Citrus Sinensis ID: 043380

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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------
Protein Sequence
IFEENEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWKGI
Secondary Structure (PSIPRED)
ccHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHccccccccHHHHHHHHHHccccHHHHHHHHHHHHHccccccccccccccEEHHHHHHHHHccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHcccHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
ifeeneivnreHWKLNTIVMNAVIEASREAQRIDEAYQILESVekglepdslSYNILISACIKtkkldvtmpfneqlkdngqkcssggfhpdIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKrvcsnpglwpkphlyVSMMHELAARVDydivkspyrrmwpdstgtispeVQEEAGHLLMEAALNDGQVDLALDKLSNtitrwkgi
Flexible Loop (DISEMBL)
ifeeneivnrehwklnTIVMNAVIEASREAQRIDEAYQILESVEkglepdslSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALdklsntitrwkgi
Low Complexity Region (SEG)
IFEENEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWKGI
Disordered region (IsUnstruct)
******IVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDS************GHLLMEAALNDGQVDLALDKLSNTIT*****
Disordered Region (DISOPRED)
IFEENEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWKGI
Disordered Region (DISEMBL)
IFEENEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWKGI
Disordered Region (DISPRO)
IFEENEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWKGI
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
IFEENEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWKGI
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	246	2.2.26 [Sep-21-2011]
Q8VYD6	580	Pentatricopeptide repeat-	yes	no	0.963	0.408	0.458	3e-53
Q9LYZ9	819	Pentatricopeptide repeat-	no	no	0.756	0.227	0.254	2e-10
Q9SZ52	1112	Pentatricopeptide repeat-	no	no	0.601	0.133	0.311	2e-10
Q9CAN6	590	Pentatricopeptide repeat-	no	no	0.540	0.225	0.270	6e-09
Q9SH60	666	Pentatricopeptide repeat-	no	no	0.439	0.162	0.313	1e-08
Q6NQ83	619	Pentatricopeptide repeat-	no	no	0.443	0.176	0.330	1e-07
O80958	867	Pentatricopeptide repeat-	no	no	0.833	0.236	0.231	1e-07
Q9S7Q2	862	Pentatricopeptide repeat-	no	no	0.650	0.185	0.270	3e-07
P0C894	761	Putative pentatricopeptid	no	no	0.890	0.287	0.226	3e-07
Q9LSQ2	659	Putative pentatricopeptid	no	no	0.487	0.182	0.274	4e-07

>sp|Q8VYD6|PP374_ARATH Pentatricopeptide repeat-containing protein At5g10690 OS=Arabidopsis thaliana GN=CBSPPR1 PE=2 SV=1

 Score =  208 bits (530), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 111/242 (45%), Positives = 152/242 (62%), Gaps = 5/242 (2%)

Query: 6   EIVNREHWKLNTIVMNAVIEASREAQRIDEAYQIL-ESVEKGLEPDSLSYNILISACIKT 64
           +I+  +H   + ++ N +++    ++    A  +L E +   LEPD L+YN LI ACIK 
Sbjct: 179 DILLLDHGTPSVLIYNLLMKGYVNSESPQAAINLLDEMLRLRLEPDRLTYNTLIHACIKC 238

Query: 65  KKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCN 124
             LD  M F   +K+  ++       PD+ TY TL+ GF  A DL SL EI  EMK C N
Sbjct: 239 GDLDAAMKFFNDMKEKAEEYYDDFLQPDVVTYTTLVKGFGDATDLLSLQEIFLEMKLCEN 298

Query: 125 LILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELA 184
           + +DR+ FTA+VDA+L  GS       ALC+FGEI+KR  +N  L PKPHLY+SMM   A
Sbjct: 299 VFIDRTAFTAVVDAMLKCGSTS----GALCVFGEILKRSGANEVLRPKPHLYLSMMRAFA 354

Query: 185 ARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK 244
            + DY +V++ Y R+WPDS+G+IS  VQ+EA +LLMEAALNDGQ+D AL  L + + RWK
Sbjct: 355 VQGDYGMVRNLYLRLWPDSSGSISKAVQQEADNLLMEAALNDGQLDEALGILLSIVRRWK 414

Query: 245 GI 246
            I
Sbjct: 415 TI 416

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LYZ9|PP362_ARATH Pentatricopeptide repeat-containing protein At5g02860 OS=Arabidopsis thaliana GN=At5g02860 PE=2 SV=1

 Score = 66.2 bits (160), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 58/228 (25%), Positives = 96/228 (42%), Gaps = 42/228 (18%)

Query: 1   IFEENEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQIL-ESVEKGLEPDSLSYNILIS 59
           +FEE +      +  + +  NA+++   ++ R  EA ++L E V  G  P  ++YN LIS
Sbjct: 301 VFEEMKAAG---FSYDKVTYNALLDVYGKSHRPKEAMKVLNEMVLNGFSPSIVTYNSLIS 357

Query: 60  ACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEM 119
           A  +   LD  M    Q+ + G K       PD+FTY TLL GF  A  ++S + I  EM
Sbjct: 358 AYARDGMLDEAMELKNQMAEKGTK-------PDVFTYTTLLSGFERAGKVESAMSIFEEM 410

Query: 120 KSC------------CNLILDRSTFTAMVDALLYSGSIKVVGLYA--------LCIFGEI 159
           ++               +  +R  FT M+        I V GL          L +FG+ 
Sbjct: 411 RNAGCKPNICTFNAFIKMYGNRGKFTEMMKIF---DEINVCGLSPDIVTWNTLLAVFGQN 467

Query: 160 --------VKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRM 199
                   V +     G  P+   + +++   +    ++   + YRRM
Sbjct: 468 GMDSEVSGVFKEMKRAGFVPERETFNTLISAYSRCGSFEQAMTVYRRM 515

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SZ52|PP344_ARATH Pentatricopeptide repeat-containing protein At4g31850, chloroplastic OS=Arabidopsis thaliana GN=PGR3 PE=1 SV=1

 Score = 65.9 bits (159), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 53/170 (31%), Positives = 81/170 (47%), Gaps = 22/170 (12%)

Query: 14  KLNTIVMNAVIEASREAQRIDEAYQILESVE-KGLEPDSLSYNILISACIKTKKLDVTMP 72
           K N       I     A +I+EAY+IL+ ++ +G  PD ++Y +LI A    +KLD    
Sbjct: 255 KPNVYTFTICIRVLGRAGKINEAYEILKRMDDEGCGPDVVTYTVLIDALCTARKLDCAKE 314

Query: 73  FNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTF 132
             E++K       +G   PD  TY TLL  F   +DL S+ +   EM+   + + D  TF
Sbjct: 315 VFEKMK-------TGRHKPDRVTYITLLDRFSDNRDLDSVKQFWSEMEKDGH-VPDVVTF 366

Query: 133 TAMVDALLYSGSIKVVGLYALCIFGEIVKR--VCSNPGLWPKPHLYVSMM 180
           T +VDAL  +G+           FGE      V  + G+ P  H Y +++
Sbjct: 367 TILVDALCKAGN-----------FGEAFDTLDVMRDQGILPNLHTYNTLI 405

Plays a role in the stabilization of the primary polycistronic transcript of the petL operon encoding subunits of the cytochrome b6-f complex.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9CAN6|PPR97_ARATH Pentatricopeptide repeat-containing protein At1g63070, mitochondrial OS=Arabidopsis thaliana GN=At1g63070 PE=1 SV=1

 Score = 61.2 bits (147), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 39/144 (27%), Positives = 76/144 (52%), Gaps = 11/144 (7%)

Query: 5   NEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQIL-ESVEKGLEPDSLSYNILISACIK 63
           +E+V  +H   + +  N +I+   + +R++E  ++  E  ++GL  ++++Y  LI    +
Sbjct: 344 DEMVKSKHCFPDVVAYNTLIKGFCKYKRVEEGMEVFREMSQRGLVGNTVTYTTLIHGFFQ 403

Query: 64  TKKLD-VTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSC 122
            +  D   M F + + D        G HPDI TY  LL G  +  ++++ L +VFE    
Sbjct: 404 ARDCDNAQMVFKQMVSD--------GVHPDIMTYNILLDGLCNNGNVETAL-VVFEYMQK 454

Query: 123 CNLILDRSTFTAMVDALLYSGSIK 146
            ++ LD  T+T M++AL  +G ++
Sbjct: 455 RDMKLDIVTYTTMIEALCKAGKVE 478

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SH60|PP103_ARATH Pentatricopeptide repeat-containing protein At1g64100 OS=Arabidopsis thaliana GN=At1g64100 PE=2 SV=2

 Score = 60.5 bits (145), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 37/118 (31%), Positives = 65/118 (55%), Gaps = 10/118 (8%)

Query: 6   EIVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVE-KGLEPDSLSYNILISA-CIK 63
           E++      L+T+  N +I    +  ++DEA+ +  S+   G+EPD  +YN++IS  C K
Sbjct: 526 EVIQMSKIDLDTVAYNIIIHGMCKGSKVDEAWDLFCSLPIHGVEPDVQTYNVMISGFCGK 585

Query: 64  TKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKS 121
           +   D  + F+ ++KDNG +       PD  TY TL+ G   A ++   +E++ EM+S
Sbjct: 586 SAISDANVLFH-KMKDNGHE-------PDNSTYNTLIRGCLKAGEIDKSIELISEMRS 635

Arabidopsis thaliana (taxid: 3702)

>sp|Q6NQ83|PP247_ARATH Pentatricopeptide repeat-containing protein At3g22470, mitochondrial OS=Arabidopsis thaliana GN=At3g22470 PE=2 SV=1

 Score = 57.0 bits (136), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 39/118 (33%), Positives = 64/118 (54%), Gaps = 9/118 (7%)

Query: 5   NEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQILE-SVEKGLEPDSLSYNILISACIK 63
           NE++ R     +TI  N++I+   +   + EA Q+ +  V KG EPD ++Y+ILI++  K
Sbjct: 339 NEMITR-GIAPDTITYNSLIDGFCKENCLHEANQMFDLMVSKGCEPDIVTYSILINSYCK 397

Query: 64  TKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKS 121
            K++D  M    ++       SS G  P+  TY TL++GF  +  L +  E+  EM S
Sbjct: 398 AKRVDDGMRLFREI-------SSKGLIPNTITYNTLVLGFCQSGKLNAAKELFQEMVS 448

Arabidopsis thaliana (taxid: 3702)

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

 Score = 57.0 bits (136), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 53/229 (23%), Positives = 102/229 (44%), Gaps = 24/229 (10%)

Query: 8   VNREHWKLNTIVMNAVIEASREAQRIDEAYQILESV--EKGLEPDSLSYNILISACIKTK 65
           +N  +++ N ++ N +I    +  +  +A ++L+++  EK       SYN +I   +K  
Sbjct: 545 MNASNFEANEVIYNTIINGLCKVGQTSKAKEMLQNLIKEKRYSMSCTSYNSIIDGFVKVG 604

Query: 66  KLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNL 125
             D  +    ++ +NG+        P++ T+ +L+ GF  +  +   LE+  EMKS   L
Sbjct: 605 DTDSAVETYREMSENGKS-------PNVVTFTSLINGFCKSNRMDLALEMTHEMKS-MEL 656

Query: 126 ILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAA 185
            LD   + A++D       +K     A  +F E+ +      GL P   +Y S++     
Sbjct: 657 KLDLPAYGALIDGFCKKNDMKT----AYTLFSELPEL-----GLMPNVSVYNSLISGFRN 707

Query: 186 RVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALD 234
               D     Y++M  D    IS ++       +++  L DG ++LA D
Sbjct: 708 LGKMDAAIDLYKKMVNDG---ISCDLFTYT--TMIDGLLKDGNINLASD 751

Involved in lateral organ development and boundary demarcation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9S7Q2|PP124_ARATH Pentatricopeptide repeat-containing protein At1g74850, chloroplastic OS=Arabidopsis thaliana GN=PTAC2 PE=2 SV=1

 Score = 55.8 bits (133), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 50/185 (27%), Positives = 89/185 (48%), Gaps = 25/185 (13%)

Query: 41  ESVEKGLEPDSLSYNILISAC-IKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATL 99
           E   +G++PD ++YN L+SAC I+    +  M F        +  + GG  PD+ TY+ L
Sbjct: 237 EMRHEGIQPDIVTYNTLLSACAIRGLGDEAEMVF--------RTMNDGGIVPDLTTYSHL 288

Query: 100 LMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEI 159
           +  F   + L+ + +++ EM S  +L  D +++  +++A   SGSIK     A+ +F ++
Sbjct: 289 VETFGKLRRLEKVCDLLGEMASGGSLP-DITSYNVLLEAYAKSGSIK----EAMGVFHQM 343

Query: 160 VKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMW-----PD-STGTISPEVQE 213
               C+     P  + Y  +++       YD V+  +  M      PD +T  I  EV  
Sbjct: 344 QAAGCT-----PNANTYSVLLNLFGQSGRYDDVRQLFLEMKSSNTDPDAATYNILIEVFG 398

Query: 214 EAGHL 218
           E G+ 
Sbjct: 399 EGGYF 403

Involved in plastid gene expression.

Arabidopsis thaliana (taxid: 3702)

>sp|P0C894|PP143_ARATH Putative pentatricopeptide repeat-containing protein At2g02150 OS=Arabidopsis thaliana GN=At2g02150 PE=3 SV=1

 Score = 55.5 bits (132), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 60/265 (22%), Positives = 110/265 (41%), Gaps = 46/265 (17%)

Query: 16  NTIVMNAVIEASREAQRIDEAYQILESVEK-GLEPDSLSYNILISACIKTKKLDVTMPFN 74
           N +   A+I+   +A+R+ EA ++   ++  G+ P+  SYN LI   +K K +D  +   
Sbjct: 436 NVVTYTALIDGLCDAERMKEAEELFGKMDTAGVIPNLASYNALIHGFVKAKNMDRALELL 495

Query: 75  EQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTA 134
            +LK  G K       PD+  Y T + G    + +++   ++ EMK  C +  +   +T 
Sbjct: 496 NELKGRGIK-------PDLLLYGTFIWGLCSLEKIEAAKVVMNEMKE-CGIKANSLIYTT 547

Query: 135 MVDALLYSGSIKVVGLYAL------------CIFGEIVKRVCSNP--------------- 167
           ++DA   SG+    GL+ L              F  ++  +C N                
Sbjct: 548 LMDAYFKSGN-PTEGLHLLDEMKELDIEVTVVTFCVLIDGLCKNKLVSKAVDYFNRISND 606

Query: 168 -GLWPKPHLYVSMMHELAARVDYDIVKSPYRRM-----WPDSTGTIS-PEVQEEAGHLLM 220
            GL     ++ +M+  L      +   + + +M      PD T   S  +   + G++L 
Sbjct: 607 FGLQANAAIFTAMIDGLCKDNQVEAATTLFEQMVQKGLVPDRTAYTSLMDGNFKQGNVLE 666

Query: 221 EAALND--GQVDLALDKLSNTITRW 243
             AL D   ++ + LD L+ T   W
Sbjct: 667 ALALRDKMAEIGMKLDLLAYTSLVW 691

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LSQ2|PP239_ARATH Putative pentatricopeptide repeat-containing protein At3g16890, mitochondrial OS=Arabidopsis thaliana GN=PPR40 PE=3 SV=1

 Score = 55.5 bits (132), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 37/135 (27%), Positives = 66/135 (48%), Gaps = 15/135 (11%)

Query: 13  WKLNTIVMNAVIEASREAQRIDEAYQIL-ESVEKGLEPDSLSYNILISACIKTKKLDVTM 71
           +K + I  + +I     A+ I +A+    E +E G+EP+ ++YNILI +C  T   D ++
Sbjct: 491 FKPDVITFSLIINCLCRAKEIKDAFDCFKEMLEWGIEPNEITYNILIRSCCSTGDTDRSV 550

Query: 72  PFNEQLKDNGQKCSSGGFHPDIFTYATLLMGF---RHAKDLQSLLEIVFEMKSCCNLILD 128
               ++K+N       G  PD++ Y   +  F   R  K  + LL+ +  +     L  D
Sbjct: 551 KLFAKMKEN-------GLSPDLYAYNATIQSFCKMRKVKKAEELLKTMLRI----GLKPD 599

Query: 129 RSTFTAMVDALLYSG 143
             T++ ++ AL  SG
Sbjct: 600 NFTYSTLIKALSESG 614

Required for the ubiqinol-cytochrome c oxidoreductase activity of mitochondrial Complex III.

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	246
225429760	609	PREDICTED: pentatricopeptide repeat-cont	0.821	0.331	0.606	2e-62
296081754	570	unnamed protein product [Vitis vinifera]	0.821	0.354	0.606	3e-62
255548570	600	pentatricopeptide repeat-containing prot	0.821	0.336	0.582	4e-62
224121168	607	predicted protein [Populus trichocarpa]	0.821	0.332	0.558	5e-60
147855724	1120	hypothetical protein VITISV_041843 [Viti	0.780	0.171	0.591	7e-56
357436759	639	Pentatricopeptide repeat-containing prot	0.955	0.367	0.5	7e-56
357436761	627	Pentatricopeptide repeat-containing prot	0.821	0.322	0.543	1e-55
356561871	558	PREDICTED: pentatricopeptide repeat-cont	0.821	0.362	0.524	5e-54
356554421	590	PREDICTED: pentatricopeptide repeat-cont	0.821	0.342	0.514	3e-53
297811171	575	pentatricopeptide repeat-containing prot	0.963	0.412	0.458	2e-52

>gi|225429760|ref|XP_002280516.1| PREDICTED: pentatricopeptide repeat-containing protein At5g10690-like [Vitis vinifera]

 Score =  244 bits (624), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 125/206 (60%), Positives = 149/206 (72%), Gaps = 4/206 (1%)

Query: 41  ESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLL 100
           E +++GL+PD L+YN LI AC+KT+KLD  M + E++K+N QK       PD  TY TLL
Sbjct: 225 EILQQGLKPDRLTYNTLIFACVKTEKLDTAMRYFEEMKENAQKTIDVDLFPDAITYTTLL 284

Query: 101 MGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIV 160
            GF HAKDL S+ +IV EMKS  NL +DR+ +TA+VDALL  GS K     ALC+FGEI+
Sbjct: 285 KGFGHAKDLLSVQKIVMEMKSSNNLFVDRTAYTAIVDALLNCGSSK----GALCMFGEII 340

Query: 161 KRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLM 220
           KR   N  L PKPHLY+SMM  LAAR DY++VKS ++RM PDS GTISP VQ EA  LLM
Sbjct: 341 KRAGQNFNLRPKPHLYISMMSALAARGDYNLVKSLHKRMRPDSAGTISPAVQIEADQLLM 400

Query: 221 EAALNDGQVDLALDKLSNTITRWKGI 246
           EAALNDGQVD A   LSN ITRWKGI
Sbjct: 401 EAALNDGQVDAATHHLSNIITRWKGI 426

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296081754|emb|CBI20759.3| unnamed protein product [Vitis vinifera]

 Score =  244 bits (622), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 125/206 (60%), Positives = 149/206 (72%), Gaps = 4/206 (1%)

Query: 41  ESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLL 100
           E +++GL+PD L+YN LI AC+KT+KLD  M + E++K+N QK       PD  TY TLL
Sbjct: 242 EILQQGLKPDRLTYNTLIFACVKTEKLDTAMRYFEEMKENAQKTIDVDLFPDAITYTTLL 301

Query: 101 MGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIV 160
            GF HAKDL S+ +IV EMKS  NL +DR+ +TA+VDALL  GS K     ALC+FGEI+
Sbjct: 302 KGFGHAKDLLSVQKIVMEMKSSNNLFVDRTAYTAIVDALLNCGSSK----GALCMFGEII 357

Query: 161 KRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLM 220
           KR   N  L PKPHLY+SMM  LAAR DY++VKS ++RM PDS GTISP VQ EA  LLM
Sbjct: 358 KRAGQNFNLRPKPHLYISMMSALAARGDYNLVKSLHKRMRPDSAGTISPAVQIEADQLLM 417

Query: 221 EAALNDGQVDLALDKLSNTITRWKGI 246
           EAALNDGQVD A   LSN ITRWKGI
Sbjct: 418 EAALNDGQVDAATHHLSNIITRWKGI 443

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255548570|ref|XP_002515341.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis] gi|223545285|gb|EEF46790.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis]

 Score =  243 bits (621), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 120/206 (58%), Positives = 148/206 (71%), Gaps = 4/206 (1%)

Query: 41  ESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLL 100
           E ++ GL PD L+YN LI AC+K+K LD  M F E++KD  ++ ++   +PD+ TY TLL
Sbjct: 218 EILQLGLTPDRLTYNTLILACVKSKSLDAAMSFFEEMKDEARQTNNVNLYPDVVTYTTLL 277

Query: 101 MGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIV 160
            GF +AKDL S+  IV EMK   NL +DR+ FTAMVDALL SGSIK     ALCIFGEI+
Sbjct: 278 KGFGNAKDLGSVKMIVLEMKLYHNLFIDRTGFTAMVDALLNSGSIK----GALCIFGEII 333

Query: 161 KRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLM 220
           KR   NP L PKPHLY+SMM   A + DY +VK+ ++R+WPDSTGTISP +Q+EA HLLM
Sbjct: 334 KRAGVNPDLRPKPHLYLSMMRAFAVQGDYSMVKNLHKRLWPDSTGTISPAIQQEADHLLM 393

Query: 221 EAALNDGQVDLALDKLSNTITRWKGI 246
           EAALN GQVD AL+ L   I RW GI
Sbjct: 394 EAALNGGQVDAALENLRKIIPRWNGI 419

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224121168|ref|XP_002330760.1| predicted protein [Populus trichocarpa] gi|222872562|gb|EEF09693.1| predicted protein [Populus trichocarpa]

 Score =  236 bits (603), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 115/206 (55%), Positives = 151/206 (73%), Gaps = 4/206 (1%)

Query: 41  ESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLL 100
           E +E GL PD L+YN LISAC+K  KLD  M F +++KD  Q  S    +PD+ TY TLL
Sbjct: 217 EILELGLTPDRLTYNTLISACVKAGKLDAAMQFFDEMKDKAQNFSRDKLYPDVVTYTTLL 276

Query: 101 MGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIV 160
            GF  AKDL S+L+IV+EMK   NL++DR+ FTAMVDALL  GS+      A+C+FGEI+
Sbjct: 277 QGFGGAKDLLSVLKIVYEMKMHRNLVIDRTAFTAMVDALLNCGSMN----GAVCVFGEII 332

Query: 161 KRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLM 220
           KR   NP L PKPHLY+S+M   A++ DY++VK+ ++R+WPDS+G IS  +QEEA HLLM
Sbjct: 333 KRAGVNPKLRPKPHLYLSLMRAFASQGDYNMVKNLHKRLWPDSSGAISLALQEEADHLLM 392

Query: 221 EAALNDGQVDLALDKLSNTITRWKGI 246
           EAALNDGQV++AL+ L+N + +WK I
Sbjct: 393 EAALNDGQVNVALENLTNVVLKWKRI 418

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147855724|emb|CAN81324.1| hypothetical protein VITISV_041843 [Vitis vinifera]

 Score =  223 bits (567), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 116/196 (59%), Positives = 141/196 (71%), Gaps = 4/196 (2%)

Query: 41  ESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLL 100
           E +++GL+PD L+YN LI AC+KT+KLD  M + E++K+N QK       PD  TY TLL
Sbjct: 225 EILQQGLKPDRLTYNTLIFACVKTEKLDTAMRYFEEMKENAQKTIDVDLFPDAITYTTLL 284

Query: 101 MGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIV 160
            GF HAKDL S+ +IV EMKS  NL +DR+ +TA+VDALL  GS K     ALCIFGEI+
Sbjct: 285 KGFGHAKDLLSVQKIVMEMKSSNNLFVDRTAYTAIVDALLNCGSSK----GALCIFGEII 340

Query: 161 KRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLM 220
           KR   N  L PKPHLY+SMM  LAAR DY++VKS ++RM PDS GTISP VQ EA  LLM
Sbjct: 341 KRAGQNFNLRPKPHLYISMMSALAARGDYNLVKSLHKRMRPDSAGTISPAVQIEADQLLM 400

Query: 221 EAALNDGQVDLALDKL 236
           EAALNDGQV + L+ L
Sbjct: 401 EAALNDGQVAVRLEAL 416

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357436759|ref|XP_003588655.1| Pentatricopeptide repeat-containing protein [Medicago truncatula] gi|355477703|gb|AES58906.1| Pentatricopeptide repeat-containing protein [Medicago truncatula]

 Score =  223 bits (567), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 120/240 (50%), Positives = 157/240 (65%), Gaps = 5/240 (2%)

Query: 8   VNREHWKLNTIVMNAVIEASREAQRIDEAYQIL-ESVEKGLEPDSLSYNILISACIKTKK 66
           V RE    +  V N +I+    +     A  +L E + +G+ PD L+YN LI AC++++K
Sbjct: 178 VLREGEHFSVSVYNLLIKGHINSGCPHTAINMLNEILHQGIMPDRLTYNTLILACVQSEK 237

Query: 67  LDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLI 126
           LDV M    ++K+  Q+       PDI TY TLL G   AKDL S+++IV EMKSC  L 
Sbjct: 238 LDVAMQLFGEMKEKAQEFIHDDLFPDIVTYTTLLKGLGQAKDLVSVMQIVLEMKSCSQLY 297

Query: 127 LDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAAR 186
           +DR+ +TA+VDALL  GS+K     ALCIFGEI K+V  NP L PKPHLY+SMM   A R
Sbjct: 298 IDRTAYTAIVDALLKCGSVK----GALCIFGEIQKQVGWNPELRPKPHLYLSMMRAFAFR 353

Query: 187 VDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWKGI 246
            DYD+VK+ ++R+ PD++GTI P  QEEA HLLMEAALN GQVD+A   L   ++RWKGI
Sbjct: 354 GDYDLVKNLHKRILPDTSGTILPVSQEEADHLLMEAALNAGQVDVATKTLMYIVSRWKGI 413

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357436761|ref|XP_003588656.1| Pentatricopeptide repeat-containing protein [Medicago truncatula] gi|355477704|gb|AES58907.1| Pentatricopeptide repeat-containing protein [Medicago truncatula]

 Score =  222 bits (565), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 112/206 (54%), Positives = 144/206 (69%), Gaps = 4/206 (1%)

Query: 41  ESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLL 100
           E + +G+ PD L+YN LI AC++++KLDV M    ++K+  Q+       PDI TY TLL
Sbjct: 200 EILHQGIMPDRLTYNTLILACVQSEKLDVAMQLFGEMKEKAQEFIHDDLFPDIVTYTTLL 259

Query: 101 MGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIV 160
            G   AKDL S+++IV EMKSC  L +DR+ +TA+VDALL  GS+K     ALCIFGEI 
Sbjct: 260 KGLGQAKDLVSVMQIVLEMKSCSQLYIDRTAYTAIVDALLKCGSVK----GALCIFGEIQ 315

Query: 161 KRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLM 220
           K+V  NP L PKPHLY+SMM   A R DYD+VK+ ++R+ PD++GTI P  QEEA HLLM
Sbjct: 316 KQVGWNPELRPKPHLYLSMMRAFAFRGDYDLVKNLHKRILPDTSGTILPVSQEEADHLLM 375

Query: 221 EAALNDGQVDLALDKLSNTITRWKGI 246
           EAALN GQVD+A   L   ++RWKGI
Sbjct: 376 EAALNAGQVDVATKTLMYIVSRWKGI 401

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356561871|ref|XP_003549200.1| PREDICTED: pentatricopeptide repeat-containing protein At5g10690-like [Glycine max]

 Score =  216 bits (551), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 108/206 (52%), Positives = 139/206 (67%), Gaps = 4/206 (1%)

Query: 41  ESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLL 100
           E + +G+ PD L+YN LI AC+++ KLD  M F  ++K   QK  +    PDI TY T+L
Sbjct: 183 EILRQGIMPDRLTYNTLILACVESGKLDAAMQFFGEMKGEAQKFVNDDLFPDIVTYTTML 242

Query: 101 MGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIV 160
            GF   KDL S+L+IV EMKSC  L +DR+ +T +VD  L  GS+K     ALCIFGEI+
Sbjct: 243 KGFGRMKDLASVLKIVLEMKSCRELYIDRTAYTEIVDVFLKCGSVK----GALCIFGEIL 298

Query: 161 KRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLM 220
           K+   NP L PKPHLY+SMM   A   DYD+VK  ++R+WPDS GTI    QEEA HLLM
Sbjct: 299 KQAGLNPELRPKPHLYLSMMRAFAFLGDYDLVKKLHKRIWPDSAGTILLVAQEEADHLLM 358

Query: 221 EAALNDGQVDLALDKLSNTITRWKGI 246
           EAALN GQV++A+  L+  ++RWKGI
Sbjct: 359 EAALNAGQVNVAIKTLTEIVSRWKGI 384

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356554421|ref|XP_003545545.1| PREDICTED: pentatricopeptide repeat-containing protein At5g10690-like [Glycine max]

 Score =  214 bits (545), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 106/206 (51%), Positives = 141/206 (68%), Gaps = 4/206 (1%)

Query: 41  ESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLL 100
           E + +G+ PD L+YN LI AC+++ KLD  M F E++K   QK S+    PDI TY T+L
Sbjct: 220 EILRQGIMPDRLTYNTLILACVQSGKLDAAMQFFEEMKGKAQKFSNHDLFPDIVTYTTML 279

Query: 101 MGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIV 160
            GF   KDL ++L+IV EMKS   L +DR+ +TA++DA L  GS+K     ALCIFGEI+
Sbjct: 280 KGFGQTKDLATVLKIVLEMKSHRELYIDRTAYTAIIDAFLKCGSVK----GALCIFGEIL 335

Query: 161 KRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLM 220
           K+   NP L PKPHLY+S+M   A   DY +VK  ++R+WPDS GTI    QEEA HLLM
Sbjct: 336 KQTGLNPELKPKPHLYLSLMRAFAFLGDYYLVKKLHKRIWPDSAGTILLVAQEEADHLLM 395

Query: 221 EAALNDGQVDLALDKLSNTITRWKGI 246
           EAALN GQV++A+  L+  +++WKGI
Sbjct: 396 EAALNAGQVNVAVKTLTEIVSKWKGI 421

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297811171|ref|XP_002873469.1| pentatricopeptide repeat-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297319306|gb|EFH49728.1| pentatricopeptide repeat-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  211 bits (537), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 111/242 (45%), Positives = 156/242 (64%), Gaps = 5/242 (2%)

Query: 6   EIVNREHWKLNTIVMNAVIEASREAQRIDEAYQIL-ESVEKGLEPDSLSYNILISACIKT 64
           +I+  +H   + ++ N +++    ++    A  +L E +   LEPD L+YN LI ACIK 
Sbjct: 176 DILLLDHGTPSVLIYNLLMKGYVNSESPQAAINLLDEMLRLRLEPDRLTYNTLIHACIKC 235

Query: 65  KKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCN 124
             +DV M F +++K+  ++       PD+ TY TL+ GF  AKDL SL +I  EMK C N
Sbjct: 236 GDMDVAMKFFKEMKEKAEEYYDDFLQPDVVTYTTLVKGFGDAKDLLSLQDIYLEMKLCDN 295

Query: 125 LILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELA 184
           + +DR+ FTA+VDA+L  GS       ALC+FGEI+KR  +N  L PKPHLY+SMM   A
Sbjct: 296 VFIDRTAFTAVVDAMLKCGSTS----GALCVFGEILKRSGANEVLRPKPHLYLSMMRAFA 351

Query: 185 ARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK 244
            + DY +V++ Y R+WPDS+G+IS  VQ+EA +LLMEAALN GQ+D AL  LS+ + RWK
Sbjct: 352 VQGDYGMVRNLYLRLWPDSSGSISKAVQQEADNLLMEAALNAGQLDEALGILSSIVRRWK 411

Query: 245 GI 246
            I
Sbjct: 412 AI 413

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	246
TAIR|locus:2159654	580	AT5G10690 [Arabidopsis thalian	0.963	0.408	0.462	1.5e-49
TAIR|locus:2151281	819	AT5G02860 [Arabidopsis thalian	0.609	0.183	0.323	1.8e-09
TAIR|locus:2116772	1112	PGR3 "AT4G31850" [Arabidopsis	0.5	0.110	0.340	2.6e-08
TAIR|locus:2024537	666	AT1G64100 [Arabidopsis thalian	0.439	0.162	0.313	4.2e-08
TAIR|locus:2056078	867	LOJ "LATERAL ORGAN JUNCTION" [	0.857	0.243	0.234	6e-08
TAIR|locus:2015218	590	AT1G63070 [Arabidopsis thalian	0.540	0.225	0.270	1.1e-07
TAIR|locus:2077061	619	AT3G22470 "AT3G22470" [Arabido	0.516	0.205	0.297	1.5e-07
TAIR|locus:2026654	257	AT1G63630 [Arabidopsis thalian	0.520	0.498	0.290	8.8e-07
TAIR|locus:2164910	747	EMB2745 "EMBRYO DEFECTIVE 2745	0.581	0.191	0.25	1.7e-06
TAIR|locus:2174008	974	AT5G61990 "AT5G61990" [Arabido	0.495	0.125	0.251	3.2e-06

TAIR|locus:2159654 AT5G10690 [Arabidopsis thaliana (taxid:3702)]

 Score = 516 (186.7 bits), Expect = 1.5e-49, P = 1.5e-49
 Identities = 112/242 (46%), Positives = 153/242 (63%)

Query:     6 EIVNREHWKLNTIVMNAVIEASREAQRIDEAYQIL-ESVEKGLEPDSLSYNILISACIKT 64
             +I+  +H   + ++ N +++    ++    A  +L E +   LEPD L+YN LI ACIK 
Sbjct:   179 DILLLDHGTPSVLIYNLLMKGYVNSESPQAAINLLDEMLRLRLEPDRLTYNTLIHACIKC 238

Query:    65 KKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCN 124
               LD  M F   +K+  ++       PD+ TY TL+ GF  A DL SL EI  EMK C N
Sbjct:   239 GDLDAAMKFFNDMKEKAEEYYDDFLQPDVVTYTTLVKGFGDATDLLSLQEIFLEMKLCEN 298

Query:   125 LILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELA 184
             + +DR+ FTA+VDA+L  GS    G  ALC+FGEI+KR  +N  L PKPHLY+SMM   A
Sbjct:   299 VFIDRTAFTAVVDAMLKCGSTS--G--ALCVFGEILKRSGANEVLRPKPHLYLSMMRAFA 354

Query:   185 ARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK 244
              + DY +V++ Y R+WPDS+G+IS  VQ+EA +LLMEAALNDGQ+D AL  L + + RWK
Sbjct:   355 VQGDYGMVRNLYLRLWPDSSGSISKAVQQEADNLLMEAALNDGQLDEALGILLSIVRRWK 414

Query:   245 GI 246
              I
Sbjct:   415 TI 416

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0005829 "cytosol" evidence=IDA

GO:0016556 "mRNA modification" evidence=RCA

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

TAIR|locus:2151281 AT5G02860 [Arabidopsis thaliana (taxid:3702)]

 Score = 163 (62.4 bits), Expect = 1.8e-09, P = 1.8e-09
 Identities = 56/173 (32%), Positives = 83/173 (47%)

Query:     1 IFEENEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQIL-ESVEKGLEPDSLSYNILIS 59
             +FEE +     + K   +  NA+++   ++ R  EA ++L E V  G  P  ++YN LIS
Sbjct:   301 VFEEMKAAGFSYDK---VTYNALLDVYGKSHRPKEAMKVLNEMVLNGFSPSIVTYNSLIS 357

Query:    60 ACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEM 119
             A  +   LD  M    Q+ + G K       PD+FTY TLL GF  A  ++S + I  EM
Sbjct:   358 AYARDGMLDEAMELKNQMAEKGTK-------PDVFTYTTLLSGFERAGKVESAMSIFEEM 410

Query:   120 KSC-CNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP 171
             ++  C   +   TF A +   +Y    K   +  + IF EI   VC   GL P
Sbjct:   411 RNAGCKPNI--CTFNAFIK--MYGNRGKFTEM--MKIFDEI--NVC---GLSP 452

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2116772 PGR3 "AT4G31850" [Arabidopsis thaliana (taxid:3702)]

 Score = 155 (59.6 bits), Expect = 2.6e-08, P = 2.6e-08
 Identities = 45/132 (34%), Positives = 68/132 (51%)

Query:    14 KLNTIVMNAVIEASREAQRIDEAYQILESVE-KGLEPDSLSYNILISACIKTKKLDVTMP 72
             K N       I     A +I+EAY+IL+ ++ +G  PD ++Y +LI A    +KLD    
Sbjct:   255 KPNVYTFTICIRVLGRAGKINEAYEILKRMDDEGCGPDVVTYTVLIDALCTARKLDCAKE 314

Query:    73 FNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTF 132
               E++K       +G   PD  TY TLL  F   +DL S+ +   EM+   + + D  TF
Sbjct:   315 VFEKMK-------TGRHKPDRVTYITLLDRFSDNRDLDSVKQFWSEMEKDGH-VPDVVTF 366

Query:   133 TAMVDALLYSGS 144
             T +VDAL  +G+
Sbjct:   367 TILVDALCKAGN 378

GO:0008150 "biological_process" evidence=ND

GO:0000023 "maltose metabolic process" evidence=RCA

GO:0000272 "polysaccharide catabolic process" evidence=RCA

GO:0005982 "starch metabolic process" evidence=RCA

GO:0006098 "pentose-phosphate shunt" evidence=RCA

GO:0006655 "phosphatidylglycerol biosynthetic process" evidence=RCA

GO:0009664 "plant-type cell wall organization" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0010075 "regulation of meristem growth" evidence=RCA

GO:0019252 "starch biosynthetic process" evidence=RCA

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

GO:0034660 "ncRNA metabolic process" evidence=RCA

GO:0046777 "protein autophosphorylation" evidence=RCA

TAIR|locus:2024537 AT1G64100 [Arabidopsis thaliana (taxid:3702)]

 Score = 151 (58.2 bits), Expect = 4.2e-08, P = 4.2e-08
 Identities = 37/118 (31%), Positives = 65/118 (55%)

Query:     6 EIVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVE-KGLEPDSLSYNILISA-CIK 63
             E++      L+T+  N +I    +  ++DEA+ +  S+   G+EPD  +YN++IS  C K
Sbjct:   526 EVIQMSKIDLDTVAYNIIIHGMCKGSKVDEAWDLFCSLPIHGVEPDVQTYNVMISGFCGK 585

Query:    64 TKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKS 121
             +   D  + F++ +KDNG +       PD  TY TL+ G   A ++   +E++ EM+S
Sbjct:   586 SAISDANVLFHK-MKDNGHE-------PDNSTYNTLIRGCLKAGEIDKSIELISEMRS 635

GO:0003677 "DNA binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

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

 Score = 151 (58.2 bits), Expect = 6.0e-08, P = 6.0e-08
 Identities = 55/235 (23%), Positives = 104/235 (44%)

Query:     8 VNREHWKLNTIVMNAVIEASREAQRIDEAYQILESV--EKGLEPDSLSYNILISACIKTK 65
             +N  +++ N ++ N +I    +  +  +A ++L+++  EK       SYN +I   +K  
Sbjct:   545 MNASNFEANEVIYNTIINGLCKVGQTSKAKEMLQNLIKEKRYSMSCTSYNSIIDGFVKVG 604

Query:    66 KLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNL 125
               D  +    ++ +NG+        P++ T+ +L+ GF  +  +   LE+  EMKS   L
Sbjct:   605 DTDSAVETYREMSENGKS-------PNVVTFTSLINGFCKSNRMDLALEMTHEMKSM-EL 656

Query:   126 ILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAA 185
              LD   + A++D       +K    Y L  F E+ +      GL P   +Y S++     
Sbjct:   657 KLDLPAYGALIDGFCKKNDMKTA--YTL--FSELPEL-----GLMPNVSVYNSLISGFRN 707

Query:   186 RVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTI 240
                 D     Y++M  D    IS ++       +++  L DG ++LA D  S  +
Sbjct:   708 LGKMDAAIDLYKKMVNDG---ISCDLFTYT--TMIDGLLKDGNINLASDLYSELL 757

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2015218 AT1G63070 [Arabidopsis thaliana (taxid:3702)]

 Score = 147 (56.8 bits), Expect = 1.1e-07, P = 1.1e-07
 Identities = 39/144 (27%), Positives = 76/144 (52%)

Query:     5 NEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQIL-ESVEKGLEPDSLSYNILISACIK 63
             +E+V  +H   + +  N +I+   + +R++E  ++  E  ++GL  ++++Y  LI    +
Sbjct:   344 DEMVKSKHCFPDVVAYNTLIKGFCKYKRVEEGMEVFREMSQRGLVGNTVTYTTLIHGFFQ 403

Query:    64 TKKLD-VTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSC 122
              +  D   M F + + D        G HPDI TY  LL G  +  ++++ L +VFE    
Sbjct:   404 ARDCDNAQMVFKQMVSD--------GVHPDIMTYNILLDGLCNNGNVETAL-VVFEYMQK 454

Query:   123 CNLILDRSTFTAMVDALLYSGSIK 146
              ++ LD  T+T M++AL  +G ++
Sbjct:   455 RDMKLDIVTYTTMIEALCKAGKVE 478

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2077061 AT3G22470 "AT3G22470" [Arabidopsis thaliana (taxid:3702)]

 Score = 146 (56.5 bits), Expect = 1.5e-07, P = 1.5e-07
 Identities = 42/141 (29%), Positives = 72/141 (51%)

Query:     1 IFEENEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESV-EKGLEPDSLSYNILIS 59
             IFE+   + +    L   + N +I     A ++D+A+ +  S+ +KG++PD ++YN++I 
Sbjct:   477 IFEK---MQKSRMTLGIGIYNIIIHGMCNASKVDDAWSLFCSLSDKGVKPDVVTYNVMIG 533

Query:    60 A-CIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFE 118
               C K    +  M F + +K++G  C+     PD FTY  L+        L S +E++ E
Sbjct:   534 GLCKKGSLSEADMLFRK-MKEDG--CT-----PDDFTYNILIRAHLGGSGLISSVELIEE 585

Query:   119 MKSCCNLILDRSTFTAMVDAL 139
             MK  C    D ST   ++D L
Sbjct:   586 MK-VCGFSADSSTIKMVIDML 605

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2026654 AT1G63630 [Arabidopsis thaliana (taxid:3702)]

 Score = 133 (51.9 bits), Expect = 8.8e-07, P = 8.8e-07
 Identities = 41/141 (29%), Positives = 72/141 (51%)

Query:     4 ENEIVNRE--HWKL--NTIVMNAVIEASREAQRIDEAYQILESV-EKGLEPDSLSYNILI 58
             E E + +E   W +   TI  N++I+   +  R+D+A ++L+S+  KG  PD ++++ LI
Sbjct:    98 EAEEIYKEMLRWSIFPTTITYNSMIDGFCKQDRVDDAKRMLDSMASKGCSPDVVTFSTLI 157

Query:    59 SACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFE 118
             +   K K++D  M    ++   G   ++        TY TL+ GF    DL +  +++ E
Sbjct:   158 NGYCKAKRVDNGMEIFCEMHRRGIVANT-------VTYTTLIHGFCQVGDLDAAQDLLNE 210

Query:   119 MKSCCNLILDRSTFTAMVDAL 139
             M SC  +  D  TF  M+  L
Sbjct:   211 MISC-GVAPDYITFHCMLAGL 230

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2164910 EMB2745 "EMBRYO DEFECTIVE 2745" [Arabidopsis thaliana (taxid:3702)]

 Score = 138 (53.6 bits), Expect = 1.7e-06, P = 1.7e-06
 Identities = 39/156 (25%), Positives = 78/156 (50%)

Query:     8 VNREHWKLNTIVMNAVIEASREAQRIDEAYQILESV-EKGLEPDSLSYNILISACIKTKK 66
             +N   +  + +  NA+I       ++++A  +LE + EKGL PD +SY+ ++S   ++  
Sbjct:   406 MNDNGFSPSVVTYNALINGHCVTGKMEDAIAVLEDMKEKGLSPDVVSYSTVLSGFCRSYD 465

Query:    67 LDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLI 126
             +D  +    ++ + G K       PD  TY++L+ GF   +  +   ++  EM     L 
Sbjct:   466 VDEALRVKREMVEKGIK-------PDTITYSSLIQGFCEQRRTKEACDLYEEMLRV-GLP 517

Query:   127 LDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR 162
              D  T+TA+++A    G ++     AL +  E+V++
Sbjct:   518 PDEFTYTALINAYCMEGDLEK----ALQLHNEMVEK 549

GO:0005739 "mitochondrion" evidence=ISM;IDA

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

TAIR|locus:2174008 AT5G61990 "AT5G61990" [Arabidopsis thaliana (taxid:3702)]

 Score = 137 (53.3 bits), Expect = 3.2e-06, P = 3.2e-06
 Identities = 33/131 (25%), Positives = 64/131 (48%)

Query:    16 NTIVMNAVIEASREAQRIDEAYQILESV-EKGLEPDSLSYNILISACIKTKKLDVTMPFN 74
             N ++   +I+   +  R  +A ++L+ + E+G+ PD   YN LI    K K++D    F 
Sbjct:   451 NVVIYTTLIKTFLQNSRFGDAMRVLKEMKEQGIAPDIFCYNSLIIGLSKAKRMDEARSFL 510

Query:    75 EQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTA 134
              ++ +NG K       P+ FTY   + G+  A +  S  + V EM+ C  ++ ++   T 
Sbjct:   511 VEMVENGLK-------PNAFTYGAFISGYIEASEFASADKYVKEMREC-GVLPNKVLCTG 562

Query:   135 MVDALLYSGSI 145
             +++     G +
Sbjct:   563 LINEYCKKGKV 573

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	246
pfam13041	50	pfam13041, PPR_2, PPR repeat family	7e-07
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	1e-05
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-05
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	5e-05
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	1e-04

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

 Score = 44.7 bits (107), Expect = 7e-07
 Identities = 11/49 (22%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 16 NTIVMNAVIEASREAQRIDEAYQILES-VEKGLEPDSLSYNILISACIK 63
          + +  N +I+   +  +++EA ++     ++G++P+  +Y+ILI    K
Sbjct: 2  DVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

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

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

 Score = 45.6 bits (108), Expect = 1e-05
 Identities = 23/71 (32%), Positives = 42/71 (59%), Gaps = 3/71 (4%)

Query: 14  KLNTIV--MNAVIEASREAQRIDEAYQILESVEK-GLEPDSLSYNILISACIKTKKLDVT 70
           KL   V  MNA+I A  E  ++ +A ++L  +++ GL P++++Y+IL+ A  +    DV 
Sbjct: 714 KLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVG 773

Query: 71  MPFNEQLKDNG 81
           +    Q K++G
Sbjct: 774 LDLLSQAKEDG 784

Length = 1060

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

 Score = 40.5 bits (96), Expect = 2e-05
 Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 7/55 (12%)

Query: 49  PDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGF 103
           PD ++YN LI    K  K++  +    ++K  G K       P+++TY+ L+ G 
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIK-------PNVYTYSILIDGL 48

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

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

 Score = 43.7 bits (103), Expect = 5e-05
 Identities = 29/111 (26%), Positives = 51/111 (45%), Gaps = 11/111 (9%)

Query: 20  MNAVIEASREAQRIDEAYQILESVEK-GLEPDSLSYNILISACIKTKKLDVTMPFNEQLK 78
            +A+++ +  A  +D+A++IL+   K G++  ++SY+ L+ AC   K     +   E +K
Sbjct: 652 FSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIK 711

Query: 79  DNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKS---CCNLI 126
                  S    P + T   L+        L   LE++ EMK    C N I
Sbjct: 712 -------SIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTI 755

Length = 1060

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

 Score = 42.6 bits (100), Expect = 1e-04
 Identities = 35/118 (29%), Positives = 54/118 (45%), Gaps = 11/118 (9%)

Query: 30  AQRIDEAYQILESV-EKGLEPDSLSYNILISACIKTKKLDVTMP-FNEQLKDNGQKCSSG 87
           +Q ID A ++L  V E GL+ D   Y  LIS C K+ K+D     F+E          + 
Sbjct: 450 SQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEM--------VNA 501

Query: 88  GFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSI 145
           G   ++ T+  L+ G   A  +         M+S  N+  DR  F A++ A   SG++
Sbjct: 502 GVEANVHTFGALIDGCARAGQVAKAFGAYGIMRS-KNVKPDRVVFNALISACGQSGAV 558

Length = 1060

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	246
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.73
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.71
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.67
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.65
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.64
PF13041	50	PPR_2: PPR repeat family	99.59
PF13041	50	PPR_2: PPR repeat family	99.58
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.57
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.48
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.47
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.47
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.46
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.43
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.41
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.4
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.37
PRK12370	553	invasion protein regulator; Provisional	99.31
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.29
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.27
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.27
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.24
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.22
PRK11189	296	lipoprotein NlpI; Provisional	99.22
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.19
KOG1126	638	consensus DNA-binding cell division cycle control	99.18
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.15
PRK12370	553	invasion protein regulator; Provisional	99.15
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.13
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.13
PF12854	34	PPR_1: PPR repeat	99.13
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.12
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.1
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.1
KOG1129	478	consensus TPR repeat-containing protein [General f	99.1
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.1
KOG1126	638	consensus DNA-binding cell division cycle control	99.09
PF12854	34	PPR_1: PPR repeat	99.08
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.05
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.04
PRK14574	822	hmsH outer membrane protein; Provisional	99.04
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.02
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	98.97
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	98.94
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.91
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.9
PRK14574	822	hmsH outer membrane protein; Provisional	98.88
KOG2003	840	consensus TPR repeat-containing protein [General f	98.88
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.87
KOG1129	478	consensus TPR repeat-containing protein [General f	98.87
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.85
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.84
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	98.82
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	98.81
KOG0547	606	consensus Translocase of outer mitochondrial membr	98.81
KOG2003	840	consensus TPR repeat-containing protein [General f	98.79
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	98.78
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.75
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	98.73
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	98.72
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.71
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	98.69
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	98.64
PRK11189	296	lipoprotein NlpI; Provisional	98.64
PRK15359	144	type III secretion system chaperone protein SscB;	98.61
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.57
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.57
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.56
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	98.54
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	98.54
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.54
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.53
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.53
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.51
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.49
KOG2076	895	consensus RNA polymerase III transcription factor	98.49
KOG0495	913	consensus HAT repeat protein [RNA processing and m	98.48
KOG0495	913	consensus HAT repeat protein [RNA processing and m	98.48
KOG1915	677	consensus Cell cycle control protein (crooked neck	98.48
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	98.47
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.47
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.46
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.46
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	98.4
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.4
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.37
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.37
KOG2076	895	consensus RNA polymerase III transcription factor	98.37
PRK15359	144	type III secretion system chaperone protein SscB;	98.36
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.35
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.34
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.34
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.34
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	98.32
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.31
KOG1125	579	consensus TPR repeat-containing protein [General f	98.3
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.3
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.28
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.25
KOG1915	677	consensus Cell cycle control protein (crooked neck	98.25
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.25
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.23
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	98.23
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.2
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	98.2
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.19
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.17
PLN02789	320	farnesyltranstransferase	98.17
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	98.16
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	98.14
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	98.12
KOG0547	606	consensus Translocase of outer mitochondrial membr	98.11
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.08
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.07
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	98.05
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.05
KOG3060	289	consensus Uncharacterized conserved protein [Funct	98.05
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	98.02
PLN02789	320	farnesyltranstransferase	98.02
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.97
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.96
KOG4340	459	consensus Uncharacterized conserved protein [Funct	97.94
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.93
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	97.91
KOG1125	579	consensus TPR repeat-containing protein [General f	97.88
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.88
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.88
PRK04841	903	transcriptional regulator MalT; Provisional	97.83
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.76
KOG3785	557	consensus Uncharacterized conserved protein [Funct	97.75
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	97.74
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.74
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	97.73
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	97.71
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.7
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.7
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.7
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.7
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.7
KOG3060	289	consensus Uncharacterized conserved protein [Funct	97.69
KOG2376	652	consensus Signal recognition particle, subunit Srp	97.68
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.65
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.62
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	97.62
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.62
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.61
KOG3616	1636	consensus Selective LIM binding factor [Transcript	97.58
PRK04841	903	transcriptional regulator MalT; Provisional	97.57
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.56
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	97.55
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.54
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	97.5
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.49
PRK10803	263	tol-pal system protein YbgF; Provisional	97.48
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.45
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	97.44
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.43
KOG2047	835	consensus mRNA splicing factor [RNA processing and	97.39
KOG3616	1636	consensus Selective LIM binding factor [Transcript	97.39
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.38
PRK10803	263	tol-pal system protein YbgF; Provisional	97.32
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.31
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	97.28
KOG2047	835	consensus mRNA splicing factor [RNA processing and	97.24
PF12688	120	TPR_5: Tetratrico peptide repeat	97.21
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.19
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	97.19
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.18
KOG4340	459	consensus Uncharacterized conserved protein [Funct	97.17
PRK14720	906	transcript cleavage factor/unknown domain fusion p	97.15
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.14
KOG3785	557	consensus Uncharacterized conserved protein [Funct	97.14
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	97.12
KOG0553	304	consensus TPR repeat-containing protein [General f	97.11
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.1
KOG0553	304	consensus TPR repeat-containing protein [General f	97.06
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	97.05
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	97.03
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	97.02
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	96.94
PF03704	146	BTAD: Bacterial transcriptional activator domain;	96.88
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	96.87
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	96.83
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	96.78
PF13371	73	TPR_9: Tetratricopeptide repeat	96.78
PF12688	120	TPR_5: Tetratrico peptide repeat	96.78
PF13371	73	TPR_9: Tetratricopeptide repeat	96.75
COG3898	531	Uncharacterized membrane-bound protein [Function u	96.72
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	96.69
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	96.69
KOG2796	366	consensus Uncharacterized conserved protein [Funct	96.65
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	96.62
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	96.62
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	96.59
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	96.59
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	96.47
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	96.47
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	96.43
COG4700	251	Uncharacterized protein conserved in bacteria cont	96.4
KOG1585	308	consensus Protein required for fusion of vesicles	96.3
COG4700	251	Uncharacterized protein conserved in bacteria cont	96.28
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	96.22
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	96.15
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	96.09
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	96.04
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	96.04
KOG2041	1189	consensus WD40 repeat protein [General function pr	96.03
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	96.02
KOG2796	366	consensus Uncharacterized conserved protein [Funct	95.99
KOG2041	1189	consensus WD40 repeat protein [General function pr	95.92
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	95.92
KOG3941	406	consensus Intermediate in Toll signal transduction	95.85
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	95.84
KOG3941	406	consensus Intermediate in Toll signal transduction	95.84
smart00299	140	CLH Clathrin heavy chain repeat homology.	95.81
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	95.81
COG3629	280	DnrI DNA-binding transcriptional activator of the	95.76
KOG2610	491	consensus Uncharacterized conserved protein [Funct	95.74
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	95.63
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	95.56
COG3629	280	DnrI DNA-binding transcriptional activator of the	95.49
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	95.43
PRK15331	165	chaperone protein SicA; Provisional	95.28
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	95.27
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	95.18
COG3118	304	Thioredoxin domain-containing protein [Posttransla	95.17
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	95.11
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	94.9
PF13512	142	TPR_18: Tetratricopeptide repeat	94.9
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	94.89
PF13512	142	TPR_18: Tetratricopeptide repeat	94.88
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	94.84
smart00299	140	CLH Clathrin heavy chain repeat homology.	94.78
PF13428	44	TPR_14: Tetratricopeptide repeat	94.7
KOG2610	491	consensus Uncharacterized conserved protein [Funct	94.7
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	94.66
KOG2376	652	consensus Signal recognition particle, subunit Srp	94.66
PF13428	44	TPR_14: Tetratricopeptide repeat	94.44
PRK15331	165	chaperone protein SicA; Provisional	94.44
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	94.41
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	94.41
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	94.4
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	94.28
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	94.26
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	94.25
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	94.1
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	93.97
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	93.91
PF13929	292	mRNA_stabil: mRNA stabilisation	93.9
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	93.85
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	93.81
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	93.7
KOG4555	175	consensus TPR repeat-containing protein [Function	93.39
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	93.31
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	93.16
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	93.0
KOG4555	175	consensus TPR repeat-containing protein [Function	92.93
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	92.9
COG1747	711	Uncharacterized N-terminal domain of the transcrip	92.66
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	92.62
KOG4570	418	consensus Uncharacterized conserved protein [Funct	92.53
COG0457	291	NrfG FOG: TPR repeat [General function prediction	92.42
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	92.3
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	92.24
COG4105	254	ComL DNA uptake lipoprotein [General function pred	92.18
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	91.86
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	91.78
KOG4570	418	consensus Uncharacterized conserved protein [Funct	91.35
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	91.26
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	91.23
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	91.22
KOG1585	308	consensus Protein required for fusion of vesicles	91.05
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	90.71
COG3898	531	Uncharacterized membrane-bound protein [Function u	90.56
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	90.46
PF04097	613	Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic9	90.42
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	90.37
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	89.82
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	89.81
PF13762	145	MNE1: Mitochondrial splicing apparatus component	89.41
PRK11906	458	transcriptional regulator; Provisional	89.35
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	89.34
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	89.33
COG4455	273	ImpE Protein of avirulence locus involved in tempe	89.26
COG3118	304	Thioredoxin domain-containing protein [Posttransla	89.13
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	89.12
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	88.86
PRK11906	458	transcriptional regulator; Provisional	88.3
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	88.13
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	87.99
PF13929	292	mRNA_stabil: mRNA stabilisation	87.43
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	87.14
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	87.07
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	87.06
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	86.97
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	86.88
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	86.77
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	86.55
KOG4077	149	consensus Cytochrome c oxidase, subunit Va/COX6 [E	86.34
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	85.89
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	85.46
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	85.26
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	85.25
KOG4077	149	consensus Cytochrome c oxidase, subunit Va/COX6 [E	85.16
COG0457	291	NrfG FOG: TPR repeat [General function prediction	84.31
PF13431	34	TPR_17: Tetratricopeptide repeat	84.2
COG3947	361	Response regulator containing CheY-like receiver a	84.19
PF13431	34	TPR_17: Tetratricopeptide repeat	84.05
KOG1258	577	consensus mRNA processing protein [RNA processing	84.0
COG4105	254	ComL DNA uptake lipoprotein [General function pred	82.95
KOG0686	466	consensus COP9 signalosome, subunit CSN1 [Posttran	82.92
KOG1941	518	consensus Acetylcholine receptor-associated protei	82.86
PF11846	193	DUF3366: Domain of unknown function (DUF3366); Int	82.14
PF10579	80	Rapsyn_N: Rapsyn N-terminal myristoylation and lin	81.82
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	80.58
COG4455	273	ImpE Protein of avirulence locus involved in tempe	80.3
PF11846	193	DUF3366: Domain of unknown function (DUF3366); Int	80.05

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=8.1e-40  Score=291.18  Aligned_cols=141  Identities=21%  Similarity=0.202  Sum_probs=66.8

Q ss_pred             CCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCC
Q 043380           88 GFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNP  167 (246)
Q Consensus        88 ~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~  167 (246)
                      ++.|+..+|+++|.+|++.|++++|.++|++|.+ .|+.||..+|+++|.+|++.|++++    |.++|+.|.+.     
T Consensus       609 gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~-~Gv~PD~~TynsLI~a~~k~G~~ee----A~~l~~eM~k~-----  678 (1060)
T PLN03218        609 NIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKK-KGVKPDEVFFSALVDVAGHAGDLDK----AFEILQDARKQ-----  678 (1060)
T ss_pred             CCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHhCCCHHH----HHHHHHHHHHc-----
Confidence            3444444444444444444444444444444444 4444444444444444444444444    44444444444     


Q ss_pred             CCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhc
Q 043380          168 GLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRW  243 (246)
Q Consensus       168 ~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  243 (246)
                      |+.||..+|++||.+|++.|++++|.++|++|...+   +.|+..  +|++||.+|++.|++++|.++|++|.+.|
T Consensus       679 G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g---~~Pdvv--tyN~LI~gy~k~G~~eeAlelf~eM~~~G  749 (1060)
T PLN03218        679 GIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIK---LRPTVS--TMNALITALCEGNQLPKALEVLSEMKRLG  749 (1060)
T ss_pred             CCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcC---CCCCHH--HHHHHHHHHHHCCCHHHHHHHHHHHHHcC
Confidence            445555555555555555555555555555554322   222222  55555555555555555555555555544

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=8.8e-40  Score=290.95  Aligned_cols=221  Identities=19%  Similarity=0.242  Sum_probs=143.7

Q ss_pred             hhhHHHHhcccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhcc
Q 043380            3 EENEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVE-KGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNG   81 (246)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~-~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~   81 (246)
                      +.+++|.+.|+.||..+||++|.+|++.|++++|.++|+.|. .|+.||..||++||.+|++.|++++|.++|++|...+
T Consensus       493 ~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~  572 (1060)
T PLN03218        493 EVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAET  572 (1060)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence            456666666666677777777777777777777777776665 5666666666666666666666666666666665421


Q ss_pred             CCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHH
Q 043380           82 QKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVK  161 (246)
Q Consensus        82 ~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~  161 (246)
                           .++.||..+|++||.+|++.|++++|.++|+.|.+ .|+.|+..+|+++|.+|++.|++++    |.++|++|.+
T Consensus       573 -----~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e-~gi~p~~~tynsLI~ay~k~G~~de----Al~lf~eM~~  642 (1060)
T PLN03218        573 -----HPIDPDHITVGALMKACANAGQVDRAKEVYQMIHE-YNIKGTPEVYTIAVNSCSQKGDWDF----ALSIYDDMKK  642 (1060)
T ss_pred             -----CCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-cCCCCChHHHHHHHHHHHhcCCHHH----HHHHHHHHHH
Confidence                 15566666666666666666666666666666666 6666666666666666666666666    6666666666


Q ss_pred             hhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          162 RVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       162 ~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      .     |+.||..+|+++|.+|++.|++++|.++|++|.+.+   +.|+..  +|++||.+|++.|++++|.++|++|.+
T Consensus       643 ~-----Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G---~~pd~~--tynsLI~ay~k~G~~eeA~~lf~eM~~  712 (1060)
T PLN03218        643 K-----GVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQG---IKLGTV--SYSSLMGACSNAKNWKKALELYEDIKS  712 (1060)
T ss_pred             c-----CCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcC---CCCCHH--HHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            6     666666666666666666666666666666665443   333322  666666666666666666666666655


Q ss_pred             hc
Q 043380          242 RW  243 (246)
Q Consensus       242 ~g  243 (246)
                      .|
T Consensus       713 ~g  714 (1060)
T PLN03218        713 IK  714 (1060)
T ss_pred             cC
Confidence            43

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

Probab=100.00  E-value=7e-37  Score=268.02  Aligned_cols=202  Identities=14%  Similarity=0.183  Sum_probs=123.5

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVE-KGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP   91 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~-~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p   91 (246)
                      .++|+.+||++|.+|++.|++++|.++|++|. .|+.||..||++++.+|++.|++++|.+++.+|.+.       |+.|
T Consensus       286 ~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~-------g~~~  358 (697)
T PLN03081        286 PEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRT-------GFPL  358 (697)
T ss_pred             CCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHh-------CCCC
Confidence            45566666666666666666666666666665 566666666666666666666666666666666666       5555


Q ss_pred             cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc
Q 043380           92 DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP  171 (246)
Q Consensus        92 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p  171 (246)
                      |..+|++|+.+|++.|++++|.++|++|.+     ||..+||+||.+|++.|+.++    |.++|++|.+.     |+.|
T Consensus       359 d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~-----~d~~t~n~lI~~y~~~G~~~~----A~~lf~~M~~~-----g~~P  424 (697)
T PLN03081        359 DIVANTALVDLYSKWGRMEDARNVFDRMPR-----KNLISWNALIAGYGNHGRGTK----AVEMFERMIAE-----GVAP  424 (697)
T ss_pred             CeeehHHHHHHHHHCCCHHHHHHHHHhCCC-----CCeeeHHHHHHHHHHcCCHHH----HHHHHHHHHHh-----CCCC
Confidence            555555555555555555555555555544     455566666666666666666    66666666655     6666


Q ss_pred             chhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHH
Q 043380          172 KPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNT  239 (246)
Q Consensus       172 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  239 (246)
                      |..||++++.+|++.|++++|.++|+.|.+.. + +.|+..  +|+.|+++|++.|++++|.+++++|
T Consensus       425 d~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~-g-~~p~~~--~y~~li~~l~r~G~~~eA~~~~~~~  488 (697)
T PLN03081        425 NHVTFLAVLSACRYSGLSEQGWEIFQSMSENH-R-IKPRAM--HYACMIELLGREGLLDEAYAMIRRA  488 (697)
T ss_pred             CHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhc-C-CCCCcc--chHhHHHHHHhcCCHHHHHHHHHHC
Confidence            66666666666666666666666666664321 1 233322  5666666666666666666665554

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

Probab=100.00  E-value=5e-36  Score=262.67  Aligned_cols=221  Identities=14%  Similarity=0.151  Sum_probs=166.1

Q ss_pred             hhhhHHHHhcccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhc
Q 043380            2 FEENEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVE-KGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDN   80 (246)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~-~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~   80 (246)
                      ++.+++|.+.|+.||..||++++.+|++.|++++|.++++.|. .|+.||..+||+||++|++.|++++|.++|++|.+ 
T Consensus       310 ~~lf~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~-  388 (697)
T PLN03081        310 LCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPR-  388 (697)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCC-
Confidence            3567788888888888888888888888888888888888876 67788888888888888888888888888887753 


Q ss_pred             cCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHH
Q 043380           81 GQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIV  160 (246)
Q Consensus        81 ~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~  160 (246)
                                ||..+||+||.+|++.|+.++|.++|++|.+ .|+.||..||++++.+|++.|.+++    |.++|+.|.
T Consensus       389 ----------~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~-~g~~Pd~~T~~~ll~a~~~~g~~~~----a~~~f~~m~  453 (697)
T PLN03081        389 ----------KNLISWNALIAGYGNHGRGTKAVEMFERMIA-EGVAPNHVTFLAVLSACRYSGLSEQ----GWEIFQSMS  453 (697)
T ss_pred             ----------CCeeeHHHHHHHHHHcCCHHHHHHHHHHHHH-hCCCCCHHHHHHHHHHHhcCCcHHH----HHHHHHHHH
Confidence                      6777888888888888888888888888877 7788888888888888888888888    888888886


Q ss_pred             HhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCC----------------------------CCCCchhh
Q 043380          161 KRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDST----------------------------GTISPEVQ  212 (246)
Q Consensus       161 ~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~----------------------------~~~~~~~~  212 (246)
                      +..    |+.|+..+|++|+++|++.|++++|.+++++|.....                            +..+... 
T Consensus       454 ~~~----g~~p~~~~y~~li~~l~r~G~~~eA~~~~~~~~~~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~~~~p~~~-  528 (697)
T PLN03081        454 ENH----RIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKL-  528 (697)
T ss_pred             Hhc----CCCCCccchHhHHHHHHhcCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHhCCCCCCC-
Confidence            532    6677777777777777777777777777666531100                            0011111 


Q ss_pred             hHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          213 EEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       213 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                       .+|..|+..|++.|++++|.++++.|+++|.
T Consensus       529 -~~y~~L~~~y~~~G~~~~A~~v~~~m~~~g~  559 (697)
T PLN03081        529 -NNYVVLLNLYNSSGRQAEAAKVVETLKRKGL  559 (697)
T ss_pred             -cchHHHHHHHHhCCCHHHHHHHHHHHHHcCC
Confidence             2688888888888888888888888888773

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=1.1e-34  Score=259.45  Aligned_cols=165  Identities=18%  Similarity=0.188  Sum_probs=69.3

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           15 LNTIVMNAVIEASREAQRIDEAYQILESVE-KGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~-~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      ||+.+||++|.+|++.|++++|+++|++|. .|+.||..||+.+|.+|++.|+.+.|.+++..|.+.       |+.||.
T Consensus       251 ~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~-------g~~~d~  323 (857)
T PLN03077        251 RDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKT-------GFAVDV  323 (857)
T ss_pred             CCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHh-------CCccch
Confidence            333333333333333333444444443333 333444444444444444444444444444443333       344444


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP  173 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~  173 (246)
                      .+||+|+.+|++.|++++|.++|++|..     ||..+||++|.+|++.|++++    |+++|++|.+.     |+.||.
T Consensus       324 ~~~n~Li~~y~k~g~~~~A~~vf~~m~~-----~d~~s~n~li~~~~~~g~~~~----A~~lf~~M~~~-----g~~Pd~  389 (857)
T PLN03077        324 SVCNSLIQMYLSLGSWGEAEKVFSRMET-----KDAVSWTAMISGYEKNGLPDK----ALETYALMEQD-----NVSPDE  389 (857)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHhhCCC-----CCeeeHHHHHHHHHhCCCHHH----HHHHHHHHHHh-----CCCCCc
Confidence            4444444444444444444444444432     333344444444444444444    44444444443     444444


Q ss_pred             hhHHHHHHHHHhcCChhHHhhHHHhhC
Q 043380          174 HLYVSMMHELAARVDYDIVKSPYRRMW  200 (246)
Q Consensus       174 ~~~~~li~~~~~~g~~~~a~~~~~~~~  200 (246)
                      .||+.++.+|++.|++++|.++++.+.
T Consensus       390 ~t~~~ll~a~~~~g~~~~a~~l~~~~~  416 (857)
T PLN03077        390 ITIASVLSACACLGDLDVGVKLHELAE  416 (857)
T ss_pred             eeHHHHHHHHhccchHHHHHHHHHHHH
Confidence            444444444444444444444444443

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=2.4e-34  Score=257.35  Aligned_cols=200  Identities=17%  Similarity=0.238  Sum_probs=137.2

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH-hCCCCCHHHH-----------------------------------HHH
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVE-KGLEPDSLSY-----------------------------------NIL   57 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~-~~~~~~~~t~-----------------------------------~~l   57 (246)
                      +||+.+||++|.+|++.|++++|+++|++|. .|+.||..||                                   |+|
T Consensus       149 ~~d~~~~n~li~~~~~~g~~~~A~~~f~~M~~~g~~Pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~n~L  228 (857)
T PLN03077        149 ERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNAL  228 (857)
T ss_pred             CCCeeEHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHhCCccchhhHHHHHHHHHHcCCCcccchHhHH
Confidence            4455555555555555555555555555554 3444444444                                   444


Q ss_pred             HHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHH
Q 043380           58 ISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVD  137 (246)
Q Consensus        58 i~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~  137 (246)
                      |.+|++.|++++|.++|++|.           .||..+||++|.+|++.|++++|+++|++|.+ .|+.||..||+.+|.
T Consensus       229 i~~y~k~g~~~~A~~lf~~m~-----------~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~-~g~~Pd~~ty~~ll~  296 (857)
T PLN03077        229 ITMYVKCGDVVSARLVFDRMP-----------RRDCISWNAMISGYFENGECLEGLELFFTMRE-LSVDPDLMTITSVIS  296 (857)
T ss_pred             HHHHhcCCCHHHHHHHHhcCC-----------CCCcchhHHHHHHHHhCCCHHHHHHHHHHHHH-cCCCCChhHHHHHHH
Confidence            444444555555555555443           36667777777777777777777778888877 778888888888888


Q ss_pred             HHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHH
Q 043380          138 ALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGH  217 (246)
Q Consensus       138 ~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  217 (246)
                      +|++.|+++.    |.+++..|.+.     |+.||..+|++||.+|++.|++++|.++|++|...+       .  .+|+
T Consensus       297 a~~~~g~~~~----a~~l~~~~~~~-----g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d-------~--~s~n  358 (857)
T PLN03077        297 ACELLGDERL----GREMHGYVVKT-----GFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKD-------A--VSWT  358 (857)
T ss_pred             HHHhcCChHH----HHHHHHHHHHh-----CCccchHHHHHHHHHHHhcCCHHHHHHHHhhCCCCC-------e--eeHH
Confidence            8888888887    88888888777     788888888888888888888888888888875432       1  1688


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhhc
Q 043380          218 LLMEAALNDGQVDLALDKLSNTITRW  243 (246)
Q Consensus       218 ~li~~~~~~g~~~~a~~~~~~m~~~g  243 (246)
                      ++|.+|++.|++++|.++|++|.+.|
T Consensus       359 ~li~~~~~~g~~~~A~~lf~~M~~~g  384 (857)
T PLN03077        359 AMISGYEKNGLPDKALETYALMEQDN  384 (857)
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHhC
Confidence            88888888888888888888887665

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.73  E-value=4e-15  Score=122.69  Aligned_cols=199  Identities=13%  Similarity=0.035  Sum_probs=113.1

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc----H
Q 043380           18 IVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD----I   93 (246)
Q Consensus        18 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~----~   93 (246)
                      ..+..+...|.+.|++++|+.+|+++.+..+++..+++.++..+.+.|++++|.+.++.+.+.       +..++    .
T Consensus       108 ~~~~~La~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~-------~~~~~~~~~~  180 (389)
T PRK11788        108 LALQELGQDYLKAGLLDRAEELFLQLVDEGDFAEGALQQLLEIYQQEKDWQKAIDVAERLEKL-------GGDSLRVEIA  180 (389)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHhchHHHHHHHHHHHHHh-------cCCcchHHHH
Confidence            345556666666666666666666655333445556666666666666666666666666554       11111    1


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK  172 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~  172 (246)
                      ..|..+...+...|++++|...|+++.+   ..|+ ...+..+...+...|++++    |.++|+++...     +-.+.
T Consensus       181 ~~~~~la~~~~~~~~~~~A~~~~~~al~---~~p~~~~~~~~la~~~~~~g~~~~----A~~~~~~~~~~-----~p~~~  248 (389)
T PRK11788        181 HFYCELAQQALARGDLDAARALLKKALA---ADPQCVRASILLGDLALAQGDYAA----AIEALERVEEQ-----DPEYL  248 (389)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHh---HCcCCHHHHHHHHHHHHHCCCHHH----HHHHHHHHHHH-----ChhhH
Confidence            2344455555666666666666666655   2233 4455556666666666666    66666666554     11111


Q ss_pred             hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          173 PHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       173 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                      ..++..+..+|...|++++|...++++....+     +..  .+..+...+.+.|++++|.++++++.+.
T Consensus       249 ~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~p-----~~~--~~~~la~~~~~~g~~~~A~~~l~~~l~~  311 (389)
T PRK11788        249 SEVLPKLMECYQALGDEAEGLEFLRRALEEYP-----GAD--LLLALAQLLEEQEGPEAAQALLREQLRR  311 (389)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-----Cch--HHHHHHHHHHHhCCHHHHHHHHHHHHHh
Confidence            34556666666666666666666666554321     111  3455666666666666666666665544

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.71  E-value=1e-14  Score=120.29  Aligned_cols=202  Identities=12%  Similarity=0.095  Sum_probs=165.1

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-----HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCC
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPD-----SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSG   87 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~-----~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~   87 (246)
                      .+++..+++.++..+.+.|++++|.+.++.+.+..+.+     ...+..+...+.+.|++++|...|+++.+.       
T Consensus       137 ~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~-------  209 (389)
T PRK11788        137 GDFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDLDAARALLKKALAA-------  209 (389)
T ss_pred             CcchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhH-------
Confidence            34578899999999999999999999999986322221     224566777888999999999999999875       


Q ss_pred             CCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC--HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcC
Q 043380           88 GFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD--RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCS  165 (246)
Q Consensus        88 ~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~--~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~  165 (246)
                       .+.+...+..+...+.+.|++++|.++|+++.. .  .|+  ..+++.++.+|...|++++    |...++.+.+.   
T Consensus       210 -~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~-~--~p~~~~~~~~~l~~~~~~~g~~~~----A~~~l~~~~~~---  278 (389)
T PRK11788        210 -DPQCVRASILLGDLALAQGDYAAAIEALERVEE-Q--DPEYLSEVLPKLMECYQALGDEAE----GLEFLRRALEE---  278 (389)
T ss_pred             -CcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-H--ChhhHHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh---
Confidence             233466888899999999999999999999998 3  344  4678899999999999999    99999999875   


Q ss_pred             CCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHh---cCChhHHHHHHHHHHhh
Q 043380          166 NPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALN---DGQVDLALDKLSNTITR  242 (246)
Q Consensus       166 ~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~---~g~~~~a~~~~~~m~~~  242 (246)
                          .|+...+..+...+.+.|++++|..+++++....    |...   +++.++..+..   .|+.+++..++++|.++
T Consensus       279 ----~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~~----P~~~---~~~~l~~~~~~~~~~g~~~~a~~~~~~~~~~  347 (389)
T PRK11788        279 ----YPGADLLLALAQLLEEQEGPEAAQALLREQLRRH----PSLR---GFHRLLDYHLAEAEEGRAKESLLLLRDLVGE  347 (389)
T ss_pred             ----CCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHhC----cCHH---HHHHHHHHhhhccCCccchhHHHHHHHHHHH
Confidence                4677777899999999999999999999887542    2222   67777777664   56899999999999876


Q ss_pred             c
Q 043380          243 W  243 (246)
Q Consensus       243 g  243 (246)
                      +
T Consensus       348 ~  348 (389)
T PRK11788        348 Q  348 (389)
T ss_pred             H
Confidence            5

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.67  E-value=3.7e-14  Score=112.24  Aligned_cols=213  Identities=14%  Similarity=0.145  Sum_probs=165.8

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVE-KGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP   91 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~-~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p   91 (246)
                      .+.+..+|.++|.+.|+-...++|.+++++.. ...+.+..+||.+|.+-+-..    ..++..+|...       .+.|
T Consensus       203 ~PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~----~K~Lv~EMisq-------km~P  271 (625)
T KOG4422|consen  203 LPKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSV----GKKLVAEMISQ-------KMTP  271 (625)
T ss_pred             cCCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhc----cHHHHHHHHHh-------hcCC
Confidence            67888999999999999999999999999987 566899999999998765433    37899999998       8999


Q ss_pred             cHHHHHHHHHHHHccCCHHH----HHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhh-c--
Q 043380           92 DIFTYATLLMGFRHAKDLQS----LLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRV-C--  164 (246)
Q Consensus        92 ~~~~~~~ll~~~~~~~~~~~----a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~-~--  164 (246)
                      |..|||+++++.++.|+++.    |.+++-+|++ -|+.|...+|+.+|..+++.++..++   |..++.++...- +  
T Consensus       272 nl~TfNalL~c~akfg~F~~ar~aalqil~EmKe-iGVePsLsSyh~iik~f~re~dp~k~---as~~i~dI~N~ltGK~  347 (625)
T KOG4422|consen  272 NLFTFNALLSCAAKFGKFEDARKAALQILGEMKE-IGVEPSLSSYHLIIKNFKRESDPQKV---ASSWINDIQNSLTGKT  347 (625)
T ss_pred             chHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHH-hCCCcchhhHHHHHHHhcccCCchhh---hHHHHHHHHHhhccCc
Confidence            99999999999999998865    5678899999 99999999999999999999888663   666666665541 1  


Q ss_pred             CCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCC-CCCCCCCchhhhHHH-HHHHHHHHhcCChhHHHHHHHHHH
Q 043380          165 SNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWP-DSTGTISPEVQEEAG-HLLMEAALNDGQVDLALDKLSNTI  240 (246)
Q Consensus       165 ~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~-~~~~~~~~~~~~~~~-~~li~~~~~~g~~~~a~~~~~~m~  240 (246)
                      ..|...-|..-|..-++.|.+..+.+.|.++..-+.. ++...+++......| ..+..+.+.....+....+|+.|.
T Consensus       348 fkp~~p~d~~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lV  425 (625)
T KOG4422|consen  348 FKPITPTDNKFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLV  425 (625)
T ss_pred             ccCCCCchhHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            1222223446678889999999999999999887763 444556666433333 335555556666666666666554

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

Probab=99.65  E-value=8.7e-14  Score=125.49  Aligned_cols=204  Identities=13%  Similarity=0.036  Sum_probs=118.7

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      +.+...|..+..+|.+.|++++|...|+.+....+.+...+..+..++...|++++|..+|+++.+.        .+.+.
T Consensus       598 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--------~~~~~  669 (899)
T TIGR02917       598 PDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQPDSALALLLLADAYAVMKNYAKAITSLKRALEL--------KPDNT  669 (899)
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--------CCCCH
Confidence            3445555555555555566666665555554322334455555555555556666666666555543        12334


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP  173 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~  173 (246)
                      .++..+...+...|++++|.++++.+.+ .+ .++...+..+...+...|++++    |...|+.+...       .|+.
T Consensus       670 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~-~~-~~~~~~~~~~~~~~~~~g~~~~----A~~~~~~~~~~-------~~~~  736 (899)
T TIGR02917       670 EAQIGLAQLLLAAKRTESAKKIAKSLQK-QH-PKAALGFELEGDLYLRQKDYPA----AIQAYRKALKR-------APSS  736 (899)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHh-hC-cCChHHHHHHHHHHHHCCCHHH----HHHHHHHHHhh-------CCCc
Confidence            5566666666666666666666666655 22 2335555566666666666666    66666666554       3444


Q ss_pred             hhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          174 HLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       174 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      .++..+..++.+.|++++|.+.++.+....+.    +.  .++..+...|...|++++|.++|+++.+..+
T Consensus       737 ~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~~~----~~--~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p  801 (899)
T TIGR02917       737 QNAIKLHRALLASGNTAEAVKTLEAWLKTHPN----DA--VLRTALAELYLAQKDYDKAIKHYRTVVKKAP  801 (899)
T ss_pred             hHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC----CH--HHHHHHHHHHHHCcCHHHHHHHHHHHHHhCC
Confidence            56666666677777777777766666544321    11  1566677777777777777777777765543

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

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

Probab=99.64  E-value=1.7e-13  Score=123.65  Aligned_cols=131  Identities=14%  Similarity=0.108  Sum_probs=65.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHH
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTY   96 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~   96 (246)
                      ..++..+...+...|++++|.++++.+....+++...+..+...+...|++++|.+.|.++...         .|+..++
T Consensus       669 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~---------~~~~~~~  739 (899)
T TIGR02917       669 TEAQIGLAQLLLAAKRTESAKKIAKSLQKQHPKAALGFELEGDLYLRQKDYPAAIQAYRKALKR---------APSSQNA  739 (899)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhh---------CCCchHH
Confidence            4444455555555555555555555544323344445555555555555555555555555543         2333444


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           97 ATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        97 ~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ..+..++.+.|++++|.+.++.+.+ . .+.+...++.+...|...|++++    |...|+++.+.
T Consensus       740 ~~l~~~~~~~g~~~~A~~~~~~~l~-~-~~~~~~~~~~la~~~~~~g~~~~----A~~~~~~~~~~  799 (899)
T TIGR02917       740 IKLHRALLASGNTAEAVKTLEAWLK-T-HPNDAVLRTALAELYLAQKDYDK----AIKHYRTVVKK  799 (899)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHH-h-CCCCHHHHHHHHHHHHHCcCHHH----HHHHHHHHHHh
Confidence            4455555555555555555555544 1 12234455555555555555555    55555555543

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.

>PF13041 PPR_2: PPR repeat family

Probab=99.59  E-value=4e-15  Score=85.33  Aligned_cols=49  Identities=31%  Similarity=0.613  Sum_probs=47.5

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHHHHh
Q 043380           15 LNTIVMNAVIEASREAQRIDEAYQILESVE-KGLEPDSLSYNILISACIK   63 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~-~~~~~~~~t~~~li~~~~~   63 (246)
                      ||+.+||++|++|++.|++++|.++|++|. +|++||..||++||++|++
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            899999999999999999999999999998 8999999999999999985

>PF13041 PPR_2: PPR repeat family

Probab=99.58  E-value=7e-15  Score=84.29  Aligned_cols=50  Identities=30%  Similarity=0.531  Sum_probs=48.8

Q ss_pred             ccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHh
Q 043380           91 PDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLY  141 (246)
Q Consensus        91 p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~  141 (246)
                      ||..+||++|.+|++.|++++|.++|++|.+ .|+.||..||+++|.+|++
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~-~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKK-RGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHcC
Confidence            8999999999999999999999999999999 9999999999999999985

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.57  E-value=6.4e-12  Score=95.58  Aligned_cols=204  Identities=11%  Similarity=-0.042  Sum_probs=167.2

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      ......+..+...+...|++++|.+.+++.....+.+...+..+...+...|++++|.+.+++..+.        .+.+.
T Consensus        28 ~~~~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~--------~~~~~   99 (234)
T TIGR02521        28 NKAAKIRVQLALGYLEQGDLEVAKENLDKALEHDPDDYLAYLALALYYQQLGELEKAEDSFRRALTL--------NPNNG   99 (234)
T ss_pred             CcHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--------CCCCH
Confidence            3446778889999999999999999999876444556788889999999999999999999999885        24456


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL-DRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK  172 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~  172 (246)
                      ..+..+...+...|++++|...+++... ....| ....+..+...+...|++++    |...+++..+.      ...+
T Consensus       100 ~~~~~~~~~~~~~g~~~~A~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~g~~~~----A~~~~~~~~~~------~~~~  168 (234)
T TIGR02521       100 DVLNNYGTFLCQQGKYEQAMQQFEQAIE-DPLYPQPARSLENAGLCALKAGDFDK----AEKYLTRALQI------DPQR  168 (234)
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHh-ccccccchHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh------CcCC
Confidence            7888889999999999999999999987 43223 35667788889999999999    99999998875      2334


Q ss_pred             hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          173 PHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       173 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                      ...+..+...+...|++++|...+++.....    +...  ..+..+...+...|+.++|..+.+.+...
T Consensus       169 ~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~----~~~~--~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  232 (234)
T TIGR02521       169 PESLLELAELYYLRGQYKDARAYLERYQQTY----NQTA--ESLWLGIRIARALGDVAAAQRYGAQLQKL  232 (234)
T ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC----CCCH--HHHHHHHHHHHHHhhHHHHHHHHHHHHhh
Confidence            5678889999999999999999999987542    1111  15667888899999999999998887654

Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.

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

Probab=99.48  E-value=4e-11  Score=104.59  Aligned_cols=205  Identities=13%  Similarity=0.013  Sum_probs=147.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHH
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTY   96 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~   96 (246)
                      ...|..+...+...|++++|...|+....-.+.+...|..+...+...|++++|...|++..+.        .+.+...+
T Consensus       365 ~~~~~~la~~~~~~g~~~eA~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l--------~P~~~~~~  436 (615)
T TIGR00990       365 TQSYIKRASMNLELGDPDKAEEDFDKALKLNSEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDL--------DPDFIFSH  436 (615)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--------CccCHHHH
Confidence            4566677777777788888888887765333455677788888888888888888888888775        23345677


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch-h
Q 043380           97 ATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP-H  174 (246)
Q Consensus        97 ~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~-~  174 (246)
                      ..+...+.+.|++++|+..|++...   ..|+ ...|+.+...+...|++++    |.+.|+..........+..++. .
T Consensus       437 ~~la~~~~~~g~~~eA~~~~~~al~---~~P~~~~~~~~lg~~~~~~g~~~~----A~~~~~~Al~l~p~~~~~~~~~~~  509 (615)
T TIGR00990       437 IQLGVTQYKEGSIASSMATFRRCKK---NFPEAPDVYNYYGELLLDQNKFDE----AIEKFDTAIELEKETKPMYMNVLP  509 (615)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHH---hCCCChHHHHHHHHHHHHccCHHH----HHHHHHHHHhcCCccccccccHHH
Confidence            7788888888999999999988877   3455 7788888899999999999    9999999877511000111111 1


Q ss_pred             hHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          175 LYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       175 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                      .++.....+...|++++|..++++....++..   .   .++..+...+...|++++|.++|++..+-
T Consensus       510 l~~~a~~~~~~~~~~~eA~~~~~kAl~l~p~~---~---~a~~~la~~~~~~g~~~eAi~~~e~A~~l  571 (615)
T TIGR00990       510 LINKALALFQWKQDFIEAENLCEKALIIDPEC---D---IAVATMAQLLLQQGDVDEALKLFERAAEL  571 (615)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHhcCCCc---H---HHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            12222333445799999999999976543211   1   16888999999999999999999887654

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.47  E-value=5.2e-11  Score=104.14  Aligned_cols=131  Identities=14%  Similarity=0.082  Sum_probs=65.6

Q ss_pred             HHHHHHHHHHHHccCCHHH----HHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCC
Q 043380           93 IFTYATLLMGFRHAKDLQS----LLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNP  167 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~----a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~  167 (246)
                      ...+..+-..+...|++++    |...|++...   ..|+ ...+..+...+...|++++    |...+++..+.     
T Consensus       246 ~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~---l~P~~~~a~~~lg~~l~~~g~~~e----A~~~l~~al~l-----  313 (656)
T PRK15174        246 AALRRSLGLAYYQSGRSREAKLQAAEHWRHALQ---FNSDNVRIVTLYADALIRTGQNEK----AIPLLQQSLAT-----  313 (656)
T ss_pred             HHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHh---hCCCCHHHHHHHHHHHHHCCCHHH----HHHHHHHHHHh-----
Confidence            3344444455555555543    4555555544   3344 4455555555555555555    55555555543     


Q ss_pred             CCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          168 GLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       168 ~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                       -..+...+..+..++...|++++|...++.+...++..    ..  .+..+..++...|+.++|.+.|++..+.
T Consensus       314 -~P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~~P~~----~~--~~~~~a~al~~~G~~deA~~~l~~al~~  381 (656)
T PRK15174        314 -HPDLPYVRAMYARALRQVGQYTAASDEFVQLAREKGVT----SK--WNRYAAAALLQAGKTSEAESVFEHYIQA  381 (656)
T ss_pred             -CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCccc----hH--HHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence             11123444555555666666666666666554332211    00  2233344555666666666666655544

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.47  E-value=4.8e-11  Score=104.37  Aligned_cols=132  Identities=11%  Similarity=-0.019  Sum_probs=72.0

Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhh
Q 043380           97 ATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHL  175 (246)
Q Consensus        97 ~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~  175 (246)
                      ..+..++...|++++|...++....   ..|+ ...+..+...+...|++++-...|...|+...+.      -+.+..+
T Consensus       216 ~~l~~~l~~~g~~~eA~~~~~~al~---~~p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l------~P~~~~a  286 (656)
T PRK15174        216 GLAVDTLCAVGKYQEAIQTGESALA---RGLDGAALRRSLGLAYYQSGRSREAKLQAAEHWRHALQF------NSDNVRI  286 (656)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHhh------CCCCHHH
Confidence            3334445555555555555555554   2233 4445555556666666552000045555555543      1223456


Q ss_pred             HHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhc
Q 043380          176 YVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRW  243 (246)
Q Consensus       176 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  243 (246)
                      +..+...+...|++++|...+++.....+.  .+    .++..+..++...|++++|.+.|+++....
T Consensus       287 ~~~lg~~l~~~g~~~eA~~~l~~al~l~P~--~~----~a~~~La~~l~~~G~~~eA~~~l~~al~~~  348 (656)
T PRK15174        287 VTLYADALIRTGQNEKAIPLLQQSLATHPD--LP----YVRAMYARALRQVGQYTAASDEFVQLAREK  348 (656)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhCCC--CH----HHHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            666666777777777777777766543221  11    145556667777777777777777666543

>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=99.46  E-value=1.3e-10  Score=101.33  Aligned_cols=208  Identities=12%  Similarity=-0.094  Sum_probs=163.5

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHH
Q 043380           15 LNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIF   94 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~   94 (246)
                      .+...|+.+...+...|++++|+..|+......+.+...|..+...+...|++++|...|++..+.        -+.+..
T Consensus       329 ~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~--------~p~~~~  400 (615)
T TIGR00990       329 KEAIALNLRGTFKCLKGKHLEALADLSKSIELDPRVTQSYIKRASMNLELGDPDKAEEDFDKALKL--------NSEDPD  400 (615)
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--------CCCCHH
Confidence            345678888889999999999999999876433445678889999999999999999999999875        234577


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP  173 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~  173 (246)
                      .|..+...+...|++++|...|+...+   +.|+ ...+..+...+.+.|++++    |...|+...+.      .+-+.
T Consensus       401 ~~~~lg~~~~~~g~~~~A~~~~~kal~---l~P~~~~~~~~la~~~~~~g~~~e----A~~~~~~al~~------~P~~~  467 (615)
T TIGR00990       401 IYYHRAQLHFIKGEFAQAGKDYQKSID---LDPDFIFSHIQLGVTQYKEGSIAS----SMATFRRCKKN------FPEAP  467 (615)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHH---cCccCHHHHHHHHHHHHHCCCHHH----HHHHHHHHHHh------CCCCh
Confidence            899999999999999999999999988   5566 7778889999999999999    99999998875      33346


Q ss_pred             hhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhh-hHHHHHHHHHHHhcCChhHHHHHHHHHHhhc
Q 043380          174 HLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQ-EEAGHLLMEAALNDGQVDLALDKLSNTITRW  243 (246)
Q Consensus       174 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  243 (246)
                      ..++.+..++...|++++|.+.|+......+...+.... ...++.....+...|++++|.+++++.....
T Consensus       468 ~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~~~~~eA~~~~~kAl~l~  538 (615)
T TIGR00990       468 DVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWKQDFIEAENLCEKALIID  538 (615)
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcC
Confidence            788999999999999999999999976543321111110 0022223334445799999999999876543

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

Probab=99.43  E-value=1.1e-12  Score=103.39  Aligned_cols=199  Identities=14%  Similarity=0.050  Sum_probs=93.2

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      ++..+..++.. ...+++++|.++++...+. .++...+..++..+.+.++++++.++++.+....      ..+++...
T Consensus        77 ~~~~~~~l~~l-~~~~~~~~A~~~~~~~~~~-~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~------~~~~~~~~  148 (280)
T PF13429_consen   77 NPQDYERLIQL-LQDGDPEEALKLAEKAYER-DGDPRYLLSALQLYYRLGDYDEAEELLEKLEELP------AAPDSARF  148 (280)
T ss_dssp             -------------------------------------------H-HHHTT-HHHHHHHHHHHHH-T---------T-HHH
T ss_pred             ccccccccccc-ccccccccccccccccccc-ccccchhhHHHHHHHHHhHHHHHHHHHHHHHhcc------CCCCCHHH
Confidence            44455566665 5677777777777655321 3555666777777777777888777777766541      33456667


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchh
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPH  174 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~  174 (246)
                      |..+...+.+.|+.++|...+++..+   ..|+ ....+.++..+...|+.++    +.++++...+.      ...|+.
T Consensus       149 ~~~~a~~~~~~G~~~~A~~~~~~al~---~~P~~~~~~~~l~~~li~~~~~~~----~~~~l~~~~~~------~~~~~~  215 (280)
T PF13429_consen  149 WLALAEIYEQLGDPDKALRDYRKALE---LDPDDPDARNALAWLLIDMGDYDE----AREALKRLLKA------APDDPD  215 (280)
T ss_dssp             HHHHHHHHHHCCHHHHHHHHHHHHHH---H-TT-HHHHHHHHHHHCTTCHHHH----HHHHHHHHHHH-------HTSCC
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH---cCCCCHHHHHHHHHHHHHCCChHH----HHHHHHHHHHH------CcCHHH
Confidence            77777777788888888888887777   5565 5667777777777788777    77777777765      244556


Q ss_pred             hHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          175 LYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       175 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      .+..+..+|...|+.++|...|++....++    .++.  ....+.+++...|+.++|.++.++...
T Consensus       216 ~~~~la~~~~~lg~~~~Al~~~~~~~~~~p----~d~~--~~~~~a~~l~~~g~~~~A~~~~~~~~~  276 (280)
T PF13429_consen  216 LWDALAAAYLQLGRYEEALEYLEKALKLNP----DDPL--WLLAYADALEQAGRKDEALRLRRQALR  276 (280)
T ss_dssp             HCHHHHHHHHHHT-HHHHHHHHHHHHHHST----T-HH--HHHHHHHHHT-----------------
T ss_pred             HHHHHHHHhccccccccccccccccccccc----cccc--ccccccccccccccccccccccccccc
Confidence            667777777888888888888887665332    1221  456677777788888888877766543

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.41  E-value=1.5e-10  Score=92.24  Aligned_cols=174  Identities=16%  Similarity=0.111  Sum_probs=138.6

Q ss_pred             CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC
Q 043380           48 EPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL  127 (246)
Q Consensus        48 ~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p  127 (246)
                      +.+..||.+||.+.|+-...+.|.++|++....       ..+.+..+||.+|.+-+-.-+    .++..+|.. ..++|
T Consensus       204 PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~-------k~kv~~~aFN~lI~~~S~~~~----K~Lv~EMis-qkm~P  271 (625)
T KOG4422|consen  204 PKTDETVSIMIAGLCKFSSLERARELYKEHRAA-------KGKVYREAFNGLIGASSYSVG----KKLVAEMIS-QKMTP  271 (625)
T ss_pred             CCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHh-------hheeeHHhhhhhhhHHHhhcc----HHHHHHHHH-hhcCC
Confidence            557789999999999999999999999999987       678999999999988654333    788999999 88999


Q ss_pred             CHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhH-HhhHHHhhC----CC
Q 043380          128 DRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDI-VKSPYRRMW----PD  202 (246)
Q Consensus       128 ~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~-a~~~~~~~~----~~  202 (246)
                      |..|||+++.+.++.|+++.-.-.|.+++.+|++-     |+.|...+|..+|..+++.++..+ +..++.++.    ..
T Consensus       272 nl~TfNalL~c~akfg~F~~ar~aalqil~EmKei-----GVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK  346 (625)
T KOG4422|consen  272 NLFTFNALLSCAAKFGKFEDARKAALQILGEMKEI-----GVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGK  346 (625)
T ss_pred             chHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHh-----CCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccC
Confidence            99999999999999998887333478899999999     999999999999999999999854 444444433    22


Q ss_pred             CCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHH
Q 043380          203 STGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNT  239 (246)
Q Consensus       203 ~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  239 (246)
                      ....+.|.- ..-|...+..|.+..+..-|.++..-+
T Consensus       347 ~fkp~~p~d-~~FF~~AM~Ic~~l~d~~LA~~v~~ll  382 (625)
T KOG4422|consen  347 TFKPITPTD-NKFFQSAMSICSSLRDLELAYQVHGLL  382 (625)
T ss_pred             cccCCCCch-hHHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence            111122221 224677788888888888888876544

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

Probab=99.40  E-value=3.7e-12  Score=100.42  Aligned_cols=202  Identities=15%  Similarity=0.148  Sum_probs=99.8

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      |+..|..+...+-..++.+.|.+.++++...-+-+...+..++.. ...+++++|.+++.+..+.         .++...
T Consensus        43 ~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~~~~~~~~~~l~~l-~~~~~~~~A~~~~~~~~~~---------~~~~~~  112 (280)
T PF13429_consen   43 DPEYWRLLADLAWSLGDYDEAIEAYEKLLASDKANPQDYERLIQL-LQDGDPEEALKLAEKAYER---------DGDPRY  112 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccccccccccc---------ccccch
Confidence            444444445555566777888888777653223345556666666 6777788888877766554         366777


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc-chh
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP-KPH  174 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p-~~~  174 (246)
                      +..++..+.+.++++++.++++.........++...|..+...+.+.|+.++    |.+++++..+.       .| |..
T Consensus       113 l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~----A~~~~~~al~~-------~P~~~~  181 (280)
T PF13429_consen  113 LLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDK----ALRDYRKALEL-------DPDDPD  181 (280)
T ss_dssp             -----H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHH----HHHHHHHHHHH--------TT-HH
T ss_pred             hhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHc-------CCCCHH
Confidence            8889999999999999999999987634445678888899999999999999    99999999886       45 467


Q ss_pred             hHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          175 LYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       175 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      ....++..+...|+.+++..++.......+  ..|.    .+..+..+|...|+.++|..+|++..+..+
T Consensus       182 ~~~~l~~~li~~~~~~~~~~~l~~~~~~~~--~~~~----~~~~la~~~~~lg~~~~Al~~~~~~~~~~p  245 (280)
T PF13429_consen  182 ARNALAWLLIDMGDYDEAREALKRLLKAAP--DDPD----LWDALAAAYLQLGRYEEALEYLEKALKLNP  245 (280)
T ss_dssp             HHHHHHHHHCTTCHHHHHHHHHHHHHHH-H--TSCC----HCHHHHHHHHHHT-HHHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHHHCCChHHHHHHHHHHHHHCc--CHHH----HHHHHHHHhccccccccccccccccccccc
Confidence            888999999999999998888888765431  1122    578899999999999999999999887554

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.37  E-value=5.8e-10  Score=100.64  Aligned_cols=202  Identities=8%  Similarity=-0.060  Sum_probs=149.3

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      .|+......+...+...|++++|...|+.+... +|+...+..+..++.+.|++++|..++++..+.       . +++.
T Consensus       506 ~Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~-~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l-------~-P~~~  576 (987)
T PRK09782        506 QPDAWQHRAVAYQAYQVEDYATALAAWQKISLH-DMSNEDLLAAANTAQAAGNGAARDRWLQQAEQR-------G-LGDN  576 (987)
T ss_pred             CCchHHHHHHHHHHHHCCCHHHHHHHHHHHhcc-CCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhc-------C-CccH
Confidence            355443333344445788888888888877532 455556667777788888999999999888875       2 2233


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP  173 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~  173 (246)
                      ..+..+.....+.|++++|...+++..+   +.|+...|..+...+.+.|++++    |...+++....      -+-+.
T Consensus       577 ~l~~~La~~l~~~Gr~~eAl~~~~~AL~---l~P~~~a~~~LA~~l~~lG~~de----A~~~l~~AL~l------~Pd~~  643 (987)
T PRK09782        577 ALYWWLHAQRYIPGQPELALNDLTRSLN---IAPSANAYVARATIYRQRHNVPA----AVSDLRAALEL------EPNNS  643 (987)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHH---hCCCHHHHHHHHHHHHHCCCHHH----HHHHHHHHHHh------CCCCH
Confidence            3344444455566999999999999888   56788888888999999999999    99999998875      22344


Q ss_pred             hhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhc
Q 043380          174 HLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRW  243 (246)
Q Consensus       174 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  243 (246)
                      ..+..+-.++...|+.++|...+++.....+..    .  .++..+..++...|++++|+..+++..+..
T Consensus       644 ~a~~nLG~aL~~~G~~eeAi~~l~~AL~l~P~~----~--~a~~nLA~al~~lGd~~eA~~~l~~Al~l~  707 (987)
T PRK09782        644 NYQAALGYALWDSGDIAQSREMLERAHKGLPDD----P--ALIRQLAYVNQRLDDMAATQHYARLVIDDI  707 (987)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC----H--HHHHHHHHHHHHCCCHHHHHHHHHHHHhcC
Confidence            677778888999999999999999887654322    1  168889999999999999999998876543

>PRK12370 invasion protein regulator; Provisional

Probab=99.31  E-value=2e-09  Score=92.70  Aligned_cols=181  Identities=13%  Similarity=0.020  Sum_probs=121.2

Q ss_pred             CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc-cHHHHHHHHHHHHccCCH
Q 043380           31 QRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP-DIFTYATLLMGFRHAKDL  109 (246)
Q Consensus        31 g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p-~~~~~~~ll~~~~~~~~~  109 (246)
                      ++.++|...+++...--+.+...+..+-..+...|++++|...|++..+.         .| +...+..+-..+...|++
T Consensus       318 ~~~~~A~~~~~~Al~ldP~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l---------~P~~~~a~~~lg~~l~~~G~~  388 (553)
T PRK12370        318 NAMIKAKEHAIKATELDHNNPQALGLLGLINTIHSEYIVGSLLFKQANLL---------SPISADIKYYYGWNLFMAGQL  388 (553)
T ss_pred             hHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHh---------CCCCHHHHHHHHHHHHHCCCH
Confidence            34678888887765433556677777777777888888888888888875         34 355677777778888888


Q ss_pred             HHHHHHHHHHHhCCCCCCCH-HHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc-hhhHHHHHHHHHhcC
Q 043380          110 QSLLEIVFEMKSCCNLILDR-STFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK-PHLYVSMMHELAARV  187 (246)
Q Consensus       110 ~~a~~~~~~m~~~~~~~p~~-~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~-~~~~~~li~~~~~~g  187 (246)
                      ++|...+++..+   +.|+. ..+..++..+...|++++    |...+++....      ..|+ ...+..+..++...|
T Consensus       389 ~eAi~~~~~Al~---l~P~~~~~~~~~~~~~~~~g~~ee----A~~~~~~~l~~------~~p~~~~~~~~la~~l~~~G  455 (553)
T PRK12370        389 EEALQTINECLK---LDPTRAAAGITKLWITYYHTGIDD----AIRLGDELRSQ------HLQDNPILLSMQVMFLSLKG  455 (553)
T ss_pred             HHHHHHHHHHHh---cCCCChhhHHHHHHHHHhccCHHH----HHHHHHHHHHh------ccccCHHHHHHHHHHHHhCC
Confidence            888888888877   44552 233334445666778888    88888887664      2343 344566677777888


Q ss_pred             ChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          188 DYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       188 ~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      +.++|...+.++....+.    ..  ...+.+...|...|  ++|...++.+.+
T Consensus       456 ~~~eA~~~~~~~~~~~~~----~~--~~~~~l~~~~~~~g--~~a~~~l~~ll~  501 (553)
T PRK12370        456 KHELARKLTKEISTQEIT----GL--IAVNLLYAEYCQNS--ERALPTIREFLE  501 (553)
T ss_pred             CHHHHHHHHHHhhhccch----hH--HHHHHHHHHHhccH--HHHHHHHHHHHH
Confidence            888888888877544321    11  14555666666666  467766666554

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

Probab=99.29  E-value=1.4e-10  Score=96.27  Aligned_cols=162  Identities=12%  Similarity=0.127  Sum_probs=88.0

Q ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-
Q 043380           51 SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-  128 (246)
Q Consensus        51 ~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-  128 (246)
                      ...||.|-+++-..|+..+|...|.+....         .|+ ...-+.|-+.|...|.+++|..+|....+   +.|. 
T Consensus       320 ~~Ay~NlanALkd~G~V~ea~~cYnkaL~l---------~p~hadam~NLgni~~E~~~~e~A~~ly~~al~---v~p~~  387 (966)
T KOG4626|consen  320 PDAYNNLANALKDKGSVTEAVDCYNKALRL---------CPNHADAMNNLGNIYREQGKIEEATRLYLKALE---VFPEF  387 (966)
T ss_pred             hHHHhHHHHHHHhccchHHHHHHHHHHHHh---------CCccHHHHHHHHHHHHHhccchHHHHHHHHHHh---hChhh
Confidence            344555555555555555555555555543         222 23445555555555555555555555554   4455 


Q ss_pred             HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch-hhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCC
Q 043380          129 RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP-HLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTI  207 (246)
Q Consensus       129 ~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  207 (246)
                      ...+|.|...|-..|++++    |+..+++...       +.|+. .+|+.+-..|-..|+++.|...+.+....++.. 
T Consensus       388 aaa~nNLa~i~kqqgnl~~----Ai~~Ykealr-------I~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~~nPt~-  455 (966)
T KOG4626|consen  388 AAAHNNLASIYKQQGNLDD----AIMCYKEALR-------IKPTFADALSNMGNTYKEMGDVSAAIQCYTRAIQINPTF-  455 (966)
T ss_pred             hhhhhhHHHHHHhcccHHH----HHHHHHHHHh-------cCchHHHHHHhcchHHHHhhhHHHHHHHHHHHHhcCcHH-
Confidence            4455555555555555555    5555555543       34543 555666666666666666666666554332211 


Q ss_pred             CchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          208 SPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       208 ~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                           ..+++.|...|-.+|++.+|++-++...+
T Consensus       456 -----AeAhsNLasi~kDsGni~~AI~sY~~aLk  484 (966)
T KOG4626|consen  456 -----AEAHSNLASIYKDSGNIPEAIQSYRTALK  484 (966)
T ss_pred             -----HHHHhhHHHHhhccCCcHHHHHHHHHHHc
Confidence                 12556666666666666666666665544

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.27  E-value=3.8e-09  Score=95.46  Aligned_cols=198  Identities=13%  Similarity=0.024  Sum_probs=153.4

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      +|+...+..+..++.+.|++++|...|+...+..+++...+..+.......|++++|...+++..+.         .|+.
T Consensus       539 ~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l---------~P~~  609 (987)
T PRK09782        539 DMSNEDLLAAANTAQAAGNGAARDRWLQQAEQRGLGDNALYWWLHAQRYIPGQPELALNDLTRSLNI---------APSA  609 (987)
T ss_pred             CCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHh---------CCCH
Confidence            4555566777888999999999999999886433344444444444555669999999999999986         6788


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK  172 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~  172 (246)
                      ..|..+..++.+.|++++|...+++...   ..|+ ...++.+...+...|++++    |+..++...+.      -+-+
T Consensus       610 ~a~~~LA~~l~~lG~~deA~~~l~~AL~---l~Pd~~~a~~nLG~aL~~~G~~ee----Ai~~l~~AL~l------~P~~  676 (987)
T PRK09782        610 NAYVARATIYRQRHNVPAAVSDLRAALE---LEPNNSNYQAALGYALWDSGDIAQ----SREMLERAHKG------LPDD  676 (987)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHCCCHHH----HHHHHHHHHHh------CCCC
Confidence            8999999999999999999999999998   5677 6778888899999999999    99999999885      2335


Q ss_pred             hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHH
Q 043380          173 PHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNT  239 (246)
Q Consensus       173 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  239 (246)
                      ...+..+..++...|++++|...+++.....+....      +.-..-....+..+++.|.+-+++-
T Consensus       677 ~~a~~nLA~al~~lGd~~eA~~~l~~Al~l~P~~a~------i~~~~g~~~~~~~~~~~a~~~~~r~  737 (987)
T PRK09782        677 PALIRQLAYVNQRLDDMAATQHYARLVIDDIDNQAL------ITPLTPEQNQQRFNFRRLHEEVGRR  737 (987)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCch------hhhhhhHHHHHHHHHHHHHHHHHHH
Confidence            578999999999999999999999998765432211      2233444455556666666655543

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.27  E-value=4.3e-09  Score=79.92  Aligned_cols=168  Identities=8%  Similarity=-0.053  Sum_probs=139.5

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      +.+...+..+...+...|++++|.+.|++.....+.+...+..+...+...|++++|.+.+.+.....      ......
T Consensus        62 p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~------~~~~~~  135 (234)
T TIGR02521        62 PDDYLAYLALALYYQQLGELEKAEDSFRRALTLNPNNGDVLNNYGTFLCQQGKYEQAMQQFEQAIEDP------LYPQPA  135 (234)
T ss_pred             cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHhcc------ccccch
Confidence            44577888899999999999999999998764445667788889999999999999999999998751      122345


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK  172 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~  172 (246)
                      ..+..+..++...|++++|...+++...   ..|+ ...+..+...+...|++++    |...+++....      ...+
T Consensus       136 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~~~~la~~~~~~~~~~~----A~~~~~~~~~~------~~~~  202 (234)
T TIGR02521       136 RSLENAGLCALKAGDFDKAEKYLTRALQ---IDPQRPESLLELAELYYLRGQYKD----ARAYLERYQQT------YNQT  202 (234)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCcCChHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh------CCCC
Confidence            5777788889999999999999999988   3344 6678889999999999999    99999998875      2345


Q ss_pred             hhhHHHHHHHHHhcCChhHHhhHHHhhC
Q 043380          173 PHLYVSMMHELAARVDYDIVKSPYRRMW  200 (246)
Q Consensus       173 ~~~~~~li~~~~~~g~~~~a~~~~~~~~  200 (246)
                      ...+..+...+...|+.++|..+.+.+.
T Consensus       203 ~~~~~~~~~~~~~~~~~~~a~~~~~~~~  230 (234)
T TIGR02521       203 AESLWLGIRIARALGDVAAAQRYGAQLQ  230 (234)
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            6777788889999999999999988765

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.

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

Probab=99.24  E-value=3.7e-10  Score=93.76  Aligned_cols=193  Identities=12%  Similarity=0.102  Sum_probs=99.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-HHHHHH
Q 043380           20 MNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-IFTYAT   98 (246)
Q Consensus        20 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~~~   98 (246)
                      |-.|-+.|-..+.+++|..-|.+...--+.....+..|-..|-..|.+|.|...|++.++.         .|+ ...|+.
T Consensus       255 YiNLGnV~ke~~~~d~Avs~Y~rAl~lrpn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~---------~P~F~~Ay~N  325 (966)
T KOG4626|consen  255 YINLGNVYKEARIFDRAVSCYLRALNLRPNHAVAHGNLACIYYEQGLLDLAIDTYKRALEL---------QPNFPDAYNN  325 (966)
T ss_pred             HhhHHHHHHHHhcchHHHHHHHHHHhcCCcchhhccceEEEEeccccHHHHHHHHHHHHhc---------CCCchHHHhH
Confidence            3334444444444444444443332111222333444444444455555555555555543         343 335666


Q ss_pred             HHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc-hhhH
Q 043380           99 LLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK-PHLY  176 (246)
Q Consensus        99 ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~-~~~~  176 (246)
                      |..++-..|+..+|.+.|+....   +.|+ ..+.+.|...|...|.+++    |.++|.....-       .|. ....
T Consensus       326 lanALkd~G~V~ea~~cYnkaL~---l~p~hadam~NLgni~~E~~~~e~----A~~ly~~al~v-------~p~~aaa~  391 (966)
T KOG4626|consen  326 LANALKDKGSVTEAVDCYNKALR---LCPNHADAMNNLGNIYREQGKIEE----ATRLYLKALEV-------FPEFAAAH  391 (966)
T ss_pred             HHHHHHhccchHHHHHHHHHHHH---hCCccHHHHHHHHHHHHHhccchH----HHHHHHHHHhh-------Chhhhhhh
Confidence            66666666666666666666555   3444 4555556666666666666    66666555442       333 2455


Q ss_pred             HHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          177 VSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       177 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      +.|...|-.+|+.++|...+++...-     .|.. ..+|+.+-..|-..|+++.|.+.+.+-..
T Consensus       392 nNLa~i~kqqgnl~~Ai~~YkealrI-----~P~f-Ada~~NmGnt~ke~g~v~~A~q~y~rAI~  450 (966)
T KOG4626|consen  392 NNLASIYKQQGNLDDAIMCYKEALRI-----KPTF-ADALSNMGNTYKEMGDVSAAIQCYTRAIQ  450 (966)
T ss_pred             hhHHHHHHhcccHHHHHHHHHHHHhc-----CchH-HHHHHhcchHHHHhhhHHHHHHHHHHHHh
Confidence            66666666666666666666665432     2221 11466666666666666666666655443

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.22  E-value=1.1e-08  Score=95.34  Aligned_cols=210  Identities=10%  Similarity=0.035  Sum_probs=136.1

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCC------------
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQK------------   83 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~------------   83 (246)
                      ++..+..+...|.+.|++++|...|+.+.+..+.+...+..+...+...++.++|...++.+......            
T Consensus       494 ~~~~~~~LA~~~~~~G~~~~A~~~l~~al~~~P~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~  573 (1157)
T PRK11447        494 SVWLTYRLAQDLRQAGQRSQADALMRRLAQQKPNDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQS  573 (1157)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhh
Confidence            45566677778888888888888887765322334444433333344455555555555443211000            


Q ss_pred             ---------------------CCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHh
Q 043380           84 ---------------------CSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLY  141 (246)
Q Consensus        84 ---------------------~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~  141 (246)
                                           +.. ..+++...+..+...+.+.|++++|...|+...+   ..|+ ...+..+...|..
T Consensus       574 ~~~l~~a~~l~~~G~~~eA~~~l~-~~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~---~~P~~~~a~~~la~~~~~  649 (1157)
T PRK11447        574 DQVLETANRLRDSGKEAEAEALLR-QQPPSTRIDLTLADWAQQRGDYAAARAAYQRVLT---REPGNADARLGLIEVDIA  649 (1157)
T ss_pred             hHHHHHHHHHHHCCCHHHHHHHHH-hCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHH
Confidence                                 000 0123444566777778888888899888888887   3455 7778888888888


Q ss_pred             cCChhhhhhHHHHHHHHHHHhhcCCCCCCc-chhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchh-hhHHHHHH
Q 043380          142 SGSIKVVGLYALCIFGEIVKRVCSNPGLWP-KPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEV-QEEAGHLL  219 (246)
Q Consensus       142 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~-~~~~~~~l  219 (246)
                      .|++++    |.+.++...+.       .| +..++..+..++...|++++|.++++.+...... .++.. ....+..+
T Consensus       650 ~g~~~e----A~~~l~~ll~~-------~p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~~~-~~~~~~~a~~~~~~  717 (1157)
T PRK11447        650 QGDLAA----ARAQLAKLPAT-------ANDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQAKS-QPPSMESALVLRDA  717 (1157)
T ss_pred             CCCHHH----HHHHHHHHhcc-------CCCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhhCcc-CCcchhhHHHHHHH
Confidence            999999    99888877653       33 3456667778888889999999999987654321 11210 11145556


Q ss_pred             HHHHHhcCChhHHHHHHHHHHh
Q 043380          220 MEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       220 i~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      ...+...|++++|.+.|+....
T Consensus       718 a~~~~~~G~~~~A~~~y~~Al~  739 (1157)
T PRK11447        718 ARFEAQTGQPQQALETYKDAMV  739 (1157)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHh
Confidence            7778888999999999887753

>PRK11189 lipoprotein NlpI; Provisional

Probab=99.22  E-value=1.6e-08  Score=80.29  Aligned_cols=200  Identities=9%  Similarity=-0.079  Sum_probs=144.7

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-HHH
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-IFT   95 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~   95 (246)
                      ...|..+-..|.+.|+.++|...|++..+.-+.+...|+.+-..+...|++++|.+.|++..+.         .|+ ..+
T Consensus        64 a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l---------~P~~~~a  134 (296)
T PRK11189         64 AQLHYERGVLYDSLGLRALARNDFSQALALRPDMADAYNYLGIYLTQAGNFDAAYEAFDSVLEL---------DPTYNYA  134 (296)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh---------CCCCHHH
Confidence            4567788888999999999999998876544667899999999999999999999999999975         454 668


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhh
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHL  175 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~  175 (246)
                      |..+..++...|++++|.+.|+....   ..|+..........+...++.++    |...|......      ..|+...
T Consensus       135 ~~~lg~~l~~~g~~~eA~~~~~~al~---~~P~~~~~~~~~~l~~~~~~~~~----A~~~l~~~~~~------~~~~~~~  201 (296)
T PRK11189        135 YLNRGIALYYGGRYELAQDDLLAFYQ---DDPNDPYRALWLYLAESKLDPKQ----AKENLKQRYEK------LDKEQWG  201 (296)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHccCCHHH----HHHHHHHHHhh------CCccccH
Confidence            88888899999999999999999988   45664322223333455678999    99999776543      3333322


Q ss_pred             HHHHHHHHHhcCChhHHhhHHHhhCCCCCC--CCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhc
Q 043380          176 YVSMMHELAARVDYDIVKSPYRRMWPDSTG--TISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRW  243 (246)
Q Consensus       176 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~--~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  243 (246)
                      + .+  .....|+...+ ..+..+......  ...|. ...+|..+...+...|++++|...|++..+..
T Consensus       202 ~-~~--~~~~lg~~~~~-~~~~~~~~~~~~~~~l~~~-~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~~  266 (296)
T PRK11189        202 W-NI--VEFYLGKISEE-TLMERLKAGATDNTELAER-LCETYFYLAKYYLSLGDLDEAAALFKLALANN  266 (296)
T ss_pred             H-HH--HHHHccCCCHH-HHHHHHHhcCCCcHHHHHH-HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            2 22  23345666554 344444321110  11111 12378999999999999999999999887644

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.19  E-value=1.3e-08  Score=94.90  Aligned_cols=199  Identities=9%  Similarity=-0.019  Sum_probs=145.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHH
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYAT   98 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~   98 (246)
                      .+..+...+...|++++|.+.|++..+..+-+...+..+...|.+.|++++|...++++.+.        .+.+...+..
T Consensus       463 ~~~~~a~~~~~~g~~~eA~~~~~~Al~~~P~~~~~~~~LA~~~~~~G~~~~A~~~l~~al~~--------~P~~~~~~~a  534 (1157)
T PRK11447        463 RLAQQAEALENQGKWAQAAELQRQRLALDPGSVWLTYRLAQDLRQAGQRSQADALMRRLAQQ--------KPNDPEQVYA  534 (1157)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--------CCCCHHHHHH
Confidence            34556677888999999999999987544556777888999999999999999999999875        1223333333


Q ss_pred             HHHHHHccCCHHHHHHHHHHHHhCC---------------------------------------CCCCCHHHHHHHHHHH
Q 043380           99 LLMGFRHAKDLQSLLEIVFEMKSCC---------------------------------------NLILDRSTFTAMVDAL  139 (246)
Q Consensus        99 ll~~~~~~~~~~~a~~~~~~m~~~~---------------------------------------~~~p~~~~~~~li~~~  139 (246)
                      +...+...++.++|...++.+.. .                                       ..+++...+..+...+
T Consensus       535 ~al~l~~~~~~~~Al~~l~~l~~-~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~~l~~~p~~~~~~~~La~~~  613 (1157)
T PRK11447        535 YGLYLSGSDRDRAALAHLNTLPR-AQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEALLRQQPPSTRIDLTLADWA  613 (1157)
T ss_pred             HHHHHHhCCCHHHHHHHHHhCCc-hhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHHHHHhCCCCchHHHHHHHHH
Confidence            33333444555555444443211 0                                       0123455677788899


Q ss_pred             HhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHH
Q 043380          140 LYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLL  219 (246)
Q Consensus       140 ~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~l  219 (246)
                      ...|++++    |+..|+...+.      -+.+...+..+...|...|++++|.+.++.+....+    ....  ++..+
T Consensus       614 ~~~g~~~~----A~~~y~~al~~------~P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~~p----~~~~--~~~~l  677 (1157)
T PRK11447        614 QQRGDYAA----ARAAYQRVLTR------EPGNADARLGLIEVDIAQGDLAAARAQLAKLPATAN----DSLN--TQRRV  677 (1157)
T ss_pred             HHcCCHHH----HHHHHHHHHHh------CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhccCC----CChH--HHHHH
Confidence            99999999    99999999886      233568899999999999999999999998865432    1121  56678


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhh
Q 043380          220 MEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       220 i~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                      ..++...|++++|.++++.+...
T Consensus       678 a~~~~~~g~~~eA~~~~~~al~~  700 (1157)
T PRK11447        678 ALAWAALGDTAAAQRTFNRLIPQ  700 (1157)
T ss_pred             HHHHHhCCCHHHHHHHHHHHhhh
Confidence            88899999999999999998764

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

Probab=99.18  E-value=1.6e-09  Score=90.40  Aligned_cols=160  Identities=13%  Similarity=0.069  Sum_probs=96.4

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHh----------------------------------CCCCCHHHHHHHHHHHHh
Q 043380           18 IVMNAVIEASREAQRIDEAYQILESVEK----------------------------------GLEPDSLSYNILISACIK   63 (246)
Q Consensus        18 ~~~~~li~~~~~~g~~~~a~~~~~~~~~----------------------------------~~~~~~~t~~~li~~~~~   63 (246)
                      .+-.-+-.+|...++.++|+++|+.+++                                  --+-.+.||.++-++|.-
T Consensus       354 wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~Ls~Laq~Li~~~~~sPesWca~GNcfSL  433 (638)
T KOG1126|consen  354 WVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVALSYLAQDLIDTDPNSPESWCALGNCFSL  433 (638)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhHHHHHHHHHHHhhCCCCcHHHHHhcchhhh
Confidence            4445567788888888888888888763                                  224456788888888888


Q ss_pred             cCCcchHHHHHHHHHhccCCCCCCCCCc-cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHh
Q 043380           64 TKKLDVTMPFNEQLKDNGQKCSSGGFHP-DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLY  141 (246)
Q Consensus        64 ~~~~~~a~~~~~~m~~~~~~~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~  141 (246)
                      .++.+.|++.|++.++.         .| ...+|+.+-.-+.....+|.|...|+....   +.|. -..|..+...|.+
T Consensus       434 Qkdh~~Aik~f~RAiQl---------dp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~---~~~rhYnAwYGlG~vy~K  501 (638)
T KOG1126|consen  434 QKDHDTAIKCFKRAIQL---------DPRFAYAYTLLGHESIATEEFDKAMKSFRKALG---VDPRHYNAWYGLGTVYLK  501 (638)
T ss_pred             hhHHHHHHHHHHHhhcc---------CCccchhhhhcCChhhhhHHHHhHHHHHHhhhc---CCchhhHHHHhhhhheec
Confidence            88888898888888875         34 445555555555555555555555555444   2222 1223344455555


Q ss_pred             cCChhhhhhHHHHHHHHHHHhhcCCCCCCc-chhhHHHHHHHHHhcCChhHHhhHHHhhC
Q 043380          142 SGSIKVVGLYALCIFGEIVKRVCSNPGLWP-KPHLYVSMMHELAARVDYDIVKSPYRRMW  200 (246)
Q Consensus       142 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~  200 (246)
                      .++++.    |+-.|+...+.       .| +.+...++...+-+.|+.|+|..++++..
T Consensus       502 qek~e~----Ae~~fqkA~~I-------NP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~  550 (638)
T KOG1126|consen  502 QEKLEF----AEFHFQKAVEI-------NPSNSVILCHIGRIQHQLKRKDKALQLYEKAI  550 (638)
T ss_pred             cchhhH----HHHHHHhhhcC-------CccchhHHhhhhHHHHHhhhhhHHHHHHHHHH
Confidence            555555    55555554442       22 23444445555555555555555555544

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.15  E-value=2.5e-08  Score=89.15  Aligned_cols=197  Identities=11%  Similarity=-0.006  Sum_probs=150.3

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCC--CCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCC--ccHHHHHHH
Q 043380           24 IEASREAQRIDEAYQILESVEKGLE--PDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFH--PDIFTYATL   99 (246)
Q Consensus        24 i~~~~~~g~~~~a~~~~~~~~~~~~--~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~--p~~~~~~~l   99 (246)
                      +..+...|+.++|+..|+.+.+.-+  |+. .-..+..+|...|++++|...|+++.+..      ...  +.......|
T Consensus       244 l~~Ll~~g~~~eA~~~~~~ll~~~~~~P~~-a~~~la~~yl~~g~~e~A~~~l~~~l~~~------p~~~~~~~~~~~~L  316 (765)
T PRK10049        244 LGALLARDRYKDVISEYQRLKAEGQIIPPW-AQRWVASAYLKLHQPEKAQSILTELFYHP------ETIADLSDEELADL  316 (765)
T ss_pred             HHHHHHhhhHHHHHHHHHHhhccCCCCCHH-HHHHHHHHHHhcCCcHHHHHHHHHHhhcC------CCCCCCChHHHHHH
Confidence            3445677999999999999874221  322 22225678999999999999999988651      111  113456677


Q ss_pred             HHHHHccCCHHHHHHHHHHHHhCCC-----------CCCC---HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcC
Q 043380          100 LMGFRHAKDLQSLLEIVFEMKSCCN-----------LILD---RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCS  165 (246)
Q Consensus       100 l~~~~~~~~~~~a~~~~~~m~~~~~-----------~~p~---~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~  165 (246)
                      ..++...|++++|..+++.+.. ..           -.|+   ...+..+...+...|+.++    |+++++++...   
T Consensus       317 ~~a~~~~g~~~eA~~~l~~~~~-~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~e----A~~~l~~al~~---  388 (765)
T PRK10049        317 FYSLLESENYPGALTVTAHTIN-NSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQ----AEMRARELAYN---  388 (765)
T ss_pred             HHHHHhcccHHHHHHHHHHHhh-cCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh---
Confidence            7788999999999999999988 31           1233   2355678889999999999    99999999886   


Q ss_pred             CCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          166 NPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       166 ~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                         .+-+...+..+...+...|++++|++.+++.....+..    ..  .+..+...+...|++++|+++++++.+..+
T Consensus       389 ---~P~n~~l~~~lA~l~~~~g~~~~A~~~l~~al~l~Pd~----~~--l~~~~a~~al~~~~~~~A~~~~~~ll~~~P  458 (765)
T PRK10049        389 ---APGNQGLRIDYASVLQARGWPRAAENELKKAEVLEPRN----IN--LEVEQAWTALDLQEWRQMDVLTDDVVAREP  458 (765)
T ss_pred             ---CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhCCCC----hH--HHHHHHHHHHHhCCHHHHHHHHHHHHHhCC
Confidence               34456889999999999999999999999988654322    22  566677789999999999999999987654

>PRK12370 invasion protein regulator; Provisional

Probab=99.15  E-value=1.3e-08  Score=87.76  Aligned_cols=200  Identities=10%  Similarity=-0.039  Sum_probs=147.2

Q ss_pred             cCHHHHHHHHHHHHh-----cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHh---------cCCcchHHHHHHHHHhc
Q 043380           15 LNTIVMNAVIEASRE-----AQRIDEAYQILESVEKGLEPDSLSYNILISACIK---------TKKLDVTMPFNEQLKDN   80 (246)
Q Consensus        15 ~~~~~~~~li~~~~~-----~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~---------~~~~~~a~~~~~~m~~~   80 (246)
                      .+...|...+.+-..     .+..++|.+.|++...--+-+...|..+..++..         .+++++|...+++..+.
T Consensus       254 ~~~da~~~~lrg~~~~~~~~~~~~~~A~~~~~~Al~ldP~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~l  333 (553)
T PRK12370        254 NSIDSTMVYLRGKHELNQYTPYSLQQALKLLTQCVNMSPNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATEL  333 (553)
T ss_pred             CChHHHHHHHHhHHHHHccCHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHhc
Confidence            455566666666322     2346789999988764334455566655555442         23478999999999986


Q ss_pred             cCCCCCCCCCc-cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHH
Q 043380           81 GQKCSSGGFHP-DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGE  158 (246)
Q Consensus        81 ~~~~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~  158 (246)
                               .| +...+..+-..+...|++++|...|++..+   ..|+ ...+..+...+...|++++    |...+++
T Consensus       334 ---------dP~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~---l~P~~~~a~~~lg~~l~~~G~~~e----Ai~~~~~  397 (553)
T PRK12370        334 ---------DHNNPQALGLLGLINTIHSEYIVGSLLFKQANL---LSPISADIKYYYGWNLFMAGQLEE----ALQTINE  397 (553)
T ss_pred             ---------CCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHCCCHHH----HHHHHHH
Confidence                     44 566788888888999999999999999998   5576 6678889999999999999    9999999


Q ss_pred             HHHhhcCCCCCCcch-hhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHH
Q 043380          159 IVKRVCSNPGLWPKP-HLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLS  237 (246)
Q Consensus       159 m~~~~~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~  237 (246)
                      ..+.       .|+. ..+..+...+...|++++|...+++....... -.+.    .+..+..++...|++++|.+.++
T Consensus       398 Al~l-------~P~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~~p-~~~~----~~~~la~~l~~~G~~~eA~~~~~  465 (553)
T PRK12370        398 CLKL-------DPTRAAAGITKLWITYYHTGIDDAIRLGDELRSQHLQ-DNPI----LLSMQVMFLSLKGKHELARKLTK  465 (553)
T ss_pred             HHhc-------CCCChhhHHHHHHHHHhccCHHHHHHHHHHHHHhccc-cCHH----HHHHHHHHHHhCCCHHHHHHHHH
Confidence            9886       3443 23344555677789999999999987643211 1111    46778888899999999999998


Q ss_pred             HHHhh
Q 043380          238 NTITR  242 (246)
Q Consensus       238 ~m~~~  242 (246)
                      ++...
T Consensus       466 ~~~~~  470 (553)
T PRK12370        466 EISTQ  470 (553)
T ss_pred             Hhhhc
Confidence            87654

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

Probab=99.13  E-value=1.2e-09  Score=93.82  Aligned_cols=171  Identities=16%  Similarity=0.166  Sum_probs=132.9

Q ss_pred             hhHHHHhcccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH-h------------------------CCCCCHHHHHHHH
Q 043380            4 ENEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVE-K------------------------GLEPDSLSYNILI   58 (246)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~-~------------------------~~~~~~~t~~~li   58 (246)
                      -+..++..|+.|+.+||..+|.-||..|+++.|- +|..|+ +                        .-.|...||..|+
T Consensus        12 fla~~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpkep~aDtyt~Ll   90 (1088)
T KOG4318|consen   12 FLALHEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPKEPLADTYTNLL   90 (1088)
T ss_pred             HHHHHHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCCCCchhHHHHHH
Confidence            3567888999999999999999999999999998 888775 3                        2357788999999


Q ss_pred             HHHHhcCCcchHHHHHHHHHh-------ccC-----------CCC-----------------------------------
Q 043380           59 SACIKTKKLDVTMPFNEQLKD-------NGQ-----------KCS-----------------------------------   85 (246)
Q Consensus        59 ~~~~~~~~~~~a~~~~~~m~~-------~~~-----------~~~-----------------------------------   85 (246)
                      .+|...|++..-..+=+.|..       .|.           .+.                                   
T Consensus        91 ~ayr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~eglwaqllkll~~~Pvsa~  170 (1088)
T KOG4318|consen   91 KAYRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVLEGLWAQLLKLLAKVPVSAW  170 (1088)
T ss_pred             HHHHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHHHHHHHHHHHHHhhCCcccc
Confidence            999999987652222111221       120           000                                   


Q ss_pred             -------------------------CCCC-CccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHH
Q 043380           86 -------------------------SGGF-HPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDAL  139 (246)
Q Consensus        86 -------------------------~~~~-~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~  139 (246)
                                               .... .|++.+|..++.+-..+|+.+.|..++.+|++ .|+..+.+-|..|+-+ 
T Consensus       171 ~~p~~vfLrqnv~~ntpvekLl~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll~emke-~gfpir~HyFwpLl~g-  248 (1088)
T KOG4318|consen  171 NAPFQVFLRQNVVDNTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLLYEMKE-KGFPIRAHYFWPLLLG-  248 (1088)
T ss_pred             cchHHHHHHHhccCCchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHHHHHHH-cCCCcccccchhhhhc-
Confidence                                     1111 58888999999999999999999999999999 9998888888877766 


Q ss_pred             HhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCC
Q 043380          140 LYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVD  188 (246)
Q Consensus       140 ~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~  188 (246)
                        .++...    +..+...|...     |+.|+..|+..-+..+...|.
T Consensus       249 --~~~~q~----~e~vlrgmqe~-----gv~p~seT~adyvip~l~N~~  286 (1088)
T KOG4318|consen  249 --INAAQV----FEFVLRGMQEK-----GVQPGSETQADYVIPQLSNGQ  286 (1088)
T ss_pred             --CccchH----HHHHHHHHHHh-----cCCCCcchhHHHHHhhhcchh
Confidence              778888    88888889888     899999998887777776444

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.13  E-value=5.7e-08  Score=80.41  Aligned_cols=206  Identities=9%  Similarity=0.029  Sum_probs=148.1

Q ss_pred             cCcCHHHHH--HHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCC-----
Q 043380           13 WKLNTIVMN--AVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCS-----   85 (246)
Q Consensus        13 ~~~~~~~~~--~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~-----   85 (246)
                      ..|+...+.  .....+...|+.+.|...++......+-+......+...|.+.|++++|.+++..+.+.+....     
T Consensus       147 ~~~~~~~~~~l~~a~l~l~~g~~~~Al~~l~~~~~~~P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~  226 (398)
T PRK10747        147 LADNDQLPVEITRVRIQLARNENHAARHGVDKLLEVAPRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAM  226 (398)
T ss_pred             cCCcchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHH
Confidence            345544333  3356888899999999999998765566788899999999999999999999999987631100     


Q ss_pred             -----------------------------CCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHH
Q 043380           86 -----------------------------SGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMV  136 (246)
Q Consensus        86 -----------------------------~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li  136 (246)
                                                   ....+.+......+..++...|+.++|..++++..+   ..||...  .++
T Consensus       227 l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~---~~~~~~l--~~l  301 (398)
T PRK10747        227 LEQQAWIGLMDQAMADQGSEGLKRWWKNQSRKTRHQVALQVAMAEHLIECDDHDTAQQIILDGLK---RQYDERL--VLL  301 (398)
T ss_pred             HHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHHHhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh---cCCCHHH--HHH
Confidence                                         001112334455566777778888888888887776   3344422  234


Q ss_pred             HHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHH
Q 043380          137 DALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAG  216 (246)
Q Consensus       137 ~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  216 (246)
                      .+....++.++    +.+..+...+.      .+-|...+.++-..+.+.+++++|.+.|+......     |+..  +|
T Consensus       302 ~~~l~~~~~~~----al~~~e~~lk~------~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~~-----P~~~--~~  364 (398)
T PRK10747        302 IPRLKTNNPEQ----LEKVLRQQIKQ------HGDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQR-----PDAY--DY  364 (398)
T ss_pred             HhhccCCChHH----HHHHHHHHHhh------CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-----CCHH--HH
Confidence            44455688888    88888887775      33344667888899999999999999999987543     2221  57


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHH
Q 043380          217 HLLMEAALNDGQVDLALDKLSNTI  240 (246)
Q Consensus       217 ~~li~~~~~~g~~~~a~~~~~~m~  240 (246)
                      ..+...+.+.|+.++|.+++++-.
T Consensus       365 ~~La~~~~~~g~~~~A~~~~~~~l  388 (398)
T PRK10747        365 AWLADALDRLHKPEEAAAMRRDGL  388 (398)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHH
Confidence            788999999999999999988653

>PF12854 PPR_1: PPR repeat

Probab=99.13  E-value=9.8e-11  Score=60.74  Aligned_cols=32  Identities=22%  Similarity=0.502  Sum_probs=20.1

Q ss_pred             ccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 043380           12 HWKLNTIVMNAVIEASREAQRIDEAYQILESV   43 (246)
Q Consensus        12 ~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~   43 (246)
                      |+.||..+||+||++|++.|++++|.++|++|
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            45666666666666666666666666666655

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

Probab=99.12  E-value=5.8e-08  Score=75.00  Aligned_cols=201  Identities=15%  Similarity=0.124  Sum_probs=147.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHH------HHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVEKGLEPDSL------SYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~------t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      +--+|-+.|-+.|.+|+|+.+.+.+..  .||..      ..-.|-.-|...|-+|.|+.+|..+.+.+        +--
T Consensus        71 ~~ltLGnLfRsRGEvDRAIRiHQ~L~~--spdlT~~qr~lAl~qL~~Dym~aGl~DRAE~~f~~L~de~--------efa  140 (389)
T COG2956          71 AHLTLGNLFRSRGEVDRAIRIHQTLLE--SPDLTFEQRLLALQQLGRDYMAAGLLDRAEDIFNQLVDEG--------EFA  140 (389)
T ss_pred             HHHHHHHHHHhcchHHHHHHHHHHHhc--CCCCchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhcch--------hhh
Confidence            334567778888999999999888763  45422      22345566777888999999999988752        233


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC----HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCC
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD----RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPG  168 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~----~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~  168 (246)
                      ......|+..|-...+|++|.++-+++.+ .+-.+.    ...|--+...+....+++.    |..+++...+.+     
T Consensus       141 ~~AlqqLl~IYQ~treW~KAId~A~~L~k-~~~q~~~~eIAqfyCELAq~~~~~~~~d~----A~~~l~kAlqa~-----  210 (389)
T COG2956         141 EGALQQLLNIYQATREWEKAIDVAERLVK-LGGQTYRVEIAQFYCELAQQALASSDVDR----ARELLKKALQAD-----  210 (389)
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHH-cCCccchhHHHHHHHHHHHHHhhhhhHHH----HHHHHHHHHhhC-----
Confidence            45677889999999999999999888877 433332    1235556666667788888    898888877751     


Q ss_pred             CCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhccC
Q 043380          169 LWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWKG  245 (246)
Q Consensus       169 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~  245 (246)
                       +-++..-..+-+.+...|+++.|.+.++.+.+.++..++     .+-..|..+|...|++++....+.++.+..+|
T Consensus       211 -~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~-----evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~~g  281 (389)
T COG2956         211 -KKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLS-----EVLEMLYECYAQLGKPAEGLNFLRRAMETNTG  281 (389)
T ss_pred             -ccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHH-----HHHHHHHHHHHHhCCHHHHHHHHHHHHHccCC
Confidence             223344445667888999999999999999887754433     25688999999999999999999988876665

>TIGR00540 hemY_coli hemY protein

Probab=99.10  E-value=8e-08  Score=79.88  Aligned_cols=200  Identities=10%  Similarity=0.020  Sum_probs=136.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCC--------------
Q 043380           20 MNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCS--------------   85 (246)
Q Consensus        20 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~--------------   85 (246)
                      --.....+...|+.+.|...++.+.+..+-+...+..+...+...|++++|.+++..+.+.+....              
T Consensus       156 ~~~~a~l~l~~~~~~~Al~~l~~l~~~~P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~  235 (409)
T TIGR00540       156 EIARTRILLAQNELHAARHGVDKLLEMAPRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGL  235 (409)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHH
Confidence            333466777788888888888887754455667788888888888888888888888886632100              


Q ss_pred             ------C---------CCCCc-----cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHH---HHHHHHHHHhc
Q 043380           86 ------S---------GGFHP-----DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRST---FTAMVDALLYS  142 (246)
Q Consensus        86 ------~---------~~~~p-----~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~---~~~li~~~~~~  142 (246)
                            .         -.-.|     +...+..+...+...|+.++|.+++++..+   ..||...   ...........
T Consensus       236 l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~---~~pd~~~~~~~~l~~~~~l~~  312 (409)
T TIGR00540       236 LDEAMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLK---KLGDDRAISLPLCLPIPRLKP  312 (409)
T ss_pred             HHHHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHh---hCCCcccchhHHHHHhhhcCC
Confidence                  0         00012     556677777778888888888888888877   3355432   11122222334


Q ss_pred             CChhhhhhHHHHHHHHHHHhhcCCCCCCcch---hhHHHHHHHHHhcCChhHHhhHHHh--hCCCCCCCCCchhhhHHHH
Q 043380          143 GSIKVVGLYALCIFGEIVKRVCSNPGLWPKP---HLYVSMMHELAARVDYDIVKSPYRR--MWPDSTGTISPEVQEEAGH  217 (246)
Q Consensus       143 ~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~---~~~~~li~~~~~~g~~~~a~~~~~~--~~~~~~~~~~~~~~~~~~~  217 (246)
                      ++.+.    +.+.++...+.       .|+.   ....++-..+.+.|++++|.+.|+.  ....     .|+..  .+.
T Consensus       313 ~~~~~----~~~~~e~~lk~-------~p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~-----~p~~~--~~~  374 (409)
T TIGR00540       313 EDNEK----LEKLIEKQAKN-------VDDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKE-----QLDAN--DLA  374 (409)
T ss_pred             CChHH----HHHHHHHHHHh-------CCCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhc-----CCCHH--HHH
Confidence            66677    77777776664       3333   4566888899999999999999994  3222     22222  567


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHH
Q 043380          218 LLMEAALNDGQVDLALDKLSNTI  240 (246)
Q Consensus       218 ~li~~~~~~g~~~~a~~~~~~m~  240 (246)
                      .+...+.+.|+.++|.+++++-.
T Consensus       375 ~La~ll~~~g~~~~A~~~~~~~l  397 (409)
T TIGR00540       375 MAADAFDQAGDKAEAAAMRQDSL  397 (409)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHH
Confidence            89999999999999999998753

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.

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.10  E-value=1.5e-07  Score=84.21  Aligned_cols=209  Identities=17%  Similarity=0.071  Sum_probs=143.9

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      +.+...+..+..++.+.|++++|.++|++....-+.+...+..+...+...|++++|...++++.+.        .+.+.
T Consensus        46 ~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~l~~~g~~~eA~~~l~~~l~~--------~P~~~  117 (765)
T PRK10049         46 QLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLEPQNDDYQRGLILTLADAGQYDEALVKAKQLVSG--------APDKA  117 (765)
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--------CCCCH
Confidence            4455568899999999999999999999876444566777888888999999999999999999885        23345


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHH----------------
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIF----------------  156 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~----------------  156 (246)
                      . +..+..++...|+.++|+..+++..+   ..|+ ...+..+...+...+..+.    |+..+                
T Consensus       118 ~-~~~la~~l~~~g~~~~Al~~l~~al~---~~P~~~~~~~~la~~l~~~~~~e~----Al~~l~~~~~~p~~~~~l~~~  189 (765)
T PRK10049        118 N-LLALAYVYKRAGRHWDELRAMTQALP---RAPQTQQYPTEYVQALRNNRLSAP----ALGAIDDANLTPAEKRDLEAD  189 (765)
T ss_pred             H-HHHHHHHHHHCCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHCCChHH----HHHHHHhCCCCHHHHHHHHHH
Confidence            5 88888889999999999999999988   5566 5555566667766666664    44333                


Q ss_pred             ------------------------------HHHHHhhcCCCCCCcch-hhHHHHHHHHHhcCChhHHhhHHHhhCCCCCC
Q 043380          157 ------------------------------GEIVKRVCSNPGLWPKP-HLYVSMMHELAARVDYDIVKSPYRRMWPDSTG  205 (246)
Q Consensus       157 ------------------------------~~m~~~~~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  205 (246)
                                                    +.+.+.....|...|.. ......+.++...|++++|...|+.+...+. 
T Consensus       190 ~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l~~Ll~~g~~~eA~~~~~~ll~~~~-  268 (765)
T PRK10049        190 AAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQRARIDRLGALLARDRYKDVISEYQRLKAEGQ-  268 (765)
T ss_pred             HHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhccCC-
Confidence                                          33332211111111111 1111113445677899999999999876532 


Q ss_pred             CCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhc
Q 043380          206 TISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRW  243 (246)
Q Consensus       206 ~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  243 (246)
                      ..|...    -..+...|...|++++|+++|+++.+..
T Consensus       269 ~~P~~a----~~~la~~yl~~g~~e~A~~~l~~~l~~~  302 (765)
T PRK10049        269 IIPPWA----QRWVASAYLKLHQPEKAQSILTELFYHP  302 (765)
T ss_pred             CCCHHH----HHHHHHHHHhcCCcHHHHHHHHHHhhcC
Confidence            122221    2225668888999999999988876543

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

Probab=99.10  E-value=6.6e-09  Score=80.36  Aligned_cols=206  Identities=11%  Similarity=0.049  Sum_probs=140.7

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      ..|-+.||-.|-.+|-+..+++.|+.+|.+-...++-|+.-..-+-+.+-..++.++|.++|+...+.        ...+
T Consensus       252 q~~~~dTfllLskvY~ridQP~~AL~~~~~gld~fP~~VT~l~g~ARi~eam~~~~~a~~lYk~vlk~--------~~~n  323 (478)
T KOG1129|consen  252 QFPHPDTFLLLSKVYQRIDQPERALLVIGEGLDSFPFDVTYLLGQARIHEAMEQQEDALQLYKLVLKL--------HPIN  323 (478)
T ss_pred             cCCchhHHHHHHHHHHHhccHHHHHHHHhhhhhcCCchhhhhhhhHHHHHHHHhHHHHHHHHHHHHhc--------CCcc
Confidence            34555566667777777777777777776655444444444445555666667777777777777664        2344


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK  172 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~  172 (246)
                      .....++-..|.-.++++.|+..|.++.. .|+ -+...|+.+.-+|...++++-    ++-.|+.....     -..|+
T Consensus       324 vEaiAcia~~yfY~~~PE~AlryYRRiLq-mG~-~speLf~NigLCC~yaqQ~D~----~L~sf~RAlst-----at~~~  392 (478)
T KOG1129|consen  324 VEAIACIAVGYFYDNNPEMALRYYRRILQ-MGA-QSPELFCNIGLCCLYAQQIDL----VLPSFQRALST-----ATQPG  392 (478)
T ss_pred             ceeeeeeeeccccCCChHHHHHHHHHHHH-hcC-CChHHHhhHHHHHHhhcchhh----hHHHHHHHHhh-----ccCcc
Confidence            55666666677777788888888888877 665 346667777777777888888    77777777665     33344


Q ss_pred             h--hhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhc
Q 043380          173 P--HLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRW  243 (246)
Q Consensus       173 ~--~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  243 (246)
                      .  ..|..+-......||+..|.+.|+-....+..+      ..+++.|.-.-.+.|++++|..++..-....
T Consensus       393 ~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~~h------~ealnNLavL~~r~G~i~~Arsll~~A~s~~  459 (478)
T KOG1129|consen  393 QAADVWYNLGFVAVTIGDFNLAKRCFRLALTSDAQH------GEALNNLAVLAARSGDILGARSLLNAAKSVM  459 (478)
T ss_pred             hhhhhhhccceeEEeccchHHHHHHHHHHhccCcch------HHHHHhHHHHHhhcCchHHHHHHHHHhhhhC
Confidence            3  567777777777888888888888766443221      2268888888889999999999988765543

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.10  E-value=2.9e-08  Score=83.02  Aligned_cols=224  Identities=12%  Similarity=0.025  Sum_probs=155.1

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh------CC-CCCHHH-HHHHHHHHHhcCCcchHHHHHHHHHhccCCC
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEK------GL-EPDSLS-YNILISACIKTKKLDVTMPFNEQLKDNGQKC   84 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~------~~-~~~~~t-~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~   84 (246)
                      .+.-..++..+...|...|+++.|+.+++...+      |. -|...+ .+.+-..|...+++++|..+|+++...-...
T Consensus       195 ~P~~~~~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~  274 (508)
T KOG1840|consen  195 DPERLRTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEV  274 (508)
T ss_pred             CchHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHh
Confidence            334445666689999999999999999987432      21 233322 3345567888999999999999998652222


Q ss_pred             CCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhC----CC------------------------------------
Q 043380           85 SSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSC----CN------------------------------------  124 (246)
Q Consensus        85 ~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~----~~------------------------------------  124 (246)
                      .....+.-..+++.|-.+|.+.|++++|...+++..+.    .|                                    
T Consensus       275 ~G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i  354 (508)
T KOG1840|consen  275 FGEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKI  354 (508)
T ss_pred             cCCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHH
Confidence            22233334568888888999999998887776654331    00                                    


Q ss_pred             ----CCC---C-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCC-CCCcc-hhhHHHHHHHHHhcCChhHHhh
Q 043380          125 ----LIL---D-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNP-GLWPK-PHLYVSMMHELAARVDYDIVKS  194 (246)
Q Consensus       125 ----~~p---~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~p~-~~~~~~li~~~~~~g~~~~a~~  194 (246)
                          +.+   . ..+++.|...|-..|++++    |+++++...+...... +..+. ...++.|-..|.+.+++++|.+
T Consensus       355 ~~~~~g~~~~~~a~~~~nl~~l~~~~gk~~e----a~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~  430 (508)
T KOG1840|consen  355 YLDAPGEDNVNLAKIYANLAELYLKMGKYKE----AEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQ  430 (508)
T ss_pred             HHhhccccchHHHHHHHHHHHHHHHhcchhH----HHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHH
Confidence                111   1 3468888888888999999    8888888776632111 12222 4678889999999999999999


Q ss_pred             HHHhhCCC--CCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          195 PYRRMWPD--STGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       195 ~~~~~~~~--~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      +|.+....  ..|.-.|++ .++|..|...|.+.|+++.|+++.+.+..
T Consensus       431 l~~~~~~i~~~~g~~~~~~-~~~~~nL~~~Y~~~g~~e~a~~~~~~~~~  478 (508)
T KOG1840|consen  431 LFEEAKDIMKLCGPDHPDV-TYTYLNLAALYRAQGNYEAAEELEEKVLN  478 (508)
T ss_pred             HHHHHHHHHHHhCCCCCch-HHHHHHHHHHHHHcccHHHHHHHHHHHHH
Confidence            99874411  112233333 34799999999999999999999888764

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

Probab=99.09  E-value=7.3e-09  Score=86.56  Aligned_cols=201  Identities=13%  Similarity=-0.020  Sum_probs=165.2

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      .+-++.+|-++-++|.-.++.+.|++.|++..+--+....+|+.+-.-+.....+|.|...|+..+..         .|.
T Consensus       417 ~~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~---------~~r  487 (638)
T KOG1126|consen  417 DPNSPESWCALGNCFSLQKDHDTAIKCFKRAIQLDPRFAYAYTLLGHESIATEEFDKAMKSFRKALGV---------DPR  487 (638)
T ss_pred             CCCCcHHHHHhcchhhhhhHHHHHHHHHHHhhccCCccchhhhhcCChhhhhHHHHhHHHHHHhhhcC---------Cch
Confidence            56678999999999999999999999999876422347888998888888999999999999997753         333


Q ss_pred             -HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCC
Q 043380           93 -IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLW  170 (246)
Q Consensus        93 -~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~  170 (246)
                       -..|.-|-..|.+.++++.|+-.|+...+   +.|. ......+...+-+.|+.++    |++++++....      -.
T Consensus       488 hYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~---INP~nsvi~~~~g~~~~~~k~~d~----AL~~~~~A~~l------d~  554 (638)
T KOG1126|consen  488 HYNAWYGLGTVYLKQEKLEFAEFHFQKAVE---INPSNSVILCHIGRIQHQLKRKDK----ALQLYEKAIHL------DP  554 (638)
T ss_pred             hhHHHHhhhhheeccchhhHHHHHHHhhhc---CCccchhHHhhhhHHHHHhhhhhH----HHHHHHHHHhc------CC
Confidence             33566677889999999999999999988   7787 5566778888999999999    99999998775      23


Q ss_pred             cchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          171 PKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       171 p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      -|+..-......+...++.++|...+++++.-    .|.+..  .|..+...|.+.|+.+.|+.-|.-+.+
T Consensus       555 kn~l~~~~~~~il~~~~~~~eal~~LEeLk~~----vP~es~--v~~llgki~k~~~~~~~Al~~f~~A~~  619 (638)
T KOG1126|consen  555 KNPLCKYHRASILFSLGRYVEALQELEELKEL----VPQESS--VFALLGKIYKRLGNTDLALLHFSWALD  619 (638)
T ss_pred             CCchhHHHHHHHHHhhcchHHHHHHHHHHHHh----CcchHH--HHHHHHHHHHHHccchHHHHhhHHHhc
Confidence            35566666778888899999999999999854    444433  789999999999999999988766544

>PF12854 PPR_1: PPR repeat

Probab=99.08  E-value=1.9e-10  Score=59.68  Aligned_cols=33  Identities=39%  Similarity=0.666  Sum_probs=24.9

Q ss_pred             CCCccHHHHHHHHHHHHccCCHHHHHHHHHHHH
Q 043380           88 GFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMK  120 (246)
Q Consensus        88 ~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  120 (246)
                      |+.||..|||+||.+|++.|++++|.++|++|.
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            677777777777777777777777777777763

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.05  E-value=2.8e-07  Score=76.32  Aligned_cols=162  Identities=14%  Similarity=0.066  Sum_probs=128.2

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHH--------HH-------------------------------
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSL--------SY-------------------------------   54 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~--------t~-------------------------------   54 (246)
                      +-++.....+...|.+.|++++|.+++..+.+....+..        +|                               
T Consensus       184 P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~~~~~~  263 (398)
T PRK10747        184 PRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQSRKTRHQV  263 (398)
T ss_pred             CCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHHHhCCH
Confidence            456778889999999999999999999998732222211        11                               


Q ss_pred             ---HHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HH
Q 043380           55 ---NILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RS  130 (246)
Q Consensus        55 ---~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~  130 (246)
                         ..+..++...|+.++|.+++++..+.         +||...  .++.+....++.+++.+..+...+   -.|+ ..
T Consensus       264 ~~~~~~A~~l~~~g~~~~A~~~L~~~l~~---------~~~~~l--~~l~~~l~~~~~~~al~~~e~~lk---~~P~~~~  329 (398)
T PRK10747        264 ALQVAMAEHLIECDDHDTAQQIILDGLKR---------QYDERL--VLLIPRLKTNNPEQLEKVLRQQIK---QHGDTPL  329 (398)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHhc---------CCCHHH--HHHHhhccCCChHHHHHHHHHHHh---hCCCCHH
Confidence               12345566788999999999888875         455422  234444566999999999999988   4466 66


Q ss_pred             HHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhC
Q 043380          131 TFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMW  200 (246)
Q Consensus       131 ~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  200 (246)
                      .+..+.+.|.+.+++++    |.+.|+...+.       .|+..++..+...+.+.|+.++|..++++-.
T Consensus       330 l~l~lgrl~~~~~~~~~----A~~~le~al~~-------~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l  388 (398)
T PRK10747        330 LWSTLGQLLMKHGEWQE----ASLAFRAALKQ-------RPDAYDYAWLADALDRLHKPEEAAAMRRDGL  388 (398)
T ss_pred             HHHHHHHHHHHCCCHHH----HHHHHHHHHhc-------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            68899999999999999    99999999875       7999999999999999999999999998753

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

Probab=99.04  E-value=8.6e-08  Score=77.37  Aligned_cols=207  Identities=11%  Similarity=0.056  Sum_probs=156.2

Q ss_pred             HHHhcccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC---CCHHHHHH---------------------------
Q 043380            7 IVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLE---PDSLSYNI---------------------------   56 (246)
Q Consensus         7 ~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~---~~~~t~~~---------------------------   56 (246)
                      .....|.+-+...-+-...+.-...+++.|+.+|+++.+.-+   -|..+|+.                           
T Consensus       252 ~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~skLs~LA~~v~~idKyR~E  331 (559)
T KOG1155|consen  252 RLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSKLSYLAQNVSNIDKYRPE  331 (559)
T ss_pred             HHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHHHHHHHHHHHHhccCCcc
Confidence            334444544444444444445556889999999999975311   14445543                           


Q ss_pred             ----HHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC-CHH
Q 043380           57 ----LISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL-DRS  130 (246)
Q Consensus        57 ----li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~  130 (246)
                          +-+-|+-.++.++|...|++..+.         .|. ...|+.+-.-|....+...|.+-|++..+   +.| |-.
T Consensus       332 TCCiIaNYYSlr~eHEKAv~YFkRALkL---------Np~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvd---i~p~DyR  399 (559)
T KOG1155|consen  332 TCCIIANYYSLRSEHEKAVMYFKRALKL---------NPKYLSAWTLMGHEYVEMKNTHAAIESYRRAVD---INPRDYR  399 (559)
T ss_pred             ceeeehhHHHHHHhHHHHHHHHHHHHhc---------CcchhHHHHHhhHHHHHhcccHHHHHHHHHHHh---cCchhHH
Confidence                333345566779999999998875         454 55788888889999999999999999888   444 467


Q ss_pred             HHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCch
Q 043380          131 TFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPE  210 (246)
Q Consensus       131 ~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  210 (246)
                      .|-.|..+|.-.+...=    |+-.|++...-      -+-|...|.+|-.+|.+.++.++|.+.|.....-+.  ..  
T Consensus       400 AWYGLGQaYeim~Mh~Y----aLyYfqkA~~~------kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~d--te--  465 (559)
T KOG1155|consen  400 AWYGLGQAYEIMKMHFY----ALYYFQKALEL------KPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGD--TE--  465 (559)
T ss_pred             HHhhhhHHHHHhcchHH----HHHHHHHHHhc------CCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccc--cc--
Confidence            89999999999999888    99999988774      234679999999999999999999999998775432  11  


Q ss_pred             hhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          211 VQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       211 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                        ..++..|.+.|-+.++..+|.++|..-.+
T Consensus       466 --~~~l~~LakLye~l~d~~eAa~~yek~v~  494 (559)
T KOG1155|consen  466 --GSALVRLAKLYEELKDLNEAAQYYEKYVE  494 (559)
T ss_pred             --hHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence              12789999999999999999999887655

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.04  E-value=1.8e-07  Score=83.27  Aligned_cols=203  Identities=12%  Similarity=0.060  Sum_probs=160.3

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHH
Q 043380           22 AVIEASREAQRIDEAYQILESVE-KGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLL  100 (246)
Q Consensus        22 ~li~~~~~~g~~~~a~~~~~~~~-~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll  100 (246)
                      -.+-++...|+..++.+-|+.++ .+.+....+-..+.++|...+.+++|+.+|.++....-+  .....++......|.
T Consensus       297 Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~~~~~~~~~~--~~~~~~~~~~~~~L~  374 (822)
T PRK14574        297 DRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPILSSLYYSDGK--TFRNSDDLLDADDLY  374 (822)
T ss_pred             HHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhcccc--ccCCCcchHHHHHHH
Confidence            44667788999999999999998 565556668889999999999999999999999775100  001123444467899


Q ss_pred             HHHHccCCHHHHHHHHHHHHhCCC------------CCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCC
Q 043380          101 MGFRHAKDLQSLLEIVFEMKSCCN------------LILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNP  167 (246)
Q Consensus       101 ~~~~~~~~~~~a~~~~~~m~~~~~------------~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~  167 (246)
                      -+|...+++++|..+++.+.+..-            ..|| ...+..++..+...|+..+    |++.++.+...     
T Consensus       375 yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~gdl~~----Ae~~le~l~~~-----  445 (822)
T PRK14574        375 YSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVALNDLPT----AQKKLEDLSST-----  445 (822)
T ss_pred             HHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh-----
Confidence            999999999999999999987211            1233 3456677888999999999    99999999875     


Q ss_pred             CCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          168 GLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       168 ~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                       -+-|......+...+...|++.+|+..++......+...      .+......++...|++++|.++.+.+...
T Consensus       446 -aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l~P~~~------~~~~~~~~~al~l~e~~~A~~~~~~l~~~  513 (822)
T PRK14574        446 -APANQNLRIALASIYLARDLPRKAEQELKAVESLAPRSL------ILERAQAETAMALQEWHQMELLTDDVISR  513 (822)
T ss_pred             -CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhCCccH------HHHHHHHHHHHhhhhHHHHHHHHHHHHhh
Confidence             455778899999999999999999999988765433221      16677888889999999999999877654

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

Probab=99.02  E-value=7.2e-08  Score=77.82  Aligned_cols=203  Identities=11%  Similarity=0.006  Sum_probs=165.0

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHH
Q 043380           15 LNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIF   94 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~   94 (246)
                      --+.|+..+.+-|+-.++.++|...|++..+--+.....|+.|..-|....+...|.+-|+..++.        .+.|-.
T Consensus       328 yR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLNp~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi--------~p~DyR  399 (559)
T KOG1155|consen  328 YRPETCCIIANYYSLRSEHEKAVMYFKRALKLNPKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDI--------NPRDYR  399 (559)
T ss_pred             CCccceeeehhHHHHHHhHHHHHHHHHHHHhcCcchhHHHHHhhHHHHHhcccHHHHHHHHHHHhc--------CchhHH
Confidence            344566677778888999999999999876533556778999999999999999999999999985        466888


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP  173 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~  173 (246)
                      .|-.|-.+|.-.+.+.=|+-.|++...   ++|+ ...|.+|..+|.+.++.++    |.+.|.....-     | ..+.
T Consensus       400 AWYGLGQaYeim~Mh~YaLyYfqkA~~---~kPnDsRlw~aLG~CY~kl~~~~e----AiKCykrai~~-----~-dte~  466 (559)
T KOG1155|consen  400 AWYGLGQAYEIMKMHFYALYYFQKALE---LKPNDSRLWVALGECYEKLNRLEE----AIKCYKRAILL-----G-DTEG  466 (559)
T ss_pred             HHhhhhHHHHHhcchHHHHHHHHHHHh---cCCCchHHHHHHHHHHHHhccHHH----HHHHHHHHHhc-----c-ccch
Confidence            999999999999999999999999988   6776 8999999999999999999    99999999885     2 3366


Q ss_pred             hhHHHHHHHHHhcCChhHHhhHHHhhCC--CCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHH
Q 043380          174 HLYVSMMHELAARVDYDIVKSPYRRMWP--DSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNT  239 (246)
Q Consensus       174 ~~~~~li~~~~~~g~~~~a~~~~~~~~~--~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  239 (246)
                      ..+..|.+.|-+.++..+|...|....+  ...|.+.+.. ..+---|..-+.+.+++++|..+....
T Consensus       467 ~~l~~LakLye~l~d~~eAa~~yek~v~~~~~eg~~~~~t-~ka~~fLA~~f~k~~~~~~As~Ya~~~  533 (559)
T KOG1155|consen  467 SALVRLAKLYEELKDLNEAAQYYEKYVEVSELEGEIDDET-IKARLFLAEYFKKMKDFDEASYYATLV  533 (559)
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccchHH-HHHHHHHHHHHHhhcchHHHHHHHHHH
Confidence            8899999999999999999999987664  2234455532 112222666677888888887765444

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

Probab=98.97  E-value=1.4e-07  Score=72.94  Aligned_cols=193  Identities=11%  Similarity=0.123  Sum_probs=149.7

Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc--HHHHHHHHHHHHcc
Q 043380           29 EAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD--IFTYATLLMGFRHA  106 (246)
Q Consensus        29 ~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~--~~~~~~ll~~~~~~  106 (246)
                      -+.+.++|.++|-+|.+.-+-+..+--+|-+.|.+.|..|.|+.+...+..+      .+..-+  .....-|-.-|...
T Consensus        47 Ls~Q~dKAvdlF~e~l~~d~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~s------pdlT~~qr~lAl~qL~~Dym~a  120 (389)
T COG2956          47 LSNQPDKAVDLFLEMLQEDPETFEAHLTLGNLFRSRGEVDRAIRIHQTLLES------PDLTFEQRLLALQQLGRDYMAA  120 (389)
T ss_pred             hhcCcchHHHHHHHHHhcCchhhHHHHHHHHHHHhcchHHHHHHHHHHHhcC------CCCchHHHHHHHHHHHHHHHHh
Confidence            3578899999999998544455566678899999999999999999999986      122211  12455566778999


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch----hhHHHHHHH
Q 043380          107 KDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP----HLYVSMMHE  182 (246)
Q Consensus       107 ~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~----~~~~~li~~  182 (246)
                      |-+|.|+++|..+.+ .+. .-....-.|+..|-...+|++    |+++-+.+.+.     +-.+..    .-|.-+...
T Consensus       121 Gl~DRAE~~f~~L~d-e~e-fa~~AlqqLl~IYQ~treW~K----AId~A~~L~k~-----~~q~~~~eIAqfyCELAq~  189 (389)
T COG2956         121 GLLDRAEDIFNQLVD-EGE-FAEGALQQLLNIYQATREWEK----AIDVAERLVKL-----GGQTYRVEIAQFYCELAQQ  189 (389)
T ss_pred             hhhhHHHHHHHHHhc-chh-hhHHHHHHHHHHHHHhhHHHH----HHHHHHHHHHc-----CCccchhHHHHHHHHHHHH
Confidence            999999999999988 322 224567789999999999999    99999988876     333322    446777777


Q ss_pred             HHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          183 LAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       183 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      +....+++.|..++.+....++..+..+      -.+-+.....|+++.|.+.++.+.++.+
T Consensus       190 ~~~~~~~d~A~~~l~kAlqa~~~cvRAs------i~lG~v~~~~g~y~~AV~~~e~v~eQn~  245 (389)
T COG2956         190 ALASSDVDRARELLKKALQADKKCVRAS------IILGRVELAKGDYQKAVEALERVLEQNP  245 (389)
T ss_pred             HhhhhhHHHHHHHHHHHHhhCccceehh------hhhhHHHHhccchHHHHHHHHHHHHhCh
Confidence            8888899999999999887766555433      3467778999999999999999987764

>TIGR00540 hemY_coli hemY protein

Probab=98.94  E-value=3.2e-07  Score=76.34  Aligned_cols=189  Identities=10%  Similarity=0.032  Sum_probs=100.1

Q ss_pred             cCCHHHHHHHHHHHHhCCCCCH-HHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHH--HHHHHHHHHHcc
Q 043380           30 AQRIDEAYQILESVEKGLEPDS-LSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIF--TYATLLMGFRHA  106 (246)
Q Consensus        30 ~g~~~~a~~~~~~~~~~~~~~~-~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~--~~~~ll~~~~~~  106 (246)
                      .|+++.|++.+....+. .|+. ..+-....+....|+++.|.+.+.+..+.         .|+..  .--.....+...
T Consensus        97 ~g~~~~A~~~l~~~~~~-~~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~---------~p~~~l~~~~~~a~l~l~~  166 (409)
T TIGR00540        97 EGDYAKAEKLIAKNADH-AAEPVLNLIKAAEAAQQRGDEARANQHLEEAAEL---------AGNDNILVEIARTRILLAQ  166 (409)
T ss_pred             CCCHHHHHHHHHHHhhc-CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh---------CCcCchHHHHHHHHHHHHC
Confidence            57777777777665432 3432 23333445556667777777777776654         24432  233345666667


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHH--
Q 043380          107 KDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHEL--  183 (246)
Q Consensus       107 ~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~--  183 (246)
                      |+++.|...++.+.+   ..|+ ...+..+...+...|+++.    |.+.+..+.+.     +..+.......-..++  
T Consensus       167 ~~~~~Al~~l~~l~~---~~P~~~~~l~ll~~~~~~~~d~~~----a~~~l~~l~k~-----~~~~~~~~~~l~~~a~~~  234 (409)
T TIGR00540       167 NELHAARHGVDKLLE---MAPRHKEVLKLAEEAYIRSGAWQA----LDDIIDNMAKA-----GLFDDEEFADLEQKAEIG  234 (409)
T ss_pred             CCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHHhhHHH----HHHHHHHHHHc-----CCCCHHHHHHHHHHHHHH
Confidence            777777777777777   3354 5566677777777777777    77777777765     3322221111111111  


Q ss_pred             -HhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          184 -AARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       184 -~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                       ...+..+++...+..+....+...+.+..  .+..+...+...|+.++|.+.+++..++
T Consensus       235 ~l~~~~~~~~~~~L~~~~~~~p~~~~~~~~--l~~~~a~~l~~~g~~~~A~~~l~~~l~~  292 (409)
T TIGR00540       235 LLDEAMADEGIDGLLNWWKNQPRHRRHNIA--LKIALAEHLIDCDDHDSAQEIIFDGLKK  292 (409)
T ss_pred             HHHHHHHhcCHHHHHHHHHHCCHHHhCCHH--HHHHHHHHHHHCCChHHHHHHHHHHHhh
Confidence             12222222222333322211111111111  4556666667777777777776666554

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.

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.91  E-value=3.1e-07  Score=70.48  Aligned_cols=170  Identities=15%  Similarity=0.112  Sum_probs=127.1

Q ss_pred             CCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc----HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCC
Q 043380           49 PDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD----IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCN  124 (246)
Q Consensus        49 ~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~  124 (246)
                      .....+-.+...+...|++++|...|+++...         .|+    ..++..+..++...|++++|...++.+.+   
T Consensus        31 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~---------~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~---   98 (235)
T TIGR03302        31 WPAEELYEEAKEALDSGDYTEAIKYFEALESR---------YPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIR---   98 (235)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---------CCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH---
Confidence            34566777888889999999999999999875         343    24677888899999999999999999988   


Q ss_pred             CCCCH----HHHHHHHHHHHhc--------CChhhhhhHHHHHHHHHHHhhcCCCCCCcch-hhH---------------
Q 043380          125 LILDR----STFTAMVDALLYS--------GSIKVVGLYALCIFGEIVKRVCSNPGLWPKP-HLY---------------  176 (246)
Q Consensus       125 ~~p~~----~~~~~li~~~~~~--------~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~-~~~---------------  176 (246)
                      ..|+.    .++..+..++...        |+.+.    |.+.|+.+...       .|+. ..+               
T Consensus        99 ~~p~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~----A~~~~~~~~~~-------~p~~~~~~~a~~~~~~~~~~~~~  167 (235)
T TIGR03302        99 LHPNHPDADYAYYLRGLSNYNQIDRVDRDQTAARE----AFEAFQELIRR-------YPNSEYAPDAKKRMDYLRNRLAG  167 (235)
T ss_pred             HCcCCCchHHHHHHHHHHHHHhcccccCCHHHHHH----HHHHHHHHHHH-------CCCChhHHHHHHHHHHHHHHHHH
Confidence            33431    2444455555544        67888    99999999886       2332 111               


Q ss_pred             --HHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          177 --VSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       177 --~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                        ..+...|.+.|++++|...++......+.. +..  ..++..+..++...|++++|..+++.+..+.+
T Consensus       168 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~-~~~--~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~~~  234 (235)
T TIGR03302       168 KELYVARFYLKRGAYVAAINRFETVVENYPDT-PAT--EEALARLVEAYLKLGLKDLAQDAAAVLGANYP  234 (235)
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHHHHCCCC-cch--HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence              134566888999999999999987654322 111  12788999999999999999999999887653

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).

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.90  E-value=4.2e-07  Score=69.77  Aligned_cols=170  Identities=11%  Similarity=0.076  Sum_probs=128.3

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCH---HHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCC
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDS---LSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFH   90 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~---~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~   90 (246)
                      ...+..+-.+...+.+.|+++.|...|+++....+.+.   ..+..+..++...|++++|...++++.+.         .
T Consensus        30 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~---------~  100 (235)
T TIGR03302        30 EWPAEELYEEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRL---------H  100 (235)
T ss_pred             cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH---------C
Confidence            34566777888899999999999999998864333333   46677888999999999999999999986         2


Q ss_pred             ccH----HHHHHHHHHHHcc--------CCHHHHHHHHHHHHhCCCCCCCHH-HH-----------------HHHHHHHH
Q 043380           91 PDI----FTYATLLMGFRHA--------KDLQSLLEIVFEMKSCCNLILDRS-TF-----------------TAMVDALL  140 (246)
Q Consensus        91 p~~----~~~~~ll~~~~~~--------~~~~~a~~~~~~m~~~~~~~p~~~-~~-----------------~~li~~~~  140 (246)
                      |+.    .++..+-.++...        |+.++|.+.|+.+..   ..|+.. .+                 ..+...|.
T Consensus       101 p~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~---~~p~~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~  177 (235)
T TIGR03302       101 PNHPDADYAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIR---RYPNSEYAPDAKKRMDYLRNRLAGKELYVARFYL  177 (235)
T ss_pred             cCCCchHHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHH---HCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            321    2455555555544        788999999999987   345422 21                 13456788


Q ss_pred             hcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCC
Q 043380          141 YSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPD  202 (246)
Q Consensus       141 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  202 (246)
                      +.|++..    |...++...+..   |+-......+..+..++...|++++|..+++.+...
T Consensus       178 ~~g~~~~----A~~~~~~al~~~---p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       178 KRGAYVA----AINRFETVVENY---PDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             HcCChHH----HHHHHHHHHHHC---CCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            8999999    999999998862   122234578999999999999999999999988643

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).

>PRK14574 hmsH outer membrane protein; Provisional

Probab=98.88  E-value=6.5e-07  Score=79.80  Aligned_cols=186  Identities=12%  Similarity=-0.001  Sum_probs=140.6

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCH-HHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHH
Q 043380           24 IEASREAQRIDEAYQILESVEKGLEPDS-LSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMG  102 (246)
Q Consensus        24 i~~~~~~g~~~~a~~~~~~~~~~~~~~~-~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~  102 (246)
                      +-...+.|+++.|++.|++..+. .|+. .....++..+...|+.++|...+++....        -.........+...
T Consensus        41 aii~~r~Gd~~~Al~~L~qaL~~-~P~~~~av~dll~l~~~~G~~~~A~~~~eka~~p--------~n~~~~~llalA~l  111 (822)
T PRK14574         41 LIIRARAGDTAPVLDYLQEESKA-GPLQSGQVDDWLQIAGWAGRDQEVIDVYERYQSS--------MNISSRGLASAARA  111 (822)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHhh-CccchhhHHHHHHHHHHcCCcHHHHHHHHHhccC--------CCCCHHHHHHHHHH
Confidence            33457899999999999988643 4543 23338888888999999999999998742        22334444444668


Q ss_pred             HHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHH
Q 043380          103 FRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMH  181 (246)
Q Consensus       103 ~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~  181 (246)
                      |...|++++|.++|+++.+   ..|+ ...+..++..+...++.++    |++.++.+...       .|+...+..++.
T Consensus       112 y~~~gdyd~Aiely~kaL~---~dP~n~~~l~gLa~~y~~~~q~~e----Al~~l~~l~~~-------dp~~~~~l~lay  177 (822)
T PRK14574        112 YRNEKRWDQALALWQSSLK---KDPTNPDLISGMIMTQADAGRGGV----VLKQATELAER-------DPTVQNYMTLSY  177 (822)
T ss_pred             HHHcCCHHHHHHHHHHHHh---hCCCCHHHHHHHHHHHhhcCCHHH----HHHHHHHhccc-------CcchHHHHHHHH
Confidence            8888999999999999998   4455 6677788899999999999    99999998775       566666655555


Q ss_pred             HHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHH
Q 043380          182 ELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSN  238 (246)
Q Consensus       182 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  238 (246)
                      .+...++..+|.+.++++....+....      .+..++.++.+.|-...|.++.++
T Consensus       178 L~~~~~~~~~AL~~~ekll~~~P~n~e------~~~~~~~~l~~~~~~~~a~~l~~~  228 (822)
T PRK14574        178 LNRATDRNYDALQASSEAVRLAPTSEE------VLKNHLEILQRNRIVEPALRLAKE  228 (822)
T ss_pred             HHHhcchHHHHHHHHHHHHHhCCCCHH------HHHHHHHHHHHcCCcHHHHHHHHh
Confidence            555566666699999999876543222      577788999999999999887764

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

Probab=98.88  E-value=2.9e-07  Score=74.45  Aligned_cols=147  Identities=10%  Similarity=0.045  Sum_probs=65.6

Q ss_pred             cCCHHHHHHHHHHHHhC-CCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCC
Q 043380           30 AQRIDEAYQILESVEKG-LEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKD  108 (246)
Q Consensus        30 ~g~~~~a~~~~~~~~~~-~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~  108 (246)
                      +|++++|.+.|.+...+ -.-....||+=+ .+-..|++++|+++|-++...        +..+.....-+.+.|-...+
T Consensus       503 ngd~dka~~~ykeal~ndasc~ealfnigl-t~e~~~~ldeald~f~klh~i--------l~nn~evl~qianiye~led  573 (840)
T KOG2003|consen  503 NGDLDKAAEFYKEALNNDASCTEALFNIGL-TAEALGNLDEALDCFLKLHAI--------LLNNAEVLVQIANIYELLED  573 (840)
T ss_pred             cCcHHHHHHHHHHHHcCchHHHHHHHHhcc-cHHHhcCHHHHHHHHHHHHHH--------HHhhHHHHHHHHHHHHHhhC
Confidence            45566666666554311 111112222222 223445555665555555432        22333344444444555555


Q ss_pred             HHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcC
Q 043380          109 LQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARV  187 (246)
Q Consensus       109 ~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g  187 (246)
                      +.+|.+++-+..+   +.|+ +...+.|...|-+.|+-..    |.+++-.--.      -++-|..|...|...|....
T Consensus       574 ~aqaie~~~q~~s---lip~dp~ilskl~dlydqegdksq----afq~~ydsyr------yfp~nie~iewl~ayyidtq  640 (840)
T KOG2003|consen  574 PAQAIELLMQANS---LIPNDPAILSKLADLYDQEGDKSQ----AFQCHYDSYR------YFPCNIETIEWLAAYYIDTQ  640 (840)
T ss_pred             HHHHHHHHHHhcc---cCCCCHHHHHHHHHHhhcccchhh----hhhhhhhccc------ccCcchHHHHHHHHHHHhhH
Confidence            5555555444433   2232 4445555555555555555    4444433322      13334444444444444444


Q ss_pred             ChhHHhhHHHh
Q 043380          188 DYDIVKSPYRR  198 (246)
Q Consensus       188 ~~~~a~~~~~~  198 (246)
                      -++++..+|++
T Consensus       641 f~ekai~y~ek  651 (840)
T KOG2003|consen  641 FSEKAINYFEK  651 (840)
T ss_pred             HHHHHHHHHHH
Confidence            44455554444

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

Probab=98.87  E-value=6.6e-07  Score=66.17  Aligned_cols=164  Identities=12%  Similarity=-0.024  Sum_probs=108.7

Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHH
Q 043380           54 YNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RST  131 (246)
Q Consensus        54 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~  131 (246)
                      ..-|--+|...|+...|..-+++.++.         .|+ ..+|..+-..|.+.|..+.|.+-|+...+   +.|+ ..+
T Consensus        38 rlqLal~YL~~gd~~~A~~nlekAL~~---------DPs~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAls---l~p~~GdV  105 (250)
T COG3063          38 RLQLALGYLQQGDYAQAKKNLEKALEH---------DPSYYLAHLVRAHYYQKLGENDLADESYRKALS---LAPNNGDV  105 (250)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHh---------CcccHHHHHHHHHHHHHcCChhhHHHHHHHHHh---cCCCccch
Confidence            334555667777777777777777765         444 44777777777777777777777777766   5555 566


Q ss_pred             HHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchh
Q 043380          132 FTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEV  211 (246)
Q Consensus       132 ~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~  211 (246)
                      .|..-..+|..|.+++    |...|+.....    |...--..||..+.-+..+.|+.+.|++.|++-...++...+   
T Consensus       106 LNNYG~FLC~qg~~~e----A~q~F~~Al~~----P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~~~~---  174 (250)
T COG3063         106 LNNYGAFLCAQGRPEE----AMQQFERALAD----PAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQFPP---  174 (250)
T ss_pred             hhhhhHHHHhCCChHH----HHHHHHHHHhC----CCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcCCCh---
Confidence            7777777777777777    77777777665    222223466777777777777777777777776544422211   


Q ss_pred             hhHHHHHHHHHHHhcCChhHHHHHHHHHHhhc
Q 043380          212 QEEAGHLLMEAALNDGQVDLALDKLSNTITRW  243 (246)
Q Consensus       212 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  243 (246)
                         +.-.+.......|++..|..+++....++
T Consensus       175 ---~~l~~a~~~~~~~~y~~Ar~~~~~~~~~~  203 (250)
T COG3063         175 ---ALLELARLHYKAGDYAPARLYLERYQQRG  203 (250)
T ss_pred             ---HHHHHHHHHHhcccchHHHHHHHHHHhcc
Confidence               34556666677777777777777666554

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

Probab=98.87  E-value=8e-08  Score=74.51  Aligned_cols=195  Identities=14%  Similarity=0.121  Sum_probs=155.2

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHH-HHH
Q 043380           21 NAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTY-ATL   99 (246)
Q Consensus        21 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~-~~l   99 (246)
                      +-+-.+|.+.|.+.+|++.|+.... ..|-+.||-.|-++|.+...+..|+.+|.+-.+.         .|-.+|| .-.
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~-q~~~~dTfllLskvY~ridQP~~AL~~~~~gld~---------fP~~VT~l~g~  296 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLT-QFPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS---------FPFDVTYLLGQ  296 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhh-cCCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc---------CCchhhhhhhh
Confidence            5677899999999999999987642 2678889999999999999999999999998875         4555554 446


Q ss_pred             HHHHHccCCHHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHH
Q 043380          100 LMGFRHAKDLQSLLEIVFEMKSCCNLIL-DRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVS  178 (246)
Q Consensus       100 l~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~  178 (246)
                      .+.+-..++.++|.++|+...+   ..| +.....++...|...++++.    |+++++.+.+.     |+ -+...|+.
T Consensus       297 ARi~eam~~~~~a~~lYk~vlk---~~~~nvEaiAcia~~yfY~~~PE~----AlryYRRiLqm-----G~-~speLf~N  363 (478)
T KOG1129|consen  297 ARIHEAMEQQEDALQLYKLVLK---LHPINVEAIACIAVGYFYDNNPEM----ALRYYRRILQM-----GA-QSPELFCN  363 (478)
T ss_pred             HHHHHHHHhHHHHHHHHHHHHh---cCCccceeeeeeeeccccCCChHH----HHHHHHHHHHh-----cC-CChHHHhh
Confidence            6677888999999999999988   334 46777888889999999999    99999999998     65 46778888


Q ss_pred             HHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          179 MMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       179 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      +--+|...+.+|.+..-|++.....   ..|......|..|-...+..|++.-|.+.|+-...
T Consensus       364 igLCC~yaqQ~D~~L~sf~RAlsta---t~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~  423 (478)
T KOG1129|consen  364 IGLCCLYAQQIDLVLPSFQRALSTA---TQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALT  423 (478)
T ss_pred             HHHHHHhhcchhhhHHHHHHHHhhc---cCcchhhhhhhccceeEEeccchHHHHHHHHHHhc
Confidence            8888999999999998888765322   12222223688888888889999999888876543

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

Probab=98.85  E-value=1.3e-06  Score=78.97  Aligned_cols=204  Identities=12%  Similarity=0.046  Sum_probs=165.1

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-----HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCC
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPD-----SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSG   87 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~-----~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~   87 (246)
                      .+-+...|-..|......++.++|++++++....+.+.     .-.|.++++.-..-|.-+...++|+++.+.       
T Consensus      1454 sPNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqy------- 1526 (1710)
T KOG1070|consen 1454 SPNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQY------- 1526 (1710)
T ss_pred             CCCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHh-------
Confidence            34456678889999999999999999999987555442     235777777777778788899999999985       


Q ss_pred             CCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCC
Q 043380           88 GFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNP  167 (246)
Q Consensus        88 ~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~  167 (246)
                        --....|..|...|.+.+..++|-++++.|.++.+  -....|...+..+.+..+-+.    |..++.+..+.     
T Consensus      1527 --cd~~~V~~~L~~iy~k~ek~~~A~ell~~m~KKF~--q~~~vW~~y~~fLl~~ne~~a----a~~lL~rAL~~----- 1593 (1710)
T KOG1070|consen 1527 --CDAYTVHLKLLGIYEKSEKNDEADELLRLMLKKFG--QTRKVWIMYADFLLRQNEAEA----ARELLKRALKS----- 1593 (1710)
T ss_pred             --cchHHHHHHHHHHHHHhhcchhHHHHHHHHHHHhc--chhhHHHHHHHHHhcccHHHH----HHHHHHHHHhh-----
Confidence              22345789999999999999999999999998544  557788889999999999999    99999998875     


Q ss_pred             CCCcc---hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          168 GLWPK---PHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       168 ~~~p~---~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                        -|-   .......+..-.+.|+.+.+..+|+......+.    ..+  .|+..++.-.+.|+.+.+..+|++....+-
T Consensus      1594 --lPk~eHv~~IskfAqLEFk~GDaeRGRtlfEgll~ayPK----RtD--lW~VYid~eik~~~~~~vR~lfeRvi~l~l 1665 (1710)
T KOG1070|consen 1594 --LPKQEHVEFISKFAQLEFKYGDAERGRTLFEGLLSAYPK----RTD--LWSVYIDMEIKHGDIKYVRDLFERVIELKL 1665 (1710)
T ss_pred             --cchhhhHHHHHHHHHHHhhcCCchhhHHHHHHHHhhCcc----chh--HHHHHHHHHHccCCHHHHHHHHHHHHhcCC
Confidence              233   345566677777899999999999998865432    222  799999999999999999999999987653

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

Probab=98.84  E-value=1.2e-05  Score=59.75  Aligned_cols=198  Identities=10%  Similarity=-0.089  Sum_probs=157.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc-cHHHHH
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP-DIFTYA   97 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p-~~~~~~   97 (246)
                      +.--|--.|.+.|+...|.+-+++..+.-+.+..+|..+-..|-+.|..+.|.+-|++....         .| +....|
T Consensus        37 arlqLal~YL~~gd~~~A~~nlekAL~~DPs~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl---------~p~~GdVLN  107 (250)
T COG3063          37 ARLQLALGYLQQGDYAQAKKNLEKALEHDPSYYLAHLVRAHYYQKLGENDLADESYRKALSL---------APNNGDVLN  107 (250)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCChhhHHHHHHHHHhc---------CCCccchhh
Confidence            44556778999999999999999876544667788999999999999999999999999875         44 456788


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhH
Q 043380           98 TLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLY  176 (246)
Q Consensus        98 ~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~  176 (246)
                      ..-.-+|..|++++|...|++... ..-.|. ..+|..+.-+..+.|+.+.    |...|++-.+.      -+-...+.
T Consensus       108 NYG~FLC~qg~~~eA~q~F~~Al~-~P~Y~~~s~t~eN~G~Cal~~gq~~~----A~~~l~raL~~------dp~~~~~~  176 (250)
T COG3063         108 NYGAFLCAQGRPEEAMQQFERALA-DPAYGEPSDTLENLGLCALKAGQFDQ----AEEYLKRALEL------DPQFPPAL  176 (250)
T ss_pred             hhhHHHHhCCChHHHHHHHHHHHh-CCCCCCcchhhhhhHHHHhhcCCchh----HHHHHHHHHHh------CcCCChHH
Confidence            888888999999999999999988 444444 6789999999999999999    99999998886      22234677


Q ss_pred             HHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          177 VSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       177 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                      ..+.......|++-.|..+++.......    +...  .....|+.--+.|+.+.+-++=..+.+.
T Consensus       177 l~~a~~~~~~~~y~~Ar~~~~~~~~~~~----~~A~--sL~L~iriak~~gd~~~a~~Y~~qL~r~  236 (250)
T COG3063         177 LELARLHYKAGDYAPARLYLERYQQRGG----AQAE--SLLLGIRIAKRLGDRAAAQRYQAQLQRL  236 (250)
T ss_pred             HHHHHHHHhcccchHHHHHHHHHHhccc----ccHH--HHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            8889999999999999999999875432    2211  3445566667789988888876666543

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

Probab=98.82  E-value=1.1e-07  Score=82.29  Aligned_cols=179  Identities=16%  Similarity=0.113  Sum_probs=105.1

Q ss_pred             HHHHHH-hCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHH
Q 043380           39 ILESVE-KGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVF  117 (246)
Q Consensus        39 ~~~~~~-~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~  117 (246)
                      ++..++ .|+.|+.+||..+|.-||..|+.+.|- +|.-|.-.       ....+...|+.++.+-..+++.+.+.    
T Consensus        12 fla~~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~k-------sLpv~e~vf~~lv~sh~~And~Enpk----   79 (1088)
T KOG4318|consen   12 FLALHEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIK-------SLPVREGVFRGLVASHKEANDAENPK----   79 (1088)
T ss_pred             HHHHHHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhcc-------cccccchhHHHHHhcccccccccCCC----
Confidence            445566 799999999999999999999999998 88888766       44555555666666555555554443    


Q ss_pred             HHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhh----------------cCCCCCCcchhhHHHHHH
Q 043380          118 EMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRV----------------CSNPGLWPKPHLYVSMMH  181 (246)
Q Consensus       118 ~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~----------------~~~~~~~p~~~~~~~li~  181 (246)
                              .|.+.||..|..+|...|++.. -..+.+.+..+...-                .+.|+.-||..+..   .
T Consensus        80 --------ep~aDtyt~Ll~ayr~hGDli~-fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~i---l  147 (1088)
T KOG4318|consen   80 --------EPLADTYTNLLKAYRIHGDLIL-FEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAI---L  147 (1088)
T ss_pred             --------CCchhHHHHHHHHHHhccchHH-HHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHH---H
Confidence                    2455556666666666655443 000222111111110                02334444443211   1


Q ss_pred             HHHhcCChhHHh------------------------------hHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhH
Q 043380          182 ELAARVDYDIVK------------------------------SPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDL  231 (246)
Q Consensus       182 ~~~~~g~~~~a~------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~  231 (246)
                      ...-.|-++.+.                              ++.+....-. +  .  ++..+|..+++.-..+|+++.
T Consensus       148 llv~eglwaqllkll~~~Pvsa~~~p~~vfLrqnv~~ntpvekLl~~cksl~-e--~--~~s~~l~a~l~~alaag~~d~  222 (1088)
T KOG4318|consen  148 LLVLEGLWAQLLKLLAKVPVSAWNAPFQVFLRQNVVDNTPVEKLLNMCKSLV-E--A--PTSETLHAVLKRALAAGDVDG  222 (1088)
T ss_pred             HHHHHHHHHHHHHHHhhCCcccccchHHHHHHHhccCCchHHHHHHHHHHhh-c--C--CChHHHHHHHHHHHhcCchhh
Confidence            111222222222                              2222221111 1  1  223389999999999999999


Q ss_pred             HHHHHHHHHhhccCC
Q 043380          232 ALDKLSNTITRWKGI  246 (246)
Q Consensus       232 a~~~~~~m~~~g~~i  246 (246)
                      |..++.+|+++|-.|
T Consensus       223 Ak~ll~emke~gfpi  237 (1088)
T KOG4318|consen  223 AKNLLYEMKEKGFPI  237 (1088)
T ss_pred             HHHHHHHHHHcCCCc
Confidence            999999999999765

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

Probab=98.81  E-value=4.6e-06  Score=68.02  Aligned_cols=199  Identities=11%  Similarity=-0.044  Sum_probs=94.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHH---HHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVEKGLEPDSLS---YNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t---~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      .|..+...+...|+.+.+...+....+..+++...   .......+...|++++|.+++++..+.        .+.|...
T Consensus         8 a~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~~~~~~g~~~~A~~~~~~~l~~--------~P~~~~a   79 (355)
T cd05804           8 GHAAAALLLLLGGERPAAAAKAAAAAQALAARATERERAHVEALSAWIAGDLPKALALLEQLLDD--------YPRDLLA   79 (355)
T ss_pred             HHHHHHHHHHhcCCcchHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--------CCCcHHH
Confidence            34444445555566666555554433212222111   111122334456666666666666654        1222223


Q ss_pred             HHH---HHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc
Q 043380           96 YAT---LLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP  171 (246)
Q Consensus        96 ~~~---ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p  171 (246)
                      +..   ........+..+.+.+.+..  . ....|+ ......+...+...|++++    |...+++..+.      -+.
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~l~~--~-~~~~~~~~~~~~~~a~~~~~~G~~~~----A~~~~~~al~~------~p~  146 (355)
T cd05804          80 LKLHLGAFGLGDFSGMRDHVARVLPL--W-APENPDYWYLLGMLAFGLEEAGQYDR----AEEAARRALEL------NPD  146 (355)
T ss_pred             HHHhHHHHHhcccccCchhHHHHHhc--c-CcCCCCcHHHHHHHHHHHHHcCCHHH----HHHHHHHHHhh------CCC
Confidence            331   11111123334444444433  1 122333 3333444556666666666    66666666654      122


Q ss_pred             chhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHH
Q 043380          172 KPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTI  240 (246)
Q Consensus       172 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  240 (246)
                      +...+..+..++...|++++|...+++.....+.  ++......|..+...+...|++++|.+++++..
T Consensus       147 ~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~--~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~  213 (355)
T cd05804         147 DAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDC--SSMLRGHNWWHLALFYLERGDYEAALAIYDTHI  213 (355)
T ss_pred             CcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCC--CcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHh
Confidence            3445555666666666666666666665433211  111111134456666666666666666666653

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

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

Probab=98.81  E-value=9.1e-07  Score=72.08  Aligned_cols=214  Identities=10%  Similarity=0.081  Sum_probs=159.9

Q ss_pred             hhHHHHhcccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCC
Q 043380            4 ENEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQK   83 (246)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~   83 (246)
                      .|+.++.....++. .|--+-..|+...+.++....|....+--+-|+.+|..--..+.-.+++++|..=|++.+..   
T Consensus       348 d~~~~I~l~~~~~~-lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp~n~dvYyHRgQm~flL~q~e~A~aDF~Kai~L---  423 (606)
T KOG0547|consen  348 DFDAAIKLDPAFNS-LYIKRAAAYADENQSEKMWKDFNKAEDLDPENPDVYYHRGQMRFLLQQYEEAIADFQKAISL---  423 (606)
T ss_pred             hHHHHHhcCcccch-HHHHHHHHHhhhhccHHHHHHHHHHHhcCCCCCchhHhHHHHHHHHHHHHHHHHHHHHHhhc---
Confidence            45555555544433 27777788999999999999998876544567788888888888889999999999998875   


Q ss_pred             CCCCCCCc-cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           84 CSSGGFHP-DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        84 ~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                            .| +...|--+--+.-+.+.+++++..|++.+++  ++-.+..|+.....+...++++.    |.+.|+..+..
T Consensus       424 ------~pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkk--FP~~~Evy~~fAeiLtDqqqFd~----A~k~YD~ai~L  491 (606)
T KOG0547|consen  424 ------DPENAYAYIQLCCALYRQHKIAESMKTFEEAKKK--FPNCPEVYNLFAEILTDQQQFDK----AVKQYDKAIEL  491 (606)
T ss_pred             ------ChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--CCCCchHHHHHHHHHhhHHhHHH----HHHHHHHHHhh
Confidence                  45 4567777777777899999999999999882  44448899999999999999999    99999998875


Q ss_pred             hcCCCCCCcchhhH--HHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHH
Q 043380          163 VCSNPGLWPKPHLY--VSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTI  240 (246)
Q Consensus       163 ~~~~~~~~p~~~~~--~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  240 (246)
                      .....++..+...+  ..++- +.=.+++..|..++++..+-++.   .   ..+|..|...-++.|+.++|+++|+.-.
T Consensus       492 E~~~~~~~v~~~plV~Ka~l~-~qwk~d~~~a~~Ll~KA~e~Dpk---c---e~A~~tlaq~~lQ~~~i~eAielFEksa  564 (606)
T KOG0547|consen  492 EPREHLIIVNAAPLVHKALLV-LQWKEDINQAENLLRKAIELDPK---C---EQAYETLAQFELQRGKIDEAIELFEKSA  564 (606)
T ss_pred             ccccccccccchhhhhhhHhh-hchhhhHHHHHHHHHHHHccCch---H---HHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            21111222222222  12221 12348999999999998765432   1   2289999999999999999999998754

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

Probab=98.79  E-value=1.5e-06  Score=70.45  Aligned_cols=186  Identities=10%  Similarity=0.064  Sum_probs=145.7

Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHc
Q 043380           26 ASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRH  105 (246)
Q Consensus        26 ~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~  105 (246)
                      .+-..|++++|++.|-.+..-...+....--+.+.|-...+...|.+++.+....        ++.|.....-|-..|-+
T Consensus       533 t~e~~~~ldeald~f~klh~il~nn~evl~qianiye~led~aqaie~~~q~~sl--------ip~dp~ilskl~dlydq  604 (840)
T KOG2003|consen  533 TAEALGNLDEALDCFLKLHAILLNNAEVLVQIANIYELLEDPAQAIELLMQANSL--------IPNDPAILSKLADLYDQ  604 (840)
T ss_pred             cHHHhcCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhCHHHHHHHHHHhccc--------CCCCHHHHHHHHHHhhc
Confidence            3456799999999998776444567778888888899999999999999988764        66678899999999999


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHH-H
Q 043380          106 AKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHEL-A  184 (246)
Q Consensus       106 ~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~-~  184 (246)
                      .|+-.+|++.+-.-.+ . ++-+..+...|..-|....-++.    +..+|+...-       +.|+..-|..||-.| .
T Consensus       605 egdksqafq~~ydsyr-y-fp~nie~iewl~ayyidtqf~ek----ai~y~ekaal-------iqp~~~kwqlmiasc~r  671 (840)
T KOG2003|consen  605 EGDKSQAFQCHYDSYR-Y-FPCNIETIEWLAAYYIDTQFSEK----AINYFEKAAL-------IQPNQSKWQLMIASCFR  671 (840)
T ss_pred             ccchhhhhhhhhhccc-c-cCcchHHHHHHHHHHHhhHHHHH----HHHHHHHHHh-------cCccHHHHHHHHHHHHH
Confidence            9999999998776555 2 55567888888888888888888    9999998754       689999999998655 5


Q ss_pred             hcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHH
Q 043380          185 ARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNT  239 (246)
Q Consensus       185 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  239 (246)
                      +.|++++|..++..+-..    .|.++.  ....|++.+...|. .++.++-+.+
T Consensus       672 rsgnyqka~d~yk~~hrk----fpedld--clkflvri~~dlgl-~d~key~~kl  719 (840)
T KOG2003|consen  672 RSGNYQKAFDLYKDIHRK----FPEDLD--CLKFLVRIAGDLGL-KDAKEYADKL  719 (840)
T ss_pred             hcccHHHHHHHHHHHHHh----CccchH--HHHHHHHHhccccc-hhHHHHHHHH
Confidence            689999999999998754    444444  66677777776663 3444444333

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

Probab=98.78  E-value=8.7e-06  Score=64.83  Aligned_cols=207  Identities=14%  Similarity=0.062  Sum_probs=131.0

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      .++...+-+........|+.+.|..-..++...-+.+.........+|.+.|++.+...+...+.+.|       .--|.
T Consensus       150 ~~~l~v~ltrarlll~~~d~~aA~~~v~~ll~~~pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~-------~l~~~  222 (400)
T COG3071         150 DDTLAVELTRARLLLNRRDYPAARENVDQLLEMTPRHPEVLRLALRAYIRLGAWQALLAILPKLRKAG-------LLSDE  222 (400)
T ss_pred             CchHHHHHHHHHHHHhCCCchhHHHHHHHHHHhCcCChHHHHHHHHHHHHhccHHHHHHHHHHHHHcc-------CCChH
Confidence            44555555556666667777777777766654446677778888888888888888888888888874       22221


Q ss_pred             -------HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhc--
Q 043380           94 -------FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVC--  164 (246)
Q Consensus        94 -------~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~--  164 (246)
                             .+|+.++.-....++.+.-...|+..-+  ..+-++..-.+++.-+..+|+.++    |.++..+-.++..  
T Consensus       223 e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~pr--~lr~~p~l~~~~a~~li~l~~~~~----A~~~i~~~Lk~~~D~  296 (400)
T COG3071         223 EAARLEQQAWEGLLQQARDDNGSEGLKTWWKNQPR--KLRNDPELVVAYAERLIRLGDHDE----AQEIIEDALKRQWDP  296 (400)
T ss_pred             HHHHHHHHHHHHHHHHHhccccchHHHHHHHhccH--HhhcChhHHHHHHHHHHHcCChHH----HHHHHHHHHHhccCh
Confidence                   2455555554444444444444444433  123334444444555555555555    5554444433310  


Q ss_pred             --------CCC---------------CCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHH
Q 043380          165 --------SNP---------------GLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLME  221 (246)
Q Consensus       165 --------~~~---------------~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~  221 (246)
                              ..+               ...-++..+.+|-..|.+.+.|.+|...|+...+..     |+  .++|+.+.+
T Consensus       297 ~L~~~~~~l~~~d~~~l~k~~e~~l~~h~~~p~L~~tLG~L~~k~~~w~kA~~~leaAl~~~-----~s--~~~~~~la~  369 (400)
T COG3071         297 RLCRLIPRLRPGDPEPLIKAAEKWLKQHPEDPLLLSTLGRLALKNKLWGKASEALEAALKLR-----PS--ASDYAELAD  369 (400)
T ss_pred             hHHHHHhhcCCCCchHHHHHHHHHHHhCCCChhHHHHHHHHHHHhhHHHHHHHHHHHHHhcC-----CC--hhhHHHHHH
Confidence                    000               123344778889999999999999999999765432     22  228999999


Q ss_pred             HHHhcCChhHHHHHHHHHH
Q 043380          222 AALNDGQVDLALDKLSNTI  240 (246)
Q Consensus       222 ~~~~~g~~~~a~~~~~~m~  240 (246)
                      ++.+.|++.+|.++.++-.
T Consensus       370 ~~~~~g~~~~A~~~r~e~L  388 (400)
T COG3071         370 ALDQLGEPEEAEQVRREAL  388 (400)
T ss_pred             HHHHcCChHHHHHHHHHHH
Confidence            9999999999999988754

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=98.75  E-value=2.1e-06  Score=64.66  Aligned_cols=159  Identities=9%  Similarity=-0.010  Sum_probs=125.7

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHH
Q 043380           21 NAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLL  100 (246)
Q Consensus        21 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll  100 (246)
                      ..+-..+-..|+-+.+..+........+.|....+..+....+.|++..|...+.+....        -++|..+|+.+-
T Consensus        70 ~~~a~a~~~~G~a~~~l~~~~~~~~~~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l--------~p~d~~~~~~lg  141 (257)
T COG5010          70 AKLATALYLRGDADSSLAVLQKSAIAYPKDRELLAAQGKNQIRNGNFGEAVSVLRKAARL--------APTDWEAWNLLG  141 (257)
T ss_pred             HHHHHHHHhcccccchHHHHhhhhccCcccHHHHHHHHHHHHHhcchHHHHHHHHHHhcc--------CCCChhhhhHHH
Confidence            445556666777777777776655444556667777888889999999999999988873        577888999999


Q ss_pred             HHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHH
Q 043380          101 MGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSM  179 (246)
Q Consensus       101 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~l  179 (246)
                      -+|-+.|+++.|..-|.+..+   +.|+ ...+|.+...|.-.|+.+.    |..++......      -.-|...-..+
T Consensus       142 aaldq~Gr~~~Ar~ay~qAl~---L~~~~p~~~nNlgms~~L~gd~~~----A~~lll~a~l~------~~ad~~v~~NL  208 (257)
T COG5010         142 AALDQLGRFDEARRAYRQALE---LAPNEPSIANNLGMSLLLRGDLED----AETLLLPAYLS------PAADSRVRQNL  208 (257)
T ss_pred             HHHHHccChhHHHHHHHHHHH---hccCCchhhhhHHHHHHHcCCHHH----HHHHHHHHHhC------CCCchHHHHHH
Confidence            999999999999999998888   5566 6678889999999999999    99998888775      23366777888


Q ss_pred             HHHHHhcCChhHHhhHHHhhC
Q 043380          180 MHELAARVDYDIVKSPYRRMW  200 (246)
Q Consensus       180 i~~~~~~g~~~~a~~~~~~~~  200 (246)
                      ..+....|++++|+.+...-.
T Consensus       209 Al~~~~~g~~~~A~~i~~~e~  229 (257)
T COG5010         209 ALVVGLQGDFREAEDIAVQEL  229 (257)
T ss_pred             HHHHhhcCChHHHHhhccccc
Confidence            888889999999988876543

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=98.73  E-value=1.5e-06  Score=73.03  Aligned_cols=183  Identities=11%  Similarity=0.056  Sum_probs=131.3

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH----h--CC-CCCHH-HHHHHHHHHHhcCCcchHHHHHHHHHhccCCC
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVE----K--GL-EPDSL-SYNILISACIKTKKLDVTMPFNEQLKDNGQKC   84 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~----~--~~-~~~~~-t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~   84 (246)
                      .+--..+++.|-.+|.+.|++++|...+++..    +  +. .|.+. -++.+...|+..+++++|..++....+.-.+.
T Consensus       279 h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~  358 (508)
T KOG1840|consen  279 HPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDA  358 (508)
T ss_pred             CHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhh
Confidence            34445677778889999999999998887631    2  22 23333 36677788889999999999998876642110


Q ss_pred             CCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCC---C--CCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHH
Q 043380           85 SSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCC---N--LILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGE  158 (246)
Q Consensus        85 ~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~---~--~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~  158 (246)
                      ......--..+++.|-..|-..|++++|.++|+......   +  ..+. ...++.|...|.+.+.+.+    |.++|.+
T Consensus       359 ~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~----a~~l~~~  434 (508)
T KOG1840|consen  359 PGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEE----AEQLFEE  434 (508)
T ss_pred             ccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccch----HHHHHHH
Confidence            000111223589999999999999999999999765521   1  1233 5668889999999999999    9998887


Q ss_pred             HHHhhc-CCCCCCcc-hhhHHHHHHHHHhcCChhHHhhHHHhhC
Q 043380          159 IVKRVC-SNPGLWPK-PHLYVSMMHELAARVDYDIVKSPYRRMW  200 (246)
Q Consensus       159 m~~~~~-~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~  200 (246)
                      -..-.. +.++ .|+ ..+|..|...|.+.|+++.|.++.+.+.
T Consensus       435 ~~~i~~~~g~~-~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  435 AKDIMKLCGPD-HPDVTYTYLNLAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             HHHHHHHhCCC-CCchHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            554321 0111 233 3789999999999999999999999766

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

Probab=98.72  E-value=1.6e-05  Score=64.92  Aligned_cols=215  Identities=13%  Similarity=0.090  Sum_probs=135.2

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH--HH
Q 043380           18 IVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI--FT   95 (246)
Q Consensus        18 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~--~~   95 (246)
                      .....+...+...|++++|...+++.....+.+...+..+-..+...|++++|..++++.....      ...|+.  ..
T Consensus       115 ~~~~~~a~~~~~~G~~~~A~~~~~~al~~~p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~------~~~~~~~~~~  188 (355)
T cd05804         115 YLLGMLAFGLEEAGQYDRAEEAARRALELNPDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTW------DCSSMLRGHN  188 (355)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhcc------CCCcchhHHH
Confidence            3444556678889999999999999875446667788889999999999999999999988751      112332  34


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHH-H--HHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCC-CCCCc
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTF-T--AMVDALLYSGSIKVVGLYALCIFGEIVKRVCSN-PGLWP  171 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~-~--~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~-~~~~p  171 (246)
                      |..+...+...|++++|..++++........+..... +  .++.-+...|....    +.+ |+.+....... ++ ..
T Consensus       189 ~~~la~~~~~~G~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~----~~~-w~~~~~~~~~~~~~-~~  262 (355)
T cd05804         189 WWHLALFYLERGDYEAALAIYDTHIAPSAESDPALDLLDAASLLWRLELAGHVDV----GDR-WEDLADYAAWHFPD-HG  262 (355)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHhccccCCChHHHHhhHHHHHHHHHhcCCCCh----HHH-HHHHHHHHHhhcCc-cc
Confidence            6678888999999999999999986512112222222 2  33444444554433    332 22222210000 11 11


Q ss_pred             chhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCC-CCchhhhHHHHHHHH--HHHhcCChhHHHHHHHHHHhhcc
Q 043380          172 KPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGT-ISPEVQEEAGHLLME--AALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       172 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~-~~~~~~~~~~~~li~--~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      ......+...++...|+.+.|..+++.+....... ........+-..++.  ++...|+.++|.+.+......+.
T Consensus       263 ~~~~~~~~a~~~~~~~~~~~a~~~L~~l~~~~~~~~~~~~~~~~~~~~~l~A~~~~~~g~~~~A~~~L~~al~~a~  338 (355)
T cd05804         263 LAFNDLHAALALAGAGDKDALDKLLAALKGRASSADDNKQPARDVGLPLAEALYAFAEGNYATALELLGPVRDDLA  338 (355)
T ss_pred             chHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhccCchhhhHHhhhHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence            22333467788889999999999999886432110 000000012233444  45689999999999998877653

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

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

Probab=98.71  E-value=7.1e-07  Score=70.38  Aligned_cols=152  Identities=12%  Similarity=0.034  Sum_probs=103.9

Q ss_pred             HHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHH---HHH
Q 043380           60 ACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFT---AMV  136 (246)
Q Consensus        60 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~---~li  136 (246)
                      .+...|++++|++++..-             .+.......+..|.+.++++.|.+.++.|.+   +..|.....   +.+
T Consensus       111 i~~~~~~~~~AL~~l~~~-------------~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~---~~eD~~l~qLa~awv  174 (290)
T PF04733_consen  111 ILFHEGDYEEALKLLHKG-------------GSLELLALAVQILLKMNRPDLAEKELKNMQQ---IDEDSILTQLAEAWV  174 (290)
T ss_dssp             HHCCCCHHHHHHCCCTTT-------------TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHC---CSCCHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHcc-------------CcccHHHHHHHHHHHcCCHHHHHHHHHHHHh---cCCcHHHHHHHHHHH
Confidence            344567777776665432             3445666788888999999999999999988   445544332   333


Q ss_pred             HHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHH
Q 043380          137 DALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAG  216 (246)
Q Consensus       137 ~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  216 (246)
                      ..+.....+.+    |..+|+++.++      ..+++.+.+.+..++...|++++|++++.+....++.    +.+  +.
T Consensus       175 ~l~~g~e~~~~----A~y~f~El~~~------~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~~----~~d--~L  238 (290)
T PF04733_consen  175 NLATGGEKYQD----AFYIFEELSDK------FGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDPN----DPD--TL  238 (290)
T ss_dssp             HHHHTTTCCCH----HHHHHHHHHCC------S--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-CC----HHH--HH
T ss_pred             HHHhCchhHHH----HHHHHHHHHhc------cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhccC----CHH--HH
Confidence            33333456888    99999998764      6678889999999999999999999999997755432    222  55


Q ss_pred             HHHHHHHHhcCCh-hHHHHHHHHHHhhc
Q 043380          217 HLLMEAALNDGQV-DLALDKLSNTITRW  243 (246)
Q Consensus       217 ~~li~~~~~~g~~-~~a~~~~~~m~~~g  243 (246)
                      ..++-+....|+. +.+.+++.+++...
T Consensus       239 aNliv~~~~~gk~~~~~~~~l~qL~~~~  266 (290)
T PF04733_consen  239 ANLIVCSLHLGKPTEAAERYLSQLKQSN  266 (290)
T ss_dssp             HHHHHHHHHTT-TCHHHHHHHHHCHHHT
T ss_pred             HHHHHHHHHhCCChhHHHHHHHHHHHhC
Confidence            5677777777777 67888888877543

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.

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

Probab=98.69  E-value=5.9e-05  Score=64.06  Aligned_cols=215  Identities=15%  Similarity=0.084  Sum_probs=136.5

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHH-HHHHHHHhc-----CCcchHHHHHHHHHhcc-----
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYN-ILISACIKT-----KKLDVTMPFNEQLKDNG-----   81 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~-~li~~~~~~-----~~~~~a~~~~~~m~~~~-----   81 (246)
                      +.............+.+.|+.++|..+|..+.+. .|+-..|. .+..+....     ...+...++|+++...-     
T Consensus        34 I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~r-NPdn~~Yy~~L~~~~g~~~~~~~~~~~~~~~~y~~l~~~yp~s~~  112 (517)
T PF12569_consen   34 ILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDR-NPDNYDYYRGLEEALGLQLQLSDEDVEKLLELYDELAEKYPRSDA  112 (517)
T ss_pred             CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-CCCcHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHhCccccc
Confidence            4444566667788889999999999999888643 45544444 444444222     23455566666664432     


Q ss_pred             -----------------------------CC-----------------------------C-----CC-----CCCCccH
Q 043380           82 -----------------------------QK-----------------------------C-----SS-----GGFHPDI   93 (246)
Q Consensus        82 -----------------------------~~-----------------------------~-----~~-----~~~~p~~   93 (246)
                                                   ++                             .     ..     ..-.|+.
T Consensus       113 ~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPslF~~lk~Ly~d~~K~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~  192 (517)
T PF12569_consen  113 PRRLPLDFLEGDEFKERLDEYLRPQLRKGVPSLFSNLKPLYKDPEKAAIIESLVEEYVNSLESNGSFSNGDDEEKEPPST  192 (517)
T ss_pred             hhHhhcccCCHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHcChhHHHHHHHHHHHHHHhhcccCCCCCccccccCCchH
Confidence                                         10                             0     00     1123444


Q ss_pred             H--HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCC
Q 043380           94 F--TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLW  170 (246)
Q Consensus        94 ~--~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~  170 (246)
                      .  ++.-+-..|-..|++++|+++++...+   ..|+ +..|..-.+.+-+.|++.+    |.+.++.....      =.
T Consensus       193 ~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~---htPt~~ely~~KarilKh~G~~~~----Aa~~~~~Ar~L------D~  259 (517)
T PF12569_consen  193 LLWTLYFLAQHYDYLGDYEKALEYIDKAIE---HTPTLVELYMTKARILKHAGDLKE----AAEAMDEAREL------DL  259 (517)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHh---cCCCcHHHHHHHHHHHHHCCCHHH----HHHHHHHHHhC------Ch
Confidence            3  334456667788888888888888777   5577 6667777888888888888    88888877765      13


Q ss_pred             cchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHH---HHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          171 PKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAG---HLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       171 p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~---~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      -|...-+..+..+.+.|++++|.+++......+.+....-....+.   .-...+|.+.|++..|++.|..+.+
T Consensus       260 ~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~r~~~~~~ALk~~~~v~k  333 (517)
T PF12569_consen  260 ADRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYLRQGDYGLALKRFHAVLK  333 (517)
T ss_pred             hhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            4566667777888888888888888888765553222211111121   1244568888888888887776654

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 [], [].

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

Probab=98.64  E-value=1.6e-05  Score=67.50  Aligned_cols=199  Identities=15%  Similarity=0.101  Sum_probs=130.6

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHH
Q 043380           24 IEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGF  103 (246)
Q Consensus        24 i~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~  103 (246)
                      ...+...|++++|++.++.-.+.+.............+.+.|+.++|..+|..+++.         .|+...|...+..+
T Consensus        11 ~~il~e~g~~~~AL~~L~~~~~~I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~r---------NPdn~~Yy~~L~~~   81 (517)
T PF12569_consen   11 NSILEEAGDYEEALEHLEKNEKQILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDR---------NPDNYDYYRGLEEA   81 (517)
T ss_pred             HHHHHHCCCHHHHHHHHHhhhhhCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH---------CCCcHHHHHHHHHH
Confidence            455678899999999998876655555666778888999999999999999999997         56666555555544


Q ss_pred             H------ccCCHHHHHHHHHHHHhCCC-----------CCCC-------------------HHHHHHHHHHHHhcCChhh
Q 043380          104 R------HAKDLQSLLEIVFEMKSCCN-----------LILD-------------------RSTFTAMVDALLYSGSIKV  147 (246)
Q Consensus       104 ~------~~~~~~~a~~~~~~m~~~~~-----------~~p~-------------------~~~~~~li~~~~~~~~~~~  147 (246)
                      .      ...+.+....+|+++.....           +.++                   +.+|+.|-..|.......-
T Consensus        82 ~g~~~~~~~~~~~~~~~~y~~l~~~yp~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPslF~~lk~Ly~d~~K~~~  161 (517)
T PF12569_consen   82 LGLQLQLSDEDVEKLLELYDELAEKYPRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVPSLFSNLKPLYKDPEKAAI  161 (517)
T ss_pred             HhhhcccccccHHHHHHHHHHHHHhCccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHcChhHHHH
Confidence            3      12356777777777655210           0000                   1234444444443333333


Q ss_pred             hhhHHHHHHHHHHHhhc----CC-----CCCCcchh--hHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHH
Q 043380          148 VGLYALCIFGEIVKRVC----SN-----PGLWPKPH--LYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAG  216 (246)
Q Consensus       148 ~~~~a~~~~~~m~~~~~----~~-----~~~~p~~~--~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  216 (246)
                          ..+++........    ..     ..-.|+..  ++.-+...|-..|++++|.+++++.....+..    +.  .|
T Consensus       162 ----i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt~----~e--ly  231 (517)
T PF12569_consen  162 ----IESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHTPTL----VE--LY  231 (517)
T ss_pred             ----HHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCc----HH--HH
Confidence                4444444433311    11     01234443  44556777889999999999999887654322    22  68


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          217 HLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       217 ~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      ..-.+.|-+.|++++|.+.++..+.
T Consensus       232 ~~KarilKh~G~~~~Aa~~~~~Ar~  256 (517)
T PF12569_consen  232 MTKARILKHAGDLKEAAEAMDEARE  256 (517)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            8888889999999999998887654

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

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.64  E-value=2.2e-05  Score=62.45  Aligned_cols=148  Identities=10%  Similarity=-0.049  Sum_probs=112.9

Q ss_pred             CCHHHHHHHHHHHHhCCC--CC--HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHcc
Q 043380           31 QRIDEAYQILESVEKGLE--PD--SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHA  106 (246)
Q Consensus        31 g~~~~a~~~~~~~~~~~~--~~--~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~  106 (246)
                      +..+.++.-+.++....+  |+  ...|..+-..|...|+.++|...|.+..+.        -+.+...|+.+-..+...
T Consensus        40 ~~~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l--------~P~~~~a~~~lg~~~~~~  111 (296)
T PRK11189         40 LQQEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALAL--------RPDMADAYNYLGIYLTQA  111 (296)
T ss_pred             hHHHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHc--------CCCCHHHHHHHHHHHHHC
Confidence            344666666666643222  22  355777888899999999999999999985        233578999999999999


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHh
Q 043380          107 KDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAA  185 (246)
Q Consensus       107 ~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~  185 (246)
                      |++++|...|+...+   +.|+ ..+|..+...+...|++++    |.+.|+...+.       .|+..........+..
T Consensus       112 g~~~~A~~~~~~Al~---l~P~~~~a~~~lg~~l~~~g~~~e----A~~~~~~al~~-------~P~~~~~~~~~~l~~~  177 (296)
T PRK11189        112 GNFDAAYEAFDSVLE---LDPTYNYAYLNRGIALYYGGRYEL----AQDDLLAFYQD-------DPNDPYRALWLYLAES  177 (296)
T ss_pred             CCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHCCCHHH----HHHHHHHHHHh-------CCCCHHHHHHHHHHHc
Confidence            999999999999988   6677 7788889999999999999    99999999876       3443222222223455


Q ss_pred             cCChhHHhhHHHhhC
Q 043380          186 RVDYDIVKSPYRRMW  200 (246)
Q Consensus       186 ~g~~~~a~~~~~~~~  200 (246)
                      .++.++|...|.+..
T Consensus       178 ~~~~~~A~~~l~~~~  192 (296)
T PRK11189        178 KLDPKQAKENLKQRY  192 (296)
T ss_pred             cCCHHHHHHHHHHHH
Confidence            778999999997644

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.61  E-value=2.9e-06  Score=59.92  Aligned_cols=109  Identities=7%  Similarity=-0.116  Sum_probs=88.0

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      +..++..+..+...+...|++++|...|+....--+.+...|..+..++...|++++|...|++....        -+.+
T Consensus        20 l~~~p~~~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l--------~p~~   91 (144)
T PRK15359         20 LSVDPETVYASGYASWQEGDYSRAVIDFSWLVMAQPWSWRAHIALAGTWMMLKEYTTAINFYGHALML--------DASH   91 (144)
T ss_pred             HHcCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc--------CCCC
Confidence            34444456667788889999999999998876544668888999999999999999999999999985        2456


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHH
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTF  132 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~  132 (246)
                      ...+..+-.++...|++++|...|+....   ..|+...+
T Consensus        92 ~~a~~~lg~~l~~~g~~~eAi~~~~~Al~---~~p~~~~~  128 (144)
T PRK15359         92 PEPVYQTGVCLKMMGEPGLAREAFQTAIK---MSYADASW  128 (144)
T ss_pred             cHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCChHH
Confidence            77888899999999999999999999888   55764433

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.57  E-value=1.2e-07  Score=49.38  Aligned_cols=34  Identities=32%  Similarity=0.381  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCH
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDR  129 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~  129 (246)
                      +||++|.+|++.|++++|.++|++|.+ .|+.||.
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~-~g~~p~~   35 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLE-RGIEPDV   35 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHH-cCCCCCC
Confidence            799999999999999999999999999 9999973

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.

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

Probab=98.57  E-value=1.4e-06  Score=71.58  Aligned_cols=131  Identities=14%  Similarity=0.147  Sum_probs=108.7

Q ss_pred             hhHHHHhcccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhc
Q 043380            4 ENEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVEK---GLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDN   80 (246)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~---~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~   80 (246)
                      .++.--....+.+......+++.+....+++.+.+++-..++   ....-..|.+++++.|.+.|..+.+..++..=...
T Consensus        53 ~l~~k~~~~~~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~y  132 (429)
T PF10037_consen   53 ELDKKFERKKPVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQY  132 (429)
T ss_pred             HHHHHHhcCCCCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhc
Confidence            344444455677777888889999989999999999988763   22233456789999999999999999999988887


Q ss_pred             cCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhc
Q 043380           81 GQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYS  142 (246)
Q Consensus        81 ~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~  142 (246)
                             |+-||..|||.||..+.+.|++..|.++...|.. .+...+..|+..-+.+|.+.
T Consensus       133 -------GiF~D~~s~n~Lmd~fl~~~~~~~A~~V~~~~~l-Qe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  133 -------GIFPDNFSFNLLMDHFLKKGNYKSAAKVATEMML-QEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             -------ccCCChhhHHHHHHHHhhcccHHHHHHHHHHHHH-hhccCCchHHHHHHHHHHHh
Confidence                   8999999999999999999999999999999988 77777788887777777666

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 [].

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

Probab=98.56  E-value=1.2e-06  Score=69.13  Aligned_cols=152  Identities=10%  Similarity=0.055  Sum_probs=114.3

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHH
Q 043380           24 IEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGF  103 (246)
Q Consensus        24 i~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~  103 (246)
                      ...+...|++++|++++...     .+.......+..|.+.+++|.|.+.++.|.+.         ..|.. ...|..++
T Consensus       109 A~i~~~~~~~~~AL~~l~~~-----~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~---------~eD~~-l~qLa~aw  173 (290)
T PF04733_consen  109 ATILFHEGDYEEALKLLHKG-----GSLELLALAVQILLKMNRPDLAEKELKNMQQI---------DEDSI-LTQLAEAW  173 (290)
T ss_dssp             HHHHCCCCHHHHHHCCCTTT-----TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCC---------SCCHH-HHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHcc-----CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhc---------CCcHH-HHHHHHHH
Confidence            34566679999998887643     45677778899999999999999999999875         34433 33344433


Q ss_pred             ----HccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHH
Q 043380          104 ----RHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSM  179 (246)
Q Consensus       104 ----~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~l  179 (246)
                          .-.+.+.+|..+|+++..  ...+++.+.+.+..++...|++++    |.+++.+....      -.-+..+...+
T Consensus       174 v~l~~g~e~~~~A~y~f~El~~--~~~~t~~~lng~A~~~l~~~~~~e----Ae~~L~~al~~------~~~~~d~LaNl  241 (290)
T PF04733_consen  174 VNLATGGEKYQDAFYIFEELSD--KFGSTPKLLNGLAVCHLQLGHYEE----AEELLEEALEK------DPNDPDTLANL  241 (290)
T ss_dssp             HHHHHTTTCCCHHHHHHHHHHC--CS--SHHHHHHHHHHHHHCT-HHH----HHHHHHHHCCC-------CCHHHHHHHH
T ss_pred             HHHHhCchhHHHHHHHHHHHHh--ccCCCHHHHHHHHHHHHHhCCHHH----HHHHHHHHHHh------ccCCHHHHHHH
Confidence                334579999999999877  356789999999999999999999    99999987654      23356788888


Q ss_pred             HHHHHhcCCh-hHHhhHHHhhCCC
Q 043380          180 MHELAARVDY-DIVKSPYRRMWPD  202 (246)
Q Consensus       180 i~~~~~~g~~-~~a~~~~~~~~~~  202 (246)
                      +-+....|+. +.+.+++.++...
T Consensus       242 iv~~~~~gk~~~~~~~~l~qL~~~  265 (290)
T PF04733_consen  242 IVCSLHLGKPTEAAERYLSQLKQS  265 (290)
T ss_dssp             HHHHHHTT-TCHHHHHHHHHCHHH
T ss_pred             HHHHHHhCCChhHHHHHHHHHHHh
Confidence            8888888988 7788899998753

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.

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

Probab=98.54  E-value=1.5e-05  Score=66.19  Aligned_cols=127  Identities=10%  Similarity=0.015  Sum_probs=93.6

Q ss_pred             HHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCC-cchhhHHHH
Q 043380          102 GFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLW-PKPHLYVSM  179 (246)
Q Consensus       102 ~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~-p~~~~~~~l  179 (246)
                      -|.+.++.+-|.++|.+...   +.|+ +...+-+.-..-..+.+.+    |..+|+.....-....+-. --..+++.|
T Consensus       389 ey~~t~n~kLAe~Ff~~A~a---i~P~Dplv~~Elgvvay~~~~y~~----A~~~f~~~l~~ik~~~~e~~~w~p~~~NL  461 (611)
T KOG1173|consen  389 EYMRTNNLKLAEKFFKQALA---IAPSDPLVLHELGVVAYTYEEYPE----ALKYFQKALEVIKSVLNEKIFWEPTLNNL  461 (611)
T ss_pred             HHHHhccHHHHHHHHHHHHh---cCCCcchhhhhhhheeehHhhhHH----HHHHHHHHHHHhhhccccccchhHHHHhH
Confidence            45667777888888887766   5565 6677777777777888999    9999988764311000111 234568889


Q ss_pred             HHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          180 MHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       180 i~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      -.+|.+.+.+++|...++......+.    +..  +|.++.-.|...|+++.|.+.|..-..
T Consensus       462 GH~~Rkl~~~~eAI~~~q~aL~l~~k----~~~--~~asig~iy~llgnld~Aid~fhKaL~  517 (611)
T KOG1173|consen  462 GHAYRKLNKYEEAIDYYQKALLLSPK----DAS--THASIGYIYHLLGNLDKAIDHFHKALA  517 (611)
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHcCCC----chh--HHHHHHHHHHHhcChHHHHHHHHHHHh
Confidence            99999999999999999997754332    222  899999999999999999999987653

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

Probab=98.54  E-value=0.00019  Score=57.44  Aligned_cols=205  Identities=13%  Similarity=0.051  Sum_probs=149.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHH
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVEK-GLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYA   97 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~~-~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~   97 (246)
                      .|-.-..+--+.|+.+.+-.++.+..+ .-.++...+-+.-+.....|+++.|..-..++.+.        -+.+.....
T Consensus       120 ~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~~aA~~~v~~ll~~--------~pr~~~vlr  191 (400)
T COG3071         120 AYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAARENVDQLLEM--------TPRHPEVLR  191 (400)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHHHHHHHHHh--------CcCChHHHH
Confidence            344445566667888888888877753 12445555666677777888888888888888876        244567788


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHhCCCCCCCH-------HHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCC
Q 043380           98 TLLMGFRHAKDLQSLLEIVFEMKSCCNLILDR-------STFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLW  170 (246)
Q Consensus        98 ~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~-------~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~  170 (246)
                      ....+|.+.|++..+..+...+.+ .|.--|+       .+|..+++-....+..+.    -...|+.....      .+
T Consensus       192 La~r~y~~~g~~~~ll~~l~~L~k-a~~l~~~e~~~le~~a~~glL~q~~~~~~~~g----L~~~W~~~pr~------lr  260 (400)
T COG3071         192 LALRAYIRLGAWQALLAILPKLRK-AGLLSDEEAARLEQQAWEGLLQQARDDNGSEG----LKTWWKNQPRK------LR  260 (400)
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHH-ccCCChHHHHHHHHHHHHHHHHHHhccccchH----HHHHHHhccHH------hh
Confidence            888999999999999999999988 7776554       367888887777777777    67777777664      56


Q ss_pred             cchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCC---------------------------CCCCchhhhHHHHHHHHHH
Q 043380          171 PKPHLYVSMMHELAARVDYDIVKSPYRRMWPDST---------------------------GTISPEVQEEAGHLLMEAA  223 (246)
Q Consensus       171 p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~---------------------------~~~~~~~~~~~~~~li~~~  223 (246)
                      -++..-.+++.-+.+.|+.++|.++..+..+...                           ...+.++  ..+.+|-..|
T Consensus       261 ~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L~~~~~~l~~~d~~~l~k~~e~~l~~h~~~p--~L~~tLG~L~  338 (400)
T COG3071         261 NDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRLCRLIPRLRPGDPEPLIKAAEKWLKQHPEDP--LLLSTLGRLA  338 (400)
T ss_pred             cChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhHHHHHhhcCCCCchHHHHHHHHHHHhCCCCh--hHHHHHHHHH
Confidence            6677778888888999999999988876543221                           0001111  2688899999


Q ss_pred             HhcCChhHHHHHHHHHHhhcc
Q 043380          224 LNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       224 ~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      .+.+.+.+|.+.|+.-.+.+.
T Consensus       339 ~k~~~w~kA~~~leaAl~~~~  359 (400)
T COG3071         339 LKNKLWGKASEALEAALKLRP  359 (400)
T ss_pred             HHhhHHHHHHHHHHHHHhcCC
Confidence            999999999999997766543

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

Probab=98.54  E-value=4e-06  Score=71.42  Aligned_cols=116  Identities=11%  Similarity=0.007  Sum_probs=88.6

Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch-hhHHHHHHHH
Q 043380          106 AKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP-HLYVSMMHEL  183 (246)
Q Consensus       106 ~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~-~~~~~li~~~  183 (246)
                      .+++.++.+.|+.-.+   +.|- ..+|-.+-.+..+.+++..    |.+.|..-..       ..||. ..||.+-.+|
T Consensus       498 ~~~fs~~~~hle~sl~---~nplq~~~wf~~G~~ALqlek~q~----av~aF~rcvt-------L~Pd~~eaWnNls~ay  563 (777)
T KOG1128|consen  498 NKDFSEADKHLERSLE---INPLQLGTWFGLGCAALQLEKEQA----AVKAFHRCVT-------LEPDNAEAWNNLSTAY  563 (777)
T ss_pred             chhHHHHHHHHHHHhh---cCccchhHHHhccHHHHHHhhhHH----HHHHHHHHhh-------cCCCchhhhhhhhHHH
Confidence            4556666666665544   3333 5567777777888888888    8888888765       35654 7899999999


Q ss_pred             HhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          184 AARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       184 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      .+.++-.+|...+.+..+-+..++.      .|...+....+-|.+++|++.+.++.+
T Consensus       564 i~~~~k~ra~~~l~EAlKcn~~~w~------iWENymlvsvdvge~eda~~A~~rll~  615 (777)
T KOG1128|consen  564 IRLKKKKRAFRKLKEALKCNYQHWQ------IWENYMLVSVDVGEFEDAIKAYHRLLD  615 (777)
T ss_pred             HHHhhhHHHHHHHHHHhhcCCCCCe------eeechhhhhhhcccHHHHHHHHHHHHH
Confidence            9999999999999998877654444      577788888899999999999988865

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.53  E-value=1.6e-07  Score=48.89  Aligned_cols=33  Identities=30%  Similarity=0.624  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHH-hCCCCCH
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVE-KGLEPDS   51 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~-~~~~~~~   51 (246)
                      +||++|.+|++.|++++|.++|++|. .|+.||.
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            79999999999999999999999997 7888873

This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.53  E-value=2e-07  Score=48.33  Aligned_cols=33  Identities=30%  Similarity=0.323  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL  127 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p  127 (246)
                      .+|+++|.+|++.|+++.|.++|++|.+ .|+.|
T Consensus         2 ~ty~~ll~a~~~~g~~~~a~~~~~~M~~-~gv~P   34 (34)
T PF13812_consen    2 HTYNALLRACAKAGDPDAALQLFDEMKE-QGVKP   34 (34)
T ss_pred             cHHHHHHHHHHHCCCHHHHHHHHHHHHH-hCCCC
Confidence            5899999999999999999999999999 89887

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=98.51  E-value=1.2e-05  Score=59.88  Aligned_cols=130  Identities=12%  Similarity=0.095  Sum_probs=100.9

Q ss_pred             CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHH-HHccCC-
Q 043380           31 QRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMG-FRHAKD-  108 (246)
Q Consensus        31 g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~-~~~~~~-  108 (246)
                      ++.+++...++...+.-+.|...|..+...|...|++++|...|++....        .+-+...+..+-.+ +...|+ 
T Consensus        53 ~~~~~~i~~l~~~L~~~P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l--------~P~~~~~~~~lA~aL~~~~g~~  124 (198)
T PRK10370         53 QTPEAQLQALQDKIRANPQNSEQWALLGEYYLWRNDYDNALLAYRQALQL--------RGENAELYAALATVLYYQAGQH  124 (198)
T ss_pred             hhHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--------CCCCHHHHHHHHHHHHHhcCCC
Confidence            44455555565544344778899999999999999999999999999986        23356677777776 467777 


Q ss_pred             -HHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHH
Q 043380          109 -LQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHE  182 (246)
Q Consensus       109 -~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~  182 (246)
                       .++|.+++++..+   ..|+ ..++..+...+...|++++    |...|+.+.+.      ..|+..-+ .+|.+
T Consensus       125 ~~~~A~~~l~~al~---~dP~~~~al~~LA~~~~~~g~~~~----Ai~~~~~aL~l------~~~~~~r~-~~i~~  186 (198)
T PRK10370        125 MTPQTREMIDKALA---LDANEVTALMLLASDAFMQADYAQ----AIELWQKVLDL------NSPRVNRT-QLVES  186 (198)
T ss_pred             CcHHHHHHHHHHHH---hCCCChhHHHHHHHHHHHcCCHHH----HHHHHHHHHhh------CCCCccHH-HHHHH
Confidence             5999999999998   5565 7888999999999999999    99999999886      45555443 34443

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.49  E-value=5.3e-05  Score=66.68  Aligned_cols=134  Identities=11%  Similarity=0.017  Sum_probs=91.6

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCC
Q 043380           46 GLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCN  124 (246)
Q Consensus        46 ~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~  124 (246)
                      ....++..+-.|.......|++++|+.+++...+.         .|| ......+...+.+.+++++|+..+++...   
T Consensus        81 ~~~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~---------~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~---  148 (694)
T PRK15179         81 RYPHTELFQVLVARALEAAHRSDEGLAVWRGIHQR---------FPDSSEAFILMLRGVKRQQGIEAGRAEIELYFS---  148 (694)
T ss_pred             hccccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhh---------CCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhh---
Confidence            34455666666777777777777777777777764         554 34566667777777777777777777776   


Q ss_pred             CCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCC
Q 043380          125 LILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWP  201 (246)
Q Consensus       125 ~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  201 (246)
                      ..|+ ....+.+..++...|++++    |..+|++....      ..-+..++..+-.++-..|+.++|...|+....
T Consensus       149 ~~p~~~~~~~~~a~~l~~~g~~~~----A~~~y~~~~~~------~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~  216 (694)
T PRK15179        149 GGSSSAREILLEAKSWDEIGQSEQ----ADACFERLSRQ------HPEFENGYVGWAQSLTRRGALWRARDVLQAGLD  216 (694)
T ss_pred             cCCCCHHHHHHHHHHHHHhcchHH----HHHHHHHHHhc------CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            4465 4555666677777777777    77777777664      122356777777777777777777777777654

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

Probab=98.49  E-value=0.00011  Score=64.36  Aligned_cols=204  Identities=14%  Similarity=0.036  Sum_probs=154.8

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      +.|.+...-...+...-.|+.++|.+++.++-+..+.+...|-+|-..|-..|+.+++...+-..--        -.+-|
T Consensus       135 l~~~l~~ll~eAN~lfarg~~eeA~~i~~EvIkqdp~~~~ay~tL~~IyEqrGd~eK~l~~~llAAH--------L~p~d  206 (895)
T KOG2076|consen  135 LAPELRQLLGEANNLFARGDLEEAEEILMEVIKQDPRNPIAYYTLGEIYEQRGDIEKALNFWLLAAH--------LNPKD  206 (895)
T ss_pred             cCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCccchhhHHHHHHHHHHcccHHHHHHHHHHHHh--------cCCCC
Confidence            4444444444455445559999999999998655677889999999999999999998876544332        22345


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP  171 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p  171 (246)
                      ...|-.+-......|+++.|.-.|.+..+   ..|+ ...+---+..|-+.|+...    |.+.|.++.+.      ..|
T Consensus       207 ~e~W~~ladls~~~~~i~qA~~cy~rAI~---~~p~n~~~~~ers~L~~~~G~~~~----Am~~f~~l~~~------~p~  273 (895)
T KOG2076|consen  207 YELWKRLADLSEQLGNINQARYCYSRAIQ---ANPSNWELIYERSSLYQKTGDLKR----AMETFLQLLQL------DPP  273 (895)
T ss_pred             hHHHHHHHHHHHhcccHHHHHHHHHHHHh---cCCcchHHHHHHHHHHHHhChHHH----HHHHHHHHHhh------CCc
Confidence            67888999999999999999999999988   3444 5555667788999999999    99999999886      222


Q ss_pred             c-----hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          172 K-----PHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       172 ~-----~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      .     ..+.-.+++.+...++-+.|.+.++.......+...    ...++.++..|.+...++.|......+..
T Consensus       274 ~d~er~~d~i~~~~~~~~~~~~~e~a~~~le~~~s~~~~~~~----~ed~ni~ael~l~~~q~d~~~~~i~~~~~  344 (895)
T KOG2076|consen  274 VDIERIEDLIRRVAHYFITHNERERAAKALEGALSKEKDEAS----LEDLNILAELFLKNKQSDKALMKIVDDRN  344 (895)
T ss_pred             hhHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhcccccc----ccHHHHHHHHHHHhHHHHHhhHHHHHHhc
Confidence            2     234455677788888889999988887653222121    12689999999999999999999888765

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

Probab=98.48  E-value=0.00023  Score=60.64  Aligned_cols=203  Identities=8%  Similarity=0.015  Sum_probs=114.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHH
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYAT   98 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~   98 (246)
                      .|......=-..|..+....+|+.....++.....|-.....+...|+...|..++.+..+.        .+.+...|-.
T Consensus       552 lWlra~~~ek~hgt~Esl~Allqkav~~~pkae~lwlM~ake~w~agdv~~ar~il~~af~~--------~pnseeiwla  623 (913)
T KOG0495|consen  552 LWLRAAMFEKSHGTRESLEALLQKAVEQCPKAEILWLMYAKEKWKAGDVPAARVILDQAFEA--------NPNSEEIWLA  623 (913)
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHHHHhCCcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHh--------CCCcHHHHHH
Confidence            33333333333444555555555544334444455555555555666666777666666664        2224556666


Q ss_pred             HHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhc--------------
Q 043380           99 LLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVC--------------  164 (246)
Q Consensus        99 ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~--------------  164 (246)
                      .+..-..+..++.|..+|.+...   ..|+...|.--+...-..++.++    |.+++++-.+.+.              
T Consensus       624 avKle~en~e~eraR~llakar~---~sgTeRv~mKs~~~er~ld~~ee----A~rllEe~lk~fp~f~Kl~lmlGQi~e  696 (913)
T KOG0495|consen  624 AVKLEFENDELERARDLLAKARS---ISGTERVWMKSANLERYLDNVEE----ALRLLEEALKSFPDFHKLWLMLGQIEE  696 (913)
T ss_pred             HHHHhhccccHHHHHHHHHHHhc---cCCcchhhHHHhHHHHHhhhHHH----HHHHHHHHHHhCCchHHHHHHHhHHHH
Confidence            66666777777777777776655   44666666655555555666666    6666665555410              


Q ss_pred             -------------CCCCCCcc-hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChh
Q 043380          165 -------------SNPGLWPK-PHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVD  230 (246)
Q Consensus       165 -------------~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~  230 (246)
                                   .....-|+ .-.|..|.+.--+.|.+-+|..+++.-...+++...      .|-..|..=.+.|+.+
T Consensus       697 ~~~~ie~aR~aY~~G~k~cP~~ipLWllLakleEk~~~~~rAR~ildrarlkNPk~~~------lwle~Ir~ElR~gn~~  770 (913)
T KOG0495|consen  697 QMENIEMAREAYLQGTKKCPNSIPLWLLLAKLEEKDGQLVRARSILDRARLKNPKNAL------LWLESIRMELRAGNKE  770 (913)
T ss_pred             HHHHHHHHHHHHHhccccCCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhcCCCcch------hHHHHHHHHHHcCCHH
Confidence                         00011222 245555556656666666777777766554433221      5666777777777777


Q ss_pred             HHHHHHHHHHhh
Q 043380          231 LALDKLSNTITR  242 (246)
Q Consensus       231 ~a~~~~~~m~~~  242 (246)
                      .|..++.+-++.
T Consensus       771 ~a~~lmakALQe  782 (913)
T KOG0495|consen  771 QAELLMAKALQE  782 (913)
T ss_pred             HHHHHHHHHHHh
Confidence            777776655543

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

Probab=98.48  E-value=9.2e-05  Score=62.92  Aligned_cols=198  Identities=8%  Similarity=-0.021  Sum_probs=113.6

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      ....|-.....+-..|++..|..++.+.-.-.+.+...|-+.+..-..+..++.|..+|.+....         .|+...
T Consensus       583 ae~lwlM~ake~w~agdv~~ar~il~~af~~~pnseeiwlaavKle~en~e~eraR~llakar~~---------sgTeRv  653 (913)
T KOG0495|consen  583 AEILWLMYAKEKWKAGDVPAARVILDQAFEANPNSEEIWLAAVKLEFENDELERARDLLAKARSI---------SGTERV  653 (913)
T ss_pred             chhHHHHHHHHHHhcCCcHHHHHHHHHHHHhCCCcHHHHHHHHHHhhccccHHHHHHHHHHHhcc---------CCcchh
Confidence            33444444444455566666666665544323334455555555555555555555555555443         344444


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhC-------------------------------CCCCCC-HHHHHHHHHHHHhcC
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSC-------------------------------CNLILD-RSTFTAMVDALLYSG  143 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~-------------------------------~~~~p~-~~~~~~li~~~~~~~  143 (246)
                      |.--+..-.-.++.++|.+++++..+.                               ....|+ ...|-.|...--+.|
T Consensus       654 ~mKs~~~er~ld~~eeA~rllEe~lk~fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~cP~~ipLWllLakleEk~~  733 (913)
T KOG0495|consen  654 WMKSANLERYLDNVEEALRLLEEALKSFPDFHKLWLMLGQIEEQMENIEMAREAYLQGTKKCPNSIPLWLLLAKLEEKDG  733 (913)
T ss_pred             hHHHhHHHHHhhhHHHHHHHHHHHHHhCCchHHHHHHHhHHHHHHHHHHHHHHHHHhccccCCCCchHHHHHHHHHHHhc
Confidence            444444444444444444444443330                               012344 445555556666666


Q ss_pred             ChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHH
Q 043380          144 SIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAA  223 (246)
Q Consensus       144 ~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~  223 (246)
                      .+-.    |..+++.-..+      -+-|...|-..|+.-.+.|+.+.|..+..+..+.-    |.+..  .|.--|...
T Consensus       734 ~~~r----AR~ildrarlk------NPk~~~lwle~Ir~ElR~gn~~~a~~lmakALQec----p~sg~--LWaEaI~le  797 (913)
T KOG0495|consen  734 QLVR----ARSILDRARLK------NPKNALLWLESIRMELRAGNKEQAELLMAKALQEC----PSSGL--LWAEAIWLE  797 (913)
T ss_pred             chhh----HHHHHHHHHhc------CCCcchhHHHHHHHHHHcCCHHHHHHHHHHHHHhC----Cccch--hHHHHHHhc
Confidence            7777    88888877665      24466889999999999999999999888776542    22211  577777777


Q ss_pred             HhcCChhHHHHHHHH
Q 043380          224 LNDGQVDLALDKLSN  238 (246)
Q Consensus       224 ~~~g~~~~a~~~~~~  238 (246)
                      -+.++-.+....++.
T Consensus       798 ~~~~rkTks~DALkk  812 (913)
T KOG0495|consen  798 PRPQRKTKSIDALKK  812 (913)
T ss_pred             cCcccchHHHHHHHh
Confidence            776665555554443

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

Probab=98.48  E-value=3e-05  Score=63.42  Aligned_cols=189  Identities=12%  Similarity=0.040  Sum_probs=148.0

Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-HHHHHHHHHHHHcc
Q 043380           28 REAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-IFTYATLLMGFRHA  106 (246)
Q Consensus        28 ~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~~~ll~~~~~~  106 (246)
                      ...+++..|.++|+....+-..++..|--.+.+=.++...+.|..+++..+..         -|- ...|---+-.=-..
T Consensus        84 esq~e~~RARSv~ERALdvd~r~itLWlkYae~Emknk~vNhARNv~dRAvt~---------lPRVdqlWyKY~ymEE~L  154 (677)
T KOG1915|consen   84 ESQKEIQRARSVFERALDVDYRNITLWLKYAEFEMKNKQVNHARNVWDRAVTI---------LPRVDQLWYKYIYMEEML  154 (677)
T ss_pred             HhHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHhhhhHhHHHHHHHHHHHh---------cchHHHHHHHHHHHHHHh
Confidence            34667888999999887555778888888888888999999999999999875         343 33555555555667


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhc
Q 043380          107 KDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAAR  186 (246)
Q Consensus       107 ~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~  186 (246)
                      |++..|.++|++-.+   ..|+...|++.|..-.+-+.++.    |..+++...-       +.|+..+|..-..---++
T Consensus       155 gNi~gaRqiferW~~---w~P~eqaW~sfI~fElRykeier----aR~IYerfV~-------~HP~v~~wikyarFE~k~  220 (677)
T KOG1915|consen  155 GNIAGARQIFERWME---WEPDEQAWLSFIKFELRYKEIER----ARSIYERFVL-------VHPKVSNWIKYARFEEKH  220 (677)
T ss_pred             cccHHHHHHHHHHHc---CCCcHHHHHHHHHHHHHhhHHHH----HHHHHHHHhe-------ecccHHHHHHHHHHHHhc
Confidence            999999999999988   88999999999999999999999    9999999876       469999999999999999


Q ss_pred             CChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          187 VDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       187 g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                      |++..|..++......- +  ........+.++...=.++..++.|.-+|+--+++
T Consensus       221 g~~~~aR~VyerAie~~-~--~d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~  273 (677)
T KOG1915|consen  221 GNVALARSVYERAIEFL-G--DDEEAEILFVAFAEFEERQKEYERARFIYKYALDH  273 (677)
T ss_pred             CcHHHHHHHHHHHHHHh-h--hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999998865322 1  11112224555555556677888888877765554

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

Probab=98.47  E-value=1.1e-05  Score=70.91  Aligned_cols=189  Identities=13%  Similarity=0.083  Sum_probs=140.3

Q ss_pred             CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHc-----
Q 043380           31 QRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRH-----  105 (246)
Q Consensus        31 g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~-----  105 (246)
                      +...+|...+.........++..++.+-+.+.+...+..|.+-|....+..      ...+|+.+.-+|-+.|.+     
T Consensus       544 ~~~~ea~~~lk~~l~~d~~np~arsl~G~~~l~k~~~~~a~k~f~~i~~~~------~~~~D~YsliaLGN~~~~~l~~~  617 (1018)
T KOG2002|consen  544 NNLYEASLLLKDALNIDSSNPNARSLLGNLHLKKSEWKPAKKKFETILKKT------STKTDAYSLIALGNVYIQALHNP  617 (1018)
T ss_pred             cCcHHHHHHHHHHHhcccCCcHHHHHHHHHHHhhhhhcccccHHHHHHhhh------ccCCchhHHHHhhHHHHHHhccc
Confidence            445566666666554455666667777777778777888888777666652      334677776666665532     


Q ss_pred             -------cCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHH
Q 043380          106 -------AKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVS  178 (246)
Q Consensus       106 -------~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~  178 (246)
                             .+..++|+++|....+ . -+.|.+.-|.+.-.++..|++..    |..+|.++.+.      ..-+..+|..
T Consensus       618 ~rn~ek~kk~~~KAlq~y~kvL~-~-dpkN~yAANGIgiVLA~kg~~~~----A~dIFsqVrEa------~~~~~dv~lN  685 (1018)
T KOG2002|consen  618 SRNPEKEKKHQEKALQLYGKVLR-N-DPKNMYAANGIGIVLAEKGRFSE----ARDIFSQVREA------TSDFEDVWLN  685 (1018)
T ss_pred             ccChHHHHHHHHHHHHHHHHHHh-c-CcchhhhccchhhhhhhccCchH----HHHHHHHHHHH------HhhCCceeee
Confidence                   2345789999998888 2 22347888899999999999999    99999999997      3345678899


Q ss_pred             HHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          179 MMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       179 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      +.++|...|++..|.++|+...+.....-.+.    ....|.+++...|.+.+|.+.+...+.
T Consensus       686 lah~~~e~~qy~~AIqmYe~~lkkf~~~~~~~----vl~~Lara~y~~~~~~eak~~ll~a~~  744 (1018)
T KOG2002|consen  686 LAHCYVEQGQYRLAIQMYENCLKKFYKKNRSE----VLHYLARAWYEAGKLQEAKEALLKARH  744 (1018)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcccCCHH----HHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            99999999999999999998775543222332    577899999999999999988765543

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=98.47  E-value=2e-05  Score=59.47  Aligned_cols=135  Identities=13%  Similarity=0.038  Sum_probs=115.8

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      .+.|...-+.++...++.|++..|...|.+....-++|..+|+.+--+|-+.|+.++|..-|.+..+.        ..-+
T Consensus        96 ~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L--------~~~~  167 (257)
T COG5010          96 YPKDRELLAAQGKNQIRNGNFGEAVSVLRKAARLAPTDWEAWNLLGAALDQLGRFDEARRAYRQALEL--------APNE  167 (257)
T ss_pred             CcccHHHHHHHHHHHHHhcchHHHHHHHHHHhccCCCChhhhhHHHHHHHHccChhHHHHHHHHHHHh--------ccCC
Confidence            44556667778999999999999999999998777999999999999999999999999999999985        3445


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHH
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVK  161 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~  161 (246)
                      ...+|.|...|.-.||.+.|..++..... .+ .-|..+-..+.......|++++    |.++...-..
T Consensus       168 p~~~nNlgms~~L~gd~~~A~~lll~a~l-~~-~ad~~v~~NLAl~~~~~g~~~~----A~~i~~~e~~  230 (257)
T COG5010         168 PSIANNLGMSLLLRGDLEDAETLLLPAYL-SP-AADSRVRQNLALVVGLQGDFRE----AEDIAVQELL  230 (257)
T ss_pred             chhhhhHHHHHHHcCCHHHHHHHHHHHHh-CC-CCchHHHHHHHHHHhhcCChHH----HHhhcccccc
Confidence            67889999999999999999999999887 32 2367778889999999999999    9987765543

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

Probab=98.46  E-value=4.4e-06  Score=68.66  Aligned_cols=126  Identities=15%  Similarity=0.106  Sum_probs=105.9

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCC
Q 043380           46 GLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNL  125 (246)
Q Consensus        46 ~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~  125 (246)
                      +.+.+......+++.+....+++.+..++-+.....     .....-..|..++++.|...|..+.++++++.=.. .|+
T Consensus        61 ~~~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~-----~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~-yGi  134 (429)
T PF10037_consen   61 KKPVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSP-----NCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQ-YGI  134 (429)
T ss_pred             CCCCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCc-----ccccccCccHHHHHHHHHhcCCHHHHHHHHhChhh-ccc
Confidence            556678888999999999999999999999888751     12222334667999999999999999999999999 999


Q ss_pred             CCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhc
Q 043380          126 ILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAAR  186 (246)
Q Consensus       126 ~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~  186 (246)
                      -||.++||.||+.+.+.|++..    |.++...|..+     ..-.+..|+..-+.+|.+-
T Consensus       135 F~D~~s~n~Lmd~fl~~~~~~~----A~~V~~~~~lQ-----e~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  135 FPDNFSFNLLMDHFLKKGNYKS----AAKVATEMMLQ-----EEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             CCChhhHHHHHHHHhhcccHHH----HHHHHHHHHHh-----hccCCchHHHHHHHHHHHh
Confidence            9999999999999999999999    99999999888     6666677777766666665

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 [].

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

Probab=98.46  E-value=1.2e-05  Score=55.99  Aligned_cols=109  Identities=12%  Similarity=0.025  Sum_probs=84.3

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      +......+...+...|+.++|.+.|+......+.+...|..+...+...|++++|..++++....        .+.+...
T Consensus        16 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~--------~p~~~~~   87 (135)
T TIGR02552        16 QLEQIYALAYNLYQQGRYDEALKLFQLLAAYDPYNSRYWLGLAACCQMLKEYEEAIDAYALAAAL--------DPDDPRP   87 (135)
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc--------CCCChHH
Confidence            34556677778888899999999998876444567788888888888899999999999988775        2445677


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHH
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAM  135 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~l  135 (246)
                      +..+-..|...|++++|...|+...+   ..|+...+..+
T Consensus        88 ~~~la~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~~  124 (135)
T TIGR02552        88 YFHAAECLLALGEPESALKALDLAIE---ICGENPEYSEL  124 (135)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH---hccccchHHHH
Confidence            77788888899999999999988888   55665554433

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

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

Probab=98.40  E-value=0.00012  Score=64.58  Aligned_cols=216  Identities=14%  Similarity=0.082  Sum_probs=120.9

Q ss_pred             hHHHHhcccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCCH------HHHHHHHHHHHhcCCcchHHHHH
Q 043380            5 NEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKG----LEPDS------LSYNILISACIKTKKLDVTMPFN   74 (246)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~----~~~~~------~t~~~li~~~~~~~~~~~a~~~~   74 (246)
                      ++.++..+-.+.+...|.+...+...|++++|...|......    ..+|.      .+--.+-...-..++.+.|.+.|
T Consensus       440 ~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YNlarl~E~l~~~~~A~e~Y  519 (1018)
T KOG2002|consen  440 LDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYNLARLLEELHDTEVAEEMY  519 (1018)
T ss_pred             HHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHHHHHHHHhhhhhhHHHHHH
Confidence            456667777788899999999999999999999999887532    23333      22222334444566788888888


Q ss_pred             HHHHhccCCCCCCCCCccHH-HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHH
Q 043380           75 EQLKDNGQKCSSGGFHPDIF-TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYAL  153 (246)
Q Consensus        75 ~~m~~~~~~~~~~~~~p~~~-~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~  153 (246)
                      ......         .|+-. .|--+.......+...+|...++.........|+.  ++.+...|.+...+..    |.
T Consensus       520 k~Ilke---------hp~YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~d~~np~a--rsl~G~~~l~k~~~~~----a~  584 (1018)
T KOG2002|consen  520 KSILKE---------HPGYIDAYLRLGCMARDKNNLYEASLLLKDALNIDSSNPNA--RSLLGNLHLKKSEWKP----AK  584 (1018)
T ss_pred             HHHHHH---------CchhHHHHHHhhHHHHhccCcHHHHHHHHHHHhcccCCcHH--HHHHHHHHHhhhhhcc----cc
Confidence            888875         45533 34444433334456666666666665522223333  3334444555555554    44


Q ss_pred             HHHHHHHHhhcCC-----------------------------------------C-CCCcchhhHHHHHHHHHhcCChhH
Q 043380          154 CIFGEIVKRVCSN-----------------------------------------P-GLWPKPHLYVSMMHELAARVDYDI  191 (246)
Q Consensus       154 ~~~~~m~~~~~~~-----------------------------------------~-~~~p~~~~~~~li~~~~~~g~~~~  191 (246)
                      +-|....+.-...                                         . .-+-|...-+.+--+++..|++.+
T Consensus       585 k~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~dpkN~yAANGIgiVLA~kg~~~~  664 (1018)
T KOG2002|consen  585 KKFETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLRNDPKNMYAANGIGIVLAEKGRFSE  664 (1018)
T ss_pred             cHHHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHhcCcchhhhccchhhhhhhccCchH
Confidence            4444433320000                                         0 012233444555555555566666


Q ss_pred             HhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          192 VKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       192 a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      |..+|.++........+      +|-.+.++|+-+|++..|+++|+...+
T Consensus       665 A~dIFsqVrEa~~~~~d------v~lNlah~~~e~~qy~~AIqmYe~~lk  708 (1018)
T KOG2002|consen  665 ARDIFSQVREATSDFED------VWLNLAHCYVEQGQYRLAIQMYENCLK  708 (1018)
T ss_pred             HHHHHHHHHHHHhhCCc------eeeeHHHHHHHHHHHHHHHHHHHHHHH
Confidence            66666655533211111      455566666666666666666665543

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=98.40  E-value=0.00014  Score=54.18  Aligned_cols=148  Identities=7%  Similarity=0.020  Sum_probs=113.1

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHH
Q 043380           24 IEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGF  103 (246)
Q Consensus        24 i~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~  103 (246)
                      +..|...|+++.+....+.+..   |. ..       +...++.+++...++.....        -+.|...|..|-..|
T Consensus        23 ~~~Y~~~g~~~~v~~~~~~~~~---~~-~~-------~~~~~~~~~~i~~l~~~L~~--------~P~~~~~w~~Lg~~~   83 (198)
T PRK10370         23 VGSYLLSPKWQAVRAEYQRLAD---PL-HQ-------FASQQTPEAQLQALQDKIRA--------NPQNSEQWALLGEYY   83 (198)
T ss_pred             HHHHHHcchHHHHHHHHHHHhC---cc-cc-------ccCchhHHHHHHHHHHHHHH--------CCCCHHHHHHHHHHH
Confidence            4568889998887555433321   11 11       11255667777777777764        356788999999999


Q ss_pred             HccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHH-HhcCC--hhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHH
Q 043380          104 RHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDAL-LYSGS--IKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSM  179 (246)
Q Consensus       104 ~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~-~~~~~--~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~l  179 (246)
                      ...|++++|...|++..+   +.|+ ...+..+..++ ...|+  .++    |.+++++..+.      -.-+..++..+
T Consensus        84 ~~~g~~~~A~~a~~~Al~---l~P~~~~~~~~lA~aL~~~~g~~~~~~----A~~~l~~al~~------dP~~~~al~~L  150 (198)
T PRK10370         84 LWRNDYDNALLAYRQALQ---LRGENAELYAALATVLYYQAGQHMTPQ----TREMIDKALAL------DANEVTALMLL  150 (198)
T ss_pred             HHCCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHhcCCCCcHH----HHHHHHHHHHh------CCCChhHHHHH
Confidence            999999999999999988   5565 77788887764 67777  488    99999999986      23356888999


Q ss_pred             HHHHHhcCChhHHhhHHHhhCCCC
Q 043380          180 MHELAARVDYDIVKSPYRRMWPDS  203 (246)
Q Consensus       180 i~~~~~~g~~~~a~~~~~~~~~~~  203 (246)
                      ...+...|++++|...|+++....
T Consensus       151 A~~~~~~g~~~~Ai~~~~~aL~l~  174 (198)
T PRK10370        151 ASDAFMQADYAQAIELWQKVLDLN  174 (198)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhhC
Confidence            999999999999999999987653

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.37  E-value=7.2e-05  Score=65.86  Aligned_cols=160  Identities=9%  Similarity=0.067  Sum_probs=103.8

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      ...++..+-.|.....+.|..++|+.+++....-.+-+......+...+.+.+++++|...+++....         .|+
T Consensus        82 ~~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~---------~p~  152 (694)
T PRK15179         82 YPHTELFQVLVARALEAAHRSDEGLAVWRGIHQRFPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSG---------GSS  152 (694)
T ss_pred             ccccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhc---------CCC
Confidence            34456666677777777777777777777765433445566677777777777777777777777765         444


Q ss_pred             -HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCC
Q 043380           93 -IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLW  170 (246)
Q Consensus        93 -~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~  170 (246)
                       ....+.+-.++.+.|++++|..+|++... .  .|+ ..++..+-..+-..|+.++    |...|+...+.      ..
T Consensus       153 ~~~~~~~~a~~l~~~g~~~~A~~~y~~~~~-~--~p~~~~~~~~~a~~l~~~G~~~~----A~~~~~~a~~~------~~  219 (694)
T PRK15179        153 SAREILLEAKSWDEIGQSEQADACFERLSR-Q--HPEFENGYVGWAQSLTRRGALWR----ARDVLQAGLDA------IG  219 (694)
T ss_pred             CHHHHHHHHHHHHHhcchHHHHHHHHHHHh-c--CCCcHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh------hC
Confidence             44555666666777777777777777776 2  244 6667777777777777777    77777777665      33


Q ss_pred             cchhhHHHHHHHHHhcCChhHHhhHHHhhC
Q 043380          171 PKPHLYVSMMHELAARVDYDIVKSPYRRMW  200 (246)
Q Consensus       171 p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  200 (246)
                      |-...|+..+.      +...-..+++.+.
T Consensus       220 ~~~~~~~~~~~------~~~~~~~~~~~~~  243 (694)
T PRK15179        220 DGARKLTRRLV------DLNADLAALRRLG  243 (694)
T ss_pred             cchHHHHHHHH------HHHHHHHHHHHcC
Confidence            44445544432      2333344555554

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=98.37  E-value=0.0005  Score=56.56  Aligned_cols=163  Identities=15%  Similarity=0.023  Sum_probs=111.4

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      ..|+...+...+.+......-..+-.++..-.+ -.-...-|..-+.. ...+.+++|+..+..++..         .||
T Consensus       270 d~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~-~~~~aa~YG~A~~~-~~~~~~d~A~~~l~~L~~~---------~P~  338 (484)
T COG4783         270 DSPDFQLARARIRAKYEALPNQQAADLLAKRSK-RGGLAAQYGRALQT-YLAGQYDEALKLLQPLIAA---------QPD  338 (484)
T ss_pred             CCccHHHHHHHHHHHhccccccchHHHHHHHhC-ccchHHHHHHHHHH-HHhcccchHHHHHHHHHHh---------CCC
Confidence            456666666666655444333333333322222 01223334444443 4567889999999998875         555


Q ss_pred             HH-HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCC
Q 043380           93 IF-TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLW  170 (246)
Q Consensus        93 ~~-~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~  170 (246)
                      .. -+......+.+.++.++|.+.++.+..   ..|+ ....-.+..+|.+.|++.+    |..+++.....      .+
T Consensus       339 N~~~~~~~~~i~~~~nk~~~A~e~~~kal~---l~P~~~~l~~~~a~all~~g~~~e----ai~~L~~~~~~------~p  405 (484)
T COG4783         339 NPYYLELAGDILLEANKAKEAIERLKKALA---LDPNSPLLQLNLAQALLKGGKPQE----AIRILNRYLFN------DP  405 (484)
T ss_pred             CHHHHHHHHHHHHHcCChHHHHHHHHHHHh---cCCCccHHHHHHHHHHHhcCChHH----HHHHHHHHhhc------CC
Confidence            44 445556668889999999999999888   6677 5556678888999999999    99999988775      56


Q ss_pred             cchhhHHHHHHHHHhcCChhHHhhHHHhh
Q 043380          171 PKPHLYVSMMHELAARVDYDIVKSPYRRM  199 (246)
Q Consensus       171 p~~~~~~~li~~~~~~g~~~~a~~~~~~~  199 (246)
                      -|+..|..|-.+|...|+..++..-.-+.
T Consensus       406 ~dp~~w~~LAqay~~~g~~~~a~~A~AE~  434 (484)
T COG4783         406 EDPNGWDLLAQAYAELGNRAEALLARAEG  434 (484)
T ss_pred             CCchHHHHHHHHHHHhCchHHHHHHHHHH
Confidence            67788999999999999887766555544

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

Probab=98.37  E-value=6.6e-05  Score=65.60  Aligned_cols=201  Identities=17%  Similarity=0.167  Sum_probs=145.8

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHH--hCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCC-----------------
Q 043380           23 VIEASREAQRIDEAYQILESVE--KGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQK-----------------   83 (246)
Q Consensus        23 li~~~~~~g~~~~a~~~~~~~~--~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-----------------   83 (246)
                      .+..|...++.+.|.+.++...  .+-..+...++++...+.+...++.|......+.....+                 
T Consensus       286 ~~~~~~~~~~~e~a~~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~  365 (895)
T KOG2076|consen  286 VAHYFITHNERERAAKALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPN  365 (895)
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhcccccc
Confidence            3455666777788888887754  244567778899999999999999999988888772110                 


Q ss_pred             ---CCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC--HHHHHHHHHHHHhcCChhhhhhHHHHHHHH
Q 043380           84 ---CSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD--RSTFTAMVDALLYSGSIKVVGLYALCIFGE  158 (246)
Q Consensus        84 ---~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~--~~~~~~li~~~~~~~~~~~~~~~a~~~~~~  158 (246)
                         .-..++.++... --+.-++.+....+....+...... ..+.|+  ...|.-+..+|...|++.+    |+++|..
T Consensus       366 ~~~~~~~~~s~~l~v-~rl~icL~~L~~~e~~e~ll~~l~~-~n~~~~d~~dL~~d~a~al~~~~~~~~----Al~~l~~  439 (895)
T KOG2076|consen  366 ALCEVGKELSYDLRV-IRLMICLVHLKERELLEALLHFLVE-DNVWVSDDVDLYLDLADALTNIGKYKE----ALRLLSP  439 (895)
T ss_pred             ccccCCCCCCccchh-HhHhhhhhcccccchHHHHHHHHHH-hcCChhhhHHHHHHHHHHHHhcccHHH----HHHHHHH
Confidence               012233444444 2233344444444444444444444 444443  6779999999999999999    9999999


Q ss_pred             HHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHH
Q 043380          159 IVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSN  238 (246)
Q Consensus       159 m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  238 (246)
                      +...     ...-+...|-.+..+|...|..++|.+.++......+....      +-.+|-..+-+.|+.++|.+.+..
T Consensus       440 i~~~-----~~~~~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~~p~~~D------~Ri~Lasl~~~~g~~EkalEtL~~  508 (895)
T KOG2076|consen  440 ITNR-----EGYQNAFVWYKLARCYMELGEYEEAIEFYEKVLILAPDNLD------ARITLASLYQQLGNHEKALETLEQ  508 (895)
T ss_pred             HhcC-----ccccchhhhHHHHHHHHHHhhHHHHHHHHHHHHhcCCCchh------hhhhHHHHHHhcCCHHHHHHHHhc
Confidence            9887     33345779999999999999999999999999876655444      445688889999999999999988


Q ss_pred             HH
Q 043380          239 TI  240 (246)
Q Consensus       239 m~  240 (246)
                      +.
T Consensus       509 ~~  510 (895)
T KOG2076|consen  509 II  510 (895)
T ss_pred             cc
Confidence            64

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.36  E-value=5.1e-05  Score=53.57  Aligned_cols=107  Identities=12%  Similarity=-0.036  Sum_probs=88.4

Q ss_pred             HHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHH
Q 043380           38 QILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVF  117 (246)
Q Consensus        38 ~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~  117 (246)
                      .+|++..+ ..|+  .+......+...|++++|...|......        -+.+...|..+-.++.+.|++++|...|+
T Consensus        14 ~~~~~al~-~~p~--~~~~~g~~~~~~g~~~~A~~~~~~al~~--------~P~~~~a~~~lg~~~~~~g~~~~A~~~y~   82 (144)
T PRK15359         14 DILKQLLS-VDPE--TVYASGYASWQEGDYSRAVIDFSWLVMA--------QPWSWRAHIALAGTWMMLKEYTTAINFYG   82 (144)
T ss_pred             HHHHHHHH-cCHH--HHHHHHHHHHHcCCHHHHHHHHHHHHHc--------CCCcHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence            44444431 2344  3556777888999999999999999885        24477899999999999999999999999


Q ss_pred             HHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          118 EMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       118 ~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ....   ..|+ ...+..+..++...|++++    |...|+.....
T Consensus        83 ~Al~---l~p~~~~a~~~lg~~l~~~g~~~e----Ai~~~~~Al~~  121 (144)
T PRK15359         83 HALM---LDASHPEPVYQTGVCLKMMGEPGL----AREAFQTAIKM  121 (144)
T ss_pred             HHHh---cCCCCcHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh
Confidence            9998   4565 7889999999999999999    99999999875

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.35  E-value=1.1e-06  Score=45.45  Aligned_cols=33  Identities=30%  Similarity=0.525  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc
Q 043380          130 STFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP  171 (246)
Q Consensus       130 ~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p  171 (246)
                      .+|+++|.+|++.|+++.    |.++|++|.+.     |++|
T Consensus         2 ~ty~~ll~a~~~~g~~~~----a~~~~~~M~~~-----gv~P   34 (34)
T PF13812_consen    2 HTYNALLRACAKAGDPDA----ALQLFDEMKEQ-----GVKP   34 (34)
T ss_pred             cHHHHHHHHHHHCCCHHH----HHHHHHHHHHh-----CCCC
Confidence            589999999999999999    99999999998     8887

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

Probab=98.34  E-value=1.5e-05  Score=52.42  Aligned_cols=81  Identities=22%  Similarity=0.398  Sum_probs=69.7

Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCC-CccHHHHHHHHHHHHccC--------CHHHHHHHHHHHHhCCC
Q 043380           54 YNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGF-HPDIFTYATLLMGFRHAK--------DLQSLLEIVFEMKSCCN  124 (246)
Q Consensus        54 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~-~p~~~~~~~ll~~~~~~~--------~~~~a~~~~~~m~~~~~  124 (246)
                      -...|..+...+++.....+|+.++..       |+ .|+..+|+.++.+.++..        +....+.+|+.|.. .+
T Consensus        28 ~i~~I~~~~~~~d~N~I~~lYqslkRN-------~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~-~~   99 (120)
T PF08579_consen   28 QIDNINSCFENEDYNIINPLYQSLKRN-------GITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILS-NK   99 (120)
T ss_pred             HHHHHHHHHhhcchHHHHHHHHHHHhc-------CCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHH-hc
Confidence            345677777889999999999999998       78 899999999999987654        24567889999999 99


Q ss_pred             CCCCHHHHHHHHHHHHhc
Q 043380          125 LILDRSTFTAMVDALLYS  142 (246)
Q Consensus       125 ~~p~~~~~~~li~~~~~~  142 (246)
                      ++|+..+|+.++..+.+.
T Consensus       100 lKP~~etYnivl~~Llkg  117 (120)
T PF08579_consen  100 LKPNDETYNIVLGSLLKG  117 (120)
T ss_pred             cCCcHHHHHHHHHHHHHh
Confidence            999999999999987653

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 [, , ].

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

Probab=98.34  E-value=4.2e-05  Score=65.47  Aligned_cols=189  Identities=12%  Similarity=0.006  Sum_probs=150.6

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      .+|-...=-.+...+.+.|-+..|..+|+++.        .|..+|.+|+..|+..+|..+..+..+.         +||
T Consensus       394 lpp~Wq~q~~laell~slGitksAl~I~Erle--------mw~~vi~CY~~lg~~~kaeei~~q~lek---------~~d  456 (777)
T KOG1128|consen  394 LPPIWQLQRLLAELLLSLGITKSALVIFERLE--------MWDPVILCYLLLGQHGKAEEINRQELEK---------DPD  456 (777)
T ss_pred             CCCcchHHHHHHHHHHHcchHHHHHHHHHhHH--------HHHHHHHHHHHhcccchHHHHHHHHhcC---------CCc
Confidence            45555555667788889999999999999986        4778899999999999999999998875         799


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK  172 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~  172 (246)
                      ...|..+.+......-+++|.++.+..-. .       .-..+.....+.+++.+    +.+.|+.-...      -...
T Consensus       457 ~~lyc~LGDv~~d~s~yEkawElsn~~sa-r-------A~r~~~~~~~~~~~fs~----~~~hle~sl~~------nplq  518 (777)
T KOG1128|consen  457 PRLYCLLGDVLHDPSLYEKAWELSNYISA-R-------AQRSLALLILSNKDFSE----ADKHLERSLEI------NPLQ  518 (777)
T ss_pred             chhHHHhhhhccChHHHHHHHHHhhhhhH-H-------HHHhhccccccchhHHH----HHHHHHHHhhc------Cccc
Confidence            99999999988877788999999887655 1       11112222333789999    99999887665      2334


Q ss_pred             hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          173 PHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       173 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                      ..+|-..-.+..+.++++.|.+.|.....-.+++      ...||.+-.+|.+.|+-.+|...+++-.+-
T Consensus       519 ~~~wf~~G~~ALqlek~q~av~aF~rcvtL~Pd~------~eaWnNls~ayi~~~~k~ra~~~l~EAlKc  582 (777)
T KOG1128|consen  519 LGTWFGLGCAALQLEKEQAAVKAFHRCVTLEPDN------AEAWNNLSTAYIRLKKKKRAFRKLKEALKC  582 (777)
T ss_pred             hhHHHhccHHHHHHhhhHHHHHHHHHHhhcCCCc------hhhhhhhhHHHHHHhhhHHHHHHHHHHhhc
Confidence            5788888888899999999999999987544332      238999999999999999999999887653

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

Probab=98.34  E-value=0.00034  Score=64.14  Aligned_cols=188  Identities=9%  Similarity=0.026  Sum_probs=153.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHH
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYAT   98 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~   98 (246)
                      .|.++++.---.|.-+...++|++..+-+. ....|..|..-|.+.+..++|.++++.|.+.        +.-....|..
T Consensus      1499 iWiA~lNlEn~yG~eesl~kVFeRAcqycd-~~~V~~~L~~iy~k~ek~~~A~ell~~m~KK--------F~q~~~vW~~ 1569 (1710)
T KOG1070|consen 1499 IWIAYLNLENAYGTEESLKKVFERACQYCD-AYTVHLKLLGIYEKSEKNDEADELLRLMLKK--------FGQTRKVWIM 1569 (1710)
T ss_pred             HHHHHHhHHHhhCcHHHHHHHHHHHHHhcc-hHHHHHHHHHHHHHhhcchhHHHHHHHHHHH--------hcchhhHHHH
Confidence            577888877778888999999999875332 2356889999999999999999999999995        5567779999


Q ss_pred             HHHHHHccCCHHHHHHHHHHHHhCCCCCCC---HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhh
Q 043380           99 LLMGFRHAKDLQSLLEIVFEMKSCCNLILD---RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHL  175 (246)
Q Consensus        99 ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~---~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~  175 (246)
                      .+..+.+..+-++|..++.+..+   ..|.   ....+-.+..-.+.|+.++    +..+|+.....      .+--...
T Consensus      1570 y~~fLl~~ne~~aa~~lL~rAL~---~lPk~eHv~~IskfAqLEFk~GDaeR----GRtlfEgll~a------yPKRtDl 1636 (1710)
T KOG1070|consen 1570 YADFLLRQNEAEAARELLKRALK---SLPKQEHVEFISKFAQLEFKYGDAER----GRTLFEGLLSA------YPKRTDL 1636 (1710)
T ss_pred             HHHHHhcccHHHHHHHHHHHHHh---hcchhhhHHHHHHHHHHHhhcCCchh----hHHHHHHHHhh------CccchhH
Confidence            99999999999999999999888   4454   3445666777778999999    99999999886      2223468


Q ss_pred             HHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhH
Q 043380          176 YVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDL  231 (246)
Q Consensus       176 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~  231 (246)
                      |+..|+.-.++|+.+.+..+|+++...+   +++.-..+.|...++.=-..|+-..
T Consensus      1637 W~VYid~eik~~~~~~vR~lfeRvi~l~---l~~kkmKfffKkwLeyEk~~Gde~~ 1689 (1710)
T KOG1070|consen 1637 WSVYIDMEIKHGDIKYVRDLFERVIELK---LSIKKMKFFFKKWLEYEKSHGDEKN 1689 (1710)
T ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhcC---CChhHhHHHHHHHHHHHHhcCchhh
Confidence            9999999999999999999999998665   5555555578888877767676543

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=98.32  E-value=3.4e-05  Score=60.80  Aligned_cols=134  Identities=10%  Similarity=0.113  Sum_probs=104.8

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP  173 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~  173 (246)
                      .+|..+++...+.+..+.|..+|.+.++...+..+.....+++.. ...++.+.    |..+|+...+.      +..+.
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E~-~~~~d~~~----A~~Ife~glk~------f~~~~   70 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALMEY-YCNKDPKR----ARKIFERGLKK------FPSDP   70 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHHH-HTCS-HHH----HHHHHHHHHHH------HTT-H
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHHH-HhCCCHHH----HHHHHHHHHHH------CCCCH
Confidence            578899999999999999999999998733344555555555543 33577888    99999999986      56677


Q ss_pred             hhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchh-hhHHHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          174 HLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEV-QEEAGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       174 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                      ..|..-+.-+...++.+.|..+|++....    +++.. ....|...++.=.+.|+++.+.++.+++.+.
T Consensus        71 ~~~~~Y~~~l~~~~d~~~aR~lfer~i~~----l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~  136 (280)
T PF05843_consen   71 DFWLEYLDFLIKLNDINNARALFERAISS----LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL  136 (280)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHCCT----SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcHHHHHHHHHHHHHh----cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            88999999999999999999999999754    44444 4458999999999999999999999887653

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.

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

Probab=98.31  E-value=8.2e-07  Score=44.84  Aligned_cols=31  Identities=26%  Similarity=0.506  Sum_probs=26.1

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCC
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNL  125 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~  125 (246)
                      +||+++|++|++.|++++|.++|++|.+ .|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~-~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRE-RGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhH-CcC
Confidence            3788999999999999999999999888 654

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.

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.30  E-value=0.00011  Score=61.26  Aligned_cols=190  Identities=14%  Similarity=0.096  Sum_probs=135.2

Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-HHHHHHHHHHH
Q 043380           25 EASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-IFTYATLLMGF  103 (246)
Q Consensus        25 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~~~ll~~~  103 (246)
                      .-+.+.|++.+|.=.|+...+.-+-+...|--|-.....+++-..|+.-+.+..+.         .|+ ....-.|--.|
T Consensus       293 ~~lm~nG~L~~A~LafEAAVkqdP~haeAW~~LG~~qaENE~E~~ai~AL~rcl~L---------dP~NleaLmaLAVSy  363 (579)
T KOG1125|consen  293 CNLMKNGDLSEAALAFEAAVKQDPQHAEAWQKLGITQAENENEQNAISALRRCLEL---------DPTNLEALMALAVSY  363 (579)
T ss_pred             HHHHhcCCchHHHHHHHHHHhhChHHHHHHHHhhhHhhhccchHHHHHHHHHHHhc---------CCccHHHHHHHHHHH
Confidence            34566777777777777654333456677777777777777777777777776654         443 33333333334


Q ss_pred             HccCCHH-----------------------------------------HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhc
Q 043380          104 RHAKDLQ-----------------------------------------SLLEIVFEMKSCCNLILDRSTFTAMVDALLYS  142 (246)
Q Consensus       104 ~~~~~~~-----------------------------------------~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~  142 (246)
                      ...|.-.                                         ...++|-++....+..+|..++..|--.|-..
T Consensus       364 tNeg~q~~Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~~~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls  443 (579)
T KOG1125|consen  364 TNEGLQNQALKMLDKWIRNKPKYVHLVSAGENEDFENTKSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLS  443 (579)
T ss_pred             hhhhhHHHHHHHHHHHHHhCccchhccccCccccccCCcCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcc
Confidence            3333333                                         33344444444244446778888899999999


Q ss_pred             CChhhhhhHHHHHHHHHHHhhcCCCCCCcc-hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHH
Q 043380          143 GSIKVVGLYALCIFGEIVKRVCSNPGLWPK-PHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLME  221 (246)
Q Consensus       143 ~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~  221 (246)
                      |++++    |.++|+...+.       +|+ ..+||.|--.++...+..+|...+++..+..++++.      +...|.-
T Consensus       444 ~efdr----aiDcf~~AL~v-------~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqLqP~yVR------~RyNlgI  506 (579)
T KOG1125|consen  444 GEFDR----AVDCFEAALQV-------KPNDYLLWNRLGATLANGNRSEEAISAYNRALQLQPGYVR------VRYNLGI  506 (579)
T ss_pred             hHHHH----HHHHHHHHHhc-------CCchHHHHHHhhHHhcCCcccHHHHHHHHHHHhcCCCeee------eehhhhh
Confidence            99999    99999999874       565 588999999999999999999999999888777776      4455788


Q ss_pred             HHHhcCChhHHHHHHHHHH
Q 043380          222 AALNDGQVDLALDKLSNTI  240 (246)
Q Consensus       222 ~~~~~g~~~~a~~~~~~m~  240 (246)
                      +|...|.+++|.+.|=..+
T Consensus       507 S~mNlG~ykEA~~hlL~AL  525 (579)
T KOG1125|consen  507 SCMNLGAYKEAVKHLLEAL  525 (579)
T ss_pred             hhhhhhhHHHHHHHHHHHH
Confidence            8999999999999886543

>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=98.30  E-value=3.9e-05  Score=62.81  Aligned_cols=122  Identities=16%  Similarity=0.150  Sum_probs=100.4

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHH
Q 043380           21 NAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLL  100 (246)
Q Consensus        21 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll  100 (246)
                      .+|+..+...++++.|.++|+++.+. .|+  ....+.+.+...++..+|.+++.+....        .+-|........
T Consensus       173 ~~Ll~~l~~t~~~~~ai~lle~L~~~-~pe--v~~~LA~v~l~~~~E~~AI~ll~~aL~~--------~p~d~~LL~~Qa  241 (395)
T PF09295_consen  173 DTLLKYLSLTQRYDEAIELLEKLRER-DPE--VAVLLARVYLLMNEEVEAIRLLNEALKE--------NPQDSELLNLQA  241 (395)
T ss_pred             HHHHHHHhhcccHHHHHHHHHHHHhc-CCc--HHHHHHHHHHhcCcHHHHHHHHHHHHHh--------CCCCHHHHHHHH
Confidence            34555666689999999999999743 355  4445788888888899999999999875        344666777777


Q ss_pred             HHHHccCCHHHHHHHHHHHHhCCCCCCCH-HHHHHHHHHHHhcCChhhhhhHHHHHHHHHH
Q 043380          101 MGFRHAKDLQSLLEIVFEMKSCCNLILDR-STFTAMVDALLYSGSIKVVGLYALCIFGEIV  160 (246)
Q Consensus       101 ~~~~~~~~~~~a~~~~~~m~~~~~~~p~~-~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~  160 (246)
                      ..+.+.++++.|+.+.+++..   ..|+. .+|..|..+|...|+++.    |+..++.+.
T Consensus       242 ~fLl~k~~~~lAL~iAk~av~---lsP~~f~~W~~La~~Yi~~~d~e~----ALlaLNs~P  295 (395)
T PF09295_consen  242 EFLLSKKKYELALEIAKKAVE---LSPSEFETWYQLAECYIQLGDFEN----ALLALNSCP  295 (395)
T ss_pred             HHHHhcCCHHHHHHHHHHHHH---hCchhHHHHHHHHHHHHhcCCHHH----HHHHHhcCc
Confidence            778999999999999999998   77884 589999999999999999    999988764

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

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

Probab=98.28  E-value=3.5e-05  Score=50.73  Aligned_cols=85  Identities=12%  Similarity=0.149  Sum_probs=70.8

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCC-CCCHHHHHHHHHHHHhcCC----hhhhhhHHHHHHHHHHHhhcCCCCC
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNL-ILDRSTFTAMVDALLYSGS----IKVVGLYALCIFGEIVKRVCSNPGL  169 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~-~p~~~~~~~li~~~~~~~~----~~~~~~~a~~~~~~m~~~~~~~~~~  169 (246)
                      |-...|..+...+++.....+|+.+++ .|+ .|+..+|+.++.+.+++.-    ++.+....+.+|+.|...     ++
T Consensus        27 t~i~~I~~~~~~~d~N~I~~lYqslkR-N~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~-----~l  100 (120)
T PF08579_consen   27 TQIDNINSCFENEDYNIINPLYQSLKR-NGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSN-----KL  100 (120)
T ss_pred             HHHHHHHHHHhhcchHHHHHHHHHHHh-cCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHh-----cc
Confidence            344566666677999999999999999 999 9999999999999988643    333333389999999998     89


Q ss_pred             CcchhhHHHHHHHHHh
Q 043380          170 WPKPHLYVSMMHELAA  185 (246)
Q Consensus       170 ~p~~~~~~~li~~~~~  185 (246)
                      +|+..||+.++..+.+
T Consensus       101 KP~~etYnivl~~Llk  116 (120)
T PF08579_consen  101 KPNDETYNIVLGSLLK  116 (120)
T ss_pred             CCcHHHHHHHHHHHHH
Confidence            9999999999998765

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 [, , ].

>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=98.25  E-value=5.8e-05  Score=61.85  Aligned_cols=124  Identities=15%  Similarity=0.128  Sum_probs=100.2

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchh
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPH  174 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~  174 (246)
                      .-.+|+..+...++++.|.++|+++.+ ..  |+.  ...+++.+...++-.+    |.+++++..+.      .+-+..
T Consensus       171 Lv~~Ll~~l~~t~~~~~ai~lle~L~~-~~--pev--~~~LA~v~l~~~~E~~----AI~ll~~aL~~------~p~d~~  235 (395)
T PF09295_consen  171 LVDTLLKYLSLTQRYDEAIELLEKLRE-RD--PEV--AVLLARVYLLMNEEVE----AIRLLNEALKE------NPQDSE  235 (395)
T ss_pred             HHHHHHHHHhhcccHHHHHHHHHHHHh-cC--CcH--HHHHHHHHHhcCcHHH----HHHHHHHHHHh------CCCCHH
Confidence            455677778888999999999999998 33  654  4458888888888888    99999998875      334566


Q ss_pred             hHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHH
Q 043380          175 LYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNT  239 (246)
Q Consensus       175 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  239 (246)
                      ....-...+...++.+.|..+.++.....    |.+..  +|..|..+|...|+++.|+..++.+
T Consensus       236 LL~~Qa~fLl~k~~~~lAL~iAk~av~ls----P~~f~--~W~~La~~Yi~~~d~e~ALlaLNs~  294 (395)
T PF09295_consen  236 LLNLQAEFLLSKKKYELALEIAKKAVELS----PSEFE--TWYQLAECYIQLGDFENALLALNSC  294 (395)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHhC----chhHH--HHHHHHHHHHhcCCHHHHHHHHhcC
Confidence            67777778999999999999999998543    33322  8999999999999999999988765

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

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

Probab=98.25  E-value=0.00091  Score=55.08  Aligned_cols=206  Identities=11%  Similarity=0.083  Sum_probs=162.4

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHH--HHHH----HHH----HHhcCCcchHHHHHHHHHhccCC
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLS--YNIL----ISA----CIKTKKLDVTMPFNEQLKDNGQK   83 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t--~~~l----i~~----~~~~~~~~~a~~~~~~m~~~~~~   83 (246)
                      +.|-.+|=..+..--..|+.+...++|+..-.+++|-..-  |--.    |+-    =....+.+.+.++|...++.   
T Consensus       319 p~nYDsWfdylrL~e~~g~~~~Ire~yErAIanvpp~~ekr~W~RYIYLWinYalyeEle~ed~ertr~vyq~~l~l---  395 (677)
T KOG1915|consen  319 PYNYDSWFDYLRLEESVGDKDRIRETYERAIANVPPASEKRYWRRYIYLWINYALYEELEAEDVERTRQVYQACLDL---  395 (677)
T ss_pred             CCCchHHHHHHHHHHhcCCHHHHHHHHHHHHccCCchhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhh---
Confidence            4556667777777778899999999999988777773321  2211    121    12467889999999999985   


Q ss_pred             CCCCCCCccHHHHHHHHHHH----HccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHH
Q 043380           84 CSSGGFHPDIFTYATLLMGF----RHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEI  159 (246)
Q Consensus        84 ~~~~~~~p~~~~~~~ll~~~----~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m  159 (246)
                           ++....||.-+=-.|    .+..++..|.+++-...   |..|-..+|-..|..-...++++.    +..+++..
T Consensus       396 -----IPHkkFtFaKiWlmyA~feIRq~~l~~ARkiLG~AI---G~cPK~KlFk~YIelElqL~efDR----cRkLYEkf  463 (677)
T KOG1915|consen  396 -----IPHKKFTFAKIWLMYAQFEIRQLNLTGARKILGNAI---GKCPKDKLFKGYIELELQLREFDR----CRKLYEKF  463 (677)
T ss_pred             -----cCcccchHHHHHHHHHHHHHHHcccHHHHHHHHHHh---ccCCchhHHHHHHHHHHHHhhHHH----HHHHHHHH
Confidence                 666777877765555    46789999999988764   578999999999999999999999    99999999


Q ss_pred             HHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHH
Q 043380          160 VKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNT  239 (246)
Q Consensus       160 ~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  239 (246)
                      ..-      -+-|..+|......-...|+.+.|..+|.-..... ..-.|.+   .|.+.|+.=...|.+++|..+++++
T Consensus       464 le~------~Pe~c~~W~kyaElE~~LgdtdRaRaifelAi~qp-~ldmpel---lwkaYIdFEi~~~E~ekaR~LYerl  533 (677)
T KOG1915|consen  464 LEF------SPENCYAWSKYAELETSLGDTDRARAIFELAISQP-ALDMPEL---LWKAYIDFEIEEGEFEKARALYERL  533 (677)
T ss_pred             Hhc------ChHhhHHHHHHHHHHHHhhhHHHHHHHHHHHhcCc-ccccHHH---HHHHhhhhhhhcchHHHHHHHHHHH
Confidence            884      23356889998888899999999999999887654 2334444   6888888888999999999999999


Q ss_pred             Hhhcc
Q 043380          240 ITRWK  244 (246)
Q Consensus       240 ~~~g~  244 (246)
                      +++.+
T Consensus       534 L~rt~  538 (677)
T KOG1915|consen  534 LDRTQ  538 (677)
T ss_pred             HHhcc
Confidence            88654

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

Probab=98.25  E-value=0.00012  Score=50.98  Aligned_cols=99  Identities=11%  Similarity=0.027  Sum_probs=83.5

Q ss_pred             CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCH
Q 043380           50 DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDR  129 (246)
Q Consensus        50 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~  129 (246)
                      +......+...+...|++++|...|+.+...        -+.+...|..+...+...|++++|...++.... .+ +.+.
T Consensus        16 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~--------~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~-~~-p~~~   85 (135)
T TIGR02552        16 QLEQIYALAYNLYQQGRYDEALKLFQLLAAY--------DPYNSRYWLGLAACCQMLKEYEEAIDAYALAAA-LD-PDDP   85 (135)
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHh--------CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cC-CCCh
Confidence            4455677778888999999999999999885        244678889999999999999999999999877 32 2346


Q ss_pred             HHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          130 STFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       130 ~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ..+..+...|...|+++.    |...|+...+.
T Consensus        86 ~~~~~la~~~~~~g~~~~----A~~~~~~al~~  114 (135)
T TIGR02552        86 RPYFHAAECLLALGEPES----ALKALDLAIEI  114 (135)
T ss_pred             HHHHHHHHHHHHcCCHHH----HHHHHHHHHHh
Confidence            778888899999999999    99999998875

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

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

Probab=98.23  E-value=1.5e-06  Score=43.80  Aligned_cols=29  Identities=21%  Similarity=0.171  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhhc
Q 043380          215 AGHLLMEAALNDGQVDLALDKLSNTITRW  243 (246)
Q Consensus       215 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g  243 (246)
                      +|++|+++|++.|++++|.++|++|.++|
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g   30 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERG   30 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCc
Confidence            68888888888888888888888888776

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.

>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=98.23  E-value=4e-05  Score=48.85  Aligned_cols=94  Identities=15%  Similarity=0.047  Sum_probs=65.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHH
Q 043380           20 MNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATL   99 (246)
Q Consensus        20 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~l   99 (246)
                      +..+...+...|++++|...|+...+-.+.+...+..+...+...+++++|.+.+......        .+.+..++..+
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~--------~~~~~~~~~~~   74 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKALEL--------DPDNAKAYYNL   74 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC--------CCcchhHHHHH
Confidence            4556667777788888888887765433444566777777777778888888888777764        23334567777


Q ss_pred             HHHHHccCCHHHHHHHHHHHHh
Q 043380          100 LMGFRHAKDLQSLLEIVFEMKS  121 (246)
Q Consensus       100 l~~~~~~~~~~~a~~~~~~m~~  121 (246)
                      ...+...|++++|...+....+
T Consensus        75 ~~~~~~~~~~~~a~~~~~~~~~   96 (100)
T cd00189          75 GLAYYKLGKYEEALEAYEKALE   96 (100)
T ss_pred             HHHHHHHHhHHHHHHHHHHHHc
Confidence            7777777888888877777655

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

Probab=98.20  E-value=0.00044  Score=62.10  Aligned_cols=205  Identities=14%  Similarity=0.094  Sum_probs=126.3

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCH-HHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDS-LSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP   91 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~-~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p   91 (246)
                      .+.+...+..|+..+...+++++|.++.+....- .|+. ..|-.+...+...++.+.+..+  .+.+.        +..
T Consensus        27 ~p~n~~a~~~Li~~~~~~~~~deai~i~~~~l~~-~P~~i~~yy~~G~l~~q~~~~~~~~lv--~~l~~--------~~~   95 (906)
T PRK14720         27 SLSKFKELDDLIDAYKSENLTDEAKDICEEHLKE-HKKSISALYISGILSLSRRPLNDSNLL--NLIDS--------FSQ   95 (906)
T ss_pred             CcchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh-CCcceehHHHHHHHHHhhcchhhhhhh--hhhhh--------ccc
Confidence            5667788999999999999999999999865432 3433 3343333456666666666555  44332        222


Q ss_pred             c-------------------HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhH
Q 043380           92 D-------------------IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLY  151 (246)
Q Consensus        92 ~-------------------~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~  151 (246)
                      +                   ...+-.|..+|-+.|+.++|..+|+++.+ ..  |+ ..+.|.+...|+.. ++++    
T Consensus        96 ~~~~~~ve~~~~~i~~~~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~-~D--~~n~~aLNn~AY~~ae~-dL~K----  167 (906)
T PRK14720         96 NLKWAIVEHICDKILLYGENKLALRTLAEAYAKLNENKKLKGVWERLVK-AD--RDNPEIVKKLATSYEEE-DKEK----  167 (906)
T ss_pred             ccchhHHHHHHHHHHhhhhhhHHHHHHHHHHHHcCChHHHHHHHHHHHh-cC--cccHHHHHHHHHHHHHh-hHHH----
Confidence            2                   25677788888899999999999999999 44  55 88899999999999 9999    


Q ss_pred             HHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhH
Q 043380          152 ALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDL  231 (246)
Q Consensus       152 a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~  231 (246)
                      |.+++.......-.......=...|..++..  ...+++.-.++.+.+.... ++   .....++-.+-..|....++++
T Consensus       168 A~~m~~KAV~~~i~~kq~~~~~e~W~k~~~~--~~~d~d~f~~i~~ki~~~~-~~---~~~~~~~~~l~~~y~~~~~~~~  241 (906)
T PRK14720        168 AITYLKKAIYRFIKKKQYVGIEEIWSKLVHY--NSDDFDFFLRIERKVLGHR-EF---TRLVGLLEDLYEPYKALEDWDE  241 (906)
T ss_pred             HHHHHHHHHHHHHhhhcchHHHHHHHHHHhc--CcccchHHHHHHHHHHhhh-cc---chhHHHHHHHHHHHhhhhhhhH
Confidence            9988888766511000000000112222111  1223334444444443221 10   0011145556666666777777


Q ss_pred             HHHHHHHHHhh
Q 043380          232 ALDKLSNTITR  242 (246)
Q Consensus       232 a~~~~~~m~~~  242 (246)
                      +..+++.+.+.
T Consensus       242 ~i~iLK~iL~~  252 (906)
T PRK14720        242 VIYILKKILEH  252 (906)
T ss_pred             HHHHHHHHHhc
Confidence            77777766553

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

Probab=98.20  E-value=0.00029  Score=56.93  Aligned_cols=211  Identities=9%  Similarity=-0.038  Sum_probs=123.1

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHH----HHHHHHHHHhcCCcchHHHHHHHHHhcc-CC----
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLS----YNILISACIKTKKLDVTMPFNEQLKDNG-QK----   83 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t----~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~----   83 (246)
                      .+-|+.....+..++...|+.+.|+..|++.+. +.|+..+    |..|+   .+.|+++....+...+.... ..    
T Consensus       228 lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~-~dpy~i~~MD~Ya~LL---~~eg~~e~~~~L~~~Lf~~~~~ta~~w  303 (564)
T KOG1174|consen  228 LRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLC-ANPDNVEAMDLYAVLL---GQEGGCEQDSALMDYLFAKVKYTASHW  303 (564)
T ss_pred             CCccHHHHHHHhhhhhhhcCchHHHHHHHHHhh-CChhhhhhHHHHHHHH---HhccCHhhHHHHHHHHHhhhhcchhhh
Confidence            677889999999999999999999999998763 1232211    22221   23333333333333332210 00    


Q ss_pred             ------------------CCCCCC--Cc-cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHh
Q 043380           84 ------------------CSSGGF--HP-DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLY  141 (246)
Q Consensus        84 ------------------~~~~~~--~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~  141 (246)
                                        ..+..+  .| +...|-.=-+++...+++++|.=.|+....   +.|. ...|-.|+..|..
T Consensus       304 fV~~~~l~~~K~~~rAL~~~eK~I~~~~r~~~alilKG~lL~~~~R~~~A~IaFR~Aq~---Lap~rL~~Y~GL~hsYLA  380 (564)
T KOG1174|consen  304 FVHAQLLYDEKKFERALNFVEKCIDSEPRNHEALILKGRLLIALERHTQAVIAFRTAQM---LAPYRLEIYRGLFHSYLA  380 (564)
T ss_pred             hhhhhhhhhhhhHHHHHHHHHHHhccCcccchHHHhccHHHHhccchHHHHHHHHHHHh---cchhhHHHHHHHHHHHHh
Confidence                              000011  22 222333334556778899999988988877   6655 7889999999999


Q ss_pred             cCChhhhhhHHHHHHHHHHHh----hc-------------------------CCCCCCcch-hhHHHHHHHHHhcCChhH
Q 043380          142 SGSIKVVGLYALCIFGEIVKR----VC-------------------------SNPGLWPKP-HLYVSMMHELAARVDYDI  191 (246)
Q Consensus       142 ~~~~~~~~~~a~~~~~~m~~~----~~-------------------------~~~~~~p~~-~~~~~li~~~~~~g~~~~  191 (246)
                      .|.+.+    |.-+-+...+.    ..                         +...+.|+- ...+.+...+...|..+.
T Consensus       381 ~~~~kE----A~~~An~~~~~~~~sA~~LtL~g~~V~~~dp~~rEKAKkf~ek~L~~~P~Y~~AV~~~AEL~~~Eg~~~D  456 (564)
T KOG1174|consen  381 QKRFKE----ANALANWTIRLFQNSARSLTLFGTLVLFPDPRMREKAKKFAEKSLKINPIYTPAVNLIAELCQVEGPTKD  456 (564)
T ss_pred             hchHHH----HHHHHHHHHHHhhcchhhhhhhcceeeccCchhHHHHHHHHHhhhccCCccHHHHHHHHHHHHhhCccch
Confidence            999999    55544443332    00                         111233432 344555566666666777


Q ss_pred             HhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          192 VKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       192 a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      +..+++......    +...   ..+.|.+.+.....+++|.+.|..-.+
T Consensus       457 ~i~LLe~~L~~~----~D~~---LH~~Lgd~~~A~Ne~Q~am~~y~~ALr  499 (564)
T KOG1174|consen  457 IIKLLEKHLIIF----PDVN---LHNHLGDIMRAQNEPQKAMEYYYKALR  499 (564)
T ss_pred             HHHHHHHHHhhc----cccH---HHHHHHHHHHHhhhHHHHHHHHHHHHh
Confidence            777766655331    1111   456666666667777777766665544

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

Probab=98.19  E-value=0.00024  Score=50.19  Aligned_cols=129  Identities=15%  Similarity=0.107  Sum_probs=95.2

Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL-DRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP  171 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p  171 (246)
                      ...|..++..+. .++...+...++.+....+-.| .....-.+...+...|++++    |...|+.....     .-.|
T Consensus        12 ~~~y~~~~~~~~-~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~----A~~~l~~~~~~-----~~d~   81 (145)
T PF09976_consen   12 SALYEQALQALQ-AGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDE----AKAALEKALAN-----APDP   81 (145)
T ss_pred             HHHHHHHHHHHH-CCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHH----HHHHHHHHHhh-----CCCH
Confidence            446777777774 8999999999999988221111 12333445678889999999    99999999987     3222


Q ss_pred             c--hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHH
Q 043380          172 K--PHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSN  238 (246)
Q Consensus       172 ~--~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  238 (246)
                      +  ......+...+...|++++|...++......   ..+.    .+...-+.|.+.|+.++|...|+.
T Consensus        82 ~l~~~a~l~LA~~~~~~~~~d~Al~~L~~~~~~~---~~~~----~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen   82 ELKPLARLRLARILLQQGQYDEALATLQQIPDEA---FKAL----AAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHhccCcc---hHHH----HHHHHHHHHHHCCCHHHHHHHHHH
Confidence            2  2355667888999999999999998753221   2222    577888999999999999999975

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

Probab=98.17  E-value=0.00031  Score=49.60  Aligned_cols=127  Identities=13%  Similarity=0.110  Sum_probs=95.1

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHH---HHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLS---YNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t---~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      ...|..++..+ ..++...+...++.+....+.+...   .-.+-..+...|++++|...|+.....       ...|+.
T Consensus        12 ~~~y~~~~~~~-~~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~-------~~d~~l   83 (145)
T PF09976_consen   12 SALYEQALQAL-QAGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALAN-------APDPEL   83 (145)
T ss_pred             HHHHHHHHHHH-HCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhh-------CCCHHH
Confidence            34677777777 4899999999999987544444222   233457778899999999999999987       323332


Q ss_pred             --HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHH
Q 043380           94 --FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGE  158 (246)
Q Consensus        94 --~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~  158 (246)
                        .....|...+...|++++|+..++.... ..  .....+......|...|++++    |...|+.
T Consensus        84 ~~~a~l~LA~~~~~~~~~d~Al~~L~~~~~-~~--~~~~~~~~~Gdi~~~~g~~~~----A~~~y~~  143 (145)
T PF09976_consen   84 KPLARLRLARILLQQGQYDEALATLQQIPD-EA--FKALAAELLGDIYLAQGDYDE----ARAAYQK  143 (145)
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHhccC-cc--hHHHHHHHHHHHHHHCCCHHH----HHHHHHH
Confidence              2455577888999999999999977544 32  345567788899999999999    9999875

>PLN02789 farnesyltranstransferase

Probab=98.17  E-value=0.0021  Score=51.63  Aligned_cols=196  Identities=9%  Similarity=-0.040  Sum_probs=125.8

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcC-CcchHHHHHHHHHhccCCCCCCCCCccHHHHH
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTK-KLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYA   97 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~-~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~   97 (246)
                      +++.+-..+...+..++|+.+.+.+..-.+-+...|+.--..+...+ ++++++.+++++.+.        -+-+..+|+
T Consensus        39 a~~~~ra~l~~~e~serAL~lt~~aI~lnP~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~--------npknyqaW~  110 (320)
T PLN02789         39 AMDYFRAVYASDERSPRALDLTADVIRLNPGNYTVWHFRRLCLEALDADLEEELDFAEDVAED--------NPKNYQIWH  110 (320)
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHCchhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHH--------CCcchHHhH
Confidence            44555556666788889999988876433445566776666666666 578899999888875        233445676


Q ss_pred             HHHHHHHccCCH--HHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchh
Q 043380           98 TLLMGFRHAKDL--QSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPH  174 (246)
Q Consensus        98 ~ll~~~~~~~~~--~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~  174 (246)
                      .--..+.+.|+.  ++++.+++.+.+   ..|. -.+|+...-.+...|++++    +++.++++.+.     . .-|..
T Consensus       111 ~R~~~l~~l~~~~~~~el~~~~kal~---~dpkNy~AW~~R~w~l~~l~~~~e----eL~~~~~~I~~-----d-~~N~s  177 (320)
T PLN02789        111 HRRWLAEKLGPDAANKELEFTRKILS---LDAKNYHAWSHRQWVLRTLGGWED----ELEYCHQLLEE-----D-VRNNS  177 (320)
T ss_pred             HHHHHHHHcCchhhHHHHHHHHHHHH---hCcccHHHHHHHHHHHHHhhhHHH----HHHHHHHHHHH-----C-CCchh
Confidence            655555555653  677888888877   3444 6778888888888888999    99999998886     2 23456


Q ss_pred             hHHHHHHHHHhc---CCh----hHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhc----CChhHHHHHHHHHHh
Q 043380          175 LYVSMMHELAAR---VDY----DIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALND----GQVDLALDKLSNTIT  241 (246)
Q Consensus       175 ~~~~li~~~~~~---g~~----~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~----g~~~~a~~~~~~m~~  241 (246)
                      +|+....++.+.   |..    +....+..+....++...+      +|+.+...+...    ++..+|.+.+.+..+
T Consensus       178 AW~~R~~vl~~~~~l~~~~~~~e~el~y~~~aI~~~P~N~S------aW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~  249 (320)
T PLN02789        178 AWNQRYFVITRSPLLGGLEAMRDSELKYTIDAILANPRNES------PWRYLRGLFKDDKEALVSDPEVSSVCLEVLS  249 (320)
T ss_pred             HHHHHHHHHHhccccccccccHHHHHHHHHHHHHhCCCCcC------HHHHHHHHHhcCCcccccchhHHHHHHHhhc
Confidence            666666555544   222    3455555444443322222      677777776662    333556666665443

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=98.16  E-value=0.00024  Score=56.02  Aligned_cols=129  Identities=12%  Similarity=0.050  Sum_probs=101.0

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhC--CCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           18 IVMNAVIEASREAQRIDEAYQILESVEKG--LEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        18 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~--~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      .+|-.+|+..-|.+.++.|..+|.+.++.  +..++....++|.. ...++.+.|.++|+...+.        +..+...
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E~-~~~~d~~~A~~Ife~glk~--------f~~~~~~   72 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALMEY-YCNKDPKRARKIFERGLKK--------FPSDPDF   72 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHHH-HTCS-HHHHHHHHHHHHHH--------HTT-HHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHHH-HhCCCHHHHHHHHHHHHHH--------CCCCHHH
Confidence            57889999999999999999999998742  22334444444443 3345677799999999985        6778888


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCH----HHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDR----STFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~----~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      |..-+.-+...++.+.|..+|++... . + |..    ..|...+.--.+.|+++.    +..+.+.+.+.
T Consensus        73 ~~~Y~~~l~~~~d~~~aR~lfer~i~-~-l-~~~~~~~~iw~~~i~fE~~~Gdl~~----v~~v~~R~~~~  136 (280)
T PF05843_consen   73 WLEYLDFLIKLNDINNARALFERAIS-S-L-PKEKQSKKIWKKFIEFESKYGDLES----VRKVEKRAEEL  136 (280)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHHHCC-T-S-SCHHHCHHHHHHHHHHHHHHS-HHH----HHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCcHHHHHHHHHHHHH-h-c-CchhHHHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHH
Confidence            99999999999999999999999988 3 3 443    489999999999999999    99999998886

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.

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

Probab=98.14  E-value=0.00034  Score=58.48  Aligned_cols=204  Identities=9%  Similarity=0.031  Sum_probs=127.3

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-   92 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-   92 (246)
                      ++....+-.-|.++...|+..+-..+=.++.+..+....+|-++.--|...|+.++|.+.|.+....         .|. 
T Consensus       275 pfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~yP~~a~sW~aVg~YYl~i~k~seARry~SKat~l---------D~~f  345 (611)
T KOG1173|consen  275 PFHLPCLPLHIACLYELGKSNKLFLLSHKLVDLYPSKALSWFAVGCYYLMIGKYSEARRYFSKATTL---------DPTF  345 (611)
T ss_pred             CCCcchHHHHHHHHHHhcccchHHHHHHHHHHhCCCCCcchhhHHHHHHHhcCcHHHHHHHHHHhhc---------Cccc
Confidence            3444444444555555555555554444554445556666666666666667777777777665543         333 


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCH-HHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDR-STFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP  171 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~-~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p  171 (246)
                      ...|-..-..|+-.|..|+|+..+....+   +.|.. -.+--+..-|.+.++.+.    |.+.|.+....      .+-
T Consensus       346 gpaWl~fghsfa~e~EhdQAmaaY~tAar---l~~G~hlP~LYlgmey~~t~n~kL----Ae~Ff~~A~ai------~P~  412 (611)
T KOG1173|consen  346 GPAWLAFGHSFAGEGEHDQAMAAYFTAAR---LMPGCHLPSLYLGMEYMRTNNLKL----AEKFFKQALAI------APS  412 (611)
T ss_pred             cHHHHHHhHHhhhcchHHHHHHHHHHHHH---hccCCcchHHHHHHHHHHhccHHH----HHHHHHHHHhc------CCC
Confidence            23566666667777777777777666555   22221 112224445666777888    88888777653      334


Q ss_pred             chhhHHHHHHHHHhcCChhHHhhHHHhhCC---CCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          172 KPHLYVSMMHELAARVDYDIVKSPYRRMWP---DSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       172 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      |+...+-+--.....+.+.+|..+|+....   ......+  ....+++.|-.+|.+.+.+++|+..++.-..
T Consensus       413 Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~--~w~p~~~NLGH~~Rkl~~~~eAI~~~q~aL~  483 (611)
T KOG1173|consen  413 DPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKI--FWEPTLNNLGHAYRKLNKYEEAIDYYQKALL  483 (611)
T ss_pred             cchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhcccccc--chhHHHHhHHHHHHHHhhHHHHHHHHHHHHH
Confidence            556667776666678899999999987651   1100010  1222789999999999999999999987654

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=98.12  E-value=0.00012  Score=49.40  Aligned_cols=102  Identities=16%  Similarity=0.111  Sum_probs=48.7

Q ss_pred             HHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchh
Q 043380          132 FTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEV  211 (246)
Q Consensus       132 ~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~  211 (246)
                      +..+...+...|++++    |.+.|+.+....   |+-......+..+..++...|+++.|...|+.+....++....  
T Consensus         5 ~~~~~~~~~~~~~~~~----A~~~~~~~~~~~---~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~--   75 (119)
T TIGR02795         5 YYDAALLVLKAGDYAD----AIQAFQAFLKKY---PKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKA--   75 (119)
T ss_pred             HHHHHHHHHHcCCHHH----HHHHHHHHHHHC---CCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcc--
Confidence            3444555555566666    666665555431   0111112344445555555666666666666554322211100  


Q ss_pred             hhHHHHHHHHHHHhcCChhHHHHHHHHHHhhc
Q 043380          212 QEEAGHLLMEAALNDGQVDLALDKLSNTITRW  243 (246)
Q Consensus       212 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  243 (246)
                       ..++..+..++...|+.++|.+.++++.+..
T Consensus        76 -~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~  106 (119)
T TIGR02795        76 -PDALLKLGMSLQELGDKEKAKATLQQVIKRY  106 (119)
T ss_pred             -cHHHHHHHHHHHHhCChHHHHHHHHHHHHHC
Confidence             0134445555555666666666665555443

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.

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

Probab=98.11  E-value=0.00049  Score=56.71  Aligned_cols=189  Identities=13%  Similarity=0.019  Sum_probs=134.5

Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHcc
Q 043380           27 SREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHA  106 (246)
Q Consensus        27 ~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~  106 (246)
                      +.-.|+.-.|..-|+..-+..+.+...|--+-.+|....+.++....|.+.....        +-|..+|..=-..+.-.
T Consensus       336 ~fL~g~~~~a~~d~~~~I~l~~~~~~lyI~~a~~y~d~~~~~~~~~~F~~A~~ld--------p~n~dvYyHRgQm~flL  407 (606)
T KOG0547|consen  336 HFLKGDSLGAQEDFDAAIKLDPAFNSLYIKRAAAYADENQSEKMWKDFNKAEDLD--------PENPDVYYHRGQMRFLL  407 (606)
T ss_pred             hhhcCCchhhhhhHHHHHhcCcccchHHHHHHHHHhhhhccHHHHHHHHHHHhcC--------CCCCchhHhHHHHHHHH
Confidence            4456788888888877654334444447778888888899999999999888751        23455666666666667


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHh
Q 043380          107 KDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAA  185 (246)
Q Consensus       107 ~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~  185 (246)
                      +++++|..=|+...+   +.|. ...|-.+--+.-+.+.+.+    +...|++.+++      ++-.+..|+-....+..
T Consensus       408 ~q~e~A~aDF~Kai~---L~pe~~~~~iQl~~a~Yr~~k~~~----~m~~Fee~kkk------FP~~~Evy~~fAeiLtD  474 (606)
T KOG0547|consen  408 QQYEEAIADFQKAIS---LDPENAYAYIQLCCALYRQHKIAE----SMKTFEEAKKK------FPNCPEVYNLFAEILTD  474 (606)
T ss_pred             HHHHHHHHHHHHHhh---cChhhhHHHHHHHHHHHHHHHHHH----HHHHHHHHHHh------CCCCchHHHHHHHHHhh
Confidence            889999999998887   6565 5566666667777889999    99999999886      66667888989999999


Q ss_pred             cCChhHHhhHHHhhCCCCCC------CCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          186 RVDYDIVKSPYRRMWPDSTG------TISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       186 ~g~~~~a~~~~~~~~~~~~~------~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      .+++++|.+.|+......+.      ...|-+    .-.++- +--.+++..|.++++.-.+
T Consensus       475 qqqFd~A~k~YD~ai~LE~~~~~~~v~~~plV----~Ka~l~-~qwk~d~~~a~~Ll~KA~e  531 (606)
T KOG0547|consen  475 QQQFDKAVKQYDKAIELEPREHLIIVNAAPLV----HKALLV-LQWKEDINQAENLLRKAIE  531 (606)
T ss_pred             HHhHHHHHHHHHHHHhhccccccccccchhhh----hhhHhh-hchhhhHHHHHHHHHHHHc
Confidence            99999999999976543322      122222    111211 1234888888888876654

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.08  E-value=0.0013  Score=50.24  Aligned_cols=152  Identities=14%  Similarity=0.120  Sum_probs=87.3

Q ss_pred             HHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHH
Q 043380           58 ISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVD  137 (246)
Q Consensus        58 i~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~  137 (246)
                      ...|+..+++++|++......         +++    ....=+..+.+..+++-|.+.++.|..   + -+..|.+.|..
T Consensus       115 a~i~~~~~~~deAl~~~~~~~---------~lE----~~Al~VqI~lk~~r~d~A~~~lk~mq~---i-ded~tLtQLA~  177 (299)
T KOG3081|consen  115 AIIYMHDGDFDEALKALHLGE---------NLE----AAALNVQILLKMHRFDLAEKELKKMQQ---I-DEDATLTQLAQ  177 (299)
T ss_pred             hHHhhcCCChHHHHHHHhccc---------hHH----HHHHHHHHHHHHHHHHHHHHHHHHHHc---c-chHHHHHHHHH
Confidence            344566777777777666511         122    222223334455677777777777777   2 13455555555


Q ss_pred             HHHh----cCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhh
Q 043380          138 ALLY----SGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQE  213 (246)
Q Consensus       138 ~~~~----~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~  213 (246)
                      ++.+    .+.+.+    |.-+|++|.++      ..|+..+.+.+..++...|++++|+.+++....+..+  .|+.  
T Consensus       178 awv~la~ggek~qd----AfyifeE~s~k------~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~~--dpet--  243 (299)
T KOG3081|consen  178 AWVKLATGGEKIQD----AFYIFEELSEK------TPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDAK--DPET--  243 (299)
T ss_pred             HHHHHhccchhhhh----HHHHHHHHhcc------cCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccCC--CHHH--
Confidence            4444    345666    77777777663      6777777777777777788888888777776654432  1221  


Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          214 EAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       214 ~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                       .-|.++.+.-...+.+-..+.+.+++.
T Consensus       244 -L~Nliv~a~~~Gkd~~~~~r~l~QLk~  270 (299)
T KOG3081|consen  244 -LANLIVLALHLGKDAEVTERNLSQLKL  270 (299)
T ss_pred             -HHHHHHHHHHhCCChHHHHHHHHHHHh
Confidence             234444444333333444455555443

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.07  E-value=0.0024  Score=48.76  Aligned_cols=164  Identities=12%  Similarity=0.075  Sum_probs=117.6

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      ..-+...-..-...|+..|++++|++......   .......+  ...+.+..+.+.|...+++|.+.          -+
T Consensus       104 ~~sn~i~~l~aa~i~~~~~~~deAl~~~~~~~---~lE~~Al~--VqI~lk~~r~d~A~~~lk~mq~i----------de  168 (299)
T KOG3081|consen  104 DGSNLIDLLLAAIIYMHDGDFDEALKALHLGE---NLEAAALN--VQILLKMHRFDLAEKELKKMQQI----------DE  168 (299)
T ss_pred             cchhHHHHHHhhHHhhcCCChHHHHHHHhccc---hHHHHHHH--HHHHHHHHHHHHHHHHHHHHHcc----------ch
Confidence            33333333334557889999999999887632   22222222  33456777899999999999985          45


Q ss_pred             HHHHHHHHHHH----HccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCC
Q 043380           93 IFTYATLLMGF----RHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPG  168 (246)
Q Consensus        93 ~~~~~~ll~~~----~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~  168 (246)
                      ..|.+-|..++    ...+...+|..+|++|-+  ...|+..+.+....++...|++++    |..++++...+      
T Consensus       169 d~tLtQLA~awv~la~ggek~qdAfyifeE~s~--k~~~T~~llnG~Av~~l~~~~~ee----Ae~lL~eaL~k------  236 (299)
T KOG3081|consen  169 DATLTQLAQAWVKLATGGEKIQDAFYIFEELSE--KTPPTPLLLNGQAVCHLQLGRYEE----AESLLEEALDK------  236 (299)
T ss_pred             HHHHHHHHHHHHHHhccchhhhhHHHHHHHHhc--ccCCChHHHccHHHHHHHhcCHHH----HHHHHHHHHhc------
Confidence            55666566665    445678999999999977  377999999999999999999999    99999999887      


Q ss_pred             CCcchhhHHHHHHHHHhcCCh-hHHhhHHHhhCCCC
Q 043380          169 LWPKPHLYVSMMHELAARVDY-DIVKSPYRRMWPDS  203 (246)
Q Consensus       169 ~~p~~~~~~~li~~~~~~g~~-~~a~~~~~~~~~~~  203 (246)
                      -.-++.+...+|-+-...|.. +-..+.+.+++...
T Consensus       237 d~~dpetL~Nliv~a~~~Gkd~~~~~r~l~QLk~~~  272 (299)
T KOG3081|consen  237 DAKDPETLANLIVLALHLGKDAEVTERNLSQLKLSH  272 (299)
T ss_pred             cCCCHHHHHHHHHHHHHhCCChHHHHHHHHHHHhcC
Confidence            234566666666665666654 55667777776543

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=98.05  E-value=0.0003  Score=47.45  Aligned_cols=102  Identities=8%  Similarity=-0.065  Sum_probs=77.8

Q ss_pred             HHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCC-CCHH
Q 043380           52 LSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLI-LDRS  130 (246)
Q Consensus        52 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~-p~~~  130 (246)
                      .++-.+...+.+.|++++|.+.|.++....     .+.......+..+..++.+.|+++.|...|+.+.....-. ....
T Consensus         3 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-----~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~   77 (119)
T TIGR02795         3 EAYYDAALLVLKAGDYADAIQAFQAFLKKY-----PKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPD   77 (119)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-----CCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccH
Confidence            355667777888999999999999998751     0111123467778899999999999999999988711111 1245


Q ss_pred             HHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          131 TFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       131 ~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      .+..+..++...|+++.    |...++++.+.
T Consensus        78 ~~~~~~~~~~~~~~~~~----A~~~~~~~~~~  105 (119)
T TIGR02795        78 ALLKLGMSLQELGDKEK----AKATLQQVIKR  105 (119)
T ss_pred             HHHHHHHHHHHhCChHH----HHHHHHHHHHH
Confidence            67788889999999999    99999999886

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.

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=98.05  E-value=0.001  Score=54.74  Aligned_cols=142  Identities=13%  Similarity=0.013  Sum_probs=117.1

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-HHHHHHHHHH
Q 043380           24 IEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-IFTYATLLMG  102 (246)
Q Consensus        24 i~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~~~ll~~  102 (246)
                      --.+...|+.++|+..+..+....+-|+.-+......+...++.++|.+.++.+...         .|+ ....-++-.+
T Consensus       313 A~~~~~~~~~d~A~~~l~~L~~~~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l---------~P~~~~l~~~~a~a  383 (484)
T COG4783         313 ALQTYLAGQYDEALKLLQPLIAAQPDNPYYLELAGDILLEANKAKEAIERLKKALAL---------DPNSPLLQLNLAQA  383 (484)
T ss_pred             HHHHHHhcccchHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhc---------CCCccHHHHHHHHH
Confidence            334557899999999999988777778888888999999999999999999999986         676 5677788899


Q ss_pred             HHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHH
Q 043380          103 FRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHE  182 (246)
Q Consensus       103 ~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~  182 (246)
                      |.+.|++.+|..+++.... . .+-|+..|..|..+|...|+..+    +..-..+.                       
T Consensus       384 ll~~g~~~eai~~L~~~~~-~-~p~dp~~w~~LAqay~~~g~~~~----a~~A~AE~-----------------------  434 (484)
T COG4783         384 LLKGGKPQEAIRILNRYLF-N-DPEDPNGWDLLAQAYAELGNRAE----ALLARAEG-----------------------  434 (484)
T ss_pred             HHhcCChHHHHHHHHHHhh-c-CCCCchHHHHHHHHHHHhCchHH----HHHHHHHH-----------------------
Confidence            9999999999999999877 2 44568899999999999999998    66544443                       


Q ss_pred             HHhcCChhHHhhHHHhhCCCC
Q 043380          183 LAARVDYDIVKSPYRRMWPDS  203 (246)
Q Consensus       183 ~~~~g~~~~a~~~~~~~~~~~  203 (246)
                      |...|+++.|...+....+..
T Consensus       435 ~~~~G~~~~A~~~l~~A~~~~  455 (484)
T COG4783         435 YALAGRLEQAIIFLMRASQQV  455 (484)
T ss_pred             HHhCCCHHHHHHHHHHHHHhc
Confidence            456788888888888776543

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.05  E-value=0.0028  Score=48.12  Aligned_cols=151  Identities=14%  Similarity=0.118  Sum_probs=84.4

Q ss_pred             CCHHHHHHHHHHHH----hC-CCCCHHH-HHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHH
Q 043380           31 QRIDEAYQILESVE----KG-LEPDSLS-YNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFR  104 (246)
Q Consensus        31 g~~~~a~~~~~~~~----~~-~~~~~~t-~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~  104 (246)
                      .+.++.++++.++.    +| ..++..+ |.-++-+....++.+.|...++++..+        ++-+...--.=-.-+-
T Consensus        26 rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~--------fp~S~RV~~lkam~lE   97 (289)
T KOG3060|consen   26 RNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDR--------FPGSKRVGKLKAMLLE   97 (289)
T ss_pred             cCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHh--------CCCChhHHHHHHHHHH
Confidence            45666666665542    23 4455433 445555556667777777777777665        2222221111111123


Q ss_pred             ccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHH
Q 043380          105 HAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELA  184 (246)
Q Consensus       105 ~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~  184 (246)
                      ..|++++|.++++.+.+ .+ +.|..+|--=+...-..|.-.+    |++-+....+.      +..|...|.-+-..|.
T Consensus        98 a~~~~~~A~e~y~~lL~-dd-pt~~v~~KRKlAilka~GK~l~----aIk~ln~YL~~------F~~D~EAW~eLaeiY~  165 (289)
T KOG3060|consen   98 ATGNYKEAIEYYESLLE-DD-PTDTVIRKRKLAILKAQGKNLE----AIKELNEYLDK------FMNDQEAWHELAEIYL  165 (289)
T ss_pred             HhhchhhHHHHHHHHhc-cC-cchhHHHHHHHHHHHHcCCcHH----HHHHHHHHHHH------hcCcHHHHHHHHHHHH
Confidence            35667777777777766 32 2234444444444444555556    66666666664      5666677777777777


Q ss_pred             hcCChhHHhhHHHhhCC
Q 043380          185 ARVDYDIVKSPYRRMWP  201 (246)
Q Consensus       185 ~~g~~~~a~~~~~~~~~  201 (246)
                      ..|++++|--.++++.-
T Consensus       166 ~~~~f~kA~fClEE~ll  182 (289)
T KOG3060|consen  166 SEGDFEKAAFCLEELLL  182 (289)
T ss_pred             hHhHHHHHHHHHHHHHH
Confidence            77777777777776653

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=98.02  E-value=0.0037  Score=52.38  Aligned_cols=153  Identities=14%  Similarity=0.136  Sum_probs=123.3

Q ss_pred             cchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHhcCCh
Q 043380           67 LDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL-DRSTFTAMVDALLYSGSI  145 (246)
Q Consensus        67 ~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~~~~  145 (246)
                      .+.....++++...      ....|+ .+|..+|+.-.+..-++.|..+|.+.++ .+..+ +..+++++|.-||. ++.
T Consensus       347 ~~~~~~~~~~ll~~------~~~~~t-Lv~~~~mn~irR~eGlkaaR~iF~kaR~-~~r~~hhVfVa~A~mEy~cs-kD~  417 (656)
T KOG1914|consen  347 EKKVHEIYNKLLKI------EDIDLT-LVYCQYMNFIRRAEGLKAARKIFKKARE-DKRTRHHVFVAAALMEYYCS-KDK  417 (656)
T ss_pred             hhhhHHHHHHHHhh------hccCCc-eehhHHHHHHHHhhhHHHHHHHHHHHhh-ccCCcchhhHHHHHHHHHhc-CCh
Confidence            56677778877765      134444 3788899999999999999999999999 77777 68889999998875 567


Q ss_pred             hhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHh
Q 043380          146 KVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALN  225 (246)
Q Consensus       146 ~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~  225 (246)
                      +.    |.++|+.=.+.      ..-++.-....++-+.+.++-..+..+|++.....   ++++-....|..+++-=+.
T Consensus       418 ~~----AfrIFeLGLkk------f~d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~---l~~~ks~~Iw~r~l~yES~  484 (656)
T KOG1914|consen  418 ET----AFRIFELGLKK------FGDSPEYVLKYLDFLSHLNDDNNARALFERVLTSV---LSADKSKEIWDRMLEYESN  484 (656)
T ss_pred             hH----HHHHHHHHHHh------cCCChHHHHHHHHHHHHhCcchhHHHHHHHHHhcc---CChhhhHHHHHHHHHHHHh
Confidence            77    99999987765      44444556778888899999999999999998662   5666556689999999999


Q ss_pred             cCChhHHHHHHHHHHh
Q 043380          226 DGQVDLALDKLSNTIT  241 (246)
Q Consensus       226 ~g~~~~a~~~~~~m~~  241 (246)
                      -|+...+.++-+++..
T Consensus       485 vGdL~si~~lekR~~~  500 (656)
T KOG1914|consen  485 VGDLNSILKLEKRRFT  500 (656)
T ss_pred             cccHHHHHHHHHHHHH
Confidence            9999999998887754

>PLN02789 farnesyltranstransferase

Probab=98.02  E-value=0.0045  Score=49.73  Aligned_cols=203  Identities=11%  Similarity=-0.008  Sum_probs=138.3

Q ss_pred             CHHHHHHHHHHHHhcC-CHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCc--chHHHHHHHHHhccCCCCCCCCCcc
Q 043380           16 NTIVMNAVIEASREAQ-RIDEAYQILESVEKGLEPDSLSYNILISACIKTKKL--DVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g-~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~--~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      +..+|+..-.++...| .++++++.++.+....+.+..+|+..-..+.+.+..  +++.++++++.+.        -+-|
T Consensus        70 ~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~npknyqaW~~R~~~l~~l~~~~~~~el~~~~kal~~--------dpkN  141 (320)
T PLN02789         70 NYTVWHFRRLCLEALDADLEEELDFAEDVAEDNPKNYQIWHHRRWLAEKLGPDAANKELEFTRKILSL--------DAKN  141 (320)
T ss_pred             hHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCCcchHHhHHHHHHHHHcCchhhHHHHHHHHHHHHh--------Cccc
Confidence            3445665555666667 579999999988755567777888766666666653  6788999999875        2446


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhc---CChhhhhhHHHHHHHHHHHhhcCCCCC
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYS---GSIKVVGLYALCIFGEIVKRVCSNPGL  169 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~---~~~~~~~~~a~~~~~~m~~~~~~~~~~  169 (246)
                      ..+|+....++.+.|+++++++.++++.+ .+. -+...|+.....+.+.   |..+.+...+..+.......      .
T Consensus       142 y~AW~~R~w~l~~l~~~~eeL~~~~~~I~-~d~-~N~sAW~~R~~vl~~~~~l~~~~~~~e~el~y~~~aI~~------~  213 (320)
T PLN02789        142 YHAWSHRQWVLRTLGGWEDELEYCHQLLE-EDV-RNNSAWNQRYFVITRSPLLGGLEAMRDSELKYTIDAILA------N  213 (320)
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHH-HCC-CchhHHHHHHHHHHhccccccccccHHHHHHHHHHHHHh------C
Confidence            78999999999999999999999999998 432 2356676665555544   22321111167777666664      2


Q ss_pred             CcchhhHHHHHHHHHhc----CChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcC------------------
Q 043380          170 WPKPHLYVSMMHELAAR----VDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDG------------------  227 (246)
Q Consensus       170 ~p~~~~~~~li~~~~~~----g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g------------------  227 (246)
                      +-|...|+-+...+...    ++..+|.+.+.+....++   ..   ..+...|++.|+...                  
T Consensus       214 P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~~---~s---~~al~~l~d~~~~~~~~~~~~~~~~~~~~~~~~  287 (320)
T PLN02789        214 PRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKDS---NH---VFALSDLLDLLCEGLQPTAEFRDTVDTLAEELS  287 (320)
T ss_pred             CCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhcccC---Cc---HHHHHHHHHHHHhhhccchhhhhhhhccccccc
Confidence            34567888888888773    445668888888655331   11   126778899888643                  


Q ss_pred             ChhHHHHHHHHHH
Q 043380          228 QVDLALDKLSNTI  240 (246)
Q Consensus       228 ~~~~a~~~~~~m~  240 (246)
                      ..++|.+++..+.
T Consensus       288 ~~~~a~~~~~~l~  300 (320)
T PLN02789        288 DSTLAQAVCSELE  300 (320)
T ss_pred             cHHHHHHHHHHHH
Confidence            2367888888773

>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=97.97  E-value=0.00036  Score=51.72  Aligned_cols=114  Identities=12%  Similarity=0.162  Sum_probs=86.0

Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHHHHhc-----CCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccC----
Q 043380           37 YQILESVEKGLEPDSLSYNILISACIKT-----KKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAK----  107 (246)
Q Consensus        37 ~~~~~~~~~~~~~~~~t~~~li~~~~~~-----~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~----  107 (246)
                      ...|+... +...|-.+|..+++.|.+.     |..+=....+..|.+-       |++-|..+|+.||+.+=+..    
T Consensus        34 ~~~f~~~~-~~~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~ef-------gv~kDL~~Y~~LLDvFPKg~fvp~  105 (228)
T PF06239_consen   34 EELFERAP-GQAKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEF-------GVEKDLEVYKALLDVFPKGKFVPR  105 (228)
T ss_pred             HHHHHHHh-hccccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHc-------CCcccHHHHHHHHHhCCCCCcccc
Confidence            34444442 2367888899999988764     5556666677777777       89999999999999975421    


Q ss_pred             ------------CHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          108 ------------DLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       108 ------------~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                                  +-+-|.+++++|.. .|+.||..++..++..+++.+..-.+   .+++.-.|.+-
T Consensus       106 n~fQ~~F~hyp~Qq~c~i~lL~qME~-~gV~Pd~Et~~~ll~iFG~~s~p~~K---~~rmmYWmpkf  168 (228)
T PF06239_consen  106 NFFQAEFMHYPRQQECAIDLLEQMEN-NGVMPDKETEQMLLNIFGRKSHPMKK---YRRMMYWMPKF  168 (228)
T ss_pred             cHHHHHhccCcHHHHHHHHHHHHHHH-cCCCCcHHHHHHHHHHhccccHHHHH---HHHHHHHHHHH
Confidence                        23679999999999 99999999999999999998876554   55555555543

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

>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=97.96  E-value=0.00016  Score=45.98  Aligned_cols=98  Identities=12%  Similarity=0.050  Sum_probs=77.9

Q ss_pred             HHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCch
Q 043380          131 TFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPE  210 (246)
Q Consensus       131 ~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  210 (246)
                      ++..+...+...|++++    |..+++...+.      ...+...+..+...+...+++++|.+.++......+...   
T Consensus         2 ~~~~~a~~~~~~~~~~~----A~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~---   68 (100)
T cd00189           2 ALLNLGNLYYKLGDYDE----ALEYYEKALEL------DPDNADAYYNLAAAYYKLGKYEEALEDYEKALELDPDNA---   68 (100)
T ss_pred             HHHHHHHHHHHHhcHHH----HHHHHHHHHhc------CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcch---
Confidence            35567778888999999    99999998875      233447788889999999999999999998765432211   


Q ss_pred             hhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          211 VQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       211 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                         .++..+...+...|++++|...+....+..+
T Consensus        69 ---~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~   99 (100)
T cd00189          69 ---KAYYNLGLAYYKLGKYEEALEAYEKALELDP   99 (100)
T ss_pred             ---hHHHHHHHHHHHHHhHHHHHHHHHHHHccCC
Confidence               2678888999999999999999998876543

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.94  E-value=0.0025  Score=49.65  Aligned_cols=195  Identities=16%  Similarity=0.146  Sum_probs=141.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHH
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYAT   98 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~   98 (246)
                      -+.+.+....+..++++|.+++..-...-+.+....+.+-.+|-...++..|-+.|+++...         .|...-|..
T Consensus        12 eftaviy~lI~d~ry~DaI~~l~s~~Er~p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql---------~P~~~qYrl   82 (459)
T KOG4340|consen   12 EFTAVVYRLIRDARYADAIQLLGSELERSPRSRAGLSLLGYCYYRLQEFALAAECYEQLGQL---------HPELEQYRL   82 (459)
T ss_pred             chHHHHHHHHHHhhHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhh---------ChHHHHHHH
Confidence            36677778888999999999998765444558888999999999999999999999999875         566554432


Q ss_pred             H-HHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHH--HhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhh
Q 043380           99 L-LMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDAL--LYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHL  175 (246)
Q Consensus        99 l-l~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~--~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~  175 (246)
                      - ...+-+++.+.+|+.+...|.. .   |....-..-+.+-  -..+++..    +..++++...        +-+..+
T Consensus        83 Y~AQSLY~A~i~ADALrV~~~~~D-~---~~L~~~~lqLqaAIkYse~Dl~g----~rsLveQlp~--------en~Ad~  146 (459)
T KOG4340|consen   83 YQAQSLYKACIYADALRVAFLLLD-N---PALHSRVLQLQAAIKYSEGDLPG----SRSLVEQLPS--------ENEADG  146 (459)
T ss_pred             HHHHHHHHhcccHHHHHHHHHhcC-C---HHHHHHHHHHHHHHhcccccCcc----hHHHHHhccC--------CCccch
Confidence            2 2345577889999999999987 2   3322222222222  23677888    7777776642        234555


Q ss_pred             HHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          176 YVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       176 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      .+..-....+.|+++.|.+-|+...+-+ | ..|-+   +||.-+--| +.|+.+.|.++..++.++|.
T Consensus       147 ~in~gCllykegqyEaAvqkFqaAlqvs-G-yqpll---AYniALaHy-~~~qyasALk~iSEIieRG~  209 (459)
T KOG4340|consen  147 QINLGCLLYKEGQYEAAVQKFQAALQVS-G-YQPLL---AYNLALAHY-SSRQYASALKHISEIIERGI  209 (459)
T ss_pred             hccchheeeccccHHHHHHHHHHHHhhc-C-CCchh---HHHHHHHHH-hhhhHHHHHHHHHHHHHhhh
Confidence            5666666778999999999999876532 3 45555   677665554 77899999999999999884

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=97.93  E-value=0.0012  Score=52.19  Aligned_cols=214  Identities=14%  Similarity=0.084  Sum_probs=134.4

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHH----hCCCC--CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCC-C
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVE----KGLEP--DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGG-F   89 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~----~~~~~--~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~-~   89 (246)
                      ...|+...+.|-..|++++|.+.|...-    +.-.+  -...|.....+|.+. ++++|...+++....-..   .| .
T Consensus        35 a~~y~~Aa~~fk~~~~~~~A~~ay~kAa~~~~~~~~~~~Aa~~~~~Aa~~~k~~-~~~~Ai~~~~~A~~~y~~---~G~~  110 (282)
T PF14938_consen   35 ADLYEKAANCFKLAKDWEKAAEAYEKAADCYEKLGDKFEAAKAYEEAANCYKKG-DPDEAIECYEKAIEIYRE---AGRF  110 (282)
T ss_dssp             HHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT-THHHHHHHHHHHHHHHHH---CT-H
T ss_pred             HHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhh-CHHHHHHHHHHHHHHHHh---cCcH
Confidence            4467777888888999999999987652    11112  223455556665555 899999999887653000   01 1


Q ss_pred             CccHHHHHHHHHHHHcc-CCHHHHHHHHHHHHhC---CCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhc
Q 043380           90 HPDIFTYATLLMGFRHA-KDLQSLLEIVFEMKSC---CNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVC  164 (246)
Q Consensus        90 ~p~~~~~~~ll~~~~~~-~~~~~a~~~~~~m~~~---~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~  164 (246)
                      ..-...+..+-..|-.. |++++|.+.|++..+.   .+-.-. ..++..+...+.+.|++++    |.++|++......
T Consensus       111 ~~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~----A~~~~e~~~~~~l  186 (282)
T PF14938_consen  111 SQAAKCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEE----AIEIYEEVAKKCL  186 (282)
T ss_dssp             HHHHHHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHH----HHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHH----HHHHHHHHHHHhh
Confidence            12244788888889888 9999999999876551   231111 3457788889999999999    9999999987522


Q ss_pred             CCCCCCcchh-hHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHh--cCChhHHHHHHHHH
Q 043380          165 SNPGLWPKPH-LYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALN--DGQVDLALDKLSNT  239 (246)
Q Consensus       165 ~~~~~~p~~~-~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~--~g~~~~a~~~~~~m  239 (246)
                      ..+..+++.. .|...+-++...||+..|.+.+++.....+++.... ....-..|+.+|-.  ...++.|+.-|+.+
T Consensus       187 ~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~-E~~~~~~l~~A~~~~D~e~f~~av~~~d~~  263 (282)
T PF14938_consen  187 ENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSR-EYKFLEDLLEAYEEGDVEAFTEAVAEYDSI  263 (282)
T ss_dssp             CHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSH-HHHHHHHHHHHHHTT-CCCHHHHCHHHTTS
T ss_pred             cccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcH-HHHHHHHHHHHHHhCCHHHHHHHHHHHccc
Confidence            1122233342 334455577778999999999999876665544433 22256667777743  23345555555544

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

Probab=97.91  E-value=0.0023  Score=54.58  Aligned_cols=193  Identities=15%  Similarity=0.078  Sum_probs=145.7

Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHcc
Q 043380           27 SREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHA  106 (246)
Q Consensus        27 ~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~  106 (246)
                      +...|+-++|.+....-.++-..+.+.|+.+.-.+....++++|.+.|......        -+-|...|.-|--.-++.
T Consensus        51 L~~lg~~~ea~~~vr~glr~d~~S~vCwHv~gl~~R~dK~Y~eaiKcy~nAl~~--------~~dN~qilrDlslLQ~Qm  122 (700)
T KOG1156|consen   51 LNCLGKKEEAYELVRLGLRNDLKSHVCWHVLGLLQRSDKKYDEAIKCYRNALKI--------EKDNLQILRDLSLLQIQM  122 (700)
T ss_pred             hhcccchHHHHHHHHHHhccCcccchhHHHHHHHHhhhhhHHHHHHHHHHHHhc--------CCCcHHHHHHHHHHHHHH
Confidence            344577888888887765555678889999888888889999999999999875        234566777776677888


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHH-----
Q 043380          107 KDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMM-----  180 (246)
Q Consensus       107 ~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li-----  180 (246)
                      ++++...+...+...   ..|+ ...|..+..++--.|+...    |..+.++..+..    ...|+...|....     
T Consensus       123 Rd~~~~~~tr~~LLq---l~~~~ra~w~~~Avs~~L~g~y~~----A~~il~ef~~t~----~~~~s~~~~e~se~~Ly~  191 (700)
T KOG1156|consen  123 RDYEGYLETRNQLLQ---LRPSQRASWIGFAVAQHLLGEYKM----ALEILEEFEKTQ----NTSPSKEDYEHSELLLYQ  191 (700)
T ss_pred             HhhhhHHHHHHHHHH---hhhhhHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHhh----ccCCCHHHHHHHHHHHHH
Confidence            999999999998888   5566 5668899999999999999    999999998871    2357776665544     


Q ss_pred             -HHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          181 -HELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       181 -~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                       ......|..++|.+.+...++.-    .....  .-..-...+.+.+++++|..++..++.+.+
T Consensus       192 n~i~~E~g~~q~ale~L~~~e~~i----~Dkla--~~e~ka~l~~kl~~lEeA~~~y~~Ll~rnP  250 (700)
T KOG1156|consen  192 NQILIEAGSLQKALEHLLDNEKQI----VDKLA--FEETKADLLMKLGQLEEAVKVYRRLLERNP  250 (700)
T ss_pred             HHHHHHcccHHHHHHHHHhhhhHH----HHHHH--HhhhHHHHHHHHhhHHhHHHHHHHHHhhCc
Confidence             33556788888888888766432    22221  123345567889999999999999988765

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.88  E-value=0.0035  Score=52.72  Aligned_cols=134  Identities=9%  Similarity=-0.010  Sum_probs=102.5

Q ss_pred             CCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCC
Q 043380           88 GFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSN  166 (246)
Q Consensus        88 ~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~  166 (246)
                      +..+|...+..|--.|--.|++++|.+.|+....   +.|+ ...||-|-..++...+.++    |+..|++..+.    
T Consensus       425 ~~~~DpdvQ~~LGVLy~ls~efdraiDcf~~AL~---v~Pnd~~lWNRLGAtLAN~~~s~E----AIsAY~rALqL----  493 (579)
T KOG1125|consen  425 PTKIDPDVQSGLGVLYNLSGEFDRAVDCFEAALQ---VKPNDYLLWNRLGATLANGNRSEE----AISAYNRALQL----  493 (579)
T ss_pred             CCCCChhHHhhhHHHHhcchHHHHHHHHHHHHHh---cCCchHHHHHHhhHHhcCCcccHH----HHHHHHHHHhc----
Confidence            4346777778888888889999999999999998   7787 7789999999999999999    99999999874    


Q ss_pred             CCCCcch-hhHHHHHHHHHhcCChhHHhhHHHhhCCCCCC----CCCchhhhHHHHHHHHHHHhcCChhHHHHH
Q 043380          167 PGLWPKP-HLYVSMMHELAARVDYDIVKSPYRRMWPDSTG----TISPEVQEEAGHLLMEAALNDGQVDLALDK  235 (246)
Q Consensus       167 ~~~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~----~~~~~~~~~~~~~li~~~~~~g~~~~a~~~  235 (246)
                         +|+- .+...|--+|...|.+++|.+.|-........    .-.+......|.+|=.+++..++.|-+.+.
T Consensus       494 ---qP~yVR~RyNlgIS~mNlG~ykEA~~hlL~AL~mq~ks~~~~~~~~~se~iw~tLR~als~~~~~D~l~~a  564 (579)
T KOG1125|consen  494 ---QPGYVRVRYNLGISCMNLGAYKEAVKHLLEALSMQRKSRNHNKAPMASENIWQTLRLALSAMNRSDLLQEA  564 (579)
T ss_pred             ---CCCeeeeehhhhhhhhhhhhHHHHHHHHHHHHHhhhcccccccCCcchHHHHHHHHHHHHHcCCchHHHHh
Confidence               6664 67778888999999999999888764411111    111111223688777777778877755554

>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=0.00026  Score=52.42  Aligned_cols=104  Identities=11%  Similarity=0.134  Sum_probs=82.1

Q ss_pred             CccHHHHHHHHHHHHc-----cCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhh------------hhhHH
Q 043380           90 HPDIFTYATLLMGFRH-----AKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKV------------VGLYA  152 (246)
Q Consensus        90 ~p~~~~~~~ll~~~~~-----~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~------------~~~~a  152 (246)
                      ..|..+|..++..|.+     .|..+-....+..|.+ .|+.-|..+|+.|++.+=+..-...            -..-|
T Consensus        44 ~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~e-fgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~  122 (228)
T PF06239_consen   44 AKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDE-FGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECA  122 (228)
T ss_pred             cccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHH-cCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHH
Confidence            5788899999999964     4677888888999999 9999999999999998876332111            02229


Q ss_pred             HHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCCh-hHHhhHHHhh
Q 043380          153 LCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDY-DIVKSPYRRM  199 (246)
Q Consensus       153 ~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~-~~a~~~~~~~  199 (246)
                      ++++++|...     |+.||..|+..++..+++.+.. .+..++.-.|
T Consensus       123 i~lL~qME~~-----gV~Pd~Et~~~ll~iFG~~s~p~~K~~rmmYWm  165 (228)
T PF06239_consen  123 IDLLEQMENN-----GVMPDKETEQMLLNIFGRKSHPMKKYRRMMYWM  165 (228)
T ss_pred             HHHHHHHHHc-----CCCCcHHHHHHHHHHhccccHHHHHHHHHHHHH
Confidence            9999999998     9999999999999999988764 3444444333

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

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.88  E-value=0.0005  Score=56.20  Aligned_cols=102  Identities=12%  Similarity=-0.020  Sum_probs=84.1

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHH
Q 043380           24 IEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGF  103 (246)
Q Consensus        24 i~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~  103 (246)
                      ...+...|++++|++.|++..+..+.+...|..+..+|...|++++|...+++++..        -+.+...|..+-.+|
T Consensus         9 a~~a~~~~~~~~Ai~~~~~Al~~~P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l--------~P~~~~a~~~lg~~~   80 (356)
T PLN03088          9 AKEAFVDDDFALAVDLYTQAIDLDPNNAELYADRAQANIKLGNFTEAVADANKAIEL--------DPSLAKAYLRKGTAC   80 (356)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--------CcCCHHHHHHHHHHH
Confidence            456678899999999999887544667888999999999999999999999999986        233567888999999


Q ss_pred             HccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHH
Q 043380          104 RHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMV  136 (246)
Q Consensus       104 ~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li  136 (246)
                      ...|++++|...|++..+   +.|+.......+
T Consensus        81 ~~lg~~~eA~~~~~~al~---l~P~~~~~~~~l  110 (356)
T PLN03088         81 MKLEEYQTAKAALEKGAS---LAPGDSRFTKLI  110 (356)
T ss_pred             HHhCCHHHHHHHHHHHHH---hCCCCHHHHHHH
Confidence            999999999999999988   557644444443

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.83  E-value=0.0083  Score=55.34  Aligned_cols=216  Identities=9%  Similarity=-0.070  Sum_probs=126.3

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHh---CC-CC--CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVEK---GL-EP--DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~~---~~-~~--~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      ..+.+...+...|++++|...+++...   .. .+  -..++..+...+...|++++|...+++................
T Consensus       493 a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~  572 (903)
T PRK04841        493 ATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMH  572 (903)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHH
Confidence            445666677789999999999987631   11 11  1234556667788899999999999887653110000000112


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCC-CCCCC--HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCC
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCC-NLILD--RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGL  169 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~-~~~p~--~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~  169 (246)
                      ...+..+...+...|++++|...+.+..... ...+.  ...+..+...+...|+++.    |.+.++......... +.
T Consensus       573 ~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~G~~~~----A~~~l~~a~~~~~~~-~~  647 (903)
T PRK04841        573 EFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISLARGDLDN----ARRYLNRLENLLGNG-RY  647 (903)
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHHHhcc-cc
Confidence            3345555666777899999999988765511 11122  3445556778888999999    999988876531100 11


Q ss_pred             CcchhhH--HHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          170 WPKPHLY--VSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       170 ~p~~~~~--~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      .+.....  ...+..+...|+.+.|...+........+.  +......+..+..++...|+.++|...+++...
T Consensus       648 ~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~--~~~~~~~~~~~a~~~~~~g~~~~A~~~l~~al~  719 (903)
T PRK04841        648 HSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFAN--NHFLQGQWRNIARAQILLGQFDEAEIILEELNE  719 (903)
T ss_pred             cHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCcc--chhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            0000000  111234455677777777776654322111  110011234566667777888888777776654

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.76  E-value=0.0025  Score=46.37  Aligned_cols=85  Identities=9%  Similarity=0.042  Sum_probs=67.1

Q ss_pred             CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc--HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC
Q 043380           50 DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD--IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL  127 (246)
Q Consensus        50 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~--~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p  127 (246)
                      ....+..+...+...|++++|...|++..+.       ...+.  ...+..+...+.+.|++++|...+.+...   ..|
T Consensus        34 ~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~-------~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~---~~p  103 (172)
T PRK02603         34 EAFVYYRDGMSAQADGEYAEALENYEEALKL-------EEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALE---LNP  103 (172)
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-------hhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCc
Confidence            4456778888888999999999999999875       22222  46788899999999999999999999888   445


Q ss_pred             C-HHHHHHHHHHHHhcCC
Q 043380          128 D-RSTFTAMVDALLYSGS  144 (246)
Q Consensus       128 ~-~~~~~~li~~~~~~~~  144 (246)
                      + ...+..+...+...|+
T Consensus       104 ~~~~~~~~lg~~~~~~g~  121 (172)
T PRK02603        104 KQPSALNNIAVIYHKRGE  121 (172)
T ss_pred             ccHHHHHHHHHHHHHcCC
Confidence            5 6667777777877776

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.75  E-value=0.00079  Score=53.48  Aligned_cols=190  Identities=12%  Similarity=0.097  Sum_probs=121.4

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHH--HHhcC-------CcchHHHHHHHHHhccCCCCCCCCCc
Q 043380           21 NAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISA--CIKTK-------KLDVTMPFNEQLKDNGQKCSSGGFHP   91 (246)
Q Consensus        21 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~--~~~~~-------~~~~a~~~~~~m~~~~~~~~~~~~~p   91 (246)
                      -.|+--|.+.+++.+|..+..++.   +.++.-|  ++.+  ++..|       ...-|..+|.-.-++       +.+.
T Consensus       289 lNL~iYyL~q~dVqeA~~L~Kdl~---PttP~Ey--ilKgvv~aalGQe~gSreHlKiAqqffqlVG~S-------a~ec  356 (557)
T KOG3785|consen  289 LNLIIYYLNQNDVQEAISLCKDLD---PTTPYEY--ILKGVVFAALGQETGSREHLKIAQQFFQLVGES-------ALEC  356 (557)
T ss_pred             hhheeeecccccHHHHHHHHhhcC---CCChHHH--HHHHHHHHHhhhhcCcHHHHHHHHHHHHHhccc-------cccc
Confidence            456667889999999999988875   3333222  2222  22222       334465555554444       3443


Q ss_pred             cHH-HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCC
Q 043380           92 DIF-TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLW  170 (246)
Q Consensus        92 ~~~-~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~  170 (246)
                      |.. --.++.+++.-..++++++-.++.++. .=..-|.+.| .+..+++..|++.+    |+++|-.+...     .++
T Consensus       357 DTIpGRQsmAs~fFL~~qFddVl~YlnSi~s-YF~NdD~Fn~-N~AQAk~atgny~e----aEelf~~is~~-----~ik  425 (557)
T KOG3785|consen  357 DTIPGRQSMASYFFLSFQFDDVLTYLNSIES-YFTNDDDFNL-NLAQAKLATGNYVE----AEELFIRISGP-----EIK  425 (557)
T ss_pred             ccccchHHHHHHHHHHHHHHHHHHHHHHHHH-HhcCcchhhh-HHHHHHHHhcChHH----HHHHHhhhcCh-----hhh
Confidence            322 334556666666788999999998888 4232334444 48889999999999    99998777553     333


Q ss_pred             cchhhHHH-HHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          171 PKPHLYVS-MMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       171 p~~~~~~~-li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                       |..+|.+ |.++|.+.+.++.|+.++-.+......       ......+..-|-+.+.+--|-+.|+.+..
T Consensus       426 -n~~~Y~s~LArCyi~nkkP~lAW~~~lk~~t~~e~-------fsLLqlIAn~CYk~~eFyyaaKAFd~lE~  489 (557)
T KOG3785|consen  426 -NKILYKSMLARCYIRNKKPQLAWDMMLKTNTPSER-------FSLLQLIANDCYKANEFYYAAKAFDELEI  489 (557)
T ss_pred             -hhHHHHHHHHHHHHhcCCchHHHHHHHhcCCchhH-------HHHHHHHHHHHHHHHHHHHHHHhhhHHHc
Confidence             4556654 558889999999999988877533211       11334455667788888777777776654

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=97.74  E-value=0.011  Score=45.53  Aligned_cols=185  Identities=15%  Similarity=0.025  Sum_probs=105.2

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHH---HHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSY---NILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~---~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      +..+-.....+.+.|++++|.+.|+.+....+-+...-   -.+..++.+.+++++|...+++..+.       ...-..
T Consensus        32 ~~~~Y~~A~~~~~~g~y~~Ai~~f~~l~~~yP~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~-------~P~~~~  104 (243)
T PRK10866         32 PSEIYATAQQKLQDGNWKQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRL-------NPTHPN  104 (243)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh-------CcCCCc
Confidence            33333445556778999999999999875333333332   34567888999999999999999987       111122


Q ss_pred             HHHHHHHHHHHc--cC---------------CH---HHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHH
Q 043380           94 FTYATLLMGFRH--AK---------------DL---QSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYAL  153 (246)
Q Consensus        94 ~~~~~ll~~~~~--~~---------------~~---~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~  153 (246)
                      .-|...+.+.+.  .+               |.   .+|...|+.+.+                -|-.+.-..+    |.
T Consensus       105 ~~~a~Y~~g~~~~~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~----------------~yP~S~ya~~----A~  164 (243)
T PRK10866        105 IDYVLYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVR----------------GYPNSQYTTD----AT  164 (243)
T ss_pred             hHHHHHHHHHhhhhcchhhhhhccCCCccccCHHHHHHHHHHHHHHHH----------------HCcCChhHHH----HH
Confidence            344444444431  11               11   233344444444                3333333444    44


Q ss_pred             HHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHH
Q 043380          154 CIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLAL  233 (246)
Q Consensus       154 ~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~  233 (246)
                      ..+..+...        .-. ---.+..-|.+.|.+..|..=++.+...-++....   ..+...++.+|...|..++|.
T Consensus       165 ~rl~~l~~~--------la~-~e~~ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~---~eal~~l~~ay~~lg~~~~a~  232 (243)
T PRK10866        165 KRLVFLKDR--------LAK-YELSVAEYYTKRGAYVAVVNRVEQMLRDYPDTQAT---RDALPLMENAYRQLQLNAQAD  232 (243)
T ss_pred             HHHHHHHHH--------HHH-HHHHHHHHHHHcCchHHHHHHHHHHHHHCCCCchH---HHHHHHHHHHHHHcCChHHHH
Confidence            444443332        001 11145566777777777777777776544332221   125666777777777777777


Q ss_pred             HHHHHHH
Q 043380          234 DKLSNTI  240 (246)
Q Consensus       234 ~~~~~m~  240 (246)
                      ++...+.
T Consensus       233 ~~~~~l~  239 (243)
T PRK10866        233 KVAKIIA  239 (243)
T ss_pred             HHHHHHh
Confidence            7766554

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A

Probab=97.74  E-value=0.00016  Score=43.70  Aligned_cols=65  Identities=23%  Similarity=0.260  Sum_probs=53.9

Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHH
Q 043380           28 REAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLM  101 (246)
Q Consensus        28 ~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~  101 (246)
                      .+.|++++|.++|+.+....+-+...+..+..+|.+.|++++|..+++++...         .|+...|..++.
T Consensus         2 l~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~---------~~~~~~~~~l~a   66 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQRNPDNPEARLLLAQCYLKQGQYDEAEELLERLLKQ---------DPDNPEYQQLLA   66 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG---------GTTHHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH---------CcCHHHHHHHHh
Confidence            56799999999999987545668888889999999999999999999999986         677666666543

...

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

Probab=97.73  E-value=0.009  Score=48.63  Aligned_cols=151  Identities=8%  Similarity=0.029  Sum_probs=101.3

Q ss_pred             CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHH
Q 043380           31 QRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQ  110 (246)
Q Consensus        31 g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~  110 (246)
                      .++..|+.+-+..-+--+.++..|-.--+.+...+++++|.--|+..+..        -+-+...|.-|+.+|...|.+.
T Consensus       314 K~~~rAL~~~eK~I~~~~r~~~alilKG~lL~~~~R~~~A~IaFR~Aq~L--------ap~rL~~Y~GL~hsYLA~~~~k  385 (564)
T KOG1174|consen  314 KKFERALNFVEKCIDSEPRNHEALILKGRLLIALERHTQAVIAFRTAQML--------APYRLEIYRGLFHSYLAQKRFK  385 (564)
T ss_pred             hhHHHHHHHHHHHhccCcccchHHHhccHHHHhccchHHHHHHHHHHHhc--------chhhHHHHHHHHHHHHhhchHH
Confidence            33444444443332112333444444445555667777777777766653        1235567777777777777766


Q ss_pred             HHHHH------------------------------------HHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHH
Q 043380          111 SLLEI------------------------------------VFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYAL  153 (246)
Q Consensus       111 ~a~~~------------------------------------~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~  153 (246)
                      +|..+                                    ++.-..   +.|+ ....+.+...|...|..++    +.
T Consensus       386 EA~~~An~~~~~~~~sA~~LtL~g~~V~~~dp~~rEKAKkf~ek~L~---~~P~Y~~AV~~~AEL~~~Eg~~~D----~i  458 (564)
T KOG1174|consen  386 EANALANWTIRLFQNSARSLTLFGTLVLFPDPRMREKAKKFAEKSLK---INPIYTPAVNLIAELCQVEGPTKD----II  458 (564)
T ss_pred             HHHHHHHHHHHHhhcchhhhhhhcceeeccCchhHHHHHHHHHhhhc---cCCccHHHHHHHHHHHHhhCccch----HH
Confidence            65543                                    322222   4466 5567778888899999999    99


Q ss_pred             HHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCC
Q 043380          154 CIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDS  203 (246)
Q Consensus       154 ~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  203 (246)
                      .+++.-...       .||...-+.|-+.+...+.+++|++.|......+
T Consensus       459 ~LLe~~L~~-------~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~ALr~d  501 (564)
T KOG1174|consen  459 KLLEKHLII-------FPDVNLHNHLGDIMRAQNEPQKAMEYYYKALRQD  501 (564)
T ss_pred             HHHHHHHhh-------ccccHHHHHHHHHHHHhhhHHHHHHHHHHHHhcC
Confidence            999988764       6899999999999999999999999999887654

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=97.71  E-value=0.014  Score=51.68  Aligned_cols=106  Identities=17%  Similarity=0.135  Sum_probs=57.3

Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHH--HhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHcc
Q 043380           29 EAQRIDEAYQILESVEKGLEPDSLSYNILISAC--IKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHA  106 (246)
Q Consensus        29 ~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~--~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~  106 (246)
                      .++++.+|++....+.+. -|| ..|..++.++  .+.|+.++|..+++.....       +.. |..|...+-.+|...
T Consensus        21 d~~qfkkal~~~~kllkk-~Pn-~~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~-------~~~-D~~tLq~l~~~y~d~   90 (932)
T KOG2053|consen   21 DSSQFKKALAKLGKLLKK-HPN-ALYAKVLKALSLFRLGKGDEALKLLEALYGL-------KGT-DDLTLQFLQNVYRDL   90 (932)
T ss_pred             hhHHHHHHHHHHHHHHHH-CCC-cHHHHHHHHHHHHHhcCchhHHHHHhhhccC-------CCC-chHHHHHHHHHHHHH
Confidence            345556666666554321 233 2234444443  3456666666655555443       111 555666666666666


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhh
Q 043380          107 KDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKV  147 (246)
Q Consensus       107 ~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~  147 (246)
                      ++.++|..+|++...   ..|+......+..+|++.+++..
T Consensus        91 ~~~d~~~~~Ye~~~~---~~P~eell~~lFmayvR~~~yk~  128 (932)
T KOG2053|consen   91 GKLDEAVHLYERANQ---KYPSEELLYHLFMAYVREKSYKK  128 (932)
T ss_pred             hhhhHHHHHHHHHHh---hCCcHHHHHHHHHHHHHHHHHHH
Confidence            666666666666554   44555555556666666666555

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.70  E-value=0.0032  Score=45.64  Aligned_cols=95  Identities=7%  Similarity=-0.112  Sum_probs=70.4

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CC--CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGL-EP--DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~--~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      ....|..+...+...|++++|+..|+....-. .|  ...+|..+-..+...|++++|...+++....        .+..
T Consensus        34 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~--------~~~~  105 (168)
T CHL00033         34 EAFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALER--------NPFL  105 (168)
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--------CcCc
Confidence            35667788888889999999999998875211 12  2357888999999999999999999999875        2233


Q ss_pred             HHHHHHHHHHHH-------ccCCHHHHHHHHHH
Q 043380           93 IFTYATLLMGFR-------HAKDLQSLLEIVFE  118 (246)
Q Consensus        93 ~~~~~~ll~~~~-------~~~~~~~a~~~~~~  118 (246)
                      ..++..+...+.       ..|+++.|...+++
T Consensus       106 ~~~~~~la~i~~~~~~~~~~~g~~~~A~~~~~~  138 (168)
T CHL00033        106 PQALNNMAVICHYRGEQAIEQGDSEIAEAWFDQ  138 (168)
T ss_pred             HHHHHHHHHHHHHhhHHHHHcccHHHHHHHHHH
Confidence            456666666666       77887765555543

>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=97.70  E-value=0.0016  Score=44.63  Aligned_cols=103  Identities=15%  Similarity=0.171  Sum_probs=72.2

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      |..++.++|.++++.|+++....+++..- |+.++...         ..+.          ..      ......|+..+
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~W-gI~~~~~~---------~~~~----------~~------~~spl~Pt~~l   54 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVW-GIDVNGKK---------KEGD----------YP------PSSPLYPTSRL   54 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhc-CCCCCCcc---------ccCc----------cC------CCCCCCCCHHH
Confidence            34566666667777777666666665543 22222100         0000          11      12367899999


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCC
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGS  144 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~  144 (246)
                      ..+++.+|+.++++..|+++.+...+..++..+..+|..|+.......+
T Consensus        55 L~AIv~sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W~~v~s~  103 (126)
T PF12921_consen   55 LIAIVHSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEWAYVLSS  103 (126)
T ss_pred             HHHHHHHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhcC
Confidence            9999999999999999999999998888988889999999997666554

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.70  E-value=0.0042  Score=45.18  Aligned_cols=116  Identities=10%  Similarity=0.025  Sum_probs=81.4

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-CCC-C-CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEK-GLE-P-DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~-~~~-~-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      ....+..+...+...|++++|...|++... .-. + ....+..+...+.+.|++++|...+.+....        .+-+
T Consensus        34 ~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--------~p~~  105 (172)
T PRK02603         34 EAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALEL--------NPKQ  105 (172)
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--------Cccc
Confidence            344677788888899999999999988752 112 2 2467888999999999999999999999885        2234


Q ss_pred             HHHHHHHHHHHHccCC--------------HHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCC
Q 043380           93 IFTYATLLMGFRHAKD--------------LQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGS  144 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~--------------~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~  144 (246)
                      ...+..+...+...|+              +++|.+++++...   ..|+.  |..++..+...|+
T Consensus       106 ~~~~~~lg~~~~~~g~~~~a~~~~~~A~~~~~~A~~~~~~a~~---~~p~~--~~~~~~~~~~~~~  166 (172)
T PRK02603        106 PSALNNIAVIYHKRGEKAEEAGDQDEAEALFDKAAEYWKQAIR---LAPNN--YIEAQNWLKTTGR  166 (172)
T ss_pred             HHHHHHHHHHHHHcCChHhHhhCHHHHHHHHHHHHHHHHHHHh---hCchh--HHHHHHHHHhcCc
Confidence            5567777777777766              3556666666555   33333  5556665555544

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.70  E-value=0.0014  Score=53.66  Aligned_cols=90  Identities=8%  Similarity=-0.053  Sum_probs=78.1

Q ss_pred             HHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHH
Q 043380           58 ISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMV  136 (246)
Q Consensus        58 i~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li  136 (246)
                      ...+...|++++|.+.|.+.++.        -+-+...|..+..+|.+.|++++|...+++...   +.|+ ...|..+.
T Consensus         9 a~~a~~~~~~~~Ai~~~~~Al~~--------~P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~---l~P~~~~a~~~lg   77 (356)
T PLN03088          9 AKEAFVDDDFALAVDLYTQAIDL--------DPNNAELYADRAQANIKLGNFTEAVADANKAIE---LDPSLAKAYLRKG   77 (356)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHh--------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCcCCHHHHHHHH
Confidence            34567789999999999999986        234567888999999999999999999999988   5565 77888899


Q ss_pred             HHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          137 DALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       137 ~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      .+|...|++++    |...|+...+.
T Consensus        78 ~~~~~lg~~~e----A~~~~~~al~l   99 (356)
T PLN03088         78 TACMKLEEYQT----AKAALEKGASL   99 (356)
T ss_pred             HHHHHhCCHHH----HHHHHHHHHHh
Confidence            99999999999    99999999875

>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=97.70  E-value=0.00096  Score=45.74  Aligned_cols=89  Identities=12%  Similarity=0.131  Sum_probs=74.9

Q ss_pred             cHHHHHHHHHHHHccCCHHHHHHHHHHHHh--------------CCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHH
Q 043380           92 DIFTYATLLMGFRHAKDLQSLLEIVFEMKS--------------CCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFG  157 (246)
Q Consensus        92 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~--------------~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~  157 (246)
                      |..++.++|.++++.|+.+....+++..-.              .....||..+..+++.+|+..+++..    |.++.+
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~~~~~spl~Pt~~lL~AIv~sf~~n~~i~~----al~~vd   76 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGDYPPSSPLYPTSRLLIAIVHSFGYNGDIFS----ALKLVD   76 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCccCCCCCCCCCHHHHHHHHHHHHhcccHHH----HHHHHH
Confidence            567899999999999999999998876422              13356999999999999999999999    999999


Q ss_pred             HHHHhhcCCCCCCcchhhHHHHHHHHHhcCC
Q 043380          158 EIVKRVCSNPGLWPKPHLYVSMMHELAARVD  188 (246)
Q Consensus       158 ~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~  188 (246)
                      ...+.+    ++..+..+|..|+.-....-+
T Consensus        77 ~fs~~Y----~I~i~~~~W~~Ll~W~~v~s~  103 (126)
T PF12921_consen   77 FFSRKY----PIPIPKEFWRRLLEWAYVLSS  103 (126)
T ss_pred             HHHHHc----CCCCCHHHHHHHHHHHHHhcC
Confidence            999985    577778999999977665544

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.69  E-value=0.013  Score=44.65  Aligned_cols=169  Identities=14%  Similarity=0.152  Sum_probs=123.8

Q ss_pred             cCcCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHH-HHHhcCCcchHHHHHHHHHhccCCCCCCCCC
Q 043380           13 WKLNT-IVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILIS-ACIKTKKLDVTMPFNEQLKDNGQKCSSGGFH   90 (246)
Q Consensus        13 ~~~~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~-~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~   90 (246)
                      ..++. ..|.-++-+....|+.+.|...++++...+ |...-...|=. -+-..|++++|.++|+.+.+.        -+
T Consensus        47 ~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~f-p~S~RV~~lkam~lEa~~~~~~A~e~y~~lL~d--------dp  117 (289)
T KOG3060|consen   47 LGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRF-PGSKRVGKLKAMLLEATGNYKEAIEYYESLLED--------DP  117 (289)
T ss_pred             cCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhC-CCChhHHHHHHHHHHHhhchhhHHHHHHHHhcc--------Cc
Confidence            33443 345666777788899999999999998656 43322222211 123478899999999999986        25


Q ss_pred             ccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCC
Q 043380           91 PDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLW  170 (246)
Q Consensus        91 p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~  170 (246)
                      .|.++|--=+...-..|+.-+|.+-+....+  .+..|...|.-+-..|...|+++.    |.-+++++.-.       .
T Consensus       118 t~~v~~KRKlAilka~GK~l~aIk~ln~YL~--~F~~D~EAW~eLaeiY~~~~~f~k----A~fClEE~ll~-------~  184 (289)
T KOG3060|consen  118 TDTVIRKRKLAILKAQGKNLEAIKELNEYLD--KFMNDQEAWHELAEIYLSEGDFEK----AAFCLEELLLI-------Q  184 (289)
T ss_pred             chhHHHHHHHHHHHHcCCcHHHHHHHHHHHH--HhcCcHHHHHHHHHHHHhHhHHHH----HHHHHHHHHHc-------C
Confidence            5777888878888788888888888887777  277889999999999999999999    99999999875       4


Q ss_pred             cch-hhHHHHHHHHHhc---CChhHHhhHHHhhCCCC
Q 043380          171 PKP-HLYVSMMHELAAR---VDYDIVKSPYRRMWPDS  203 (246)
Q Consensus       171 p~~-~~~~~li~~~~~~---g~~~~a~~~~~~~~~~~  203 (246)
                      |-. .-+..+...+.-.   .+...+.+++.+..+.+
T Consensus       185 P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alkl~  221 (289)
T KOG3060|consen  185 PFNPLYFQRLAEVLYTQGGAENLELARKYYERALKLN  221 (289)
T ss_pred             CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhC
Confidence            443 4444444444443   45678888888877544

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

Probab=97.68  E-value=0.012  Score=49.89  Aligned_cols=201  Identities=14%  Similarity=0.087  Sum_probs=128.6

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHH
Q 043380           22 AVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLM  101 (246)
Q Consensus        22 ~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~  101 (246)
                      +=++-+...|++++|......+..+.+.+...+..=+-+..+.+++++|+.+.+.-..         ...+.+-+  +=.
T Consensus        17 t~ln~~~~~~e~e~a~k~~~Kil~~~pdd~~a~~cKvValIq~~ky~~ALk~ikk~~~---------~~~~~~~~--fEK   85 (652)
T KOG2376|consen   17 TDLNRHGKNGEYEEAVKTANKILSIVPDDEDAIRCKVVALIQLDKYEDALKLIKKNGA---------LLVINSFF--FEK   85 (652)
T ss_pred             HHHHHhccchHHHHHHHHHHHHHhcCCCcHhhHhhhHhhhhhhhHHHHHHHHHHhcch---------hhhcchhh--HHH
Confidence            4466777889999999999998866666777788888888889999999865554221         11111111  244


Q ss_pred             HHH--ccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhc---------------
Q 043380          102 GFR--HAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVC---------------  164 (246)
Q Consensus       102 ~~~--~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~---------------  164 (246)
                      +||  +.+..++|+..++-...     .|..+...-...+-+.|++++    |+++|+.+.+...               
T Consensus        86 AYc~Yrlnk~Dealk~~~~~~~-----~~~~ll~L~AQvlYrl~~yde----aldiY~~L~kn~~dd~d~~~r~nl~a~~  156 (652)
T KOG2376|consen   86 AYCEYRLNKLDEALKTLKGLDR-----LDDKLLELRAQVLYRLERYDE----ALDIYQHLAKNNSDDQDEERRANLLAVA  156 (652)
T ss_pred             HHHHHHcccHHHHHHHHhcccc-----cchHHHHHHHHHHHHHhhHHH----HHHHHHHHHhcCCchHHHHHHHHHHHHH
Confidence            443  67888888888874333     234455556667778888888    8888888855411               


Q ss_pred             --------CCCCCCcchhhHHH---HHHHHHhcCChhHHhhHHHhh--------CCCCCC--CCCchhhhHHHHHHHHHH
Q 043380          165 --------SNPGLWPKPHLYVS---MMHELAARVDYDIVKSPYRRM--------WPDSTG--TISPEVQEEAGHLLMEAA  223 (246)
Q Consensus       165 --------~~~~~~p~~~~~~~---li~~~~~~g~~~~a~~~~~~~--------~~~~~~--~~~~~~~~~~~~~li~~~  223 (246)
                              ......| ..+|..   ....+...|++.+|+++++..        ...+..  .+...++ .+---|.-.+
T Consensus       157 a~l~~~~~q~v~~v~-e~syel~yN~Ac~~i~~gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~-~IrvQlayVl  234 (652)
T KOG2376|consen  157 AALQVQLLQSVPEVP-EDSYELLYNTACILIENGKYNQAIELLEKALRICREKLEDEDTNEEEIEEELN-PIRVQLAYVL  234 (652)
T ss_pred             HhhhHHHHHhccCCC-cchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHH-HHHHHHHHHH
Confidence                    0011223 223433   345567789999999999987        222111  0111111 1223355667


Q ss_pred             HhcCChhHHHHHHHHHHhhcc
Q 043380          224 LNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       224 ~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      -..|+.++|.+++..+.++.+
T Consensus       235 Q~~Gqt~ea~~iy~~~i~~~~  255 (652)
T KOG2376|consen  235 QLQGQTAEASSIYVDIIKRNP  255 (652)
T ss_pred             HHhcchHHHHHHHHHHHHhcC
Confidence            789999999999998887654

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.65  E-value=0.0074  Score=51.78  Aligned_cols=139  Identities=9%  Similarity=0.002  Sum_probs=97.5

Q ss_pred             cccCcCHHHHHHHHHHHHhc-----CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCc--------chHHHHHHHH
Q 043380           11 EHWKLNTIVMNAVIEASREA-----QRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKL--------DVTMPFNEQL   77 (246)
Q Consensus        11 ~~~~~~~~~~~~li~~~~~~-----g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~--------~~a~~~~~~m   77 (246)
                      ...+.|...|...+.+....     ++.+.|..+|++..+.-+-+...|..+..++.....+        ..+.+...+.
T Consensus       331 ~~~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ldP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a  410 (517)
T PRK10153        331 QGLPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSEPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNI  410 (517)
T ss_pred             ccCCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHh
Confidence            44678889999999986543     2377899999987643334455566554444332222        2233333332


Q ss_pred             HhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHH
Q 043380           78 KDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFG  157 (246)
Q Consensus        78 ~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~  157 (246)
                      ...      .....+...|..+--.....|++++|...+++...   +.|+...|..+...+...|+.++    |.+.++
T Consensus       411 ~al------~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~---L~ps~~a~~~lG~~~~~~G~~~e----A~~~~~  477 (517)
T PRK10153        411 VAL------PELNVLPRIYEILAVQALVKGKTDEAYQAINKAID---LEMSWLNYVLLGKVYELKGDNRL----AADAYS  477 (517)
T ss_pred             hhc------ccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHH---cCCCHHHHHHHHHHHHHcCCHHH----HHHHHH
Confidence            221      01233456787776666778999999999999999   55888899999999999999999    999999


Q ss_pred             HHHHh
Q 043380          158 EIVKR  162 (246)
Q Consensus       158 ~m~~~  162 (246)
                      +....
T Consensus       478 ~A~~L  482 (517)
T PRK10153        478 TAFNL  482 (517)
T ss_pred             HHHhc
Confidence            98765

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=97.62  E-value=0.00023  Score=45.14  Aligned_cols=81  Identities=12%  Similarity=0.140  Sum_probs=60.8

Q ss_pred             cCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhc
Q 043380           64 TKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYS  142 (246)
Q Consensus        64 ~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~  142 (246)
                      .|+++.|+.+++++.+..      ...|+...+..+..+|.+.|++++|..+++. ..   ..|+ ......+..+|...
T Consensus         2 ~~~y~~Ai~~~~k~~~~~------~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~---~~~~~~~~~~l~a~~~~~l   71 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELD------PTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LK---LDPSNPDIHYLLARCLLKL   71 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHH------CGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HT---HHHCHHHHHHHHHHHHHHT
T ss_pred             CccHHHHHHHHHHHHHHC------CCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hC---CCCCCHHHHHHHHHHHHHh
Confidence            578999999999999871      1012455666689999999999999999988 33   2233 34444668899999


Q ss_pred             CChhhhhhHHHHHHHH
Q 043380          143 GSIKVVGLYALCIFGE  158 (246)
Q Consensus       143 ~~~~~~~~~a~~~~~~  158 (246)
                      |++++    |++++++
T Consensus        72 ~~y~e----Ai~~l~~   83 (84)
T PF12895_consen   72 GKYEE----AIKALEK   83 (84)
T ss_dssp             T-HHH----HHHHHHH
T ss_pred             CCHHH----HHHHHhc
Confidence            99999    9999875

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

Probab=97.62  E-value=0.032  Score=47.89  Aligned_cols=139  Identities=12%  Similarity=0.069  Sum_probs=91.7

Q ss_pred             CccHHH--HHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCC
Q 043380           90 HPDIFT--YATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSN  166 (246)
Q Consensus        90 ~p~~~~--~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~  166 (246)
                      +|+...  +--+...|-+.|+++.|+..++....   -+|+ ...|..=.+.+...|++++    |...+++..+-    
T Consensus       366 ~PttllWt~y~laqh~D~~g~~~~A~~yId~AId---HTPTliEly~~KaRI~kH~G~l~e----Aa~~l~ea~el----  434 (700)
T KOG1156|consen  366 PPTTLLWTLYFLAQHYDKLGDYEVALEYIDLAID---HTPTLIELYLVKARIFKHAGLLDE----AAAWLDEAQEL----  434 (700)
T ss_pred             CchHHHHHHHHHHHHHHHcccHHHHHHHHHHHhc---cCchHHHHHHHHHHHHHhcCChHH----HHHHHHHHHhc----
Confidence            444443  34456667788888888888888766   5566 4556666788888888888    88888888775    


Q ss_pred             CCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHH---HHHHHhcCChhHHHHHHHHHHh
Q 043380          167 PGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLL---MEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       167 ~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~l---i~~~~~~g~~~~a~~~~~~m~~  241 (246)
                        -.||...=..-..-..++.+.++|.++.......+.+.+..-....+...+   ..+|.+.|++..|++-|..+-+
T Consensus       435 --D~aDR~INsKcAKYmLrAn~i~eA~~~~skFTr~~~~~~~~L~~mqcmWf~~E~g~ay~r~~k~g~ALKkfh~i~k  510 (700)
T KOG1156|consen  435 --DTADRAINSKCAKYMLRANEIEEAEEVLSKFTREGFGAVNNLAEMQCMWFQLEDGEAYLRQNKLGLALKKFHEIEK  510 (700)
T ss_pred             --cchhHHHHHHHHHHHHHccccHHHHHHHHHhhhcccchhhhHHHhhhHHHhHhhhHHHHHHHHHHHHHHHHhhHHH
Confidence              245555555666777788888888888888776554333322222222222   2357788888888777766543

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.62  E-value=0.0036  Score=45.35  Aligned_cols=95  Identities=9%  Similarity=0.030  Sum_probs=71.9

Q ss_pred             CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc--cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC
Q 043380           50 DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP--DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL  127 (246)
Q Consensus        50 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p--~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p  127 (246)
                      ....|..+...+...|++++|...|++....       ...|  ...+|..+-..+...|++++|...++....   +.|
T Consensus        34 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~l-------~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~---~~~  103 (168)
T CHL00033         34 EAFTYYRDGMSAQSEGEYAEALQNYYEAMRL-------EIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALE---RNP  103 (168)
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc-------cccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCc
Confidence            4566778888888899999999999999875       2122  235888999999999999999999999888   345


Q ss_pred             C-HHHHHHHHHHHH-------hcCChhhhhhHHHHHHHH
Q 043380          128 D-RSTFTAMVDALL-------YSGSIKVVGLYALCIFGE  158 (246)
Q Consensus       128 ~-~~~~~~li~~~~-------~~~~~~~~~~~a~~~~~~  158 (246)
                      + ..++..+...+.       ..|+++.    |+..+++
T Consensus       104 ~~~~~~~~la~i~~~~~~~~~~~g~~~~----A~~~~~~  138 (168)
T CHL00033        104 FLPQALNNMAVICHYRGEQAIEQGDSEI----AEAWFDQ  138 (168)
T ss_pred             CcHHHHHHHHHHHHHhhHHHHHcccHHH----HHHHHHH
Confidence            4 555666666666       7778776    5555554

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=97.61  E-value=0.0003  Score=44.61  Aligned_cols=76  Identities=12%  Similarity=0.183  Sum_probs=34.5

Q ss_pred             CCHHHHHHHHHHHHhCCCCCC---CHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc-chhhHHHHHHH
Q 043380          107 KDLQSLLEIVFEMKSCCNLIL---DRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP-KPHLYVSMMHE  182 (246)
Q Consensus       107 ~~~~~a~~~~~~m~~~~~~~p---~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p-~~~~~~~li~~  182 (246)
                      |+++.|..+++.+.+   ..|   +...+..+..+|.+.|++++    |..+++.. +       ..| +......+..+
T Consensus         3 ~~y~~Ai~~~~k~~~---~~~~~~~~~~~~~la~~~~~~~~y~~----A~~~~~~~-~-------~~~~~~~~~~l~a~~   67 (84)
T PF12895_consen    3 GNYENAIKYYEKLLE---LDPTNPNSAYLYNLAQCYFQQGKYEE----AIELLQKL-K-------LDPSNPDIHYLLARC   67 (84)
T ss_dssp             T-HHHHHHHHHHHHH---HHCGTHHHHHHHHHHHHHHHTTHHHH----HHHHHHCH-T-------HHHCHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHH---HCCCChhHHHHHHHHHHHHHCCCHHH----HHHHHHHh-C-------CCCCCHHHHHHHHHH
Confidence            455555555555555   222   22233335555555555555    55555551 1       111 11222233455


Q ss_pred             HHhcCChhHHhhHHH
Q 043380          183 LAARVDYDIVKSPYR  197 (246)
Q Consensus       183 ~~~~g~~~~a~~~~~  197 (246)
                      |...|++++|.++++
T Consensus        68 ~~~l~~y~eAi~~l~   82 (84)
T PF12895_consen   68 LLKLGKYEEAIKALE   82 (84)
T ss_dssp             HHHTT-HHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHh
Confidence            555555555555554

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=97.58  E-value=0.0018  Score=56.26  Aligned_cols=123  Identities=13%  Similarity=0.142  Sum_probs=82.5

Q ss_pred             hhhHHHHhcccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccC
Q 043380            3 EENEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQ   82 (246)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~   82 (246)
                      +.++.++.++++.+..  -..+.+......+.+|+.+++.++.. +.-..-|..+...|+..|+++-|+++|-+.-    
T Consensus       720 ~q~daainhfiea~~~--~kaieaai~akew~kai~ildniqdq-k~~s~yy~~iadhyan~~dfe~ae~lf~e~~----  792 (1636)
T KOG3616|consen  720 GQLDAAINHFIEANCL--IKAIEAAIGAKEWKKAISILDNIQDQ-KTASGYYGEIADHYANKGDFEIAEELFTEAD----  792 (1636)
T ss_pred             HhHHHHHHHHHHhhhH--HHHHHHHhhhhhhhhhHhHHHHhhhh-ccccccchHHHHHhccchhHHHHHHHHHhcc----
Confidence            3455666666655443  34566777888999999999988731 2333346777888889999999988886632    


Q ss_pred             CCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhh
Q 043380           83 KCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKV  147 (246)
Q Consensus        83 ~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~  147 (246)
                                  .++-.|..|.++|+|++|.++-.+...   -..+...|-+-..-+-+.|++.+
T Consensus       793 ------------~~~dai~my~k~~kw~da~kla~e~~~---~e~t~~~yiakaedldehgkf~e  842 (1636)
T KOG3616|consen  793 ------------LFKDAIDMYGKAGKWEDAFKLAEECHG---PEATISLYIAKAEDLDEHGKFAE  842 (1636)
T ss_pred             ------------hhHHHHHHHhccccHHHHHHHHHHhcC---chhHHHHHHHhHHhHHhhcchhh
Confidence                        345667888899999888887665433   23334555555555556666666

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.57  E-value=0.033  Score=51.49  Aligned_cols=211  Identities=13%  Similarity=0.053  Sum_probs=132.1

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCC-------CCHH--HHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc
Q 043380           21 NAVIEASREAQRIDEAYQILESVEKGLE-------PDSL--SYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP   91 (246)
Q Consensus        21 ~~li~~~~~~g~~~~a~~~~~~~~~~~~-------~~~~--t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p   91 (246)
                      ......+...|++++|..+++.......       +...  ....+-..+...|++++|...+++....- .   .+..+
T Consensus       413 ~~~a~~~~~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-~---~~~~~  488 (903)
T PRK04841        413 LLQAWLAQSQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQVAINDGDPEEAERLAELALAEL-P---LTWYY  488 (903)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC-C---CccHH
Confidence            3445556678999999999987642111       1111  11222344567899999999999987630 0   00000


Q ss_pred             -cHHHHHHHHHHHHccCCHHHHHHHHHHHHhC---CCC-CCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCC
Q 043380           92 -DIFTYATLLMGFRHAKDLQSLLEIVFEMKSC---CNL-ILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSN  166 (246)
Q Consensus        92 -~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~---~~~-~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~  166 (246)
                       -....+.+...+...|++++|...+.+....   .|- .+...++..+...+...|+++.    |...+++........
T Consensus       489 ~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~G~~~~----A~~~~~~al~~~~~~  564 (903)
T PRK04841        489 SRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQGFLQA----AYETQEKAFQLIEEQ  564 (903)
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHCCCHHH----HHHHHHHHHHHHHHh
Confidence             1234566666778899999999998887641   111 1112345666778889999999    999988866541110


Q ss_pred             CCCC--c-chhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          167 PGLW--P-KPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       167 ~~~~--p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                       +..  | ....+..+...+...|++++|...+++....... ..+.....++..+...+...|++++|.+.+.....
T Consensus       565 -~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~-~~~~~~~~~~~~la~~~~~~G~~~~A~~~l~~a~~  640 (903)
T PRK04841        565 -HLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSN-YQPQQQLQCLAMLAKISLARGDLDNARRYLNRLEN  640 (903)
T ss_pred             -ccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhc-cCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence             111  1 2334555666778889999999999876532111 11111122566677788899999999999887754

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=97.56  E-value=0.0096  Score=47.08  Aligned_cols=181  Identities=10%  Similarity=0.038  Sum_probs=109.3

Q ss_pred             HHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhC---CCCCCC-
Q 043380           53 SYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSC---CNLILD-  128 (246)
Q Consensus        53 t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~---~~~~p~-  128 (246)
                      .|.-.-+.|-..+++++|.+.|.+.-....+.  .....-...|.....+|.+. ++++|...+++..+.   .|- |+ 
T Consensus        37 ~y~~Aa~~fk~~~~~~~A~~ay~kAa~~~~~~--~~~~~Aa~~~~~Aa~~~k~~-~~~~Ai~~~~~A~~~y~~~G~-~~~  112 (282)
T PF14938_consen   37 LYEKAANCFKLAKDWEKAAEAYEKAADCYEKL--GDKFEAAKAYEEAANCYKKG-DPDEAIECYEKAIEIYREAGR-FSQ  112 (282)
T ss_dssp             HHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHT--T-HHHHHHHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHCT--HHH
T ss_pred             HHHHHHHHHHHHhccchhHHHHHHHHHHHHHc--CCHHHHHHHHHHHHHHHHhh-CHHHHHHHHHHHHHHHHhcCc-HHH
Confidence            35555566677788888888887764431110  01112233566666666555 888888877765441   222 22 


Q ss_pred             -HHHHHHHHHHHHhc-CChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCC-
Q 043380          129 -RSTFTAMVDALLYS-GSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTG-  205 (246)
Q Consensus       129 -~~~~~~li~~~~~~-~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~-  205 (246)
                       ...+..+...|-.. |+++.    |.+.|++...-........--...+..+...+.+.|++++|.++|+++...... 
T Consensus       113 aA~~~~~lA~~ye~~~~d~e~----Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~  188 (282)
T PF14938_consen  113 AAKCLKELAEIYEEQLGDYEK----AIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLEN  188 (282)
T ss_dssp             HHHHHHHHHHHHCCTT--HHH----HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCH
T ss_pred             HHHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcc
Confidence             44677778888888 89999    999999877653211111112356778889999999999999999987643211 


Q ss_pred             -CCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          206 -TISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       206 -~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                       ........ .|-..+-++...|++-.|.+.|++....
T Consensus       189 ~l~~~~~~~-~~l~a~l~~L~~~D~v~A~~~~~~~~~~  225 (282)
T PF14938_consen  189 NLLKYSAKE-YFLKAILCHLAMGDYVAARKALERYCSQ  225 (282)
T ss_dssp             CTTGHHHHH-HHHHHHHHHHHTT-HHHHHHHHHHHGTT
T ss_pred             cccchhHHH-HHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence             12222221 2333455777789999999999987654

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=97.55  E-value=0.051  Score=48.40  Aligned_cols=210  Identities=13%  Similarity=0.079  Sum_probs=137.5

Q ss_pred             cCHHHHHHHHHHH--HhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           15 LNTIVMNAVIEAS--REAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        15 ~~~~~~~~li~~~--~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      |+. .|..++.++  .|.|+.++|..+++....--..|..|..++-.+|...+..++|..+|++..+.         -|+
T Consensus        40 Pn~-~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~~---------~P~  109 (932)
T KOG2053|consen   40 PNA-LYAKVLKALSLFRLGKGDEALKLLEALYGLKGTDDLTLQFLQNVYRDLGKLDEAVHLYERANQK---------YPS  109 (932)
T ss_pred             CCc-HHHHHHHHHHHHHhcCchhHHHHHhhhccCCCCchHHHHHHHHHHHHHhhhhHHHHHHHHHHhh---------CCc
Confidence            444 344555544  57899999999998876322448899999999999999999999999999976         688


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCC-hhh-----hhhHHHHHHHHHHHhhcCC
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGS-IKV-----VGLYALCIFGEIVKRVCSN  166 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~-~~~-----~~~~a~~~~~~m~~~~~~~  166 (246)
                      ..-...+..+|+|.+++.+-.++=-++.+  .++-....|.+++..+...-. .+.     ....|.+.++.+.+..   
T Consensus       110 eell~~lFmayvR~~~yk~qQkaa~~LyK--~~pk~~yyfWsV~Slilqs~~~~~~~~~~i~l~LA~~m~~~~l~~~---  184 (932)
T KOG2053|consen  110 EELLYHLFMAYVREKSYKKQQKAALQLYK--NFPKRAYYFWSVISLILQSIFSENELLDPILLALAEKMVQKLLEKK---  184 (932)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--hCCcccchHHHHHHHHHHhccCCcccccchhHHHHHHHHHHHhccC---
Confidence            88888899999999988765554444444  133346666677766655432 111     1223667777776651   


Q ss_pred             CCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          167 PGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       167 ~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                       |-.-+..=...-...+-..|++++|..++..=.-......++.    .-+.-++.+...+++++..++-.++..+|.
T Consensus       185 -gk~~s~aE~~Lyl~iL~~~~k~~eal~~l~~~la~~l~~~~~~----l~~~~~dllk~l~~w~~l~~l~~~Ll~k~~  257 (932)
T KOG2053|consen  185 -GKIESEAEIILYLLILELQGKYQEALEFLAITLAEKLTSANLY----LENKKLDLLKLLNRWQELFELSSRLLEKGN  257 (932)
T ss_pred             -CccchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhccccchH----HHHHHHHHHHHhcChHHHHHHHHHHHHhCC
Confidence             2111222222233445668889999999843221111112222    344567777888888888888888877764

>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=0.00036  Score=42.13  Aligned_cols=64  Identities=9%  Similarity=0.067  Sum_probs=51.6

Q ss_pred             HhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHH
Q 043380           62 IKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMV  136 (246)
Q Consensus        62 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li  136 (246)
                      ...|++++|.++|+++.+.        .+-+...+..+..+|.+.|++++|..+++.+..   ..|+...|..++
T Consensus         2 l~~~~~~~A~~~~~~~l~~--------~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~---~~~~~~~~~~l~   65 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQR--------NPDNPEARLLLAQCYLKQGQYDEAEELLERLLK---QDPDNPEYQQLL   65 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHH--------TTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHG---GGTTHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHH--------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---HCcCHHHHHHHH
Confidence            4678999999999999986        233677888899999999999999999999988   557766665554

...

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=97.50  E-value=0.046  Score=46.16  Aligned_cols=147  Identities=13%  Similarity=0.138  Sum_probs=115.8

Q ss_pred             HHHHHHHHHHHH--hCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc-cHHHHHHHHHHHHccCCH
Q 043380           33 IDEAYQILESVE--KGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP-DIFTYATLLMGFRHAKDL  109 (246)
Q Consensus        33 ~~~a~~~~~~~~--~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p-~~~~~~~ll~~~~~~~~~  109 (246)
                      .+....+++.+.  ..+.|+ .+|...|+...+..-+..|..+|.+..+.       +..+ .+..++++|.-|| .+|.
T Consensus       347 ~~~~~~~~~~ll~~~~~~~t-Lv~~~~mn~irR~eGlkaaR~iF~kaR~~-------~r~~hhVfVa~A~mEy~c-skD~  417 (656)
T KOG1914|consen  347 EKKVHEIYNKLLKIEDIDLT-LVYCQYMNFIRRAEGLKAARKIFKKARED-------KRTRHHVFVAAALMEYYC-SKDK  417 (656)
T ss_pred             hhhhHHHHHHHHhhhccCCc-eehhHHHHHHHHhhhHHHHHHHHHHHhhc-------cCCcchhhHHHHHHHHHh-cCCh
Confidence            445556666554  233444 56888889888988899999999999987       5555 7889999999887 5778


Q ss_pred             HHHHHHHHHHHhCCCCCCCHHHH-HHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch--hhHHHHHHHHHhc
Q 043380          110 QSLLEIVFEMKSCCNLILDRSTF-TAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP--HLYVSMMHELAAR  186 (246)
Q Consensus       110 ~~a~~~~~~m~~~~~~~p~~~~~-~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~--~~~~~li~~~~~~  186 (246)
                      +-|..+|+.=.+..   +|...| ...++-+...++-..    +..+|+....+     ++.||.  ..|..+|.--..-
T Consensus       418 ~~AfrIFeLGLkkf---~d~p~yv~~YldfL~~lNdd~N----~R~LFEr~l~s-----~l~~~ks~~Iw~r~l~yES~v  485 (656)
T KOG1914|consen  418 ETAFRIFELGLKKF---GDSPEYVLKYLDFLSHLNDDNN----ARALFERVLTS-----VLSADKSKEIWDRMLEYESNV  485 (656)
T ss_pred             hHHHHHHHHHHHhc---CCChHHHHHHHHHHHHhCcchh----HHHHHHHHHhc-----cCChhhhHHHHHHHHHHHHhc
Confidence            99999999755523   454444 577888888999999    99999999987     677665  7899999999999


Q ss_pred             CChhHHhhHHHhhC
Q 043380          187 VDYDIVKSPYRRMW  200 (246)
Q Consensus       187 g~~~~a~~~~~~~~  200 (246)
                      |+...+.++-+++.
T Consensus       486 GdL~si~~lekR~~  499 (656)
T KOG1914|consen  486 GDLNSILKLEKRRF  499 (656)
T ss_pred             ccHHHHHHHHHHHH
Confidence            99999888888765

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.49  E-value=0.0007  Score=40.48  Aligned_cols=58  Identities=16%  Similarity=0.151  Sum_probs=50.6

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhc
Q 043380           23 VIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDN   80 (246)
Q Consensus        23 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~   80 (246)
                      +...+.+.|++++|.+.|+++.+..+-+...+..+-.++...|++++|..+|+++.+.
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~   60 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQALKQDPDNPEAWYLLGRILYQQGRYDEALAYYERALEL   60 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHHHCCSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            4567889999999999999998655668888999999999999999999999999875

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=97.48  E-value=0.0029  Score=49.32  Aligned_cols=106  Identities=11%  Similarity=0.071  Sum_probs=78.4

Q ss_pred             HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCC
Q 043380          129 RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTIS  208 (246)
Q Consensus       129 ~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  208 (246)
                      ...|..-+..+.+.|++++    |...|+.+.+.+   |+-.-...++..+..+|...|++++|...|..+....+.+..
T Consensus       143 ~~~Y~~A~~l~~~~~~y~~----Ai~af~~fl~~y---P~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~  215 (263)
T PRK10803        143 NTDYNAAIALVQDKSRQDD----AIVAFQNFVKKY---PDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPK  215 (263)
T ss_pred             HHHHHHHHHHHHhcCCHHH----HHHHHHHHHHHC---cCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcc
Confidence            3456666655577899999    999999999872   111111257788999999999999999999999854433211


Q ss_pred             chhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          209 PEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       209 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                       ...  ++-.+...+...|+.++|.++|+.+.+.-+
T Consensus       216 -~~d--Al~klg~~~~~~g~~~~A~~~~~~vi~~yP  248 (263)
T PRK10803        216 -AAD--AMFKVGVIMQDKGDTAKAKAVYQQVIKKYP  248 (263)
T ss_pred             -hhH--HHHHHHHHHHHcCCHHHHHHHHHHHHHHCc
Confidence             111  566677788899999999999999987654

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.45  E-value=0.0041  Score=44.03  Aligned_cols=95  Identities=9%  Similarity=-0.006  Sum_probs=77.1

Q ss_pred             HHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc-cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-H
Q 043380           52 LSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP-DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-R  129 (246)
Q Consensus        52 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~  129 (246)
                      ...-.+-..+...|++++|.++|+-+...         .| +..-|-.|-.++-..|++++|...|.....   +.|| +
T Consensus        36 ~~lY~~A~~ly~~G~l~~A~~~f~~L~~~---------Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~---L~~ddp  103 (157)
T PRK15363         36 NTLYRYAMQLMEVKEFAGAARLFQLLTIY---------DAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQ---IKIDAP  103 (157)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHh---------CcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHh---cCCCCc
Confidence            34445555667889999999999998875         45 455777888888899999999999999888   4455 7


Q ss_pred             HHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          130 STFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       130 ~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ..+-.+-.++...|+.+.    |.+.|+.....
T Consensus       104 ~~~~~ag~c~L~lG~~~~----A~~aF~~Ai~~  132 (157)
T PRK15363        104 QAPWAAAECYLACDNVCY----AIKALKAVVRI  132 (157)
T ss_pred             hHHHHHHHHHHHcCCHHH----HHHHHHHHHHH
Confidence            778888999999999999    99999988776

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=97.44  E-value=0.0078  Score=54.00  Aligned_cols=183  Identities=12%  Similarity=0.047  Sum_probs=122.8

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHH
Q 043380           33 IDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSL  112 (246)
Q Consensus        33 ~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a  112 (246)
                      ...|+..|-+..+--..=...|..|-.-|+...+...|.+.|+...+.        -.-|...+......|++..+++.|
T Consensus       474 ~~~al~ali~alrld~~~apaf~~LG~iYrd~~Dm~RA~kCf~KAFeL--------Datdaeaaaa~adtyae~~~we~a  545 (1238)
T KOG1127|consen  474 SALALHALIRALRLDVSLAPAFAFLGQIYRDSDDMKRAKKCFDKAFEL--------DATDAEAAAASADTYAEESTWEEA  545 (1238)
T ss_pred             HHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--------CchhhhhHHHHHHHhhccccHHHH
Confidence            455555443322111223466888888888877888899999888875        133556788888999999999999


Q ss_pred             HHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHH
Q 043380          113 LEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIV  192 (246)
Q Consensus       113 ~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a  192 (246)
                      ..+.-...++.....-..-|.-.--.|...++...    |..-|+.....      -+-|...|..+..+|.+.|++..|
T Consensus       546 ~~I~l~~~qka~a~~~k~nW~~rG~yyLea~n~h~----aV~~fQsALR~------dPkD~n~W~gLGeAY~~sGry~~A  615 (1238)
T KOG1127|consen  546 FEICLRAAQKAPAFACKENWVQRGPYYLEAHNLHG----AVCEFQSALRT------DPKDYNLWLGLGEAYPESGRYSHA  615 (1238)
T ss_pred             HHHHHHHhhhchHHHHHhhhhhccccccCccchhh----HHHHHHHHhcC------CchhHHHHHHHHHHHHhcCceehH
Confidence            98844333311111112223334446777888888    88888877664      234568899999999999999999


Q ss_pred             hhHHHhhCCCCCCCCCchhhhHHHHHHHHH--HHhcCChhHHHHHHHHHHh
Q 043380          193 KSPYRRMWPDSTGTISPEVQEEAGHLLMEA--ALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~~~~li~~--~~~~g~~~~a~~~~~~m~~  241 (246)
                      .++|.+...-     .|..   +|.....+  -+..|.+.+|...+..+..
T Consensus       616 lKvF~kAs~L-----rP~s---~y~~fk~A~~ecd~GkYkeald~l~~ii~  658 (1238)
T KOG1127|consen  616 LKVFTKASLL-----RPLS---KYGRFKEAVMECDNGKYKEALDALGLIIY  658 (1238)
T ss_pred             HHhhhhhHhc-----CcHh---HHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            9999887643     3332   45554444  3457888888888877654

>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=97.43  E-value=0.0069  Score=42.70  Aligned_cols=75  Identities=20%  Similarity=0.282  Sum_probs=55.3

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL-DRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP  173 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~  173 (246)
                      +...++..+...|++++|..+...+..   ..| |...|..+|.+|...|+...    |.++|+.+...-....|+.|+.
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~---~dP~~E~~~~~lm~~~~~~g~~~~----A~~~Y~~~~~~l~~elg~~Ps~  136 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALA---LDPYDEEAYRLLMRALAAQGRRAE----ALRVYERYRRRLREELGIEPSP  136 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHH---HSTT-HHHHHHHHHHHHHTT-HHH----HHHHHHHHHHHHHHHHS----H
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHCcCHHH----HHHHHHHHHHHHHHHhCcCcCH
Confidence            566778888899999999999999988   445 47889999999999999999    9999998866533334788887


Q ss_pred             hhH
Q 043380          174 HLY  176 (246)
Q Consensus       174 ~~~  176 (246)
                      .+-
T Consensus       137 ~~~  139 (146)
T PF03704_consen  137 ETR  139 (146)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            653

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

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

Probab=97.39  E-value=0.073  Score=45.95  Aligned_cols=115  Identities=11%  Similarity=0.082  Sum_probs=69.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCC--------------
Q 043380           20 MNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCS--------------   85 (246)
Q Consensus        20 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~--------------   85 (246)
                      |...+......+-++.+..++++..   +.++..-+--|..+++.+++++|.+.+........-.+              
T Consensus       141 W~lyl~Fv~~~~lPets~rvyrRYL---k~~P~~~eeyie~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elc  217 (835)
T KOG2047|consen  141 WDLYLKFVESHGLPETSIRVYRRYL---KVAPEAREEYIEYLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELC  217 (835)
T ss_pred             hHHHHHHHHhCCChHHHHHHHHHHH---hcCHHHHHHHHHHHHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHH
Confidence            4444444444555556666665543   23333466677778888888888888877765421000              


Q ss_pred             ---------------------CCCCCccH--HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHH
Q 043380           86 ---------------------SGGFHPDI--FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALL  140 (246)
Q Consensus        86 ---------------------~~~~~p~~--~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~  140 (246)
                                           ..+.-+|.  ..|++|..-|.+.|.+++|.++|++-.. .  ..+..-|+.+.++|+
T Consensus       218 dlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw~SLAdYYIr~g~~ekarDvyeeai~-~--v~tvrDFt~ifd~Ya  292 (835)
T KOG2047|consen  218 DLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLWCSLADYYIRSGLFEKARDVYEEAIQ-T--VMTVRDFTQIFDAYA  292 (835)
T ss_pred             HHHHhCcchhcccCHHHHHHhhcccCcHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHH-h--heehhhHHHHHHHHH
Confidence                                 11222332  3688999999999999999999988776 2  234444444444444

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=97.39  E-value=0.0037  Score=54.40  Aligned_cols=22  Identities=14%  Similarity=0.252  Sum_probs=10.8

Q ss_pred             HHHHHHHHHccCCHHHHHHHHH
Q 043380           96 YATLLMGFRHAKDLQSLLEIVF  117 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~  117 (246)
                      |.-+...|+..|+++-|.++|.
T Consensus       768 y~~iadhyan~~dfe~ae~lf~  789 (1636)
T KOG3616|consen  768 YGEIADHYANKGDFEIAEELFT  789 (1636)
T ss_pred             chHHHHHhccchhHHHHHHHHH
Confidence            4444444555555555555544

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.38  E-value=0.018  Score=49.46  Aligned_cols=138  Identities=14%  Similarity=0.114  Sum_probs=99.4

Q ss_pred             CCCCCHHHHHHHHHHHHhcCC-----cchHHHHHHHHHhccCCCCCCCCCccH-HHHHHHHHHHHcc--------CCHHH
Q 043380           46 GLEPDSLSYNILISACIKTKK-----LDVTMPFNEQLKDNGQKCSSGGFHPDI-FTYATLLMGFRHA--------KDLQS  111 (246)
Q Consensus        46 ~~~~~~~t~~~li~~~~~~~~-----~~~a~~~~~~m~~~~~~~~~~~~~p~~-~~~~~ll~~~~~~--------~~~~~  111 (246)
                      ..+.|...|...+++.....+     .+.|..+|++..+.         .|+- ..|..+..++...        .+...
T Consensus       332 ~~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~l---------dP~~a~a~A~la~~~~~~~~~~~~~~~~l~~  402 (517)
T PRK10153        332 GLPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKS---------EPDFTYAQAEKALADIVRHSQQPLDEKQLAA  402 (517)
T ss_pred             cCCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHh---------CCCcHHHHHHHHHHHHHHHhcCCccHHHHHH
Confidence            446788999999998765433     66899999999986         6764 4555444433221        12334


Q ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhH
Q 043380          112 LLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDI  191 (246)
Q Consensus       112 a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~  191 (246)
                      +.+.............+...|.++...+...|++++    |...+++....       .|+...|..+...+...|+.++
T Consensus       403 a~~~~~~a~al~~~~~~~~~~~ala~~~~~~g~~~~----A~~~l~rAl~L-------~ps~~a~~~lG~~~~~~G~~~e  471 (517)
T PRK10153        403 LSTELDNIVALPELNVLPRIYEILAVQALVKGKTDE----AYQAINKAIDL-------EMSWLNYVLLGKVYELKGDNRL  471 (517)
T ss_pred             HHHHHHHhhhcccCcCChHHHHHHHHHHHhcCCHHH----HHHHHHHHHHc-------CCCHHHHHHHHHHHHHcCCHHH
Confidence            444444433311233446778888777778899999    99999999886       5788899999999999999999


Q ss_pred             HhhHHHhhCCCC
Q 043380          192 VKSPYRRMWPDS  203 (246)
Q Consensus       192 a~~~~~~~~~~~  203 (246)
                      |...+++....+
T Consensus       472 A~~~~~~A~~L~  483 (517)
T PRK10153        472 AADAYSTAFNLR  483 (517)
T ss_pred             HHHHHHHHHhcC
Confidence            999999876544

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=97.32  E-value=0.0051  Score=47.94  Aligned_cols=101  Identities=11%  Similarity=0.031  Sum_probs=80.1

Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCH----HHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCC
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDR----STFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPG  168 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~----~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~  168 (246)
                      ...|...+..+.+.|++++|...|+.+..   ..|+.    ..+..+...|...|++++    |...|+.+.+.+   |+
T Consensus       143 ~~~Y~~A~~l~~~~~~y~~Ai~af~~fl~---~yP~s~~a~~A~y~LG~~y~~~g~~~~----A~~~f~~vv~~y---P~  212 (263)
T PRK10803        143 NTDYNAAIALVQDKSRQDDAIVAFQNFVK---KYPDSTYQPNANYWLGQLNYNKGKKDD----AAYYFASVVKNY---PK  212 (263)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHH---HCcCCcchHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHHC---CC
Confidence            34677777776778999999999999998   44653    467789999999999999    999999999862   12


Q ss_pred             CCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCC
Q 043380          169 LWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDS  203 (246)
Q Consensus       169 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  203 (246)
                      -......+..+...+...|+.++|..+++.+....
T Consensus       213 s~~~~dAl~klg~~~~~~g~~~~A~~~~~~vi~~y  247 (263)
T PRK10803        213 SPKAADAMFKVGVIMQDKGDTAKAKAVYQQVIKKY  247 (263)
T ss_pred             CcchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence            22234566667778889999999999999987654

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.31  E-value=0.021  Score=40.46  Aligned_cols=98  Identities=6%  Similarity=-0.072  Sum_probs=79.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHH
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYAT   98 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~   98 (246)
                      ..-.+-.-+...|++++|..+|+.+-.--+-+..-|-.|--++-..|++.+|...|......       . +-|...+-.
T Consensus        37 ~lY~~A~~ly~~G~l~~A~~~f~~L~~~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L-------~-~ddp~~~~~  108 (157)
T PRK15363         37 TLYRYAMQLMEVKEFAGAARLFQLLTIYDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQI-------K-IDAPQAPWA  108 (157)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc-------C-CCCchHHHH
Confidence            33355566778999999999999986423456666777888888899999999999999986       2 346788999


Q ss_pred             HHHHHHccCCHHHHHHHHHHHHhCCC
Q 043380           99 LLMGFRHAKDLQSLLEIVFEMKSCCN  124 (246)
Q Consensus        99 ll~~~~~~~~~~~a~~~~~~m~~~~~  124 (246)
                      +-.++...|+.+.|.+.|+......+
T Consensus       109 ag~c~L~lG~~~~A~~aF~~Ai~~~~  134 (157)
T PRK15363        109 AAECYLACDNVCYAIKALKAVVRICG  134 (157)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHhc
Confidence            99999999999999999998877333

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

Probab=97.28  E-value=0.0057  Score=53.90  Aligned_cols=166  Identities=17%  Similarity=0.125  Sum_probs=99.2

Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccC
Q 043380           28 REAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAK  107 (246)
Q Consensus        28 ~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~  107 (246)
                      ...|.+++|+.+|.+-++        |..|=..|-..|++++|.++-+.- ++         ..=..||..-..-+-..+
T Consensus       811 ieLgMlEeA~~lYr~ckR--------~DLlNKlyQs~g~w~eA~eiAE~~-DR---------iHLr~Tyy~yA~~Lear~  872 (1416)
T KOG3617|consen  811 IELGMLEEALILYRQCKR--------YDLLNKLYQSQGMWSEAFEIAETK-DR---------IHLRNTYYNYAKYLEARR  872 (1416)
T ss_pred             HHHhhHHHHHHHHHHHHH--------HHHHHHHHHhcccHHHHHHHHhhc-cc---------eehhhhHHHHHHHHHhhc
Confidence            455677777777777653        334445566677777777654432 21         122346666666666777


Q ss_pred             CHHHHHHHHHHHHhCCC-------------------CCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCC
Q 043380          108 DLQSLLEIVFEMKSCCN-------------------LILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPG  168 (246)
Q Consensus       108 ~~~~a~~~~~~m~~~~~-------------------~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~  168 (246)
                      |.+.|++.|+.... ..                   -..|...|.-...-+-..|+.+.    |+.+|...+.       
T Consensus       873 Di~~AleyyEK~~~-hafev~rmL~e~p~~~e~Yv~~~~d~~L~~WWgqYlES~Gemda----Al~~Y~~A~D-------  940 (1416)
T KOG3617|consen  873 DIEAALEYYEKAGV-HAFEVFRMLKEYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDA----ALSFYSSAKD-------  940 (1416)
T ss_pred             cHHHHHHHHHhcCC-hHHHHHHHHHhChHHHHHHHHhccchHHHHHHHHHHhcccchHH----HHHHHHHhhh-------
Confidence            88888777764322 10                   01223333333333344555555    5555555443       


Q ss_pred             CCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          169 LWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       169 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                             |-++++..|-.|+.++|-.+.++-...     .      +...|.+.|-..|++.+|...|-+...
T Consensus       941 -------~fs~VrI~C~qGk~~kAa~iA~esgd~-----A------AcYhlaR~YEn~g~v~~Av~FfTrAqa  995 (1416)
T KOG3617|consen  941 -------YFSMVRIKCIQGKTDKAARIAEESGDK-----A------ACYHLARMYENDGDVVKAVKFFTRAQA  995 (1416)
T ss_pred             -------hhhheeeEeeccCchHHHHHHHhcccH-----H------HHHHHHHHhhhhHHHHHHHHHHHHHHH
Confidence                   456777778888888888887764321     1      455678888888888888888876543

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

Probab=97.24  E-value=0.11  Score=44.86  Aligned_cols=169  Identities=9%  Similarity=-0.022  Sum_probs=113.0

Q ss_pred             HHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHH
Q 043380           53 SYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTF  132 (246)
Q Consensus        53 t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~  132 (246)
                      .|-..+....+.+++......|+.....      .-+.--...|...+.-....+-++.+..+|++..+   +.|.  .-
T Consensus       104 Iwl~Ylq~l~~Q~~iT~tR~tfdrALra------LpvtqH~rIW~lyl~Fv~~~~lPets~rvyrRYLk---~~P~--~~  172 (835)
T KOG2047|consen  104 IWLDYLQFLIKQGLITRTRRTFDRALRA------LPVTQHDRIWDLYLKFVESHGLPETSIRVYRRYLK---VAPE--AR  172 (835)
T ss_pred             HHHHHHHHHHhcchHHHHHHHHHHHHHh------CchHhhccchHHHHHHHHhCCChHHHHHHHHHHHh---cCHH--HH
Confidence            4555555556677777777777776654      01222334677788888888889999999999888   4444  47


Q ss_pred             HHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCC-CCCcchhhHHHHHHHHHhcCChh---HHhhHHHhhCCCCCCCCC
Q 043380          133 TAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNP-GLWPKPHLYVSMMHELAARVDYD---IVKSPYRRMWPDSTGTIS  208 (246)
Q Consensus       133 ~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~p~~~~~~~li~~~~~~g~~~---~a~~~~~~~~~~~~~~~~  208 (246)
                      +-.|.-+++.+++++    |-+.+.....++.... ..+.+...|.-+-...++..+.-   ....+++.+...    .+
T Consensus       173 eeyie~L~~~d~~~e----aa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~r----ft  244 (835)
T KOG2047|consen  173 EEYIEYLAKSDRLDE----AAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRR----FT  244 (835)
T ss_pred             HHHHHHHHhccchHH----HHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhccc----Cc
Confidence            788899999999999    9988888776533221 22334456666666666554433   344445544322    22


Q ss_pred             chhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          209 PEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       209 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      ... ...|.+|.+-|++.|.+++|..+|++-..
T Consensus       245 Dq~-g~Lw~SLAdYYIr~g~~ekarDvyeeai~  276 (835)
T KOG2047|consen  245 DQL-GFLWCSLADYYIRSGLFEKARDVYEEAIQ  276 (835)
T ss_pred             HHH-HHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence            222 33799999999999999999999887554

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.21  E-value=0.031  Score=37.96  Aligned_cols=105  Identities=15%  Similarity=0.121  Sum_probs=72.0

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHH-hCCCCC--HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc----HHH
Q 043380           23 VIEASREAQRIDEAYQILESVE-KGLEPD--SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD----IFT   95 (246)
Q Consensus        23 li~~~~~~g~~~~a~~~~~~~~-~~~~~~--~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~----~~~   95 (246)
                      +-.++-..|+.++|+.+|++.. .|....  ...+-.+-+.+...|++++|..++++....         .|+    ...
T Consensus         7 ~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~---------~p~~~~~~~l   77 (120)
T PF12688_consen    7 LAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEE---------FPDDELNAAL   77 (120)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH---------CCCccccHHH
Confidence            4456677899999999998875 454433  334556777788899999999999988875         243    222


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHh
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLY  141 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~  141 (246)
                      ...+-.++...|+.++|...+-....     ++...|.--|..|+.
T Consensus        78 ~~f~Al~L~~~gr~~eAl~~~l~~la-----~~~~~y~ra~~~ya~  118 (120)
T PF12688_consen   78 RVFLALALYNLGRPKEALEWLLEALA-----ETLPRYRRAIRFYAD  118 (120)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHH-----HHHHHHHHHHHHHHh
Confidence            22333466788999999888876655     455567666666653

>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=97.19  E-value=0.0023  Score=38.67  Aligned_cols=65  Identities=14%  Similarity=-0.005  Sum_probs=56.4

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcC-CcchHHHHHHHHHhc
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTK-KLDVTMPFNEQLKDN   80 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~-~~~~a~~~~~~m~~~   80 (246)
                      ++.+|..+-..+.+.|++++|+..|++..+-.+.+...|..+-.+|...| ++++|.+.+++.++.
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~l   67 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELDPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALKL   67 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHHc
Confidence            46789999999999999999999998875433567888999999999999 799999999998764

...

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=97.19  E-value=0.057  Score=40.44  Aligned_cols=181  Identities=16%  Similarity=0.119  Sum_probs=96.0

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCC---CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH--HHH
Q 043380           22 AVIEASREAQRIDEAYQILESVEKGLEP---DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI--FTY   96 (246)
Q Consensus        22 ~li~~~~~~g~~~~a~~~~~~~~~~~~~---~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~--~~~   96 (246)
                      .....+...|++++|.+.|+.+....+.   -....-.+..++.+.|++++|...+++++..         -|+.  .-+
T Consensus        10 ~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~---------yP~~~~~~~   80 (203)
T PF13525_consen   10 QKALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKL---------YPNSPKADY   80 (203)
T ss_dssp             HHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH----------TT-TTHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH---------CCCCcchhh
Confidence            3445567788888888888887632222   2234456677788888888888888888875         2332  223


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHhCCCCCC---CHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch
Q 043380           97 ATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL---DRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP  173 (246)
Q Consensus        97 ~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p---~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~  173 (246)
                      ...+.+.+.........     ... .....   -...+..++.-|=.+.-..+    |...+..+...        . .
T Consensus        81 A~Y~~g~~~~~~~~~~~-----~~~-~D~~~~~~A~~~~~~li~~yP~S~y~~~----A~~~l~~l~~~--------l-a  141 (203)
T PF13525_consen   81 ALYMLGLSYYKQIPGIL-----RSD-RDQTSTRKAIEEFEELIKRYPNSEYAEE----AKKRLAELRNR--------L-A  141 (203)
T ss_dssp             HHHHHHHHHHHHHHHHH------TT----HHHHHHHHHHHHHHHH-TTSTTHHH----HHHHHHHHHHH--------H-H
T ss_pred             HHHHHHHHHHHhCccch-----hcc-cChHHHHHHHHHHHHHHHHCcCchHHHH----HHHHHHHHHHH--------H-H
Confidence            33333332211111111     000 00000   02235555666655655666    55555554443        0 1


Q ss_pred             hhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHH
Q 043380          174 HLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLAL  233 (246)
Q Consensus       174 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~  233 (246)
                      ..--.+..-|.+.|.+..|..-++.+.+.-++....   ..+...++.+|.+.|..+.|.
T Consensus       142 ~~e~~ia~~Y~~~~~y~aA~~r~~~v~~~yp~t~~~---~~al~~l~~~y~~l~~~~~a~  198 (203)
T PF13525_consen  142 EHELYIARFYYKRGKYKAAIIRFQYVIENYPDTPAA---EEALARLAEAYYKLGLKQAAD  198 (203)
T ss_dssp             HHHHHHHHHHHCTT-HHHHHHHHHHHHHHSTTSHHH---HHHHHHHHHHHHHTT-HHHHH
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCCchH---HHHHHHHHHHHHHhCChHHHH
Confidence            111235667888888888888888887654432222   226677888888888877443

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.18  E-value=0.0049  Score=36.74  Aligned_cols=57  Identities=12%  Similarity=0.102  Sum_probs=49.3

Q ss_pred             HHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           99 LLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        99 ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      +...+...|++++|...|++..+   ..|+ ...+..+..++...|++++    |...|+...+.
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~l~---~~P~~~~a~~~lg~~~~~~g~~~~----A~~~~~~a~~~   60 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQALK---QDPDNPEAWYLLGRILYQQGRYDE----ALAYYERALEL   60 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHHHC---CSTTHHHHHHHHHHHHHHTT-HHH----HHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHH---HCCCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHH
Confidence            44667889999999999999999   3365 7788899999999999999    99999999876

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.17  E-value=0.019  Score=44.88  Aligned_cols=206  Identities=11%  Similarity=0.114  Sum_probs=132.0

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHH--hCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCC--------C
Q 043380           15 LNTIVMNAVIEASREAQRIDEAYQILESVE--KGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQK--------C   84 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~--~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~--------~   84 (246)
                      -+..+-+..-+...+.|+.+.|.+-|+...  +|..|- ..||..+..| +.++++.|++...+++++|++        +
T Consensus       142 n~Ad~~in~gCllykegqyEaAvqkFqaAlqvsGyqpl-lAYniALaHy-~~~qyasALk~iSEIieRG~r~HPElgIGm  219 (459)
T KOG4340|consen  142 NEADGQINLGCLLYKEGQYEAAVQKFQAALQVSGYQPL-LAYNLALAHY-SSRQYASALKHISEIIERGIRQHPELGIGM  219 (459)
T ss_pred             CccchhccchheeeccccHHHHHHHHHHHHhhcCCCch-hHHHHHHHHH-hhhhHHHHHHHHHHHHHhhhhcCCccCccc
Confidence            344555556666678999999999998764  676654 6688776654 557899999999999999854        1


Q ss_pred             CCCCCCc----cH--H-------HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhH
Q 043380           85 SSGGFHP----DI--F-------TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLY  151 (246)
Q Consensus        85 ~~~~~~p----~~--~-------~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~  151 (246)
                      .-.|+..    |.  -       .||.-...+-+.++++.|.+-+..|-....-..|+.|.+.+.-.=. .+++.+    
T Consensus       220 ~tegiDvrsvgNt~~lh~Sal~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n~-~~~p~~----  294 (459)
T KOG4340|consen  220 TTEGIDVRSVGNTLVLHQSALVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMNM-DARPTE----  294 (459)
T ss_pred             eeccCchhcccchHHHHHHHHHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhcc-cCCccc----
Confidence            1112111    11  1       2333333356789999999999888764556678888776544322 344555    


Q ss_pred             HHHHHHHHHHhhcCCCCCCc-chhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHH-hcCCh
Q 043380          152 ALCIFGEIVKRVCSNPGLWP-KPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAAL-NDGQV  229 (246)
Q Consensus       152 a~~~~~~m~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~-~~g~~  229 (246)
                      ..+-+.-+...       .| ...||..++-.||+..-++.|-.++.+=...-    -...+.+.|+ |+++++ ..-.+
T Consensus       295 g~~KLqFLL~~-------nPfP~ETFANlLllyCKNeyf~lAADvLAEn~~lT----yk~L~~Yly~-LLdaLIt~qT~p  362 (459)
T KOG4340|consen  295 GFEKLQFLLQQ-------NPFPPETFANLLLLYCKNEYFDLAADVLAENAHLT----YKFLTPYLYD-LLDALITCQTAP  362 (459)
T ss_pred             cHHHHHHHHhc-------CCCChHHHHHHHHHHhhhHHHhHHHHHHhhCcchh----HHHhhHHHHH-HHHHHHhCCCCH
Confidence            55555555553       33 34899999999999999999988887643221    1112223444 344443 45567


Q ss_pred             hHHHHHHHHH
Q 043380          230 DLALDKLSNT  239 (246)
Q Consensus       230 ~~a~~~~~~m  239 (246)
                      ++|++-+..+
T Consensus       363 Eea~KKL~~L  372 (459)
T KOG4340|consen  363 EEAFKKLDGL  372 (459)
T ss_pred             HHHHHHHHHH
Confidence            7777666554

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

Probab=97.15  E-value=0.014  Score=52.78  Aligned_cols=132  Identities=9%  Similarity=0.040  Sum_probs=96.2

Q ss_pred             CCCcc-HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCH-HHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcC
Q 043380           88 GFHPD-IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDR-STFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCS  165 (246)
Q Consensus        88 ~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~-~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~  165 (246)
                      ++.|+ ...+..|+..|...+++++|.++.+.-.+   ..|+. ..|-.+...+...++...    +..+  .+...   
T Consensus        25 ~~~p~n~~a~~~Li~~~~~~~~~deai~i~~~~l~---~~P~~i~~yy~~G~l~~q~~~~~~----~~lv--~~l~~---   92 (906)
T PRK14720         25 NYSLSKFKELDDLIDAYKSENLTDEAKDICEEHLK---EHKKSISALYISGILSLSRRPLND----SNLL--NLIDS---   92 (906)
T ss_pred             cCCcchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH---hCCcceehHHHHHHHHHhhcchhh----hhhh--hhhhh---
Confidence            55554 56899999999999999999999997777   55663 334444446777777777    5555  33332   


Q ss_pred             CCCCCcch-------------------hhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhc
Q 043380          166 NPGLWPKP-------------------HLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALND  226 (246)
Q Consensus       166 ~~~~~p~~-------------------~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~  226 (246)
                         +..+.                   .++..+..+|-+.|+.+++..+++++.+.++..    +.  +-|.+...|...
T Consensus        93 ---~~~~~~~~~ve~~~~~i~~~~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D~~n----~~--aLNn~AY~~ae~  163 (906)
T PRK14720         93 ---FSQNLKWAIVEHICDKILLYGENKLALRTLAEAYAKLNENKKLKGVWERLVKADRDN----PE--IVKKLATSYEEE  163 (906)
T ss_pred             ---cccccchhHHHHHHHHHHhhhhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcCccc----HH--HHHHHHHHHHHh
Confidence               22222                   677788889999999999999999998765322    11  678888888888


Q ss_pred             CChhHHHHHHHHHHh
Q 043380          227 GQVDLALDKLSNTIT  241 (246)
Q Consensus       227 g~~~~a~~~~~~m~~  241 (246)
                       ++++|++++.....
T Consensus       164 -dL~KA~~m~~KAV~  177 (906)
T PRK14720        164 -DKEKAITYLKKAIY  177 (906)
T ss_pred             -hHHHHHHHHHHHHH
Confidence             99999998877654

>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=97.14  E-value=0.0042  Score=37.47  Aligned_cols=64  Identities=14%  Similarity=0.083  Sum_probs=56.7

Q ss_pred             cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcC-ChhhhhhHHHHHHHHHHHh
Q 043380           92 DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSG-SIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        92 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~-~~~~~~~~a~~~~~~m~~~  162 (246)
                      +..+|..+-..+...|++++|...|++..+   +.|+ ...|..+..+|...| ++++    |.+.|+...+.
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~---~~p~~~~~~~~~g~~~~~~~~~~~~----A~~~~~~al~l   67 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIE---LDPNNAEAYYNLGLAYMKLGKDYEE----AIEDFEKALKL   67 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHH---HSTTHHHHHHHHHHHHHHTTTHHHH----HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---cCCCCHHHHHHHHHHHHHhCccHHH----HHHHHHHHHHc
Confidence            456888999999999999999999999999   5576 778899999999999 7999    99999988764

...

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.14  E-value=0.096  Score=42.11  Aligned_cols=149  Identities=9%  Similarity=0.068  Sum_probs=101.7

Q ss_pred             HHHHHHHHHHHH-hCCCCC-HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHH
Q 043380           33 IDEAYQILESVE-KGLEPD-SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQ  110 (246)
Q Consensus        33 ~~~a~~~~~~~~-~~~~~~-~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~  110 (246)
                      +..|...|+..- ++..-| +.---++.+++.-...+|+++..+.....-        +.-|...--.+..+++..|++.
T Consensus       339 lKiAqqffqlVG~Sa~ecDTIpGRQsmAs~fFL~~qFddVl~YlnSi~sY--------F~NdD~Fn~N~AQAk~atgny~  410 (557)
T KOG3785|consen  339 LKIAQQFFQLVGESALECDTIPGRQSMASYFFLSFQFDDVLTYLNSIESY--------FTNDDDFNLNLAQAKLATGNYV  410 (557)
T ss_pred             HHHHHHHHHHhcccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHH--------hcCcchhhhHHHHHHHHhcChH
Confidence            455666666654 333322 233456666777778899999998888875        3334434445788999999999


Q ss_pred             HHHHHHHHHHhCCCCCCCHHHH-HHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchh-hHHHHHHHHHhcCC
Q 043380          111 SLLEIVFEMKSCCNLILDRSTF-TAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPH-LYVSMMHELAARVD  188 (246)
Q Consensus       111 ~a~~~~~~m~~~~~~~p~~~~~-~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~-~~~~li~~~~~~g~  188 (246)
                      +|+++|-++.. ..++ |..+| +.|.++|.+++.++.    ||+++-.+.        ...+.. ....+...|.+.+.
T Consensus       411 eaEelf~~is~-~~ik-n~~~Y~s~LArCyi~nkkP~l----AW~~~lk~~--------t~~e~fsLLqlIAn~CYk~~e  476 (557)
T KOG3785|consen  411 EAEELFIRISG-PEIK-NKILYKSMLARCYIRNKKPQL----AWDMMLKTN--------TPSERFSLLQLIANDCYKANE  476 (557)
T ss_pred             HHHHHHhhhcC-hhhh-hhHHHHHHHHHHHHhcCCchH----HHHHHHhcC--------CchhHHHHHHHHHHHHHHHHH
Confidence            99999988866 4343 45555 567789999999999    987765542        223333 34455577888888


Q ss_pred             hhHHhhHHHhhCCCC
Q 043380          189 YDIVKSPYRRMWPDS  203 (246)
Q Consensus       189 ~~~a~~~~~~~~~~~  203 (246)
                      +--|-+.|+.++..+
T Consensus       477 FyyaaKAFd~lE~lD  491 (557)
T KOG3785|consen  477 FYYAAKAFDELEILD  491 (557)
T ss_pred             HHHHHHhhhHHHccC
Confidence            887778888776443

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

Probab=97.12  E-value=0.054  Score=49.16  Aligned_cols=81  Identities=16%  Similarity=0.201  Sum_probs=37.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHH
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYAT   98 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~   98 (246)
                      +|+.+..+-.+.|.+.+|.+-|-.     ..|+..|..+++...+.|.+++-.+++.-.++.       .-+|.+.+  .
T Consensus      1106 vWsqlakAQL~~~~v~dAieSyik-----adDps~y~eVi~~a~~~~~~edLv~yL~MaRkk-------~~E~~id~--e 1171 (1666)
T KOG0985|consen 1106 VWSQLAKAQLQGGLVKDAIESYIK-----ADDPSNYLEVIDVASRTGKYEDLVKYLLMARKK-------VREPYIDS--E 1171 (1666)
T ss_pred             HHHHHHHHHHhcCchHHHHHHHHh-----cCCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHh-------hcCccchH--H
Confidence            344444444444444444433321     123344555555555555555555555444443       33343332  4


Q ss_pred             HHHHHHccCCHHHHH
Q 043380           99 LLMGFRHAKDLQSLL  113 (246)
Q Consensus        99 ll~~~~~~~~~~~a~  113 (246)
                      |+-+|++.++..+.+
T Consensus      1172 Li~AyAkt~rl~elE 1186 (1666)
T KOG0985|consen 1172 LIFAYAKTNRLTELE 1186 (1666)
T ss_pred             HHHHHHHhchHHHHH
Confidence            555555555554433

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.11  E-value=0.012  Score=45.75  Aligned_cols=97  Identities=12%  Similarity=0.065  Sum_probs=76.4

Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-HHHHHHHHHHHH
Q 043380           26 ASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-IFTYATLLMGFR  104 (246)
Q Consensus        26 ~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~~~ll~~~~  104 (246)
                      -..+.+++++|+..|.+...-.+-|.+-|..--.+|++.|.++.|.+=-+..+..         .|. ..+|..|-.+|.
T Consensus        90 ~~m~~~~Y~eAv~kY~~AI~l~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~i---------Dp~yskay~RLG~A~~  160 (304)
T KOG0553|consen   90 KLMKNKDYQEAVDKYTEAIELDPTNAVYYCNRAAAYSKLGEYEDAVKDCESALSI---------DPHYSKAYGRLGLAYL  160 (304)
T ss_pred             HHHHhhhHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHhcchHHHHHHHHHHHhc---------ChHHHHHHHHHHHHHH
Confidence            3556788888888888766544667788888888999999998888777776653         554 458999999999


Q ss_pred             ccCCHHHHHHHHHHHHhCCCCCCCHHHHHH
Q 043380          105 HAKDLQSLLEIVFEMKSCCNLILDRSTFTA  134 (246)
Q Consensus       105 ~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~  134 (246)
                      ..|++++|.+.|+...+   +.|+-.+|-.
T Consensus       161 ~~gk~~~A~~aykKaLe---ldP~Ne~~K~  187 (304)
T KOG0553|consen  161 ALGKYEEAIEAYKKALE---LDPDNESYKS  187 (304)
T ss_pred             ccCcHHHHHHHHHhhhc---cCCCcHHHHH
Confidence            99999999999988888   7888666643

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

Probab=97.10  E-value=0.072  Score=42.85  Aligned_cols=106  Identities=10%  Similarity=0.003  Sum_probs=77.3

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchh
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPH  174 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~  174 (246)
                      +.+.-|.-+...|+...|.++-.+.+-     ||..-|..-+.+++..++|++    -.++-..   +        -++.
T Consensus       179 Sl~~Ti~~li~~~~~k~A~kl~k~Fkv-----~dkrfw~lki~aLa~~~~w~e----L~~fa~s---k--------KsPI  238 (319)
T PF04840_consen  179 SLNDTIRKLIEMGQEKQAEKLKKEFKV-----PDKRFWWLKIKALAENKDWDE----LEKFAKS---K--------KSPI  238 (319)
T ss_pred             CHHHHHHHHHHCCCHHHHHHHHHHcCC-----cHHHHHHHHHHHHHhcCCHHH----HHHHHhC---C--------CCCC
Confidence            444556666777888888877666543     788888999999999999998    5544221   1        1346


Q ss_pred             hHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHH
Q 043380          175 LYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDK  235 (246)
Q Consensus       175 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~  235 (246)
                      -|..++.+|.+.|+..+|..+...+.               +..-+..|+++|++.+|.+.
T Consensus       239 GyepFv~~~~~~~~~~eA~~yI~k~~---------------~~~rv~~y~~~~~~~~A~~~  284 (319)
T PF04840_consen  239 GYEPFVEACLKYGNKKEASKYIPKIP---------------DEERVEMYLKCGDYKEAAQE  284 (319)
T ss_pred             ChHHHHHHHHHCCCHHHHHHHHHhCC---------------hHHHHHHHHHCCCHHHHHHH
Confidence            78889999999999999988888742               34467777888888887665

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

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.06  E-value=0.01  Score=46.13  Aligned_cols=100  Identities=12%  Similarity=0.093  Sum_probs=83.7

Q ss_pred             HHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHH
Q 043380           61 CIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDAL  139 (246)
Q Consensus        61 ~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~  139 (246)
                      ..+.+++.+|...|.+.++.        .+-|.+-|..=-.+|++.|.++.|.+=.+....   +.|. ..+|..|-.+|
T Consensus        91 ~m~~~~Y~eAv~kY~~AI~l--------~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~---iDp~yskay~RLG~A~  159 (304)
T KOG0553|consen   91 LMKNKDYQEAVDKYTEAIEL--------DPTNAVYYCNRAAAYSKLGEYEDAVKDCESALS---IDPHYSKAYGRLGLAY  159 (304)
T ss_pred             HHHhhhHHHHHHHHHHHHhc--------CCCcchHHHHHHHHHHHhcchHHHHHHHHHHHh---cChHHHHHHHHHHHHH
Confidence            45678999999999999985        345778888899999999999999998888877   6677 78999999999


Q ss_pred             HhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHH
Q 043380          140 LYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHE  182 (246)
Q Consensus       140 ~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~  182 (246)
                      ...|++++    |.+.|+....       +.|+-.+|-.=+..
T Consensus       160 ~~~gk~~~----A~~aykKaLe-------ldP~Ne~~K~nL~~  191 (304)
T KOG0553|consen  160 LALGKYEE----AIEAYKKALE-------LDPDNESYKSNLKI  191 (304)
T ss_pred             HccCcHHH----HHHHHHhhhc-------cCCCcHHHHHHHHH
Confidence            99999999    9999988776       46776666554443

>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=97.05  E-value=0.0015  Score=40.57  Aligned_cols=69  Identities=20%  Similarity=0.189  Sum_probs=51.6

Q ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-HHHHHHHHHHHHccCCHHHHHHHHHHHHh
Q 043380           51 SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-IFTYATLLMGFRHAKDLQSLLEIVFEMKS  121 (246)
Q Consensus        51 ~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~  121 (246)
                      ..+|+.+-..|...|++++|++.|++..+. .+... .-.|+ ..+++.+-.+|...|++++|++.+++..+
T Consensus         5 a~~~~~la~~~~~~~~~~~A~~~~~~al~~-~~~~~-~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~   74 (78)
T PF13424_consen    5 ANAYNNLARVYRELGRYDEALDYYEKALDI-EEQLG-DDHPDTANTLNNLGECYYRLGDYEEALEYYQKALD   74 (78)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-HHHTT-THHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHHHC-CCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            356788888899999999999999888754 11100 12243 56899999999999999999999987654

...

>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=97.03  E-value=0.0014  Score=40.71  Aligned_cols=68  Identities=10%  Similarity=0.065  Sum_probs=51.5

Q ss_pred             HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc-hhhHHHHHHHHHhcCChhHHhhHHHhhC
Q 043380          129 RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK-PHLYVSMMHELAARVDYDIVKSPYRRMW  200 (246)
Q Consensus       129 ~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~  200 (246)
                      ..+|+.+...|...|++++    |+..|++..+.....+.-.|+ ..++..+-.+|...|++++|.+++++..
T Consensus         5 a~~~~~la~~~~~~~~~~~----A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al   73 (78)
T PF13424_consen    5 ANAYNNLARVYRELGRYDE----ALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKAL   73 (78)
T ss_dssp             HHHHHHHHHHHHHTT-HHH----HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHH----HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            5678999999999999999    999999887652111112233 5778888899999999999999888753

...

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=97.02  E-value=0.14  Score=41.89  Aligned_cols=191  Identities=10%  Similarity=0.024  Sum_probs=112.2

Q ss_pred             hhHHHHhcccCcCHH---HHHHHHHHHHhcCCHHHHHHHHHHHHhC--C--CCCHHHHHHHHHHHHh---cCCcchHHHH
Q 043380            4 ENEIVNREHWKLNTI---VMNAVIEASREAQRIDEAYQILESVEKG--L--EPDSLSYNILISACIK---TKKLDVTMPF   73 (246)
Q Consensus         4 ~~~~~~~~~~~~~~~---~~~~li~~~~~~g~~~~a~~~~~~~~~~--~--~~~~~t~~~li~~~~~---~~~~~~a~~~   73 (246)
                      .+..++++-..|...   +-..++-+|-..++++...++.+.+..-  +  .-....--...-++-+   .|+.++|..+
T Consensus       125 ~L~~i~~rLd~~~~ls~div~~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~i  204 (374)
T PF13281_consen  125 ELRRIRQRLDDPELLSPDIVINLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQI  204 (374)
T ss_pred             HHHHHHHhhCCHhhcChhHHHHHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHH
Confidence            344555555333222   2235566799999999999999999741  1  1111111122233345   7899999999


Q ss_pred             HHHHHhccCCCCCCCCCccHHHHHHHHHHHHc---------cCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCC
Q 043380           74 NEQLKDNGQKCSSGGFHPDIFTYATLLMGFRH---------AKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGS  144 (246)
Q Consensus        74 ~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~---------~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~  144 (246)
                      +..+...       .-.++..||..+-+.|-.         ....++|.+.|.+--+   +.||..+--.+...+...|.
T Consensus       205 l~~~l~~-------~~~~~~d~~gL~GRIyKD~~~~s~~~d~~~ldkAi~~Y~kgFe---~~~~~Y~GIN~AtLL~~~g~  274 (374)
T PF13281_consen  205 LLPVLES-------DENPDPDTLGLLGRIYKDLFLESNFTDRESLDKAIEWYRKGFE---IEPDYYSGINAATLLMLAGH  274 (374)
T ss_pred             HHHHHhc-------cCCCChHHHHHHHHHHHHHHHHcCccchHHHHHHHHHHHHHHc---CCccccchHHHHHHHHHcCC
Confidence            9996554       456777788888887632         2236778888877665   44665443233333333343


Q ss_pred             -hhhhhhHHHHHH---HHHH-HhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCC
Q 043380          145 -IKVVGLYALCIF---GEIV-KRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTI  207 (246)
Q Consensus       145 -~~~~~~~a~~~~---~~m~-~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  207 (246)
                       .+. .....++-   ..+. ++ + ...-..|-..+.+++.++.-.|+.++|.+..+.+....+..+
T Consensus       275 ~~~~-~~el~~i~~~l~~llg~k-g-~~~~~~dYWd~ATl~Ea~vL~~d~~ka~~a~e~~~~l~~~~W  339 (374)
T PF13281_consen  275 DFET-SEELRKIGVKLSSLLGRK-G-SLEKMQDYWDVATLLEASVLAGDYEKAIQAAEKAFKLKPPAW  339 (374)
T ss_pred             cccc-hHHHHHHHHHHHHHHHhh-c-cccccccHHHHHHHHHHHHHcCCHHHHHHHHHHHhhcCCcch
Confidence             222 00022222   2211 12 0 012235557788999999999999999999999886654333

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=96.94  E-value=0.064  Score=48.51  Aligned_cols=161  Identities=8%  Similarity=-0.050  Sum_probs=115.4

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHH
Q 043380           18 IVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYA   97 (246)
Q Consensus        18 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~   97 (246)
                      ..|..|-..|+..-+...|.+-|+....--..+...+....+.|+...+++.|..+.-..-+.        -+.-...+|
T Consensus       493 paf~~LG~iYrd~~Dm~RA~kCf~KAFeLDatdaeaaaa~adtyae~~~we~a~~I~l~~~qk--------a~a~~~k~n  564 (1238)
T KOG1127|consen  493 PAFAFLGQIYRDSDDMKRAKKCFDKAFELDATDAEAAAASADTYAEESTWEEAFEICLRAAQK--------APAFACKEN  564 (1238)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchhhhhHHHHHHHhhccccHHHHHHHHHHHhhh--------chHHHHHhh
Confidence            467777777877778888888888776433567788889999999999999999983333221        122233344


Q ss_pred             HHHH--HHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch-
Q 043380           98 TLLM--GFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP-  173 (246)
Q Consensus        98 ~ll~--~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~-  173 (246)
                      .+-.  .|...++..+|..-|+...+   ..|. ...|..+..+|..+|++..    |.++|.....-       .|+. 
T Consensus       565 W~~rG~yyLea~n~h~aV~~fQsALR---~dPkD~n~W~gLGeAY~~sGry~~----AlKvF~kAs~L-------rP~s~  630 (1238)
T KOG1127|consen  565 WVQRGPYYLEAHNLHGAVCEFQSALR---TDPKDYNLWLGLGEAYPESGRYSH----ALKVFTKASLL-------RPLSK  630 (1238)
T ss_pred             hhhccccccCccchhhHHHHHHHHhc---CCchhHHHHHHHHHHHHhcCceeh----HHHhhhhhHhc-------CcHhH
Confidence            4333  36788899999999998887   4454 6788999999999999999    99999888663       5554 


Q ss_pred             hhHHHHHHHHHhcCChhHHhhHHHhhC
Q 043380          174 HLYVSMMHELAARVDYDIVKSPYRRMW  200 (246)
Q Consensus       174 ~~~~~li~~~~~~g~~~~a~~~~~~~~  200 (246)
                      ..-.-..-..+..|.+.+|...++.+.
T Consensus       631 y~~fk~A~~ecd~GkYkeald~l~~ii  657 (1238)
T KOG1127|consen  631 YGRFKEAVMECDNGKYKEALDALGLII  657 (1238)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            221222233567888888888888765

>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=96.88  E-value=0.01  Score=41.85  Aligned_cols=76  Identities=20%  Similarity=0.166  Sum_probs=54.7

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           18 IVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        18 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      .....++..+...|++++|..+.+.+...-+.|...|..+|.+|...|+..+|.+.|+++...=  ..+.|+.|+..+
T Consensus        63 ~~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l--~~elg~~Ps~~~  138 (146)
T PF03704_consen   63 DALERLAEALLEAGDYEEALRLLQRALALDPYDEEAYRLLMRALAAQGRRAEALRVYERYRRRL--REELGIEPSPET  138 (146)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH--HHHHS----HHH
T ss_pred             HHHHHHHHHHHhccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHH--HHHhCcCcCHHH
Confidence            4566677778889999999999999875557789999999999999999999999999885420  001277888765

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

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

Probab=96.87  E-value=0.14  Score=46.73  Aligned_cols=53  Identities=8%  Similarity=-0.011  Sum_probs=32.2

Q ss_pred             cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhh
Q 043380           92 DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKV  147 (246)
Q Consensus        92 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~  147 (246)
                      |...|.-++....+.|.|++-...+...++ ..-.|..  =+.||.+|++.+++.+
T Consensus      1132 Dps~y~eVi~~a~~~~~~edLv~yL~MaRk-k~~E~~i--d~eLi~AyAkt~rl~e 1184 (1666)
T KOG0985|consen 1132 DPSNYLEVIDVASRTGKYEDLVKYLLMARK-KVREPYI--DSELIFAYAKTNRLTE 1184 (1666)
T ss_pred             CcHHHHHHHHHHHhcCcHHHHHHHHHHHHH-hhcCccc--hHHHHHHHHHhchHHH
Confidence            444666777777777777776666665555 3333433  3456666777666665

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

Probab=96.83  E-value=0.032  Score=49.45  Aligned_cols=185  Identities=16%  Similarity=0.084  Sum_probs=107.4

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHh--C--------CCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCC
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEK--G--------LEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCS   85 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~--~--------~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~   85 (246)
                      +..+|..+.+.|.+.+++|-|.--+..|++  |        ..|+ .+=.-+--.....|.+++|+.+|.+-+..     
T Consensus       756 S~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~-e~eakvAvLAieLgMlEeA~~lYr~ckR~-----  829 (1416)
T KOG3617|consen  756 SDSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQNGE-EDEAKVAVLAIELGMLEEALILYRQCKRY-----  829 (1416)
T ss_pred             hhHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhCCc-chhhHHHHHHHHHhhHHHHHHHHHHHHHH-----
Confidence            444566666666666666666555555431  1        1121 11111112224456666666666665542     


Q ss_pred             CCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHH----
Q 043380           86 SGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVK----  161 (246)
Q Consensus        86 ~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~----  161 (246)
                                 ..|-..|-..|.|++|.++-+.=.+   +.. ..||.....-+-.+++++.    |++.|+.-..    
T Consensus       830 -----------DLlNKlyQs~g~w~eA~eiAE~~DR---iHL-r~Tyy~yA~~Lear~Di~~----AleyyEK~~~hafe  890 (1416)
T KOG3617|consen  830 -----------DLLNKLYQSQGMWSEAFEIAETKDR---IHL-RNTYYNYAKYLEARRDIEA----ALEYYEKAGVHAFE  890 (1416)
T ss_pred             -----------HHHHHHHHhcccHHHHHHHHhhccc---eeh-hhhHHHHHHHHHhhccHHH----HHHHHHhcCChHHH
Confidence                       3455566677888888887655433   222 4566667777777888888    8877764311    


Q ss_pred             ------hhcC----CCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhH
Q 043380          162 ------RVCS----NPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDL  231 (246)
Q Consensus       162 ------~~~~----~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~  231 (246)
                            .+..    .-.-.-|...|..--..+-..|++|.|..++...+              -|-++++..|-+|+.++
T Consensus       891 v~rmL~e~p~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~--------------D~fs~VrI~C~qGk~~k  956 (1416)
T KOG3617|consen  891 VFRMLKEYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAK--------------DYFSMVRIKCIQGKTDK  956 (1416)
T ss_pred             HHHHHHhChHHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhh--------------hhhhheeeEeeccCchH
Confidence                  1000    00112334444444555566788888888888775              25667777788899999


Q ss_pred             HHHHHHHH
Q 043380          232 ALDKLSNT  239 (246)
Q Consensus       232 a~~~~~~m  239 (246)
                      |-++-++-
T Consensus       957 Aa~iA~es  964 (1416)
T KOG3617|consen  957 AARIAEES  964 (1416)
T ss_pred             HHHHHHhc
Confidence            88876653

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=96.78  E-value=0.34  Score=42.78  Aligned_cols=126  Identities=12%  Similarity=-0.022  Sum_probs=98.0

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL-DRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP  173 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~  173 (246)
                      .|......+.+.+..++|...+.+...   +.| ....|.-....+...|.+++    |.+.|.....-       .|+.
T Consensus       652 lwllaa~~~~~~~~~~~a~~CL~Ea~~---~~~l~~~~~~~~G~~~~~~~~~~E----A~~af~~Al~l-------dP~h  717 (799)
T KOG4162|consen  652 LWLLAADLFLLSGNDDEARSCLLEASK---IDPLSASVYYLRGLLLEVKGQLEE----AKEAFLVALAL-------DPDH  717 (799)
T ss_pred             HHHHHHHHHHhcCCchHHHHHHHHHHh---cchhhHHHHHHhhHHHHHHHhhHH----HHHHHHHHHhc-------CCCC
Confidence            355566667788888888888888766   334 36677777788888999999    99999887764       4543


Q ss_pred             -hhHHHHHHHHHhcCChhHHhh--HHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHH
Q 043380          174 -HLYVSMMHELAARVDYDIVKS--PYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTI  240 (246)
Q Consensus       174 -~~~~~li~~~~~~g~~~~a~~--~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  240 (246)
                       ...+++..++...|+...|..  ++..+.+-++  ..+.    +|..+-..+-+.|+.++|-+.|..-.
T Consensus       718 v~s~~Ala~~lle~G~~~la~~~~~L~dalr~dp--~n~e----aW~~LG~v~k~~Gd~~~Aaecf~aa~  781 (799)
T KOG4162|consen  718 VPSMTALAELLLELGSPRLAEKRSLLSDALRLDP--LNHE----AWYYLGEVFKKLGDSKQAAECFQAAL  781 (799)
T ss_pred             cHHHHHHHHHHHHhCCcchHHHHHHHHHHHhhCC--CCHH----HHHHHHHHHHHccchHHHHHHHHHHH
Confidence             677888899999998888887  8888876543  2222    79999999999999999999997654

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.78  E-value=0.014  Score=35.57  Aligned_cols=56  Identities=16%  Similarity=0.115  Sum_probs=49.6

Q ss_pred             HHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          100 LMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       100 l~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      -..|.+.+++++|.++++.+..   +.|+ ...+......+...|++.+    |.+.|+...+.
T Consensus         2 ~~~~~~~~~~~~A~~~~~~~l~---~~p~~~~~~~~~a~~~~~~g~~~~----A~~~l~~~l~~   58 (73)
T PF13371_consen    2 KQIYLQQEDYEEALEVLERALE---LDPDDPELWLQRARCLFQLGRYEE----ALEDLERALEL   58 (73)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHH---hCcccchhhHHHHHHHHHhccHHH----HHHHHHHHHHH
Confidence            3568899999999999999999   5566 6678889999999999999    99999999886

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=96.78  E-value=0.086  Score=35.82  Aligned_cols=104  Identities=16%  Similarity=0.062  Sum_probs=75.7

Q ss_pred             HHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc--HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC----HHH
Q 043380           58 ISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD--IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD----RST  131 (246)
Q Consensus        58 i~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~--~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~----~~~  131 (246)
                      -.++-..|+.++|..+|++....       |+...  ...+-.+-+.+...|++++|..+++.... .  .|+    ...
T Consensus         8 A~a~d~~G~~~~Ai~~Y~~Al~~-------gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~-~--~p~~~~~~~l   77 (120)
T PF12688_consen    8 AWAHDSLGREEEAIPLYRRALAA-------GLSGADRRRALIQLASTLRNLGRYDEALALLEEALE-E--FPDDELNAAL   77 (120)
T ss_pred             HHHHHhcCCHHHHHHHHHHHHHc-------CCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-H--CCCccccHHH
Confidence            34566789999999999999997       55544  34677788889999999999999999887 2  243    222


Q ss_pred             HHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHH
Q 043380          132 FTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELA  184 (246)
Q Consensus       132 ~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~  184 (246)
                      ...+..++...|+.++    |++.+-.....         +...|..-|..|+
T Consensus        78 ~~f~Al~L~~~gr~~e----Al~~~l~~la~---------~~~~y~ra~~~ya  117 (120)
T PF12688_consen   78 RVFLALALYNLGRPKE----ALEWLLEALAE---------TLPRYRRAIRFYA  117 (120)
T ss_pred             HHHHHHHHHHCCCHHH----HHHHHHHHHHH---------HHHHHHHHHHHHH
Confidence            2334457788899999    99888665443         3336666666655

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.75  E-value=0.013  Score=35.70  Aligned_cols=57  Identities=11%  Similarity=0.016  Sum_probs=50.5

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhc
Q 043380           24 IEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDN   80 (246)
Q Consensus        24 i~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~   80 (246)
                      -..|.+.+++++|.++++.+..-.+.+...|...-.++...|++++|.+.|+...+.
T Consensus         2 ~~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~   58 (73)
T PF13371_consen    2 KQIYLQQEDYEEALEVLERALELDPDDPELWLQRARCLFQLGRYEEALEDLERALEL   58 (73)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHhCcccchhhHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            357889999999999999987545667888888999999999999999999999986

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=96.72  E-value=0.25  Score=40.37  Aligned_cols=127  Identities=13%  Similarity=0.005  Sum_probs=94.2

Q ss_pred             HHHHHHHHHHh--cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHH--hcCCcchHHHHHHHHHhccCCCCCCCCCccHH
Q 043380           19 VMNAVIEASRE--AQRIDEAYQILESVEKGLEPDSLSYNILISACI--KTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIF   94 (246)
Q Consensus        19 ~~~~li~~~~~--~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~--~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~   94 (246)
                      -|.+|-.++.-  .|+-..|.++-.+-.+-+..|....-.++.+-.  -.|+++.|.+-|+.|...          |...
T Consensus        84 gyqALStGliAagAGda~lARkmt~~~~~llssDqepLIhlLeAQaal~eG~~~~Ar~kfeAMl~d----------PEtR  153 (531)
T COG3898          84 GYQALSTGLIAAGAGDASLARKMTARASKLLSSDQEPLIHLLEAQAALLEGDYEDARKKFEAMLDD----------PETR  153 (531)
T ss_pred             HHHHHhhhhhhhccCchHHHHHHHHHHHhhhhccchHHHHHHHHHHHHhcCchHHHHHHHHHHhcC----------hHHH
Confidence            45555555544  577788888877665556667777766776654  379999999999999874          4433


Q ss_pred             --HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           95 --TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        95 --~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                        -...|.-.--+.|+.+.|.++-+....   ..|. ...+.+.+...|..|+|+.    |+++++.-++.
T Consensus       154 llGLRgLyleAqr~GareaAr~yAe~Aa~---~Ap~l~WA~~AtLe~r~~~gdWd~----AlkLvd~~~~~  217 (531)
T COG3898         154 LLGLRGLYLEAQRLGAREAARHYAERAAE---KAPQLPWAARATLEARCAAGDWDG----ALKLVDAQRAA  217 (531)
T ss_pred             HHhHHHHHHHHHhcccHHHHHHHHHHHHh---hccCCchHHHHHHHHHHhcCChHH----HHHHHHHHHHH
Confidence              233444445678999999988888766   5677 7888999999999999999    99999987665

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=96.69  E-value=0.37  Score=41.94  Aligned_cols=201  Identities=14%  Similarity=0.066  Sum_probs=117.5

Q ss_pred             hhhhHHHHhcccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHH------
Q 043380            2 FEENEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNE------   75 (246)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~------   75 (246)
                      ..++++++++|..|+...   +...|+-.|.+.+|-++|.+--.  .      |-.+..|...+.+|.|.+++.      
T Consensus       620 i~EL~~~k~rge~P~~iL---lA~~~Ay~gKF~EAAklFk~~G~--e------nRAlEmyTDlRMFD~aQE~~~~g~~~e  688 (1081)
T KOG1538|consen  620 ISELEERKKRGETPNDLL---LADVFAYQGKFHEAAKLFKRSGH--E------NRALEMYTDLRMFDYAQEFLGSGDPKE  688 (1081)
T ss_pred             HHHHHHHHhcCCCchHHH---HHHHHHhhhhHHHHHHHHHHcCc--h------hhHHHHHHHHHHHHHHHHHhhcCChHH
Confidence            457889999999888863   45566777888888888866431  1      122333444444444443332      


Q ss_pred             ------HHHhccCCCCCCCC-CccHHHHHHHHHHHHccCCHHHHHHHHH-----HHHhCCCCCC---CHHHHHHHHHHHH
Q 043380           76 ------QLKDNGQKCSSGGF-HPDIFTYATLLMGFRHAKDLQSLLEIVF-----EMKSCCNLIL---DRSTFTAMVDALL  140 (246)
Q Consensus        76 ------~m~~~~~~~~~~~~-~p~~~~~~~ll~~~~~~~~~~~a~~~~~-----~m~~~~~~~p---~~~~~~~li~~~~  140 (246)
                            +--+-.     .++ +|.     +....+..+|+.++|..+.-     +|.-+-+-+.   +..+.-.+..-+.
T Consensus       689 KKmL~RKRA~WA-----r~~kePk-----aAAEmLiSaGe~~KAi~i~~d~gW~d~lidI~rkld~~ere~l~~~a~ylk  758 (1081)
T KOG1538|consen  689 KKMLIRKRADWA-----RNIKEPK-----AAAEMLISAGEHVKAIEICGDHGWVDMLIDIARKLDKAEREPLLLCATYLK  758 (1081)
T ss_pred             HHHHHHHHHHHh-----hhcCCcH-----HHHHHhhcccchhhhhhhhhcccHHHHHHHHHhhcchhhhhHHHHHHHHHh
Confidence                  111100     011 222     23344556677777776522     1111011112   2445555555566


Q ss_pred             hcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchh----hhHHH
Q 043380          141 YSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEV----QEEAG  216 (246)
Q Consensus       141 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~----~~~~~  216 (246)
                      +...+..    |-++|..|-..              ..++..+...++|++|..+.++..+-.....-|..    ...-|
T Consensus       759 ~l~~~gL----AaeIF~k~gD~--------------ksiVqlHve~~~W~eAFalAe~hPe~~~dVy~pyaqwLAE~DrF  820 (1081)
T KOG1538|consen  759 KLDSPGL----AAEIFLKMGDL--------------KSLVQLHVETQRWDEAFALAEKHPEFKDDVYMPYAQWLAENDRF  820 (1081)
T ss_pred             hccccch----HHHHHHHhccH--------------HHHhhheeecccchHhHhhhhhCccccccccchHHHHhhhhhhH
Confidence            6777888    99999988654              45788888999999999999886543222111110    00023


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          217 HLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       217 ~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      .-.=++|.+.|+-++|.++++++..
T Consensus       821 eEAqkAfhkAGr~~EA~~vLeQLtn  845 (1081)
T KOG1538|consen  821 EEAQKAFHKAGRQREAVQVLEQLTN  845 (1081)
T ss_pred             HHHHHHHHHhcchHHHHHHHHHhhh
Confidence            3455688999999999999988754

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.69  E-value=0.038  Score=42.60  Aligned_cols=105  Identities=25%  Similarity=0.246  Sum_probs=81.3

Q ss_pred             HHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCc
Q 043380          130 STFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISP  209 (246)
Q Consensus       130 ~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  209 (246)
                      ..|+.-+. +.+.|++..    |...|....+.+   |+-.-....+..|..++...|+++.|-.+|..+.+..+.+-. 
T Consensus       143 ~~Y~~A~~-~~ksgdy~~----A~~~F~~fi~~Y---P~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~K-  213 (262)
T COG1729         143 KLYNAALD-LYKSGDYAE----AEQAFQAFIKKY---PNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPK-  213 (262)
T ss_pred             HHHHHHHH-HHHcCCHHH----HHHHHHHHHHcC---CCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCC-
Confidence            35776655 556777999    999999999973   333344567788999999999999999999998865543222 


Q ss_pred             hhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhccC
Q 043380          210 EVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWKG  245 (246)
Q Consensus       210 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~  245 (246)
                      .++  +.-.|..+..+.|+.++|..+|+++.++=+|
T Consensus       214 Apd--allKlg~~~~~l~~~d~A~atl~qv~k~YP~  247 (262)
T COG1729         214 APD--ALLKLGVSLGRLGNTDEACATLQQVIKRYPG  247 (262)
T ss_pred             ChH--HHHHHHHHHHHhcCHHHHHHHHHHHHHHCCC
Confidence            112  5677888899999999999999999987665

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.65  E-value=0.21  Score=38.62  Aligned_cols=133  Identities=11%  Similarity=-0.068  Sum_probs=98.2

Q ss_pred             HHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHH
Q 043380           55 NILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTA  134 (246)
Q Consensus        55 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~  134 (246)
                      +.++..+.-.+.+.-...++.+.++.       ..+.+......|.+.-.+.||.+.|...|++..+ ..-..|..+++.
T Consensus       181 y~~~~~llG~kEy~iS~d~~~~vi~~-------~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek-~~~kL~~~q~~~  252 (366)
T KOG2796|consen  181 YSMANCLLGMKEYVLSVDAYHSVIKY-------YPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEK-VTQKLDGLQGKI  252 (366)
T ss_pred             HHHHHHHhcchhhhhhHHHHHHHHHh-------CCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHH-HHhhhhccchhH
Confidence            45666666678888888999999886       5566788888899999999999999999998877 444455444444


Q ss_pred             HH-----HHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCC
Q 043380          135 MV-----DALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTG  205 (246)
Q Consensus       135 li-----~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  205 (246)
                      ++     ..|...+++-.    |.+.|.+....+      .-|....|.-.-+..-.|+...|.+..+.|.+..++
T Consensus       253 ~V~~n~a~i~lg~nn~a~----a~r~~~~i~~~D------~~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~~P~  318 (366)
T KOG2796|consen  253 MVLMNSAFLHLGQNNFAE----AHRFFTEILRMD------PRNAVANNNKALCLLYLGKLKDALKQLEAMVQQDPR  318 (366)
T ss_pred             HHHhhhhhheecccchHH----HHHHHhhccccC------CCchhhhchHHHHHHHHHHHHHHHHHHHHHhccCCc
Confidence            43     35566778888    898888887762      224444555455555678999999999999877654

>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=96.62  E-value=0.19  Score=42.45  Aligned_cols=157  Identities=13%  Similarity=0.114  Sum_probs=96.4

Q ss_pred             HHHHhcCCHHHHHHHHHH--HHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHH
Q 043380           25 EASREAQRIDEAYQILES--VEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMG  102 (246)
Q Consensus        25 ~~~~~~g~~~~a~~~~~~--~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~  102 (246)
                      ....-.++++++.++.+.  +...++  ..-.+.++.-+-+.|.++.|+.+-..-.                   .=...
T Consensus       269 k~av~~~d~~~v~~~i~~~~ll~~i~--~~~~~~i~~fL~~~G~~e~AL~~~~D~~-------------------~rFeL  327 (443)
T PF04053_consen  269 KTAVLRGDFEEVLRMIAASNLLPNIP--KDQGQSIARFLEKKGYPELALQFVTDPD-------------------HRFEL  327 (443)
T ss_dssp             HHHHHTT-HHH-----HHHHTGGG----HHHHHHHHHHHHHTT-HHHHHHHSS-HH-------------------HHHHH
T ss_pred             HHHHHcCChhhhhhhhhhhhhcccCC--hhHHHHHHHHHHHCCCHHHHHhhcCChH-------------------HHhHH
Confidence            344556788887777752  222222  3447777777788888888876544322                   12334


Q ss_pred             HHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHH
Q 043380          103 FRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHE  182 (246)
Q Consensus       103 ~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~  182 (246)
                      ..+.|+++.|.++-+       -.++...|..|.......|+++-    |++.|++...              |..|+-.
T Consensus       328 Al~lg~L~~A~~~a~-------~~~~~~~W~~Lg~~AL~~g~~~l----Ae~c~~k~~d--------------~~~L~lL  382 (443)
T PF04053_consen  328 ALQLGNLDIALEIAK-------ELDDPEKWKQLGDEALRQGNIEL----AEECYQKAKD--------------FSGLLLL  382 (443)
T ss_dssp             HHHCT-HHHHHHHCC-------CCSTHHHHHHHHHHHHHTTBHHH----HHHHHHHCT---------------HHHHHHH
T ss_pred             HHhcCCHHHHHHHHH-------hcCcHHHHHHHHHHHHHcCCHHH----HHHHHHhhcC--------------ccccHHH
Confidence            456688888877633       23457788888888888888888    8888877654              4667778


Q ss_pred             HHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHH
Q 043380          183 LAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSN  238 (246)
Q Consensus       183 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  238 (246)
                      |...|+.+...++.+.....+           -++..+.++.-.|++++..+++.+
T Consensus       383 y~~~g~~~~L~kl~~~a~~~~-----------~~n~af~~~~~lgd~~~cv~lL~~  427 (443)
T PF04053_consen  383 YSSTGDREKLSKLAKIAEERG-----------DINIAFQAALLLGDVEECVDLLIE  427 (443)
T ss_dssp             HHHCT-HHHHHHHHHHHHHTT------------HHHHHHHHHHHT-HHHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHHcc-----------CHHHHHHHHHHcCCHHHHHHHHHH
Confidence            888888888888777765443           256666666677777777777654

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.

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=96.62  E-value=0.067  Score=44.32  Aligned_cols=132  Identities=9%  Similarity=0.029  Sum_probs=101.9

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCC-CCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCN-LILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK  172 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~-~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~  172 (246)
                      ..|..+|+.-.+..-.+.|..+|-...+ .| +.++...++++|..++. |+...    |.++|+.=...      +.-+
T Consensus       398 ~v~C~~~N~v~r~~Gl~aaR~~F~k~rk-~~~~~h~vyi~~A~~E~~~~-~d~~t----a~~ifelGl~~------f~d~  465 (660)
T COG5107         398 FVFCVHLNYVLRKRGLEAARKLFIKLRK-EGIVGHHVYIYCAFIEYYAT-GDRAT----AYNIFELGLLK------FPDS  465 (660)
T ss_pred             hHHHHHHHHHHHHhhHHHHHHHHHHHhc-cCCCCcceeeeHHHHHHHhc-CCcch----HHHHHHHHHHh------CCCc
Confidence            4688899999999999999999999999 88 67889999999998775 56777    99999986664      3333


Q ss_pred             hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          173 PHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       173 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      ..-.+..+.-+.+.++-..|..+|+.-.+.-    ...-....|..+|+-=..-|+...|..+=++|..
T Consensus       466 ~~y~~kyl~fLi~inde~naraLFetsv~r~----~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e  530 (660)
T COG5107         466 TLYKEKYLLFLIRINDEENARALFETSVERL----EKTQLKRIYDKMIEYESMVGSLNNVYSLEERFRE  530 (660)
T ss_pred             hHHHHHHHHHHHHhCcHHHHHHHHHHhHHHH----HHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHH
Confidence            3444677888889999999999999544321    1111122799999999999999888777666654

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=96.59  E-value=0.47  Score=41.94  Aligned_cols=215  Identities=12%  Similarity=0.012  Sum_probs=137.6

Q ss_pred             HHhcccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCC
Q 043380            8 VNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSG   87 (246)
Q Consensus         8 ~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~   87 (246)
                      +......-|...|..|--+..+.|+++.+-+.|++...+.--....|+.+-..|...|.-..|..+.+.-...       
T Consensus       314 ~r~~~~qnd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~~~~~e~w~~~als~saag~~s~Av~ll~~~~~~-------  386 (799)
T KOG4162|consen  314 LRLKKFQNDAAIFDHLTFALSRCGQFEVLAEQFEQALPFSFGEHERWYQLALSYSAAGSDSKAVNLLRESLKK-------  386 (799)
T ss_pred             HHHhhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhHHHHHHHHHHHHHhccchHHHHHHHhhccc-------
Confidence            3333456788999999999999999999999999976555667788999999999999988899988876654       


Q ss_pred             CCCcc-HHHHHHHHHHHH-ccCCHHHHHHHHHHHHhC-----CCCCCCHHHHHHHHHHHHhc----CChhh-h--hhHHH
Q 043380           88 GFHPD-IFTYATLLMGFR-HAKDLQSLLEIVFEMKSC-----CNLILDRSTFTAMVDALLYS----GSIKV-V--GLYAL  153 (246)
Q Consensus        88 ~~~p~-~~~~~~ll~~~~-~~~~~~~a~~~~~~m~~~-----~~~~p~~~~~~~li~~~~~~----~~~~~-~--~~~a~  153 (246)
                      .-.|+ ...+-..-..|. +-+..++++++-.+....     ..+.  ...|..+.-+|...    ..+.+ .  ...++
T Consensus       387 ~~~ps~~s~~Lmasklc~e~l~~~eegldYA~kai~~~~~~~~~l~--~~~~l~lGi~y~~~A~~a~~~seR~~~h~ksl  464 (799)
T KOG4162|consen  387 SEQPSDISVLLMASKLCIERLKLVEEGLDYAQKAISLLGGQRSHLK--PRGYLFLGIAYGFQARQANLKSERDALHKKSL  464 (799)
T ss_pred             ccCCCcchHHHHHHHHHHhchhhhhhHHHHHHHHHHHhhhhhhhhh--hhHHHHHHHHHHhHhhcCCChHHHHHHHHHHH
Confidence            11243 333333333333 345555555554443331     1122  33344444444332    11111 0  11166


Q ss_pred             HHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHH
Q 043380          154 CIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLAL  233 (246)
Q Consensus       154 ~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~  233 (246)
                      +.+++-.+.+    +-.|+..-|  +---|+-.++++.|.....+...-+.+...     ..|..|...+..++++.+|+
T Consensus       465 qale~av~~d----~~dp~~if~--lalq~A~~R~l~sAl~~~~eaL~l~~~~~~-----~~whLLALvlSa~kr~~~Al  533 (799)
T KOG4162|consen  465 QALEEAVQFD----PTDPLVIFY--LALQYAEQRQLTSALDYAREALALNRGDSA-----KAWHLLALVLSAQKRLKEAL  533 (799)
T ss_pred             HHHHHHHhcC----CCCchHHHH--HHHHHHHHHhHHHHHHHHHHHHHhcCCccH-----HHHHHHHHHHhhhhhhHHHH
Confidence            6666665542    233443333  444467788999999999988765433222     16888999999999999999


Q ss_pred             HHHHHHHhh
Q 043380          234 DKLSNTITR  242 (246)
Q Consensus       234 ~~~~~m~~~  242 (246)
                      .+.+...+.
T Consensus       534 ~vvd~al~E  542 (799)
T KOG4162|consen  534 DVVDAALEE  542 (799)
T ss_pred             HHHHHHHHH
Confidence            999877654

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

Probab=96.59  E-value=0.29  Score=39.43  Aligned_cols=88  Identities=19%  Similarity=0.191  Sum_probs=69.9

Q ss_pred             HHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCc
Q 043380          130 STFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISP  209 (246)
Q Consensus       130 ~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  209 (246)
                      .+.+..|.-+...|+...    |.++-.+.        ++ |+..-|...+.+++..++|++.+++... .      -+|
T Consensus       178 ~Sl~~Ti~~li~~~~~k~----A~kl~k~F--------kv-~dkrfw~lki~aLa~~~~w~eL~~fa~s-k------KsP  237 (319)
T PF04840_consen  178 LSLNDTIRKLIEMGQEKQ----AEKLKKEF--------KV-PDKRFWWLKIKALAENKDWDELEKFAKS-K------KSP  237 (319)
T ss_pred             CCHHHHHHHHHHCCCHHH----HHHHHHHc--------CC-cHHHHHHHHHHHHHhcCCHHHHHHHHhC-C------CCC
Confidence            356666778888899888    88776665        23 8899999999999999999998887654 1      122


Q ss_pred             hhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          210 EVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       210 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      -    .|..++++|.+.|+.++|..++..+..
T Consensus       238 I----GyepFv~~~~~~~~~~eA~~yI~k~~~  265 (319)
T PF04840_consen  238 I----GYEPFVEACLKYGNKKEASKYIPKIPD  265 (319)
T ss_pred             C----ChHHHHHHHHHCCCHHHHHHHHHhCCh
Confidence            1    488899999999999999999987543

Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=96.47  E-value=0.11  Score=43.29  Aligned_cols=64  Identities=6%  Similarity=-0.064  Sum_probs=51.8

Q ss_pred             CCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH----HHHHHHHHHHHccCCHHHHHHHHHHHHh
Q 043380           49 PDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI----FTYATLLMGFRHAKDLQSLLEIVFEMKS  121 (246)
Q Consensus        49 ~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~----~~~~~ll~~~~~~~~~~~a~~~~~~m~~  121 (246)
                      .+...++.+-.+|...|++++|...|++.++.         .|+.    .+|..+-.+|...|+.++|.+.+++..+
T Consensus        73 ~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL---------~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALe  140 (453)
T PLN03098         73 KTAEDAVNLGLSLFSKGRVKDALAQFETALEL---------NPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALR  140 (453)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh---------CCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            35677888888888888888888888888875         5663    3588888888888888888888888777

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=96.47  E-value=0.25  Score=42.14  Aligned_cols=164  Identities=13%  Similarity=0.076  Sum_probs=112.6

Q ss_pred             HHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH-----HHHHHHHHHHHc----cCCHHHHHHHHHHHHhCCCCC
Q 043380           56 ILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI-----FTYATLLMGFRH----AKDLQSLLEIVFEMKSCCNLI  126 (246)
Q Consensus        56 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~-----~~~~~ll~~~~~----~~~~~~a~~~~~~m~~~~~~~  126 (246)
                      .+++..+=.|+-+.+++++.+..+.+      ++.-..     -+|+..+..++.    ..+.+.|.++++.+..   -.
T Consensus       193 kll~~vGF~gdR~~GL~~L~~~~~~~------~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~---~y  263 (468)
T PF10300_consen  193 KLLSFVGFSGDRELGLRLLWEASKSE------NIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLK---RY  263 (468)
T ss_pred             HHHhhcCcCCcHHHHHHHHHHHhccC------CcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHH---hC
Confidence            44455556788899999998876652      444322     256666666554    4578899999999998   56


Q ss_pred             CCHHHHHH-HHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCC-CcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCC
Q 043380          127 LDRSTFTA-MVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGL-WPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDST  204 (246)
Q Consensus       127 p~~~~~~~-li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~-~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  204 (246)
                      |+...|.. --+.+...|++++    |.+.|+.......   .. +.....+--+.-++...++|++|.+.|..+.+.+ 
T Consensus       264 P~s~lfl~~~gR~~~~~g~~~~----Ai~~~~~a~~~q~---~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s-  335 (468)
T PF10300_consen  264 PNSALFLFFEGRLERLKGNLEE----AIESFERAIESQS---EWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKES-  335 (468)
T ss_pred             CCcHHHHHHHHHHHHHhcCHHH----HHHHHHHhccchh---hHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhcc-
Confidence            88777653 3456777899999    9999997554200   11 1223456667777888999999999999998653 


Q ss_pred             CCCCchhhhHHHHHHHHH-HHhcCCh-------hHHHHHHHHHHh
Q 043380          205 GTISPEVQEEAGHLLMEA-ALNDGQV-------DLALDKLSNTIT  241 (246)
Q Consensus       205 ~~~~~~~~~~~~~~li~~-~~~~g~~-------~~a~~~~~~m~~  241 (246)
                       .+++.    .|..+.-+ +...|+.       ++|.++|+++..
T Consensus       336 -~WSka----~Y~Y~~a~c~~~l~~~~~~~~~~~~a~~l~~~vp~  375 (468)
T PF10300_consen  336 -KWSKA----FYAYLAAACLLMLGREEEAKEHKKEAEELFRKVPK  375 (468)
T ss_pred             -ccHHH----HHHHHHHHHHHhhccchhhhhhHHHHHHHHHHHHH
Confidence             24433    35444444 3557877       889999887743

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.

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=96.43  E-value=0.32  Score=38.13  Aligned_cols=102  Identities=8%  Similarity=-0.042  Sum_probs=82.2

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHcc---CCHHHHHHHHHHHHhC
Q 043380           46 GLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHA---KDLQSLLEIVFEMKSC  122 (246)
Q Consensus        46 ~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~---~~~~~a~~~~~~m~~~  122 (246)
                      .-+-|...|-.|-..|...|+.+.|..-|....+.        -.++...+..+-.++...   .+-.++..+|+++.. 
T Consensus       151 ~nP~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL--------~g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~-  221 (287)
T COG4235         151 QNPGDAEGWDLLGRAYMALGRASDALLAYRNALRL--------AGDNPEILLGLAEALYYQAGQQMTAKARALLRQALA-  221 (287)
T ss_pred             hCCCCchhHHHHHHHHHHhcchhHHHHHHHHHHHh--------CCCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHh-
Confidence            34668899999999999999999999999999886        234455555555554333   345789999999998 


Q ss_pred             CCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          123 CNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       123 ~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                        ..|+ ..+...|...+...|++.+    |...|+.|.+.
T Consensus       222 --~D~~~iral~lLA~~afe~g~~~~----A~~~Wq~lL~~  256 (287)
T COG4235         222 --LDPANIRALSLLAFAAFEQGDYAE----AAAAWQMLLDL  256 (287)
T ss_pred             --cCCccHHHHHHHHHHHHHcccHHH----HHHHHHHHHhc
Confidence              5565 6677788889999999999    99999999986

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=96.40  E-value=0.24  Score=36.29  Aligned_cols=135  Identities=13%  Similarity=0.058  Sum_probs=98.5

Q ss_pred             CCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCC
Q 043380           89 FHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPG  168 (246)
Q Consensus        89 ~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~  168 (246)
                      ..|+...--.|-.+....|+..+|...|++... .-+.-|....-.+..+....+++-.    |..+++.+.+..  -.+
T Consensus        85 ~ApTvqnr~rLa~al~elGr~~EA~~hy~qals-G~fA~d~a~lLglA~Aqfa~~~~A~----a~~tLe~l~e~~--pa~  157 (251)
T COG4700          85 IAPTVQNRYRLANALAELGRYHEAVPHYQQALS-GIFAHDAAMLLGLAQAQFAIQEFAA----AQQTLEDLMEYN--PAF  157 (251)
T ss_pred             hchhHHHHHHHHHHHHHhhhhhhhHHHHHHHhc-cccCCCHHHHHHHHHHHHhhccHHH----HHHHHHHHhhcC--Ccc
Confidence            467777777889999999999999999999887 5455668888889999999999999    999999988761  012


Q ss_pred             CCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHH
Q 043380          169 LWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNT  239 (246)
Q Consensus       169 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  239 (246)
                      -.||  +.-.+-+.+...|+...|+.-|+....--+|..       .-...-..+.++|+.++|..-+.++
T Consensus       158 r~pd--~~Ll~aR~laa~g~~a~Aesafe~a~~~ypg~~-------ar~~Y~e~La~qgr~~ea~aq~~~v  219 (251)
T COG4700         158 RSPD--GHLLFARTLAAQGKYADAESAFEVAISYYPGPQ-------ARIYYAEMLAKQGRLREANAQYVAV  219 (251)
T ss_pred             CCCC--chHHHHHHHHhcCCchhHHHHHHHHHHhCCCHH-------HHHHHHHHHHHhcchhHHHHHHHHH
Confidence            2344  445667889999999999999998765432211       2222444566778777665544444

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.30  E-value=0.34  Score=37.05  Aligned_cols=207  Identities=14%  Similarity=0.089  Sum_probs=112.4

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHH------HHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCC
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNI------LISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFH   90 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~------li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~   90 (246)
                      ...|.---.+|-.+.++++|..-+....++...|...|++      .+-..-....+.++..+|++....-++    .=.
T Consensus        31 as~yekAAvafRnAk~feKakdcLlkA~~~yEnnrslfhAAKayEqaamLake~~klsEvvdl~eKAs~lY~E----~Gs  106 (308)
T KOG1585|consen   31 ASLYEKAAVAFRNAKKFEKAKDCLLKASKGYENNRSLFHAAKAYEQAAMLAKELSKLSEVVDLYEKASELYVE----CGS  106 (308)
T ss_pred             HHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH----hCC
Confidence            3456666778888899999988777665555555555543      222223344555666666555432100    012


Q ss_pred             ccHHHHHHHHHH--HHccCCHHHHHHHHHHHHhCC---C-CCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhc
Q 043380           91 PDIFTYATLLMG--FRHAKDLQSLLEIVFEMKSCC---N-LILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVC  164 (246)
Q Consensus        91 p~~~~~~~ll~~--~~~~~~~~~a~~~~~~m~~~~---~-~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~  164 (246)
                      |+... -+|=.+  ...+-++++|+++|++-....   + ...-...|..+-+.+.+...+++    |-..|..-..-.-
T Consensus       107 pdtAA-maleKAak~lenv~Pd~AlqlYqralavve~~dr~~ma~el~gk~sr~lVrl~kf~E----aa~a~lKe~~~~~  181 (308)
T KOG1585|consen  107 PDTAA-MALEKAAKALENVKPDDALQLYQRALAVVEEDDRDQMAFELYGKCSRVLVRLEKFTE----AATAFLKEGVAAD  181 (308)
T ss_pred             cchHH-HHHHHHHHHhhcCCHHHHHHHHHHHHHHHhccchHHHHHHHHHHhhhHhhhhHHhhH----HHHHHHHhhhHHH
Confidence            33211 011111  123455677777776654410   0 01112345666667777777777    5544443222100


Q ss_pred             CCCCCCcch-hhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHH
Q 043380          165 SNPGLWPKP-HLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKL  236 (246)
Q Consensus       165 ~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~  236 (246)
                      .. .--|+. ..|...|-.|....++..|++.++.--+.. ++..+.- ..+...|+.+| ..|+.+++..++
T Consensus       182 ~~-~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~~~qip-~f~~sed-~r~lenLL~ay-d~gD~E~~~kvl  250 (308)
T KOG1585|consen  182 KC-DAYNSQCKAYVAAILVYLYAHDYVQAEKCYRDCSQIP-AFLKSED-SRSLENLLTAY-DEGDIEEIKKVL  250 (308)
T ss_pred             HH-hhcccHHHHHHHHHHHHhhHHHHHHHHHHhcchhcCc-cccChHH-HHHHHHHHHHh-ccCCHHHHHHHH
Confidence            00 112232 457777778888889999999999854333 2232221 22677888888 678888877765

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=96.28  E-value=0.28  Score=35.94  Aligned_cols=154  Identities=13%  Similarity=0.093  Sum_probs=94.0

Q ss_pred             HHHHHhcCCHHHHHHHH-HHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHH
Q 043380           24 IEASREAQRIDEAYQIL-ESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMG  102 (246)
Q Consensus        24 i~~~~~~g~~~~a~~~~-~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~  102 (246)
                      ..+..+.=+++...+-. +.+.  +.|++..--.|-++....|+..+|...|.+...-       -+.-|....-.+-++
T Consensus        63 ~~a~~q~ldP~R~~Rea~~~~~--~ApTvqnr~rLa~al~elGr~~EA~~hy~qalsG-------~fA~d~a~lLglA~A  133 (251)
T COG4700          63 LMALQQKLDPERHLREATEELA--IAPTVQNRYRLANALAELGRYHEAVPHYQQALSG-------IFAHDAAMLLGLAQA  133 (251)
T ss_pred             HHHHHHhcChhHHHHHHHHHHh--hchhHHHHHHHHHHHHHhhhhhhhHHHHHHHhcc-------ccCCCHHHHHHHHHH
Confidence            33334444444443322 2232  3566666667777788888888888888887763       344566677777777


Q ss_pred             HHccCCHHHHHHHHHHHHhCCC---CCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHH
Q 043380          103 FRHAKDLQSLLEIVFEMKSCCN---LILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSM  179 (246)
Q Consensus       103 ~~~~~~~~~a~~~~~~m~~~~~---~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~l  179 (246)
                      ....+++..|...++.+.+ ..   -.||  +.-.+.+.|...|.+..    |+.-|+.....       -|+...-.--
T Consensus       134 qfa~~~~A~a~~tLe~l~e-~~pa~r~pd--~~Ll~aR~laa~g~~a~----Aesafe~a~~~-------ypg~~ar~~Y  199 (251)
T COG4700         134 QFAIQEFAAAQQTLEDLME-YNPAFRSPD--GHLLFARTLAAQGKYAD----AESAFEVAISY-------YPGPQARIYY  199 (251)
T ss_pred             HHhhccHHHHHHHHHHHhh-cCCccCCCC--chHHHHHHHHhcCCchh----HHHHHHHHHHh-------CCCHHHHHHH
Confidence            7788888888888887776 32   1233  34456677788888888    88888887775       2333222222


Q ss_pred             HHHHHhcCChhHHh----hHHHhhC
Q 043380          180 MHELAARVDYDIVK----SPYRRMW  200 (246)
Q Consensus       180 i~~~~~~g~~~~a~----~~~~~~~  200 (246)
                      -..+++.|+.+++.    .+++.+.
T Consensus       200 ~e~La~qgr~~ea~aq~~~v~d~~~  224 (251)
T COG4700         200 AEMLAKQGRLREANAQYVAVVDTAK  224 (251)
T ss_pred             HHHHHHhcchhHHHHHHHHHHHHHH
Confidence            23345666555444    4444444

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=96.22  E-value=0.26  Score=39.24  Aligned_cols=123  Identities=16%  Similarity=0.217  Sum_probs=80.7

Q ss_pred             cchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHc--cCC----HHHHHHHHHHHHhCCCC--CCCHHHHHHHHHH
Q 043380           67 LDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRH--AKD----LQSLLEIVFEMKSCCNL--ILDRSTFTAMVDA  138 (246)
Q Consensus        67 ~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~--~~~----~~~a~~~~~~m~~~~~~--~p~~~~~~~li~~  138 (246)
                      +++...+++.|++.       |+.-+..+|-+.......  ..+    ...|..+|+.|++...+  .++..++..++..
T Consensus        78 ~~~~~~~y~~L~~~-------gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~  150 (297)
T PF13170_consen   78 FKEVLDIYEKLKEA-------GFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM  150 (297)
T ss_pred             HHHHHHHHHHHHHh-------ccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc
Confidence            45677889999998       788888877775444433  333    46789999999994443  2445666666555


Q ss_pred             HHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch--hhHHHHHHHHHhcCC--hhHHhhHHHhhCCCC
Q 043380          139 LLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP--HLYVSMMHELAARVD--YDIVKSPYRRMWPDS  203 (246)
Q Consensus       139 ~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~--~~~~~li~~~~~~g~--~~~a~~~~~~~~~~~  203 (246)
                        ..++++...+.++.+|+.+...     |+..+.  ...+.++........  ..++.++++.+.+.+
T Consensus       151 --~~~~~e~l~~~~E~~Y~~L~~~-----~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~  212 (297)
T PF13170_consen  151 --TSEDVEELAERMEQCYQKLADA-----GFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNG  212 (297)
T ss_pred             --ccccHHHHHHHHHHHHHHHHHh-----CCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcC
Confidence              5566666556689999999987     665443  333444433332222  347888888887665

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=96.15  E-value=0.26  Score=38.63  Aligned_cols=113  Identities=10%  Similarity=-0.046  Sum_probs=85.0

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhc---CCcchHHHHHHHHHhccCCCCCCCC
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKT---KKLDVTMPFNEQLKDNGQKCSSGGF   89 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~---~~~~~a~~~~~~m~~~~~~~~~~~~   89 (246)
                      -+-|...|-.|-..|...|+...|..-|....+--++|...+..+-.++...   ..-.++..+|+++...         
T Consensus       152 nP~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~---------  222 (287)
T COG4235         152 NPGDAEGWDLLGRAYMALGRASDALLAYRNALRLAGDNPEILLGLAEALYYQAGQQMTAKARALLRQALAL---------  222 (287)
T ss_pred             CCCCchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhc---------
Confidence            5668889999999999999999999999887643456666666666555443   3456799999999986         


Q ss_pred             Cc-cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHH
Q 043380           90 HP-DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVD  137 (246)
Q Consensus        90 ~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~  137 (246)
                      .| |+.+-.-|-..+...|++.+|...|+.|.+   ..|....+..+|.
T Consensus       223 D~~~iral~lLA~~afe~g~~~~A~~~Wq~lL~---~lp~~~~rr~~ie  268 (287)
T COG4235         223 DPANIRALSLLAFAAFEQGDYAEAAAAWQMLLD---LLPADDPRRSLIE  268 (287)
T ss_pred             CCccHHHHHHHHHHHHHcccHHHHHHHHHHHHh---cCCCCCchHHHHH
Confidence            45 556666777788999999999999999999   3343333444443

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=96.09  E-value=0.67  Score=38.70  Aligned_cols=147  Identities=12%  Similarity=0.102  Sum_probs=106.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHH-hC-CCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHH
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVE-KG-LEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIF   94 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~-~~-~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~   94 (246)
                      ..+|-..|+.-.+..-++.|..+|-..+ .+ +.+++..++++|..++. |++.-|..+|+-=...         .||..
T Consensus       397 t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~~-~d~~ta~~ifelGl~~---------f~d~~  466 (660)
T COG5107         397 TFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYAT-GDRATAYNIFELGLLK---------FPDST  466 (660)
T ss_pred             hhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhc-CCcchHHHHHHHHHHh---------CCCch
Confidence            4567778888888888999999999887 55 56888999999998775 5678888888765543         35544


Q ss_pred             -HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC--HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc
Q 043380           95 -TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD--RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP  171 (246)
Q Consensus        95 -~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~--~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p  171 (246)
                       --+-.+.-+.+-++-+.|..+|+.... . +..+  ...|-.+|.--..-|+...    +..+=+.|...       -|
T Consensus       467 ~y~~kyl~fLi~inde~naraLFetsv~-r-~~~~q~k~iy~kmi~YEs~~G~lN~----v~sLe~rf~e~-------~p  533 (660)
T COG5107         467 LYKEKYLLFLIRINDEENARALFETSVE-R-LEKTQLKRIYDKMIEYESMVGSLNN----VYSLEERFREL-------VP  533 (660)
T ss_pred             HHHHHHHHHHHHhCcHHHHHHHHHHhHH-H-HHHhhhhHHHHHHHHHHHhhcchHH----HHhHHHHHHHH-------cC
Confidence             345566777888999999999995443 1 3234  6789999999899999988    88777777664       35


Q ss_pred             chhhHHHHHHHHHhc
Q 043380          172 KPHLYVSMMHELAAR  186 (246)
Q Consensus       172 ~~~~~~~li~~~~~~  186 (246)
                      ...+.....+-|+-.
T Consensus       534 Qen~~evF~Sry~ik  548 (660)
T COG5107         534 QENLIEVFTSRYAIK  548 (660)
T ss_pred             cHhHHHHHHHHHhhh
Confidence            555555555444433

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=96.04  E-value=0.46  Score=37.85  Aligned_cols=155  Identities=14%  Similarity=0.187  Sum_probs=94.7

Q ss_pred             HHHHHHHHHHHH-hCCCCCHHHHHHHHHHHHh--cC----CcchHHHHHHHHHhccCCCCCCCC-CccHHHHHHHHHHHH
Q 043380           33 IDEAYQILESVE-KGLEPDSLSYNILISACIK--TK----KLDVTMPFNEQLKDNGQKCSSGGF-HPDIFTYATLLMGFR  104 (246)
Q Consensus        33 ~~~a~~~~~~~~-~~~~~~~~t~~~li~~~~~--~~----~~~~a~~~~~~m~~~~~~~~~~~~-~p~~~~~~~ll~~~~  104 (246)
                      +++...+++.|. .|++.+..+|-+.......  ..    ....|.++|+.|++..     ..+ .++..++..||..  
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H-----~fLTs~~D~~~a~lLA~--  150 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKH-----PFLTSPEDYPFAALLAM--  150 (297)
T ss_pred             HHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhC-----ccccCccchhHHHHHhc--
Confidence            455667778887 6798888777664433333  22    3467999999999872     011 2456677777666  


Q ss_pred             ccCCH----HHHHHHHHHHHhCCCCCCCHH-HHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHH
Q 043380          105 HAKDL----QSLLEIVFEMKSCCNLILDRS-TFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSM  179 (246)
Q Consensus       105 ~~~~~----~~a~~~~~~m~~~~~~~p~~~-~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~l  179 (246)
                      ...+.    +.++.+|+.+.+ .|+..+.. -+-+-+-+++....-+. ..++.++++.+.+.     |+++....|..+
T Consensus       151 ~~~~~e~l~~~~E~~Y~~L~~-~~f~kgn~LQ~LS~iLaL~~~~~~~~-v~r~~~l~~~l~~~-----~~kik~~~yp~l  223 (297)
T PF13170_consen  151 TSEDVEELAERMEQCYQKLAD-AGFKKGNDLQFLSHILALSEGDDQEK-VARVIELYNALKKN-----GVKIKYMHYPTL  223 (297)
T ss_pred             ccccHHHHHHHHHHHHHHHHH-hCCCCCcHHHHHHHHHHhccccchHH-HHHHHHHHHHHHHc-----CCccccccccHH
Confidence            44444    567888999998 88887733 23233333333222222 33399999999998     888777665543


Q ss_pred             HHHHHhcCC-----hhHHhhHHHhhCCC
Q 043380          180 MHELAARVD-----YDIVKSPYRRMWPD  202 (246)
Q Consensus       180 i~~~~~~g~-----~~~a~~~~~~~~~~  202 (246)
                       ..++-.++     .+...++.+.+.+.
T Consensus       224 -GlLall~~~~~~~~~~i~ev~~~L~~~  250 (297)
T PF13170_consen  224 -GLLALLEDPEEKIVEEIKEVIDELKEQ  250 (297)
T ss_pred             -HHHHhcCCchHHHHHHHHHHHHHHhhC
Confidence             33343333     33455555555443

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.04  E-value=0.3  Score=37.84  Aligned_cols=100  Identities=12%  Similarity=-0.001  Sum_probs=81.2

Q ss_pred             HHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHH
Q 043380           53 SYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RST  131 (246)
Q Consensus        53 t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~  131 (246)
                      .|+..+.. .+.|++..|..-|...++..     .+-.-....+-.|..++...|++++|..+|..+.+..+-.|- +..
T Consensus       144 ~Y~~A~~~-~ksgdy~~A~~~F~~fi~~Y-----P~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApda  217 (262)
T COG1729         144 LYNAALDL-YKSGDYAEAEQAFQAFIKKY-----PNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDA  217 (262)
T ss_pred             HHHHHHHH-HHcCCHHHHHHHHHHHHHcC-----CCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHH
Confidence            58887776 45677999999999999862     111123346778999999999999999999999885555555 467


Q ss_pred             HHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          132 FTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       132 ~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      +--|.....+.|+.++    |..+|+++.++
T Consensus       218 llKlg~~~~~l~~~d~----A~atl~qv~k~  244 (262)
T COG1729         218 LLKLGVSLGRLGNTDE----ACATLQQVIKR  244 (262)
T ss_pred             HHHHHHHHHHhcCHHH----HHHHHHHHHHH
Confidence            8889999999999999    99999999998

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=96.03  E-value=0.17  Score=44.27  Aligned_cols=134  Identities=13%  Similarity=0.114  Sum_probs=76.7

Q ss_pred             ccHHHHHHHHHHHHccCCHHHHHHHHHHHHh------C-CCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhh
Q 043380           91 PDIFTYATLLMGFRHAKDLQSLLEIVFEMKS------C-CNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRV  163 (246)
Q Consensus        91 p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~------~-~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~  163 (246)
                      .+...|......|...|+.+.-.+.+-....      . ..++-|......+..++.+.|..+.    |.+.|-+-..  
T Consensus       807 a~~~~We~A~~yY~~~~~~e~~~ecly~le~f~~LE~la~~Lpe~s~llp~~a~mf~svGMC~q----AV~a~Lr~s~--  880 (1189)
T KOG2041|consen  807 AEMMEWEEAAKYYSYCGDTENQIECLYRLELFGELEVLARTLPEDSELLPVMADMFTSVGMCDQ----AVEAYLRRSL--  880 (1189)
T ss_pred             HHHHHHHHHHHHHHhccchHhHHHHHHHHHhhhhHHHHHHhcCcccchHHHHHHHHHhhchHHH----HHHHHHhccC--
Confidence            4445566666666666665544333222211      0 1133456677788889999999998    8876644322  


Q ss_pred             cCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhH-----HHHHHHHHHHhcCChhHHHHHHHH
Q 043380          164 CSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEE-----AGHLLMEAALNDGQVDLALDKLSN  238 (246)
Q Consensus       164 ~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~-----~~~~li~~~~~~g~~~~a~~~~~~  238 (246)
                             |     .+-+..|....+|.+|.++.+.......+.+-......     -..--|..+.+.|+.-.|-+++.+
T Consensus       881 -------p-----kaAv~tCv~LnQW~~avelaq~~~l~qv~tliak~aaqll~~~~~~eaIe~~Rka~~~~daarll~q  948 (1189)
T KOG2041|consen  881 -------P-----KAAVHTCVELNQWGEAVELAQRFQLPQVQTLIAKQAAQLLADANHMEAIEKDRKAGRHLDAARLLSQ  948 (1189)
T ss_pred             -------c-----HHHHHHHHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHhhcchHHHHHHhhhcccchhHHHHHHH
Confidence                   2     34567778888888888888876532211111000000     011134556777777777777777


Q ss_pred             HHhh
Q 043380          239 TITR  242 (246)
Q Consensus       239 m~~~  242 (246)
                      |.++
T Consensus       949 mae~  952 (1189)
T KOG2041|consen  949 MAER  952 (1189)
T ss_pred             HhHH
Confidence            7654

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=96.02  E-value=0.4  Score=35.91  Aligned_cols=152  Identities=9%  Similarity=0.044  Sum_probs=82.5

Q ss_pred             HHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHH
Q 043380           58 ISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVD  137 (246)
Q Consensus        58 i~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~  137 (246)
                      ...+...|++++|.+.|+++....     .+-+--....-.+..++-+.|+++.|...+++..+...-.|. ..+...+.
T Consensus        12 a~~~~~~g~y~~Ai~~f~~l~~~~-----P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~~-~~~A~Y~~   85 (203)
T PF13525_consen   12 ALEALQQGDYEEAIKLFEKLIDRY-----PNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNSPK-ADYALYML   85 (203)
T ss_dssp             HHHHHHCT-HHHHHHHHHHHHHH------TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-TT-HHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHC-----CCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcc-hhhHHHHH
Confidence            344567788999999999998751     111122345667788888999999999999998772322222 22333344


Q ss_pred             HHHhcCChhh---------hhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCC
Q 043380          138 ALLYSGSIKV---------VGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTIS  208 (246)
Q Consensus       138 ~~~~~~~~~~---------~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  208 (246)
                      +.+.......         ....|..                    .+..++.-|-.+....+|...+..+...    +.
T Consensus        86 g~~~~~~~~~~~~~~~D~~~~~~A~~--------------------~~~~li~~yP~S~y~~~A~~~l~~l~~~----la  141 (203)
T PF13525_consen   86 GLSYYKQIPGILRSDRDQTSTRKAIE--------------------EFEELIKRYPNSEYAEEAKKRLAELRNR----LA  141 (203)
T ss_dssp             HHHHHHHHHHHH-TT---HHHHHHHH--------------------HHHHHHHH-TTSTTHHHHHHHHHHHHHH----HH
T ss_pred             HHHHHHhCccchhcccChHHHHHHHH--------------------HHHHHHHHCcCchHHHHHHHHHHHHHHH----HH
Confidence            3333222222         0000333                    3444555555555555665555554321    00


Q ss_pred             chhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          209 PEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       209 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      .     .--.+.+.|.+.|.+..|..-++.+.++=+
T Consensus       142 ~-----~e~~ia~~Y~~~~~y~aA~~r~~~v~~~yp  172 (203)
T PF13525_consen  142 E-----HELYIARFYYKRGKYKAAIIRFQYVIENYP  172 (203)
T ss_dssp             H-----HHHHHHHHHHCTT-HHHHHHHHHHHHHHST
T ss_pred             H-----HHHHHHHHHHHcccHHHHHHHHHHHHHHCC
Confidence            0     122356677888888888888877776543

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.99  E-value=0.53  Score=36.48  Aligned_cols=135  Identities=10%  Similarity=0.005  Sum_probs=98.0

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchh
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPH  174 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~  174 (246)
                      .-++++....-.+.+.-....+++..+ ..-..++...+.|.+.--..|+.+.    |..+|+...+.     .-+.|..
T Consensus       179 Vmy~~~~~llG~kEy~iS~d~~~~vi~-~~~e~~p~L~s~Lgr~~MQ~GD~k~----a~~yf~~vek~-----~~kL~~~  248 (366)
T KOG2796|consen  179 VMYSMANCLLGMKEYVLSVDAYHSVIK-YYPEQEPQLLSGLGRISMQIGDIKT----AEKYFQDVEKV-----TQKLDGL  248 (366)
T ss_pred             HHHHHHHHHhcchhhhhhHHHHHHHHH-hCCcccHHHHHHHHHHHHhcccHHH----HHHHHHHHHHH-----Hhhhhcc
Confidence            446677777778888889999999988 6556678888899999999999999    99999988876     3444554


Q ss_pred             hHHHHH-----HHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhccC
Q 043380          175 LYVSMM-----HELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWKG  245 (246)
Q Consensus       175 ~~~~li-----~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~  245 (246)
                      +.+.++     ..|.-+.++..|...++++...+.....      ..|.=.-+..-.|+..+|++.++.|..+-++
T Consensus       249 q~~~~V~~n~a~i~lg~nn~a~a~r~~~~i~~~D~~~~~------a~NnKALcllYlg~l~DAiK~~e~~~~~~P~  318 (366)
T KOG2796|consen  249 QGKIMVLMNSAFLHLGQNNFAEAHRFFTEILRMDPRNAV------ANNNKALCLLYLGKLKDALKQLEAMVQQDPR  318 (366)
T ss_pred             chhHHHHhhhhhheecccchHHHHHHHhhccccCCCchh------hhchHHHHHHHHHHHHHHHHHHHHHhccCCc
Confidence            444443     4566677899999999888755432221      2233222333478999999999999876553

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=95.92  E-value=0.42  Score=42.01  Aligned_cols=148  Identities=9%  Similarity=-0.043  Sum_probs=86.2

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH--hCCCCC--HHH------HHHHHHHHHhcCCcchHHHHHHHHHhccC
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVE--KGLEPD--SLS------YNILISACIKTKKLDVTMPFNEQLKDNGQ   82 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~--~~~~~~--~~t------~~~li~~~~~~~~~~~a~~~~~~m~~~~~   82 (246)
                      ..|.+..|..|.......-.++.|+..|-+..  .|++.-  ..|      -.+=+.+|  -|++++|+++|-+|-.+  
T Consensus       688 dnPHprLWrllAe~Al~Kl~l~tAE~AFVrc~dY~Gik~vkrl~~i~s~~~q~aei~~~--~g~feeaek~yld~drr--  763 (1189)
T KOG2041|consen  688 DNPHPRLWRLLAEYALFKLALDTAEHAFVRCGDYAGIKLVKRLRTIHSKEQQRAEISAF--YGEFEEAEKLYLDADRR--  763 (1189)
T ss_pred             cCCchHHHHHHHHHHHHHHhhhhHhhhhhhhccccchhHHHHhhhhhhHHHHhHhHhhh--hcchhHhhhhhhccchh--
Confidence            56888889888887777777888888876654  343211  011      11112222  36788888888887665  


Q ss_pred             CCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC----HHHHHHHHHHHHhcCChhhhhhHHHHHHHH
Q 043380           83 KCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD----RSTFTAMVDALLYSGSIKVVGLYALCIFGE  158 (246)
Q Consensus        83 ~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~----~~~~~~li~~~~~~~~~~~~~~~a~~~~~~  158 (246)
                                    ...+..+.+.|||-.+.++++.    .|-..|    ...|+.+...++....|++    |.+.|..
T Consensus       764 --------------DLAielr~klgDwfrV~qL~r~----g~~d~dD~~~e~A~r~ig~~fa~~~~We~----A~~yY~~  821 (1189)
T KOG2041|consen  764 --------------DLAIELRKKLGDWFRVYQLIRN----GGSDDDDEGKEDAFRNIGETFAEMMEWEE----AAKYYSY  821 (1189)
T ss_pred             --------------hhhHHHHHhhhhHHHHHHHHHc----cCCCcchHHHHHHHHHHHHHHHHHHHHHH----HHHHHHh
Confidence                          1345566677777555554432    222222    3467777777777777777    7766655


Q ss_pred             HHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhC
Q 043380          159 IVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMW  200 (246)
Q Consensus       159 m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  200 (246)
                      -...              ...+.++.+..++++.+.+...+.
T Consensus       822 ~~~~--------------e~~~ecly~le~f~~LE~la~~Lp  849 (1189)
T KOG2041|consen  822 CGDT--------------ENQIECLYRLELFGELEVLARTLP  849 (1189)
T ss_pred             ccch--------------HhHHHHHHHHHhhhhHHHHHHhcC
Confidence            4332              224455555555555555555543

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=95.92  E-value=0.72  Score=39.09  Aligned_cols=166  Identities=14%  Similarity=0.117  Sum_probs=92.0

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHH-hCCCCCHHHHH-------HHHHHHHhcCCcchHHHHHHHHHhccCCCCC
Q 043380           15 LNTIVMNAVIEASREAQRIDEAYQILESVE-KGLEPDSLSYN-------ILISACIKTKKLDVTMPFNEQLKDNGQKCSS   86 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~-~~~~~~~~t~~-------~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~   86 (246)
                      -+..-++..-.+|...|...++....+... .| .-...-|+       .+-++|.+.++++.+...|.+....      
T Consensus       255 ~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~g-re~rad~klIak~~~r~g~a~~k~~~~~~ai~~~~kaLte------  327 (539)
T KOG0548|consen  255 TDITYLNNIAAVYLERGKYAECIELCEKAVEVG-RELRADYKLIAKALARLGNAYTKREDYEGAIKYYQKALTE------  327 (539)
T ss_pred             hhhHHHHHHHHHHHhccHHHHhhcchHHHHHHh-HHHHHHHHHHHHHHHHhhhhhhhHHhHHHHHHHHHHHhhh------
Confidence            444455666667777777766666554432 21 11112222       2334566667788888888877665      


Q ss_pred             CCCCccHHH-------------------------HHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHH
Q 043380           87 GGFHPDIFT-------------------------YATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALL  140 (246)
Q Consensus        87 ~~~~p~~~~-------------------------~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~  140 (246)
                       ...|+..+                         .-.--+.+.+.|++..|...|.++.. ..  |+ ...|+...-+|.
T Consensus       328 -~Rt~~~ls~lk~~Ek~~k~~e~~a~~~pe~A~e~r~kGne~Fk~gdy~~Av~~YteAIk-r~--P~Da~lYsNRAac~~  403 (539)
T KOG0548|consen  328 -HRTPDLLSKLKEAEKALKEAERKAYINPEKAEEEREKGNEAFKKGDYPEAVKHYTEAIK-RD--PEDARLYSNRAACYL  403 (539)
T ss_pred             -hcCHHHHHHHHHHHHHHHHHHHHHhhChhHHHHHHHHHHHHHhccCHHHHHHHHHHHHh-cC--CchhHHHHHHHHHHH
Confidence             22333221                         11113334556777777777777666 32  44 666777777777


Q ss_pred             hcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc-hhhHHHHHHHHHhcCChhHHhhHHHhhCCC
Q 043380          141 YSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK-PHLYVSMMHELAARVDYDIVKSPYRRMWPD  202 (246)
Q Consensus       141 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  202 (246)
                      +.|.+..    |++--+.-.+.       .|+ ...|.-=..++....++++|.+.|++-.+.
T Consensus       404 kL~~~~~----aL~Da~~~ieL-------~p~~~kgy~RKg~al~~mk~ydkAleay~eale~  455 (539)
T KOG0548|consen  404 KLGEYPE----ALKDAKKCIEL-------DPNFIKAYLRKGAALRAMKEYDKALEAYQEALEL  455 (539)
T ss_pred             HHhhHHH----HHHHHHHHHhc-------CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            7777777    66665555443       222 233333344444445666777777666543

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=95.85  E-value=0.11  Score=40.57  Aligned_cols=105  Identities=12%  Similarity=0.120  Sum_probs=79.9

Q ss_pred             CccHHHHHHHHHHHHc-----cCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhh-----h-------hhHH
Q 043380           90 HPDIFTYATLLMGFRH-----AKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKV-----V-------GLYA  152 (246)
Q Consensus        90 ~p~~~~~~~ll~~~~~-----~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~-----~-------~~~a  152 (246)
                      +.|..+|-..+..+..     .+.++-....++.|++ .|+.-|..+|+.|+..+-+-.-...     +       -.-+
T Consensus        64 ~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~e-yGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C~  142 (406)
T KOG3941|consen   64 KRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKE-YGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNCA  142 (406)
T ss_pred             cccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHH-hcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhHH
Confidence            5577788888877743     3556777777899999 9999999999999998776543222     0       0117


Q ss_pred             HHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCCh-hHHhhHHHhhC
Q 043380          153 LCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDY-DIVKSPYRRMW  200 (246)
Q Consensus       153 ~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~-~~a~~~~~~~~  200 (246)
                      ++++++|...     |+.||-.+-..|++++++.+.. .+..++.-.|-
T Consensus       143 I~vLeqME~h-----GVmPdkE~e~~lvn~FGr~~~p~~K~~Rm~yWmP  186 (406)
T KOG3941|consen  143 IKVLEQMEWH-----GVMPDKEIEDILVNAFGRWNFPTKKVKRMLYWMP  186 (406)
T ss_pred             HHHHHHHHHc-----CCCCchHHHHHHHHHhccccccHHHHHHHHHhhh
Confidence            8999999999     9999999999999999998874 35555555444

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=95.84  E-value=0.76  Score=37.06  Aligned_cols=193  Identities=11%  Similarity=0.020  Sum_probs=128.9

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHH
Q 043380           24 IEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGF  103 (246)
Q Consensus        24 i~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~  103 (246)
                      +..+.-.|+...|++....+..-.+.|...|..--.+|...|++..|..=++...+.        ..-+..++--+-..+
T Consensus       162 l~s~~~~GD~~~ai~~i~~llEi~~Wda~l~~~Rakc~i~~~e~k~AI~Dlk~askL--------s~DnTe~~ykis~L~  233 (504)
T KOG0624|consen  162 LKSASGSGDCQNAIEMITHLLEIQPWDASLRQARAKCYIAEGEPKKAIHDLKQASKL--------SQDNTEGHYKISQLL  233 (504)
T ss_pred             HHHHhcCCchhhHHHHHHHHHhcCcchhHHHHHHHHHHHhcCcHHHHHHHHHHHHhc--------cccchHHHHHHHHHH
Confidence            445566788899999888877655779999999999999999999888766666553        234555666677777


Q ss_pred             HccCCHHHHHHHHHHHHhCCCCCCCHH-HHH---HH---------HHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCC
Q 043380          104 RHAKDLQSLLEIVFEMKSCCNLILDRS-TFT---AM---------VDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLW  170 (246)
Q Consensus       104 ~~~~~~~~a~~~~~~m~~~~~~~p~~~-~~~---~l---------i~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~  170 (246)
                      -..|+.+.++....+..+   +.||-. .|.   .|         +......++|.+    +++..+...+.   .|...
T Consensus       234 Y~vgd~~~sL~~iRECLK---ldpdHK~Cf~~YKklkKv~K~les~e~~ie~~~~t~----cle~ge~vlk~---ep~~~  303 (504)
T KOG0624|consen  234 YTVGDAENSLKEIRECLK---LDPDHKLCFPFYKKLKKVVKSLESAEQAIEEKHWTE----CLEAGEKVLKN---EPEET  303 (504)
T ss_pred             HhhhhHHHHHHHHHHHHc---cCcchhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHH----HHHHHHHHHhc---CCccc
Confidence            889999999999888887   667732 222   11         223344556666    66666666554   11211


Q ss_pred             -cchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHH
Q 043380          171 -PKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTI  240 (246)
Q Consensus       171 -p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  240 (246)
                       .....+..+-.++...|++.+|.....++....    +.++.  ++.-=.++|.--..+|.|++=|+...
T Consensus       304 ~ir~~~~r~~c~C~~~d~~~~eAiqqC~evL~~d----~~dv~--~l~dRAeA~l~dE~YD~AI~dye~A~  368 (504)
T KOG0624|consen  304 MIRYNGFRVLCTCYREDEQFGEAIQQCKEVLDID----PDDVQ--VLCDRAEAYLGDEMYDDAIHDYEKAL  368 (504)
T ss_pred             ceeeeeeheeeecccccCCHHHHHHHHHHHHhcC----chHHH--HHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence             112345566677778889999999888877543    22222  44445566666667777776665543

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=95.84  E-value=0.24  Score=38.67  Aligned_cols=103  Identities=15%  Similarity=0.124  Sum_probs=77.1

Q ss_pred             CCCHHHHHHHHHHHHhc-----CCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCC--------------
Q 043380           48 EPDSLSYNILISACIKT-----KKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKD--------------  108 (246)
Q Consensus        48 ~~~~~t~~~li~~~~~~-----~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~--------------  108 (246)
                      ..|-.+|-+++..+...     +..+-....++.|.+-       |++.|..+|+.||+.+=+-.-              
T Consensus        64 ~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~ey-------GVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP  136 (406)
T KOG3941|consen   64 KRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEY-------GVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYP  136 (406)
T ss_pred             cccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHh-------cchhhHHHHHHHHHhCcccccccHHHHHHHHhhCc
Confidence            55677777777776543     4556666667788887       899999999999998755322              


Q ss_pred             --HHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHH
Q 043380          109 --LQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVK  161 (246)
Q Consensus       109 --~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~  161 (246)
                        -+-+.+++++|.. .|+.||..+-..|+.++.+.+-.-.+   .+++.-.|-+
T Consensus       137 ~QQ~C~I~vLeqME~-hGVmPdkE~e~~lvn~FGr~~~p~~K---~~Rm~yWmPk  187 (406)
T KOG3941|consen  137 QQQNCAIKVLEQMEW-HGVMPDKEIEDILVNAFGRWNFPTKK---VKRMLYWMPK  187 (406)
T ss_pred             hhhhHHHHHHHHHHH-cCCCCchHHHHHHHHHhccccccHHH---HHHHHHhhhh
Confidence              2558899999999 99999999999999999998875543   4444444444

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=95.81  E-value=0.39  Score=33.46  Aligned_cols=127  Identities=11%  Similarity=0.056  Sum_probs=78.2

Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHH
Q 043380           54 YNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFT  133 (246)
Q Consensus        54 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~  133 (246)
                      ...++..+...+.+.....+++.+...       + ..+...++.++..|++.+ ..+..+.+..  .     ++.....
T Consensus        10 ~~~vv~~~~~~~~~~~l~~yLe~~~~~-------~-~~~~~~~~~li~ly~~~~-~~~ll~~l~~--~-----~~~yd~~   73 (140)
T smart00299       10 VSEVVELFEKRNLLEELIPYLESALKL-------N-SENPALQTKLIELYAKYD-PQKEIERLDN--K-----SNHYDIE   73 (140)
T ss_pred             HHHHHHHHHhCCcHHHHHHHHHHHHcc-------C-ccchhHHHHHHHHHHHHC-HHHHHHHHHh--c-----cccCCHH
Confidence            445677777777788888888888776       3 256667888888887653 3444444442  1     2233344


Q ss_pred             HHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhc-CChhHHhhHHHhhCCCCCCCCCchhh
Q 043380          134 AMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAAR-VDYDIVKSPYRRMWPDSTGTISPEVQ  212 (246)
Q Consensus       134 ~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~-g~~~~a~~~~~~~~~~~~~~~~~~~~  212 (246)
                      .+++.|.+.+.+++    +..++..+...              ...+..+... ++++.|.+++.+-.       .+.  
T Consensus        74 ~~~~~c~~~~l~~~----~~~l~~k~~~~--------------~~Al~~~l~~~~d~~~a~~~~~~~~-------~~~--  126 (140)
T smart00299       74 KVGKLCEKAKLYEE----AVELYKKDGNF--------------KDAIVTLIEHLGNYEKAIEYFVKQN-------NPE--  126 (140)
T ss_pred             HHHHHHHHcCcHHH----HHHHHHhhcCH--------------HHHHHHHHHcccCHHHHHHHHHhCC-------CHH--
Confidence            47777777888888    88777776332              2233333333 77888888777632       112  


Q ss_pred             hHHHHHHHHHHHh
Q 043380          213 EEAGHLLMEAALN  225 (246)
Q Consensus       213 ~~~~~~li~~~~~  225 (246)
                        .|..++..+..
T Consensus       127 --lw~~~~~~~l~  137 (140)
T smart00299      127 --LWAEVLKALLD  137 (140)
T ss_pred             --HHHHHHHHHHc
Confidence              56667666653

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=95.81  E-value=0.21  Score=41.63  Aligned_cols=67  Identities=9%  Similarity=-0.035  Sum_probs=57.9

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCH----HHHHHHHHHHHhcCCcchHHHHHHHHHhc
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDS----LSYNILISACIKTKKLDVTMPFNEQLKDN   80 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~----~t~~~li~~~~~~~~~~~a~~~~~~m~~~   80 (246)
                      .+.+...|+.+-.+|.+.|++++|+..|++... +.|+.    .+|..+-.+|...|+.++|.+.+++.++.
T Consensus        71 dP~~a~a~~NLG~AL~~lGryeEAIa~f~rALe-L~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         71 DVKTAEDAVNLGLSLFSKGRVKDALAQFETALE-LNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh-hCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            456788999999999999999999999998653 35653    45999999999999999999999999885

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=95.76  E-value=0.16  Score=39.83  Aligned_cols=85  Identities=19%  Similarity=0.085  Sum_probs=71.2

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      =..++..++..+...|+.+.+.+.++++-.--+-+...|..+|.+|.+.|+...|+..|+++.+.  ...+.|+.|...+
T Consensus       152 ~~~~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~--~~edlgi~P~~~~  229 (280)
T COG3629         152 FIKALTKLAEALIACGRADAVIEHLERLIELDPYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKT--LAEELGIDPAPEL  229 (280)
T ss_pred             HHHHHHHHHHHHHhcccHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCchHHHHHHHHHHHH--hhhhcCCCccHHH
Confidence            34567778888899999999999999987545779999999999999999999999999999874  3345688998888


Q ss_pred             HHHHHHH
Q 043380           96 YATLLMG  102 (246)
Q Consensus        96 ~~~ll~~  102 (246)
                      .......
T Consensus       230 ~~~y~~~  236 (280)
T COG3629         230 RALYEEI  236 (280)
T ss_pred             HHHHHHH
Confidence            7777666

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.74  E-value=0.48  Score=38.02  Aligned_cols=152  Identities=13%  Similarity=0.033  Sum_probs=90.9

Q ss_pred             cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHH--HH--HHHHHHHHc
Q 043380           30 AQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIF--TY--ATLLMGFRH  105 (246)
Q Consensus        30 ~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~--~~--~~ll~~~~~  105 (246)
                      +|+..+|-..++++.+..+.|...++..=.+|...|+.+.-...+++....        ..||..  +|  ...--++..
T Consensus       116 ~g~~h~a~~~wdklL~d~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~--------wn~dlp~~sYv~GmyaFgL~E  187 (491)
T KOG2610|consen  116 RGKHHEAAIEWDKLLDDYPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPK--------WNADLPCYSYVHGMYAFGLEE  187 (491)
T ss_pred             cccccHHHHHHHHHHHhCchhhhhhhhhhhHHHhccchhhhhhHHHHhccc--------cCCCCcHHHHHHHHHHhhHHH
Confidence            455556666666666556777777777777777777777777777777653        233332  22  222233456


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHH
Q 043380          106 AKDLQSLLEIVFEMKSCCNLIL-DRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELA  184 (246)
Q Consensus       106 ~~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~  184 (246)
                      +|-+++|++.-++..+   +.| |...-++....+-..+++.+    +.+...+-...  .+.+...-.+.|-+..-.+.
T Consensus       188 ~g~y~dAEk~A~ralq---iN~~D~Wa~Ha~aHVlem~~r~Ke----g~eFM~~ted~--Wr~s~mlasHNyWH~Al~~i  258 (491)
T KOG2610|consen  188 CGIYDDAEKQADRALQ---INRFDCWASHAKAHVLEMNGRHKE----GKEFMYKTEDD--WRQSWMLASHNYWHTALFHI  258 (491)
T ss_pred             hccchhHHHHHHhhcc---CCCcchHHHHHHHHHHHhcchhhh----HHHHHHhcccc--hhhhhHHHhhhhHHHHHhhh
Confidence            7777777777666655   333 46666777777777777777    77665544332  00112222344545555566


Q ss_pred             hcCChhHHhhHHHh
Q 043380          185 ARVDYDIVKSPYRR  198 (246)
Q Consensus       185 ~~g~~~~a~~~~~~  198 (246)
                      ..+.++.|+++|+.
T Consensus       259 E~aeye~aleIyD~  272 (491)
T KOG2610|consen  259 EGAEYEKALEIYDR  272 (491)
T ss_pred             cccchhHHHHHHHH
Confidence            66777777777764

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=95.63  E-value=0.14  Score=43.23  Aligned_cols=104  Identities=11%  Similarity=0.104  Sum_probs=87.4

Q ss_pred             HHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHH
Q 043380           59 SACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVD  137 (246)
Q Consensus        59 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~  137 (246)
                      ++.+..|+++.|...|.+.+..        -++|.+.|..=..+|+..|++++|++==..-.+   +.|+ ...|+-...
T Consensus        10 naa~s~~d~~~ai~~~t~ai~l--------~p~nhvlySnrsaa~a~~~~~~~al~da~k~~~---l~p~w~kgy~r~Ga   78 (539)
T KOG0548|consen   10 NAAFSSGDFETAIRLFTEAIML--------SPTNHVLYSNRSAAYASLGSYEKALKDATKTRR---LNPDWAKGYSRKGA   78 (539)
T ss_pred             HhhcccccHHHHHHHHHHHHcc--------CCCccchhcchHHHHHHHhhHHHHHHHHHHHHh---cCCchhhHHHHhHH
Confidence            4567889999999999999985        356888999999999999999999876666555   8899 778999999


Q ss_pred             HHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHH
Q 043380          138 ALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHEL  183 (246)
Q Consensus       138 ~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~  183 (246)
                      ++...|++++    |..-|.+-.+.      -.-|...++.+..++
T Consensus        79 a~~~lg~~~e----A~~ay~~GL~~------d~~n~~L~~gl~~a~  114 (539)
T KOG0548|consen   79 ALFGLGDYEE----AILAYSEGLEK------DPSNKQLKTGLAQAY  114 (539)
T ss_pred             HHHhcccHHH----HHHHHHHHhhc------CCchHHHHHhHHHhh
Confidence            9999999999    99999988775      334557778888777

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=95.56  E-value=1.2  Score=37.30  Aligned_cols=141  Identities=14%  Similarity=0.146  Sum_probs=96.4

Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCHH------HHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHH
Q 043380           29 EAQRIDEAYQILESVEKGLEPDSL------SYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMG  102 (246)
Q Consensus        29 ~~g~~~~a~~~~~~~~~~~~~~~~------t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~  102 (246)
                      +.+++.+|+++|.++-+....+..      .-+-+|++|...+ .+.....+....+.         .| ...|-.|..+
T Consensus        18 kq~~~~esEkifskI~~e~~~~~f~lkeEvl~grilnAffl~n-ld~Me~~l~~l~~~---------~~-~s~~l~LF~~   86 (549)
T PF07079_consen   18 KQKKFQESEKIFSKIYDEKESSPFLLKEEVLGGRILNAFFLNN-LDLMEKQLMELRQQ---------FG-KSAYLPLFKA   86 (549)
T ss_pred             HHhhhhHHHHHHHHHHHHhhcchHHHHHHHHhhHHHHHHHHhh-HHHHHHHHHHHHHh---------cC-CchHHHHHHH
Confidence            578899999999998643344433      3467888887754 78888888888775         34 3455566555


Q ss_pred             H--HccCCHHHHHHHHHHHHhCC--CCC------------CCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCC
Q 043380          103 F--RHAKDLQSLLEIVFEMKSCC--NLI------------LDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSN  166 (246)
Q Consensus       103 ~--~~~~~~~~a~~~~~~m~~~~--~~~------------p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~  166 (246)
                      .  -+.+.+.+|.+.+....+ .  +-.            +|-..=+..+.++...|++.+    +..+++++...-- .
T Consensus        87 L~~Y~~k~~~kal~~ls~w~~-~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~E----gR~iLn~i~~~ll-k  160 (549)
T PF07079_consen   87 LVAYKQKEYRKALQALSVWKE-QIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSE----GRAILNRIIERLL-K  160 (549)
T ss_pred             HHHHHhhhHHHHHHHHHHHHh-hhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcch----HHHHHHHHHHHHh-h
Confidence            3  477889999998887766 3  211            222233567888899999999    9999999887610 0


Q ss_pred             CCCCcchhhHHHHHHHHHhc
Q 043380          167 PGLWPKPHLYVSMMHELAAR  186 (246)
Q Consensus       167 ~~~~p~~~~~~~li~~~~~~  186 (246)
                      ....-+..+|+.++-.++++
T Consensus       161 rE~~w~~d~yd~~vlmlsrS  180 (549)
T PF07079_consen  161 RECEWNSDMYDRAVLMLSRS  180 (549)
T ss_pred             hhhcccHHHHHHHHHHHhHH
Confidence            12235778888877666643

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=95.49  E-value=0.3  Score=38.29  Aligned_cols=82  Identities=15%  Similarity=0.221  Sum_probs=69.6

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchh
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPH  174 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~  174 (246)
                      ++..++..+...|+.+.+...++++.. . -+-+...|..+|.+|...|+...    |++.|+++.+......|+.|-..
T Consensus       155 ~l~~lae~~~~~~~~~~~~~~l~~Li~-~-dp~~E~~~~~lm~~y~~~g~~~~----ai~~y~~l~~~~~edlgi~P~~~  228 (280)
T COG3629         155 ALTKLAEALIACGRADAVIEHLERLIE-L-DPYDEPAYLRLMEAYLVNGRQSA----AIRAYRQLKKTLAEELGIDPAPE  228 (280)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHh-c-CccchHHHHHHHHHHHHcCCchH----HHHHHHHHHHHhhhhcCCCccHH
Confidence            466678888999999999999999988 2 23468899999999999999999    99999999886555679999988


Q ss_pred             hHHHHHHH
Q 043380          175 LYVSMMHE  182 (246)
Q Consensus       175 ~~~~li~~  182 (246)
                      +.......
T Consensus       229 ~~~~y~~~  236 (280)
T COG3629         229 LRALYEEI  236 (280)
T ss_pred             HHHHHHHH
Confidence            87777666

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome

Probab=95.43  E-value=0.36  Score=35.30  Aligned_cols=124  Identities=13%  Similarity=0.018  Sum_probs=82.6

Q ss_pred             HHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc--cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-
Q 043380           52 LSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP--DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-  128 (246)
Q Consensus        52 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p--~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-  128 (246)
                      ..+..+...|++.|+.++|.+.|.++.+.       ...|  -...+-.+|+.....+++..+.....+... .--.++ 
T Consensus        37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~-------~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~-~~~~~~d  108 (177)
T PF10602_consen   37 MALEDLADHYCKIGDLEEALKAYSRARDY-------CTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAES-LIEKGGD  108 (177)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhhh-------cCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH-HHhccch
Confidence            56888999999999999999999999886       3333  345788899999999999999999887766 222222 


Q ss_pred             HH------HHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcC---CCCCCcchhhHHHHHHHHHhcCCh
Q 043380          129 RS------TFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCS---NPGLWPKPHLYVSMMHELAARVDY  189 (246)
Q Consensus       129 ~~------~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~---~~~~~p~~~~~~~li~~~~~~g~~  189 (246)
                      ..      .|..+  .+...+++..    |-+.|-+.......   ..=+.|+..++...+.+++...+.
T Consensus       109 ~~~~nrlk~~~gL--~~l~~r~f~~----AA~~fl~~~~t~~~~~~~el~s~~d~a~Y~~l~aLat~~R~  172 (177)
T PF10602_consen  109 WERRNRLKVYEGL--ANLAQRDFKE----AAELFLDSLSTFTSLQYTELISYNDFAIYGGLCALATLDRS  172 (177)
T ss_pred             HHHHHHHHHHHHH--HHHHhchHHH----HHHHHHccCcCCCCCchhhhcCHHHHHHHHHHHHHHhCCHH
Confidence            22      22222  3344678888    88777766544211   112345555555566666655543

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.

>PRK15331 chaperone protein SicA; Provisional

Probab=95.28  E-value=0.48  Score=33.94  Aligned_cols=121  Identities=7%  Similarity=-0.044  Sum_probs=77.1

Q ss_pred             chHHHHHHHHHhccCCCC-CCCCCccHH--HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCC
Q 043380           68 DVTMPFNEQLKDNGQKCS-SGGFHPDIF--TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGS  144 (246)
Q Consensus        68 ~~a~~~~~~m~~~~~~~~-~~~~~p~~~--~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~  144 (246)
                      ++..+.+.+....|.++. -.|+.++.-  .|..--. +-..|++++|..+|.-+.. .+. -+..-+..|..+|-..++
T Consensus        10 ~~~~~~i~~al~~G~tlk~l~gis~~~le~iY~~Ay~-~y~~Gk~~eA~~~F~~L~~-~d~-~n~~Y~~GLaa~~Q~~k~   86 (165)
T PRK15331         10 ERVAEMIWDAVSEGATLKDVHGIPQDMMDGLYAHAYE-FYNQGRLDEAETFFRFLCI-YDF-YNPDYTMGLAAVCQLKKQ   86 (165)
T ss_pred             HHHHHHHHHHHHCCCCHHHHhCCCHHHHHHHHHHHHH-HHHCCCHHHHHHHHHHHHH-hCc-CcHHHHHHHHHHHHHHHH
Confidence            333444444555443322 233443321  3333333 3467899999999998888 332 123345667777777888


Q ss_pred             hhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCC
Q 043380          145 IKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWP  201 (246)
Q Consensus       145 ~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  201 (246)
                      ++.    |...|......     . .-|+..+-..-.+|...|+.+.|...|.....
T Consensus        87 y~~----Ai~~Y~~A~~l-----~-~~dp~p~f~agqC~l~l~~~~~A~~~f~~a~~  133 (165)
T PRK15331         87 FQK----ACDLYAVAFTL-----L-KNDYRPVFFTGQCQLLMRKAAKARQCFELVNE  133 (165)
T ss_pred             HHH----HHHHHHHHHHc-----c-cCCCCccchHHHHHHHhCCHHHHHHHHHHHHh
Confidence            998    99888877664     2 24555667778888889999999998888764

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=95.27  E-value=0.55  Score=38.44  Aligned_cols=125  Identities=5%  Similarity=-0.059  Sum_probs=90.4

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHh------CC---------CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCC
Q 043380           24 IEASREAQRIDEAYQILESVEK------GL---------EPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGG   88 (246)
Q Consensus        24 i~~~~~~g~~~~a~~~~~~~~~------~~---------~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~   88 (246)
                      -+.|.+.|++..|..-|+...+      +.         ..-..+++.+.-+|.+.+++.+|+..-.+.+..+       
T Consensus       215 Gn~~fK~gk~~~A~~~Yerav~~l~~~~~~~~ee~~~~~~~k~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~-------  287 (397)
T KOG0543|consen  215 GNVLFKEGKFKLAKKRYERAVSFLEYRRSFDEEEQKKAEALKLACHLNLAACYLKLKEYKEAIESCNKVLELD-------  287 (397)
T ss_pred             hhHHHhhchHHHHHHHHHHHHHHhhccccCCHHHHHHHHHHHHHHhhHHHHHHHhhhhHHHHHHHHHHHHhcC-------
Confidence            3567889999999988877432      11         1223457778888899999999999999998862       


Q ss_pred             CCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHH-HHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           89 FHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFT-AMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        89 ~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~-~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                       ++|.-..--=-.++...|+++.|+..|+.+.+   +.|+...-+ .|+..--+......+   ..++|..|...
T Consensus       288 -~~N~KALyRrG~A~l~~~e~~~A~~df~ka~k---~~P~Nka~~~el~~l~~k~~~~~~k---ekk~y~~mF~k  355 (397)
T KOG0543|consen  288 -PNNVKALYRRGQALLALGEYDLARDDFQKALK---LEPSNKAARAELIKLKQKIREYEEK---EKKMYANMFAK  355 (397)
T ss_pred             -CCchhHHHHHHHHHHhhccHHHHHHHHHHHHH---hCCCcHHHHHHHHHHHHHHHHHHHH---HHHHHHHHhhc
Confidence             55666767777889999999999999999999   778855544 444444444443331   56777777665

>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=95.18  E-value=0.8  Score=33.04  Aligned_cols=136  Identities=13%  Similarity=0.099  Sum_probs=91.0

Q ss_pred             HHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhh
Q 043380           71 MPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGL  150 (246)
Q Consensus        71 ~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~  150 (246)
                      .++++.+.+.       +++|+...|..+++.+.+.|.+...    .++.. .++-+|.......+-.+...  ......
T Consensus        14 lEYirSl~~~-------~i~~~~~L~~lli~lLi~~~~~~~L----~qllq-~~Vi~DSk~lA~~LLs~~~~--~~~~~Q   79 (167)
T PF07035_consen   14 LEYIRSLNQH-------NIPVQHELYELLIDLLIRNGQFSQL----HQLLQ-YHVIPDSKPLACQLLSLGNQ--YPPAYQ   79 (167)
T ss_pred             HHHHHHHHHc-------CCCCCHHHHHHHHHHHHHcCCHHHH----HHHHh-hcccCCcHHHHHHHHHhHcc--ChHHHH
Confidence            3455566666       8899999999999999999987554    44455 66778876666555444432  333112


Q ss_pred             HHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChh
Q 043380          151 YALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVD  230 (246)
Q Consensus       151 ~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~  230 (246)
                      .|.+.+.++..             .+..++..+...|++-+|.++.+.....  ..+++       ..++++-.+.++..
T Consensus        80 l~lDMLkRL~~-------------~~~~iievLL~~g~vl~ALr~ar~~~~~--~~~~~-------~~fLeAA~~~~D~~  137 (167)
T PF07035_consen   80 LGLDMLKRLGT-------------AYEEIIEVLLSKGQVLEALRYARQYHKV--DSVPA-------RKFLEAAANSNDDQ  137 (167)
T ss_pred             HHHHHHHHhhh-------------hHHHHHHHHHhCCCHHHHHHHHHHcCCc--ccCCH-------HHHHHHHHHcCCHH
Confidence            25555555542             3567888999999999999999886432  22443       34888888888876


Q ss_pred             HHHHHHHHHHhh
Q 043380          231 LALDKLSNTITR  242 (246)
Q Consensus       231 ~a~~~~~~m~~~  242 (246)
                      .=..+++-...+
T Consensus       138 lf~~V~~ff~~~  149 (167)
T PF07035_consen  138 LFYAVFRFFEER  149 (167)
T ss_pred             HHHHHHHHHHHh
Confidence            666666555543

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=95.17  E-value=1.2  Score=35.06  Aligned_cols=153  Identities=12%  Similarity=0.034  Sum_probs=106.4

Q ss_pred             HHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHH
Q 043380           60 ACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDAL  139 (246)
Q Consensus        60 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~  139 (246)
                      .....|++.+|..+|....+.        .+-+...--.+..+|...|+.+.|..++..+-. .--.........-|..+
T Consensus       143 ~~~~~e~~~~a~~~~~~al~~--------~~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~-~~~~~~~~~l~a~i~ll  213 (304)
T COG3118         143 ELIEAEDFGEAAPLLKQALQA--------APENSEAKLLLAECLLAAGDVEAAQAILAALPL-QAQDKAAHGLQAQIELL  213 (304)
T ss_pred             hhhhccchhhHHHHHHHHHHh--------CcccchHHHHHHHHHHHcCChHHHHHHHHhCcc-cchhhHHHHHHHHHHHH
Confidence            346678899999999998886        233455667888999999999999999998766 21112222333456666


Q ss_pred             HhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc-chhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHH
Q 043380          140 LYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP-KPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHL  218 (246)
Q Consensus       140 ~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  218 (246)
                      .+.....+    ...+-...-..        | |...-..+...+...|+.+.|.+.+-.+.+.+.+.-...    .-..
T Consensus       214 ~qaa~~~~----~~~l~~~~aad--------Pdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~d~~~~d~~----~Rk~  277 (304)
T COG3118         214 EQAAATPE----IQDLQRRLAAD--------PDDVEAALALADQLHLVGRNEAALEHLLALLRRDRGFEDGE----ARKT  277 (304)
T ss_pred             HHHhcCCC----HHHHHHHHHhC--------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccCcH----HHHH
Confidence            66777776    66665666553        5 667777888899999999999988888777665544444    4567


Q ss_pred             HHHHHHhcCChhHHHHHHH
Q 043380          219 LMEAALNDGQVDLALDKLS  237 (246)
Q Consensus       219 li~~~~~~g~~~~a~~~~~  237 (246)
                      |++.+.--|.-|.+.--++
T Consensus       278 lle~f~~~g~~Dp~~~~~R  296 (304)
T COG3118         278 LLELFEAFGPADPLVLAYR  296 (304)
T ss_pred             HHHHHHhcCCCCHHHHHHH
Confidence            8887777775555444443

>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=95.11  E-value=1.3  Score=37.52  Aligned_cols=135  Identities=10%  Similarity=-0.002  Sum_probs=97.0

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHH
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTY   96 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~   96 (246)
                      ..-.+.++..+-+.|..+.|+++-.+-..           -.....+.|+++.|.++-++             .++...|
T Consensus       295 ~~~~~~i~~fL~~~G~~e~AL~~~~D~~~-----------rFeLAl~lg~L~~A~~~a~~-------------~~~~~~W  350 (443)
T PF04053_consen  295 KDQGQSIARFLEKKGYPELALQFVTDPDH-----------RFELALQLGNLDIALEIAKE-------------LDDPEKW  350 (443)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHSS-HHH-----------HHHHHHHCT-HHHHHHHCCC-------------CSTHHHH
T ss_pred             hhHHHHHHHHHHHCCCHHHHHhhcCChHH-----------HhHHHHhcCCHHHHHHHHHh-------------cCcHHHH
Confidence            44578888888899999999988755432           12344678999888765332             3467799


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhH
Q 043380           97 ATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLY  176 (246)
Q Consensus        97 ~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~  176 (246)
                      ..|-....+.|+++-|++.|.+...          |..|+-.|.-.|+.+.    ..++-+....+     |      -+
T Consensus       351 ~~Lg~~AL~~g~~~lAe~c~~k~~d----------~~~L~lLy~~~g~~~~----L~kl~~~a~~~-----~------~~  405 (443)
T PF04053_consen  351 KQLGDEALRQGNIELAEECYQKAKD----------FSGLLLLYSSTGDREK----LSKLAKIAEER-----G------DI  405 (443)
T ss_dssp             HHHHHHHHHTTBHHHHHHHHHHCT-----------HHHHHHHHHHCT-HHH----HHHHHHHHHHT-----T-------H
T ss_pred             HHHHHHHHHcCCHHHHHHHHHhhcC----------ccccHHHHHHhCCHHH----HHHHHHHHHHc-----c------CH
Confidence            9999999999999999999998877          7788888889999888    66666665554     2      25


Q ss_pred             HHHHHHHHhcCChhHHhhHHHhhC
Q 043380          177 VSMMHELAARVDYDIVKSPYRRMW  200 (246)
Q Consensus       177 ~~li~~~~~~g~~~~a~~~~~~~~  200 (246)
                      +....++.-.|+.++..+++.+-.
T Consensus       406 n~af~~~~~lgd~~~cv~lL~~~~  429 (443)
T PF04053_consen  406 NIAFQAALLLGDVEECVDLLIETG  429 (443)
T ss_dssp             HHHHHHHHHHT-HHHHHHHHHHTT
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHcC
Confidence            666666777888888888887753

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.

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=94.90  E-value=2.1  Score=38.03  Aligned_cols=100  Identities=15%  Similarity=0.113  Sum_probs=67.0

Q ss_pred             HHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhH
Q 043380          116 VFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSP  195 (246)
Q Consensus       116 ~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~  195 (246)
                      .+.+....|.....-+.+--+.-+...|+-.+    |.++-.+.+         .||-..|-.-+.+++..++|++-+++
T Consensus       671 Q~~Le~q~~~~f~dlSl~dTv~~li~~g~~k~----a~ql~~~Fk---------ipdKr~~wLk~~aLa~~~kweeLekf  737 (829)
T KOG2280|consen  671 QRTLEDQFGGSFVDLSLHDTVTTLILIGQNKR----AEQLKSDFK---------IPDKRLWWLKLTALADIKKWEELEKF  737 (829)
T ss_pred             HHHHHHHhccccccCcHHHHHHHHHHccchHH----HHHHHHhcC---------CcchhhHHHHHHHHHhhhhHHHHHHH
Confidence            33444334444444455666667777788888    776655542         37778888888888888888888877


Q ss_pred             HHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHH
Q 043380          196 YRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNT  239 (246)
Q Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  239 (246)
                      -++... ..          -|.-++.+|.+.|+.++|.+++-++
T Consensus       738 Akskks-PI----------Gy~PFVe~c~~~~n~~EA~KYiprv  770 (829)
T KOG2280|consen  738 AKSKKS-PI----------GYLPFVEACLKQGNKDEAKKYIPRV  770 (829)
T ss_pred             HhccCC-CC----------CchhHHHHHHhcccHHHHhhhhhcc
Confidence            777653 21          2555788888888888888877654

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=94.90  E-value=0.85  Score=31.89  Aligned_cols=62  Identities=15%  Similarity=0.101  Sum_probs=34.5

Q ss_pred             HHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCC
Q 043380          136 VDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDST  204 (246)
Q Consensus       136 i~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  204 (246)
                      .......|++++    |.+.|+.+..+.   |.-.-...+--.++.+|.+.+++++|...+++..+.++
T Consensus        17 a~~~l~~~~Y~~----A~~~le~L~~ry---P~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP   78 (142)
T PF13512_consen   17 AQEALQKGNYEE----AIKQLEALDTRY---PFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHP   78 (142)
T ss_pred             HHHHHHhCCHHH----HHHHHHHHHhcC---CCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCC
Confidence            334455666666    666666666652   11122234455566666666666666666666655444

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=94.89  E-value=0.15  Score=41.88  Aligned_cols=135  Identities=12%  Similarity=0.037  Sum_probs=87.5

Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHH----HhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCC
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEM----KSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLW  170 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m----~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~  170 (246)
                      |.+|-+.|--.|+++.|....+.=    ++ .|-... ...++.+..++.-.|+++.    |.+.|+.-......-..-.
T Consensus       198 ~GnLGNTyYlLGdf~~ai~~H~~RL~ia~e-fGDrAaeRRA~sNlgN~hiflg~fe~----A~ehYK~tl~LAielg~r~  272 (639)
T KOG1130|consen  198 YGNLGNTYYLLGDFDQAIHFHKLRLEIAQE-FGDRAAERRAHSNLGNCHIFLGNFEL----AIEHYKLTLNLAIELGNRT  272 (639)
T ss_pred             hcccCceeeeeccHHHHHHHHHHHHHHHHH-hhhHHHHHHhhcccchhhhhhcccHh----HHHHHHHHHHHHHHhcchh
Confidence            334444444467788888776532    22 333222 4578889999999999999    9988886443200000112


Q ss_pred             cchhhHHHHHHHHHhcCChhHHhhHHHhhC------CCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          171 PKPHLYVSMMHELAARVDYDIVKSPYRRMW------PDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       171 p~~~~~~~li~~~~~~g~~~~a~~~~~~~~------~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      ....+..+|-..|.-..++++|..++.+=.      .+..|..      .++.+|-.+|...|.-++|+.+.+.-++
T Consensus       273 vEAQscYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~------RacwSLgna~~alg~h~kAl~fae~hl~  343 (639)
T KOG1130|consen  273 VEAQSCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGEL------RACWSLGNAFNALGEHRKALYFAELHLR  343 (639)
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhH------HHHHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence            344667778888888888899988877522      1211211      1788999999999999999988765443

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=94.88  E-value=0.74  Score=32.17  Aligned_cols=81  Identities=12%  Similarity=0.053  Sum_probs=58.5

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCC---HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHH
Q 043380           22 AVIEASREAQRIDEAYQILESVEKGLEPD---SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYAT   98 (246)
Q Consensus        22 ~li~~~~~~g~~~~a~~~~~~~~~~~~~~---~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~   98 (246)
                      .-.....+.|++++|.+.|+.+....+.+   ...--.++.+|.+.+++++|...+++.++.       ....-..-|..
T Consensus        15 ~~a~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirL-------hP~hp~vdYa~   87 (142)
T PF13512_consen   15 QEAQEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRL-------HPTHPNVDYAY   87 (142)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh-------CCCCCCccHHH
Confidence            33445578899999999999998655443   344567899999999999999999999987       22222346666


Q ss_pred             HHHHHHccCCH
Q 043380           99 LLMGFRHAKDL  109 (246)
Q Consensus        99 ll~~~~~~~~~  109 (246)
                      .+.+++.-...
T Consensus        88 Y~~gL~~~~~~   98 (142)
T PF13512_consen   88 YMRGLSYYEQD   98 (142)
T ss_pred             HHHHHHHHHHh
Confidence            66666544433

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=94.84  E-value=2.2  Score=36.45  Aligned_cols=162  Identities=10%  Similarity=0.052  Sum_probs=107.4

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHH--hCCCCCH-----HHHHHHHHHHHhc----CCcchHHHHHHHHHhccCCCCCCCC
Q 043380           21 NAVIEASREAQRIDEAYQILESVE--KGLEPDS-----LSYNILISACIKT----KKLDVTMPFNEQLKDNGQKCSSGGF   89 (246)
Q Consensus        21 ~~li~~~~~~g~~~~a~~~~~~~~--~~~~~~~-----~t~~~li~~~~~~----~~~~~a~~~~~~m~~~~~~~~~~~~   89 (246)
                      ..++...+=.|+=+.+++.+.+..  .++.-..     -.|+.++..++..    ...+.|.+++..+.+.         
T Consensus       192 ~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~---------  262 (468)
T PF10300_consen  192 LKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKR---------  262 (468)
T ss_pred             HHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHh---------
Confidence            456666667899999999987764  2333222     2355666555543    4567899999999986         


Q ss_pred             CccHHHHHHHH-HHHHccCCHHHHHHHHHHHHhCCCC--CCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCC
Q 043380           90 HPDIFTYATLL-MGFRHAKDLQSLLEIVFEMKSCCNL--ILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSN  166 (246)
Q Consensus        90 ~p~~~~~~~ll-~~~~~~~~~~~a~~~~~~m~~~~~~--~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~  166 (246)
                      -|+...|...- +.+...|++++|.+.|+.......-  ......+--+.-.+....+|++    |.+.|..+.+.+   
T Consensus       263 yP~s~lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~----A~~~f~~L~~~s---  335 (468)
T PF10300_consen  263 YPNSALFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEE----AAEYFLRLLKES---  335 (468)
T ss_pred             CCCcHHHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHH----HHHHHHHHHhcc---
Confidence            68776665443 3356789999999999975541111  1223456667778889999999    999999999862   


Q ss_pred             CCCCcchhhHHHHHHHHHhcCCh-------hHHhhHHHhhC
Q 043380          167 PGLWPKPHLYVSMMHELAARVDY-------DIVKSPYRRMW  200 (246)
Q Consensus       167 ~~~~p~~~~~~~li~~~~~~g~~-------~~a~~~~~~~~  200 (246)
                       .+.+...+|.. ..++...|+.       ++|.++|.++.
T Consensus       336 -~WSka~Y~Y~~-a~c~~~l~~~~~~~~~~~~a~~l~~~vp  374 (468)
T PF10300_consen  336 -KWSKAFYAYLA-AACLLMLGREEEAKEHKKEAEELFRKVP  374 (468)
T ss_pred             -ccHHHHHHHHH-HHHHHhhccchhhhhhHHHHHHHHHHHH
Confidence             23222222222 2234456777       88888888765

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.

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=94.78  E-value=0.9  Score=31.58  Aligned_cols=110  Identities=8%  Similarity=0.034  Sum_probs=76.9

Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhH
Q 043380           97 ATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLY  176 (246)
Q Consensus        97 ~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~  176 (246)
                      ..++..+...+.+.....+++.+.. .+ ..+...++.++..|++... ..    ..+.++.   .        ++....
T Consensus        11 ~~vv~~~~~~~~~~~l~~yLe~~~~-~~-~~~~~~~~~li~ly~~~~~-~~----ll~~l~~---~--------~~~yd~   72 (140)
T smart00299       11 SEVVELFEKRNLLEELIPYLESALK-LN-SENPALQTKLIELYAKYDP-QK----EIERLDN---K--------SNHYDI   72 (140)
T ss_pred             HHHHHHHHhCCcHHHHHHHHHHHHc-cC-ccchhHHHHHHHHHHHHCH-HH----HHHHHHh---c--------cccCCH
Confidence            4677778888899999999999988 65 3677889999999997643 33    4444442   2        234455


Q ss_pred             HHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhc-CChhHHHHHHHH
Q 043380          177 VSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALND-GQVDLALDKLSN  238 (246)
Q Consensus       177 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~-g~~~~a~~~~~~  238 (246)
                      ..+++.|.+.+.++++..++..+..              |...+..+... ++++.|.+++.+
T Consensus        73 ~~~~~~c~~~~l~~~~~~l~~k~~~--------------~~~Al~~~l~~~~d~~~a~~~~~~  121 (140)
T smart00299       73 EKVGKLCEKAKLYEEAVELYKKDGN--------------FKDAIVTLIEHLGNYEKAIEYFVK  121 (140)
T ss_pred             HHHHHHHHHcCcHHHHHHHHHhhcC--------------HHHHHHHHHHcccCHHHHHHHHHh
Confidence            6688888888888888888887742              33344444444 677777777665

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=94.70  E-value=0.15  Score=27.56  Aligned_cols=40  Identities=23%  Similarity=0.137  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHH
Q 043380           18 IVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNIL   57 (246)
Q Consensus        18 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~l   57 (246)
                      .+|..+-..|.+.|++++|+++|++..+..+-|...+..+
T Consensus         2 ~~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~~~a~~~L   41 (44)
T PF13428_consen    2 AAWLALARAYRRLGQPDEAERLLRRALALDPDDPEAWRAL   41 (44)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCHHHHHHh
Confidence            3577888999999999999999999875445565555544

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.70  E-value=1.9  Score=34.83  Aligned_cols=153  Identities=9%  Similarity=-0.100  Sum_probs=112.0

Q ss_pred             hcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHH----HHH
Q 043380           63 KTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAM----VDA  138 (246)
Q Consensus        63 ~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~l----i~~  138 (246)
                      ..|+..+|...++++.+.        .+.|...+.-.=.+|.-.|+.+.-...++.+.. . ..||.+.|+-+    .-+
T Consensus       115 ~~g~~h~a~~~wdklL~d--------~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip-~-wn~dlp~~sYv~GmyaFg  184 (491)
T KOG2610|consen  115 GRGKHHEAAIEWDKLLDD--------YPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIP-K-WNADLPCYSYVHGMYAFG  184 (491)
T ss_pred             ccccccHHHHHHHHHHHh--------CchhhhhhhhhhhHHHhccchhhhhhHHHHhcc-c-cCCCCcHHHHHHHHHHhh
Confidence            457788888889999884        777888999999999999999999999998877 2 35665444433    334


Q ss_pred             HHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCC-CCCCCchhhhHHHH
Q 043380          139 LLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDS-TGTISPEVQEEAGH  217 (246)
Q Consensus       139 ~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~  217 (246)
                      +...|-+++    |++.-++..+.      -+.|.-+-.++...+-..|++.++.+...+-..+= .+......   -|.
T Consensus       185 L~E~g~y~d----AEk~A~ralqi------N~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~s~mlasH---NyW  251 (491)
T KOG2610|consen  185 LEECGIYDD----AEKQADRALQI------NRFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWMLASH---NYW  251 (491)
T ss_pred             HHHhccchh----HHHHHHhhccC------CCcchHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHHHhh---hhH
Confidence            556899999    99887777664      24566777788888888999999998887764321 11111111   355


Q ss_pred             HHHHHHHhcCChhHHHHHHHH
Q 043380          218 LLMEAALNDGQVDLALDKLSN  238 (246)
Q Consensus       218 ~li~~~~~~g~~~~a~~~~~~  238 (246)
                      ...-.++..+.++.|+++|++
T Consensus       252 H~Al~~iE~aeye~aleIyD~  272 (491)
T KOG2610|consen  252 HTALFHIEGAEYEKALEIYDR  272 (491)
T ss_pred             HHHHhhhcccchhHHHHHHHH
Confidence            566667788999999999975

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=94.66  E-value=1.9  Score=34.85  Aligned_cols=196  Identities=8%  Similarity=-0.008  Sum_probs=124.5

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHH-HHH
Q 043380           21 NAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTY-ATL   99 (246)
Q Consensus        21 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~-~~l   99 (246)
                      --+-..+.-.|++.+|+.-|.....+-+.+-.++----..|...|+-..|+.=+...++.         +||-..- .--
T Consensus        42 lElGk~lla~~Q~sDALt~yHaAve~dp~~Y~aifrRaT~yLAmGksk~al~Dl~rVlel---------KpDF~~ARiQR  112 (504)
T KOG0624|consen   42 LELGKELLARGQLSDALTHYHAAVEGDPNNYQAIFRRATVYLAMGKSKAALQDLSRVLEL---------KPDFMAARIQR  112 (504)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhcCCccchhhHHHHHhc---------CccHHHHHHHh
Confidence            344455556667777776666655443334444444455677778888888888887765         6774321 111


Q ss_pred             HHHHHccCCHHHHHHHHHHHHhCCCCC------------CCHHH--HHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcC
Q 043380          100 LMGFRHAKDLQSLLEIVFEMKSCCNLI------------LDRST--FTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCS  165 (246)
Q Consensus       100 l~~~~~~~~~~~a~~~~~~m~~~~~~~------------p~~~~--~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~  165 (246)
                      -..+.+.|.++.|..=|+.... ..-.            +....  .-..+..+...|+...    |+.....+.+.   
T Consensus       113 g~vllK~Gele~A~~DF~~vl~-~~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~----ai~~i~~llEi---  184 (504)
T KOG0624|consen  113 GVVLLKQGELEQAEADFDQVLQ-HEPSNGLVLEAQSKLALIQEHWVLVQQLKSASGSGDCQN----AIEMITHLLEI---  184 (504)
T ss_pred             chhhhhcccHHHHHHHHHHHHh-cCCCcchhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhh----HHHHHHHHHhc---
Confidence            2335688999999999998887 3211            11111  2234556677888888    99988888875   


Q ss_pred             CCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          166 NPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       166 ~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                         ..-|...|..=..+|...|++..|..=+....+....+.      .++--+-..+...|+.+.++..+++.++-
T Consensus       185 ---~~Wda~l~~~Rakc~i~~~e~k~AI~Dlk~askLs~DnT------e~~ykis~L~Y~vgd~~~sL~~iRECLKl  252 (504)
T KOG0624|consen  185 ---QPWDASLRQARAKCYIAEGEPKKAIHDLKQASKLSQDNT------EGHYKISQLLYTVGDAENSLKEIRECLKL  252 (504)
T ss_pred             ---CcchhHHHHHHHHHHHhcCcHHHHHHHHHHHHhccccch------HHHHHHHHHHHhhhhHHHHHHHHHHHHcc
Confidence               344667788888899999999888877666553321111      14445556666777777777777666543

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

Probab=94.66  E-value=2.6  Score=36.42  Aligned_cols=164  Identities=14%  Similarity=0.140  Sum_probs=112.8

Q ss_pred             HHHHHHHHHHhc--CCHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHHhcCCcchHHHHHH--------HHHhccCCCCCC
Q 043380           19 VMNAVIEASREA--QRIDEAYQILESVEKGLEPD-SLSYNILISACIKTKKLDVTMPFNE--------QLKDNGQKCSSG   87 (246)
Q Consensus        19 ~~~~li~~~~~~--g~~~~a~~~~~~~~~~~~~~-~~t~~~li~~~~~~~~~~~a~~~~~--------~m~~~~~~~~~~   87 (246)
                      .+.+++..+.+.  ....++.+++...-.+.+-+ ....-+++......|+++.|.+++.        .+.+.       
T Consensus       341 ~~~~ll~~~t~~~~~~~~ka~e~L~~~~~~~p~~s~~v~L~~aQl~is~gn~~~A~~il~~~~~~~~ss~~~~-------  413 (652)
T KOG2376|consen  341 LFPILLQEATKVREKKHKKAIELLLQFADGHPEKSKVVLLLRAQLKISQGNPEVALEILSLFLESWKSSILEA-------  413 (652)
T ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHhccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhhhhhhhh-------
Confidence            445555554443  23677778877776544433 4555667777888999999999999        44443       


Q ss_pred             CCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhC----CCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           88 GFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSC----CNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        88 ~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~----~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      +..|-  +...+...+.+.++-+.|-.++++...-    ....+. ..++.-....-.+.|+.++    |..+++++.+.
T Consensus       414 ~~~P~--~V~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~~l~~~~~~aa~f~lr~G~~~e----a~s~leel~k~  487 (652)
T KOG2376|consen  414 KHLPG--TVGAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGSIALLSLMREAAEFKLRHGNEEE----ASSLLEELVKF  487 (652)
T ss_pred             ccChh--HHHHHHHHHHhccCCccHHHHHHHHHHHHHHhcccchHHHhHHHHHhHHHHhcCchHH----HHHHHHHHHHh
Confidence            44444  5556777787888777777776654330    001111 2334444555566899999    99999999985


Q ss_pred             hcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCC
Q 043380          163 VCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPD  202 (246)
Q Consensus       163 ~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  202 (246)
                            ..+|..+...++.+|++. +++.|+.+-..+.+.
T Consensus       488 ------n~~d~~~l~~lV~a~~~~-d~eka~~l~k~L~p~  520 (652)
T KOG2376|consen  488 ------NPNDTDLLVQLVTAYARL-DPEKAESLSKKLPPL  520 (652)
T ss_pred             ------CCchHHHHHHHHHHHHhc-CHHHHHHHhhcCCCc
Confidence                  568889999999999977 889999988887643

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=94.44  E-value=0.11  Score=28.09  Aligned_cols=30  Identities=27%  Similarity=0.003  Sum_probs=23.1

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          215 AGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       215 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      ++..+...|...|++++|+++|++..+..+
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~~P   32 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALALDP   32 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCc
Confidence            567777888888888888888888777654

>PRK15331 chaperone protein SicA; Provisional

Probab=94.44  E-value=0.43  Score=34.17  Aligned_cols=87  Identities=13%  Similarity=-0.076  Sum_probs=41.1

Q ss_pred             HhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHh
Q 043380           62 IKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLY  141 (246)
Q Consensus        62 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~  141 (246)
                      ...|++++|..+|.-+.-.+        .-+..-|..|-.++-..+++++|...|.......--.|.+  +-....+|..
T Consensus        48 y~~Gk~~eA~~~F~~L~~~d--------~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~~dp~p--~f~agqC~l~  117 (165)
T PRK15331         48 YNQGRLDEAETFFRFLCIYD--------FYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLKNDYRP--VFFTGQCQLL  117 (165)
T ss_pred             HHCCCHHHHHHHHHHHHHhC--------cCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCCc--cchHHHHHHH
Confidence            34555666666665555431        1122234444444455555666655555432222111222  2224455555


Q ss_pred             cCChhhhhhHHHHHHHHHHHh
Q 043380          142 SGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       142 ~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      .|+.+.    |...|+.....
T Consensus       118 l~~~~~----A~~~f~~a~~~  134 (165)
T PRK15331        118 MRKAAK----ARQCFELVNER  134 (165)
T ss_pred             hCCHHH----HHHHHHHHHhC
Confidence            556665    66666555555

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=94.41  E-value=0.11  Score=26.70  Aligned_cols=26  Identities=15%  Similarity=0.138  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHH
Q 043380          215 AGHLLMEAALNDGQVDLALDKLSNTI  240 (246)
Q Consensus       215 ~~~~li~~~~~~g~~~~a~~~~~~m~  240 (246)
                      +|..|...|.+.|++++|+++|++..
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL   26 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQAL   26 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            46778888899999999999988843

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=94.41  E-value=2.8  Score=35.63  Aligned_cols=108  Identities=11%  Similarity=0.099  Sum_probs=70.3

Q ss_pred             cCCcchHHHHHHHHHhccCCC-------C----------CCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCC
Q 043380           64 TKKLDVTMPFNEQLKDNGQKC-------S----------SGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLI  126 (246)
Q Consensus        64 ~~~~~~a~~~~~~m~~~~~~~-------~----------~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~  126 (246)
                      .....+++++|++..+.|-..       .          .....|-..+=..|-.++.+.|+.++|.+.|.+|.+.....
T Consensus       213 A~Ti~Eae~l~rqAvkAgE~~lg~s~~~~~~g~~~e~~~~Rdt~~~~y~KrRLAmCarklGr~~EAIk~~rdLlke~p~~  292 (539)
T PF04184_consen  213 ASTIVEAEELLRQAVKAGEASLGKSQFLQHHGHFWEAWHRRDTNVLVYAKRRLAMCARKLGRLREAIKMFRDLLKEFPNL  292 (539)
T ss_pred             ccCHHHHHHHHHHHHHHHHHhhchhhhhhcccchhhhhhccccchhhhhHHHHHHHHHHhCChHHHHHHHHHHHhhCCcc
Confidence            344677888888777654110       0          11112223334456777788999999999999998723211


Q ss_pred             CCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch--hhHHHHHH
Q 043380          127 LDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP--HLYVSMMH  181 (246)
Q Consensus       127 p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~--~~~~~li~  181 (246)
                      -.......|+.++...+.+.+    +..++..-.+.      ..|..  ..|+..+-
T Consensus       293 ~~l~IrenLie~LLelq~Yad----~q~lL~kYdDi------~lpkSAti~YTaALL  339 (539)
T PF04184_consen  293 DNLNIRENLIEALLELQAYAD----VQALLAKYDDI------SLPKSATICYTAALL  339 (539)
T ss_pred             chhhHHHHHHHHHHhcCCHHH----HHHHHHHhccc------cCCchHHHHHHHHHH
Confidence            224567789999999999999    99999887543      23443  55666553

The molecular function of this protein is uncertain.

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=94.40  E-value=0.0037  Score=43.94  Aligned_cols=129  Identities=16%  Similarity=0.142  Sum_probs=75.6

Q ss_pred             HHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHH
Q 043380           57 LISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMV  136 (246)
Q Consensus        57 li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li  136 (246)
                      ++..+.+.+.+.....+++.+...       +...+....+.++..|++.++.++..++++..   .+     .-...++
T Consensus        13 vi~~~~~~~~~~~l~~yLe~~~~~-------~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~~---~~-----yd~~~~~   77 (143)
T PF00637_consen   13 VISAFEERNQPEELIEYLEALVKE-------NKENNPDLHTLLLELYIKYDPYEKLLEFLKTS---NN-----YDLDKAL   77 (143)
T ss_dssp             CHHHCTTTT-GGGCTCCHHHHHHT-------STC-SHHHHHHHHHHHHCTTTCCHHHHTTTSS---SS-----S-CTHHH
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHhc-------ccccCHHHHHHHHHHHHhcCCchHHHHHcccc---cc-----cCHHHHH
Confidence            455666677778888888888765       44566777888888888887777777776621   11     2223466


Q ss_pred             HHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHH
Q 043380          137 DALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAG  216 (246)
Q Consensus       137 ~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  216 (246)
                      ..|-+.|.+++    |.-++..+...        ..      .+..+...++++.|.+++.+...       +.    .|
T Consensus        78 ~~c~~~~l~~~----a~~Ly~~~~~~--------~~------al~i~~~~~~~~~a~e~~~~~~~-------~~----l~  128 (143)
T PF00637_consen   78 RLCEKHGLYEE----AVYLYSKLGNH--------DE------ALEILHKLKDYEEAIEYAKKVDD-------PE----LW  128 (143)
T ss_dssp             HHHHTTTSHHH----HHHHHHCCTTH--------TT------CSSTSSSTHCSCCCTTTGGGCSS-------SH----HH
T ss_pred             HHHHhcchHHH----HHHHHHHcccH--------HH------HHHHHHHHccHHHHHHHHHhcCc-------HH----HH
Confidence            66667777777    66666554332        00      11113344556666644444422       11    67


Q ss_pred             HHHHHHHHhcCCh
Q 043380          217 HLLMEAALNDGQV  229 (246)
Q Consensus       217 ~~li~~~~~~g~~  229 (246)
                      ..+++.|...+..
T Consensus       129 ~~l~~~~l~~~~~  141 (143)
T PF00637_consen  129 EQLLKYCLDSKPF  141 (143)
T ss_dssp             HHHHHHHCTSTCT
T ss_pred             HHHHHHHHhcCcc
Confidence            8888877766543

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.

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=94.28  E-value=0.32  Score=31.34  Aligned_cols=51  Identities=18%  Similarity=0.207  Sum_probs=34.2

Q ss_pred             HhcccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 043380            9 NREHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILIS   59 (246)
Q Consensus         9 ~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~   59 (246)
                      ....+-|++.+.++.+.+|-|.+++..|.++|+-++..+..+...|..++.
T Consensus        34 ~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~~~~~~~y~~~lq   84 (103)
T cd00923          34 FGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKCGAHKEIYPYILQ   84 (103)
T ss_pred             hccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccCchhhHHHHHH
Confidence            333467777778888888888888888888888776434444445655543

Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=94.26  E-value=0.28  Score=31.94  Aligned_cols=49  Identities=16%  Similarity=0.229  Sum_probs=31.4

Q ss_pred             cccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 043380           11 EHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILIS   59 (246)
Q Consensus        11 ~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~   59 (246)
                      ..+-|++.+..+.+.+|-|.+++..|.++|+-++..+.+....|..++.
T Consensus        39 ~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~~~~~~Y~~~lq   87 (108)
T PF02284_consen   39 YDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKCGNKKEIYPYILQ   87 (108)
T ss_dssp             SSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTTT-TTHHHHHHH
T ss_pred             cccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccChHHHHHHHHH
Confidence            3377888888888888888888888888888887434444446666544

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 ....

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=94.25  E-value=0.63  Score=30.37  Aligned_cols=62  Identities=15%  Similarity=0.127  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHH
Q 043380          109 LQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMH  181 (246)
Q Consensus       109 ~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~  181 (246)
                      .-+..+-++.+.. ..+.|++....+.+++|.+.+++..    |.++|+.++.+      +.+....|..++.
T Consensus        26 ~we~rrglN~l~~-~DlVP~P~ii~aALrAcRRvND~a~----AVR~lE~iK~K------~~~~~~~Y~~~lq   87 (108)
T PF02284_consen   26 GWELRRGLNNLFG-YDLVPEPKIIEAALRACRRVNDFAL----AVRILEGIKDK------CGNKKEIYPYILQ   87 (108)
T ss_dssp             HHHHHHHHHHHTT-SSB---HHHHHHHHHHHHHTT-HHH----HHHHHHHHHHH------TTT-TTHHHHHHH
T ss_pred             HHHHHHHHHHHhc-cccCCChHHHHHHHHHHHHhhhHHH----HHHHHHHHHHH------ccChHHHHHHHHH
Confidence            3456667777777 7788888888888888888888888    88888888886      3333336666654

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 ....

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=94.10  E-value=1.3  Score=30.60  Aligned_cols=139  Identities=14%  Similarity=0.131  Sum_probs=79.9

Q ss_pred             HhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHh
Q 043380           62 IKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLY  141 (246)
Q Consensus        62 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~  141 (246)
                      .-.|..++..+++.+...+          .+..-||.+|--...+-+=+-..++++.+-+...+.              .
T Consensus        13 ildG~V~qGveii~k~v~S----------sni~E~NWvICNiiDaa~C~yvv~~LdsIGkiFDis--------------~   68 (161)
T PF09205_consen   13 ILDGDVKQGVEIIEKTVNS----------SNIKEYNWVICNIIDAADCDYVVETLDSIGKIFDIS--------------K   68 (161)
T ss_dssp             HHTT-HHHHHHHHHHHHHH----------S-HHHHTHHHHHHHHH--HHHHHHHHHHHGGGS-GG--------------G
T ss_pred             HHhchHHHHHHHHHHHcCc----------CCccccceeeeecchhhchhHHHHHHHHHhhhcCch--------------h
Confidence            3467888888999888875          456677777766666666677777777776632222              1


Q ss_pred             cCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHH
Q 043380          142 SGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLME  221 (246)
Q Consensus       142 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~  221 (246)
                      +|++..    ....+-.+..          +..-+..-+..+..+|+-|+-.++...+.+.+.  .+|.    ..-.+..
T Consensus        69 C~NlKr----Vi~C~~~~n~----------~se~vD~ALd~lv~~~kkDqLdki~~~l~kn~~--~~p~----~L~kia~  128 (161)
T PF09205_consen   69 CGNLKR----VIECYAKRNK----------LSEYVDLALDILVKQGKKDQLDKIYNELKKNEE--INPE----FLVKIAN  128 (161)
T ss_dssp             -S-THH----HHHHHHHTT-------------HHHHHHHHHHHHTT-HHHHHHHHHHH-------S-HH----HHHHHHH
T ss_pred             hcchHH----HHHHHHHhcc----------hHHHHHHHHHHHHHhccHHHHHHHHHHHhhccC--CCHH----HHHHHHH
Confidence            333333    3333322211          222334456666777888888888888775322  4444    3567888


Q ss_pred             HHHhcCChhHHHHHHHHHHhhcc
Q 043380          222 AALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       222 ~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      +|.+.|+..++-+++++..++|.
T Consensus       129 Ay~klg~~r~~~ell~~ACekG~  151 (161)
T PF09205_consen  129 AYKKLGNTREANELLKEACEKGL  151 (161)
T ss_dssp             HHHHTT-HHHHHHHHHHHHHTT-
T ss_pred             HHHHhcchhhHHHHHHHHHHhch
Confidence            88888888888888888887773

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>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=93.97  E-value=1.8  Score=31.70  Aligned_cols=101  Identities=9%  Similarity=0.032  Sum_probs=72.9

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC--HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD--RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP  171 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~--~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p  171 (246)
                      ..+..+...|++.|+.+.|.+.|.++.+ ....|.  ...+-.+|+.....+++..    +.....+.......  +-.+
T Consensus        37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~-~~~~~~~~id~~l~~irv~i~~~d~~~----v~~~i~ka~~~~~~--~~d~  109 (177)
T PF10602_consen   37 MALEDLADHYCKIGDLEEALKAYSRARD-YCTSPGHKIDMCLNVIRVAIFFGDWSH----VEKYIEKAESLIEK--GGDW  109 (177)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhh-hcCCHHHHHHHHHHHHHHHHHhCCHHH----HHHHHHHHHHHHhc--cchH
Confidence            4788999999999999999999999998 655555  4557789999999999999    88888777665110  1112


Q ss_pred             ch----hhHHHHHHHHHhcCChhHHhhHHHhhCCCC
Q 043380          172 KP----HLYVSMMHELAARVDYDIVKSPYRRMWPDS  203 (246)
Q Consensus       172 ~~----~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  203 (246)
                      +.    ..|..+.  +...+++..|-+.|-+.....
T Consensus       110 ~~~nrlk~~~gL~--~l~~r~f~~AA~~fl~~~~t~  143 (177)
T PF10602_consen  110 ERRNRLKVYEGLA--NLAQRDFKEAAELFLDSLSTF  143 (177)
T ss_pred             HHHHHHHHHHHHH--HHHhchHHHHHHHHHccCcCC
Confidence            22    2222222  234678999999888876443

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.

>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=93.91  E-value=1.7  Score=31.35  Aligned_cols=136  Identities=11%  Similarity=0.112  Sum_probs=83.1

Q ss_pred             hhhhHHHHhcccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhcc
Q 043380            2 FEENEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNG   81 (246)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~   81 (246)
                      .+-+....+.+++|+...|..+++.+.+.|++.....++.   .++-+|.......+-.+..  ....+..+=-+|..+ 
T Consensus        14 lEYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~L~qllq---~~Vi~DSk~lA~~LLs~~~--~~~~~~Ql~lDMLkR-   87 (167)
T PF07035_consen   14 LEYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQLHQLLQ---YHVIPDSKPLACQLLSLGN--QYPPAYQLGLDMLKR-   87 (167)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHHHHHHHh---hcccCCcHHHHHHHHHhHc--cChHHHHHHHHHHHH-
Confidence            3455666777888898899999999999988766555443   3345555555544433332  233344444444432 


Q ss_pred             CCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHH
Q 043380           82 QKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVK  161 (246)
Q Consensus        82 ~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~  161 (246)
                             +   ...+..++..+...|++-+|.++...... .    +......++.+-...++...    -..+|+-...
T Consensus        88 -------L---~~~~~~iievLL~~g~vl~ALr~ar~~~~-~----~~~~~~~fLeAA~~~~D~~l----f~~V~~ff~~  148 (167)
T PF07035_consen   88 -------L---GTAYEEIIEVLLSKGQVLEALRYARQYHK-V----DSVPARKFLEAAANSNDDQL----FYAVFRFFEE  148 (167)
T ss_pred             -------h---hhhHHHHHHHHHhCCCHHHHHHHHHHcCC-c----ccCCHHHHHHHHHHcCCHHH----HHHHHHHHHH
Confidence                   0   01345677778888999888888877544 1    11222446777777777666    6666665555


Q ss_pred             h
Q 043380          162 R  162 (246)
Q Consensus       162 ~  162 (246)
                      +
T Consensus       149 ~  149 (167)
T PF07035_consen  149 R  149 (167)
T ss_pred             h
Confidence            4

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=93.90  E-value=1.4  Score=34.69  Aligned_cols=116  Identities=13%  Similarity=0.118  Sum_probs=86.0

Q ss_pred             CHHHHHHHHHHHH--hCCCCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccC
Q 043380           32 RIDEAYQILESVE--KGLEPDSLSYNILISACIKT--KKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAK  107 (246)
Q Consensus        32 ~~~~a~~~~~~~~--~~~~~~~~t~~~li~~~~~~--~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~  107 (246)
                      .+-+|+++|+...  ..+-.|......+++.....  .....-.++.+-+...      .+-.++..+...+|..++..+
T Consensus       143 ~Vv~aL~L~~~~~~~~~Ii~d~evislLL~sMv~~~~~~l~alYEvV~~l~~t------~~~~l~~~vi~~Il~~L~~~~  216 (292)
T PF13929_consen  143 IVVEALKLYDGLNPDESIIFDEEVISLLLKSMVIDENTKLNALYEVVDFLVST------FSKSLTRNVIISILEILAESR  216 (292)
T ss_pred             HHHHHHHHhhccCcccceeeChHHHHHHHHHHHhccccchhhHHHHHHHHHhc------cccCCChhHHHHHHHHHHhcc
Confidence            3566777777443  23566778888888887762  2345555566666543      245788889999999999999


Q ss_pred             CHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHH
Q 043380          108 DLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFG  157 (246)
Q Consensus       108 ~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~  157 (246)
                      +|.+-.++++......+..-|...|..+|......|+..-    ...+.+
T Consensus       217 dW~kl~~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~----~~kiI~  262 (292)
T PF13929_consen  217 DWNKLFQFWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEV----MRKIID  262 (292)
T ss_pred             cHHHHHHHHHHhcccCCCCCCCchHHHHHHHHHHcCCHHH----HHHHhh
Confidence            9999999999887733566678889999999999999887    665554

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=93.85  E-value=2.8  Score=37.84  Aligned_cols=83  Identities=10%  Similarity=0.093  Sum_probs=44.4

Q ss_pred             CHHHHHHHHHHHH----hcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCC
Q 043380           50 DSLSYNILISACI----KTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNL  125 (246)
Q Consensus        50 ~~~t~~~li~~~~----~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~  125 (246)
                      |..+...++..|+    +.|++++|...|-+-+..        ++|..     ++.-|.....+..--.+++.+.+ .|+
T Consensus       363 d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~--------le~s~-----Vi~kfLdaq~IknLt~YLe~L~~-~gl  428 (933)
T KOG2114|consen  363 DEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGF--------LEPSE-----VIKKFLDAQRIKNLTSYLEALHK-KGL  428 (933)
T ss_pred             CHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHccc--------CChHH-----HHHHhcCHHHHHHHHHHHHHHHH-ccc
Confidence            3334444444433    467777777777666653        45543     33444444455555555556555 544


Q ss_pred             CCCHHHHHHHHHHHHhcCChhh
Q 043380          126 ILDRSTFTAMVDALLYSGSIKV  147 (246)
Q Consensus       126 ~p~~~~~~~li~~~~~~~~~~~  147 (246)
                       .+...-+.|+.+|.+.++.+.
T Consensus       429 -a~~dhttlLLncYiKlkd~~k  449 (933)
T KOG2114|consen  429 -ANSDHTTLLLNCYIKLKDVEK  449 (933)
T ss_pred             -ccchhHHHHHHHHHHhcchHH
Confidence             233444556666666666655

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=93.81  E-value=0.87  Score=29.41  Aligned_cols=63  Identities=14%  Similarity=0.150  Sum_probs=46.0

Q ss_pred             CHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHH
Q 043380          108 DLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMH  181 (246)
Q Consensus       108 ~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~  181 (246)
                      |.-++.+-++.+.. ..+.|++....+-+++|.+.+++..    |.++|+.++.+      ...+...|..++.
T Consensus        22 D~we~rr~mN~l~~-~DlVP~P~ii~aaLrAcRRvND~al----AVR~lE~vK~K------~~~~~~~y~~~lq   84 (103)
T cd00923          22 DGWELRRGLNNLFG-YDLVPEPKVIEAALRACRRVNDFAL----AVRILEAIKDK------CGAHKEIYPYILQ   84 (103)
T ss_pred             cHHHHHHHHHHHhc-cccCCCcHHHHHHHHHHHHhhhHHH----HHHHHHHHHHH------ccCchhhHHHHHH
Confidence            45566777777777 7788888888888888888888888    88888888765      2333445555543

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.

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=93.70  E-value=2  Score=35.33  Aligned_cols=128  Identities=15%  Similarity=0.105  Sum_probs=89.4

Q ss_pred             HHHHhcCCcchHHHHHHHHHhccCCCCCCCC---------CccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCH
Q 043380           59 SACIKTKKLDVTMPFNEQLKDNGQKCSSGGF---------HPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDR  129 (246)
Q Consensus        59 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~---------~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~  129 (246)
                      +.|.+.|++..|..-|++....= . ...+.         ..-..+++.|..+|.+.+++..|++..+.... .+ .+|.
T Consensus       216 n~~fK~gk~~~A~~~Yerav~~l-~-~~~~~~~ee~~~~~~~k~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe-~~-~~N~  291 (397)
T KOG0543|consen  216 NVLFKEGKFKLAKKRYERAVSFL-E-YRRSFDEEEQKKAEALKLACHLNLAACYLKLKEYKEAIESCNKVLE-LD-PNNV  291 (397)
T ss_pred             hHHHhhchHHHHHHHHHHHHHHh-h-ccccCCHHHHHHHHHHHHHHhhHHHHHHHhhhhHHHHHHHHHHHHh-cC-CCch
Confidence            45778889999988888865430 0 00011         12234688899999999999999999999988 32 2446


Q ss_pred             HHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHH-HHHHHHhcCCh-hHHhhHHHhhCC
Q 043380          130 STFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVS-MMHELAARVDY-DIVKSPYRRMWP  201 (246)
Q Consensus       130 ~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~-li~~~~~~g~~-~~a~~~~~~~~~  201 (246)
                      -..----.+|...|+++.    |+..|+.+.+.       .|+...... ++.+-.+.... +...++|..|..
T Consensus       292 KALyRrG~A~l~~~e~~~----A~~df~ka~k~-------~P~Nka~~~el~~l~~k~~~~~~kekk~y~~mF~  354 (397)
T KOG0543|consen  292 KALYRRGQALLALGEYDL----ARDDFQKALKL-------EPSNKAARAELIKLKQKIREYEEKEKKMYANMFA  354 (397)
T ss_pred             hHHHHHHHHHHhhccHHH----HHHHHHHHHHh-------CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            677777889999999999    99999999885       676655544 44444444443 345677777763

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=93.39  E-value=1.8  Score=29.90  Aligned_cols=90  Identities=14%  Similarity=0.008  Sum_probs=71.1

Q ss_pred             HHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHH---HHHHH
Q 043380           60 ACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRST---FTAMV  136 (246)
Q Consensus        60 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~---~~~li  136 (246)
                      +.+..|+++.|++.|.+.+..        .+-....||.-..++.-.|+.++|++=+++..+-.|-. +...   |-.-.
T Consensus        52 alaE~g~Ld~AlE~F~qal~l--------~P~raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~-trtacqa~vQRg  122 (175)
T KOG4555|consen   52 ALAEAGDLDGALELFGQALCL--------APERASAYNNRAQALRLQGDDEEALDDLNKALELAGDQ-TRTACQAFVQRG  122 (175)
T ss_pred             HHHhccchHHHHHHHHHHHHh--------cccchHhhccHHHHHHHcCChHHHHHHHHHHHHhcCcc-chHHHHHHHHHH
Confidence            457789999999999999875        45578899999999999999999999999988844433 3333   33334


Q ss_pred             HHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          137 DALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       137 ~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ..|...|+-+.    |..=|+..-+.
T Consensus       123 ~lyRl~g~dd~----AR~DFe~AA~L  144 (175)
T KOG4555|consen  123 LLYRLLGNDDA----ARADFEAAAQL  144 (175)
T ss_pred             HHHHHhCchHH----HHHhHHHHHHh
Confidence            46777899999    98888877665

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=93.31  E-value=0.21  Score=25.68  Aligned_cols=23  Identities=17%  Similarity=0.232  Sum_probs=11.9

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHH
Q 043380           20 MNAVIEASREAQRIDEAYQILES   42 (246)
Q Consensus        20 ~~~li~~~~~~g~~~~a~~~~~~   42 (246)
                      |+.|-..|.+.|++++|.++|++
T Consensus         2 l~~Lg~~~~~~g~~~~Ai~~y~~   24 (36)
T PF13176_consen    2 LNNLGRIYRQQGDYEKAIEYYEQ   24 (36)
T ss_dssp             HHHHHHHHHHCT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHH
Confidence            44555555555555555555544

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=93.16  E-value=3.2  Score=32.11  Aligned_cols=159  Identities=8%  Similarity=0.049  Sum_probs=98.3

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCC--CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-----HH
Q 043380           22 AVIEASREAQRIDEAYQILESVEKGL--EPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-----IF   94 (246)
Q Consensus        22 ~li~~~~~~g~~~~a~~~~~~~~~~~--~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-----~~   94 (246)
                      .+..++.+.++.+.|...|++..+..  .|+ ..|...+.+.+....   ...++.......  .  ..-.++     ..
T Consensus        74 ~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~-~~~a~Y~~g~~~~~~---~~~~~~~~~~~~--~--~~rD~~~~~~A~~  145 (243)
T PRK10866         74 DLIYAYYKNADLPLAQAAIDRFIRLNPTHPN-IDYVLYMRGLTNMAL---DDSALQGFFGVD--R--SDRDPQHARAAFR  145 (243)
T ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHhCcCCCc-hHHHHHHHHHhhhhc---chhhhhhccCCC--c--cccCHHHHHHHHH
Confidence            45677889999999999999875322  232 334444554442110   001111111000  0  000111     12


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchh
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPH  174 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~  174 (246)
                      ++..+++-|=...-..+|..-+..+.. .   . ...--.+.+-|.+.|.+..    |..-++.+.+.+   |+.+....
T Consensus       146 ~~~~li~~yP~S~ya~~A~~rl~~l~~-~---l-a~~e~~ia~~Y~~~~~y~A----A~~r~~~v~~~Y---p~t~~~~e  213 (243)
T PRK10866        146 DFSKLVRGYPNSQYTTDATKRLVFLKD-R---L-AKYELSVAEYYTKRGAYVA----VVNRVEQMLRDY---PDTQATRD  213 (243)
T ss_pred             HHHHHHHHCcCChhHHHHHHHHHHHHH-H---H-HHHHHHHHHHHHHcCchHH----HHHHHHHHHHHC---CCCchHHH
Confidence            455555555555556777776666655 1   1 1112257778999999999    999999999984   45566678


Q ss_pred             hHHHHHHHHHhcCChhHHhhHHHhhC
Q 043380          175 LYVSMMHELAARVDYDIVKSPYRRMW  200 (246)
Q Consensus       175 ~~~~li~~~~~~g~~~~a~~~~~~~~  200 (246)
                      ....++.+|...|..++|..+...+.
T Consensus       214 al~~l~~ay~~lg~~~~a~~~~~~l~  239 (243)
T PRK10866        214 ALPLMENAYRQLQLNAQADKVAKIIA  239 (243)
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHh
Confidence            88899999999999999998887664

>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=93.00  E-value=3.7  Score=32.43  Aligned_cols=105  Identities=7%  Similarity=-0.003  Sum_probs=70.2

Q ss_pred             CHHHHHHHHHHHHhcCCH---HHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           16 NTIVMNAVIEASREAQRI---DEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~---~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      -..+...++.+|...+..   ++|..+++.+.+..+-.+..+-.-++.+.+.++.+++.+.+.+|+..        +.-.
T Consensus        83 r~~iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~~~~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~--------~~~~  154 (278)
T PF08631_consen   83 RLSILRLLANAYLEWDTYESVEKALNALRLLESEYGNKPEVFLLKLEILLKSFDEEEYEEILMRMIRS--------VDHS  154 (278)
T ss_pred             HHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHhccCChhHHHHHHHHHHHh--------cccc
Confidence            345677788888887775   45666777776544444667777788888889999999999999985        3324


Q ss_pred             HHHHHHHHHHH---HccCCHHHHHHHHHHHHhCCCCCCCHH
Q 043380           93 IFTYATLLMGF---RHAKDLQSLLEIVFEMKSCCNLILDRS  130 (246)
Q Consensus        93 ~~~~~~ll~~~---~~~~~~~~a~~~~~~m~~~~~~~p~~~  130 (246)
                      ...+..++..+   .... ...|...++.+.. ..+.|...
T Consensus       155 e~~~~~~l~~i~~l~~~~-~~~a~~~ld~~l~-~r~~~~~~  193 (278)
T PF08631_consen  155 ESNFDSILHHIKQLAEKS-PELAAFCLDYLLL-NRFKSSED  193 (278)
T ss_pred             cchHHHHHHHHHHHHhhC-cHHHHHHHHHHHH-HHhCCChh
Confidence            44555555555   4333 4556666666665 45656543

It is also involved in sporulation [].

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=92.93  E-value=2.2  Score=29.52  Aligned_cols=92  Identities=11%  Similarity=-0.046  Sum_probs=71.6

Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHH---HHHHHHH
Q 043380           25 EASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIF---TYATLLM  101 (246)
Q Consensus        25 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~---~~~~ll~  101 (246)
                      -+.+..|+++.|++.|.+...-.+-....||.--.++.-.|+.++|++=+++..+..      |-. +..   .|.---.
T Consensus        51 valaE~g~Ld~AlE~F~qal~l~P~raSayNNRAQa~RLq~~~e~ALdDLn~AleLa------g~~-trtacqa~vQRg~  123 (175)
T KOG4555|consen   51 IALAEAGDLDGALELFGQALCLAPERASAYNNRAQALRLQGDDEEALDDLNKALELA------GDQ-TRTACQAFVQRGL  123 (175)
T ss_pred             HHHHhccchHHHHHHHHHHHHhcccchHhhccHHHHHHHcCChHHHHHHHHHHHHhc------Ccc-chHHHHHHHHHHH
Confidence            356789999999999988765456788999999999999999999999998888762      222 222   3444445


Q ss_pred             HHHccCCHHHHHHHHHHHHhCCC
Q 043380          102 GFRHAKDLQSLLEIVFEMKSCCN  124 (246)
Q Consensus       102 ~~~~~~~~~~a~~~~~~m~~~~~  124 (246)
                      .|...|+.+.|..=|+...+ .|
T Consensus       124 lyRl~g~dd~AR~DFe~AA~-LG  145 (175)
T KOG4555|consen  124 LYRLLGNDDAARADFEAAAQ-LG  145 (175)
T ss_pred             HHHHhCchHHHHHhHHHHHH-hC
Confidence            57788999999998888777 55

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=92.90  E-value=2.2  Score=29.53  Aligned_cols=60  Identities=15%  Similarity=0.026  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHH
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEI  159 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m  159 (246)
                      ..+...+......|+-++-.+++..+.+ . -.+++...-.+..+|.+.|+..+    +.+++.+.
T Consensus        87 e~vD~ALd~lv~~~kkDqLdki~~~l~k-n-~~~~p~~L~kia~Ay~klg~~r~----~~ell~~A  146 (161)
T PF09205_consen   87 EYVDLALDILVKQGKKDQLDKIYNELKK-N-EEINPEFLVKIANAYKKLGNTRE----ANELLKEA  146 (161)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHH-------S-HHHHHHHHHHHHHTT-HHH----HHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHhh-c-cCCCHHHHHHHHHHHHHhcchhh----HHHHHHHH
Confidence            3444555555555655555555555543 1 22444445555556666666555    55555544

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]

Probab=92.66  E-value=6  Score=33.95  Aligned_cols=167  Identities=10%  Similarity=0.073  Sum_probs=119.0

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCC
Q 043380           46 GLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNL  125 (246)
Q Consensus        46 ~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~  125 (246)
                      ....|....-+++..++.+....-++.+-.+|..-         --+...|-.++.+|..+ ..++-..+|+++.+ .. 
T Consensus        61 ~~~l~d~~l~~~~~~f~~n~k~~~veh~c~~~l~~---------~e~kmal~el~q~y~en-~n~~l~~lWer~ve-~d-  128 (711)
T COG1747          61 KQLLDDSCLVTLLTIFGDNHKNQIVEHLCTRVLEY---------GESKMALLELLQCYKEN-GNEQLYSLWERLVE-YD-  128 (711)
T ss_pred             hccccchHHHHHHHHhccchHHHHHHHHHHHHHHh---------cchHHHHHHHHHHHHhc-CchhhHHHHHHHHH-hc-
Confidence            44667778888999999998888899999999886         36777899999999988 67788899998888 43 


Q ss_pred             CCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc------hhhHHHHHHHHHhcCChhHHhhHHHhh
Q 043380          126 ILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK------PHLYVSMMHELAARVDYDIVKSPYRRM  199 (246)
Q Consensus       126 ~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~------~~~~~~li~~~~~~g~~~~a~~~~~~~  199 (246)
                       -+.....--+..+...++...    +...|.....+      +.|-      ...|..++..  -..+.+....+...+
T Consensus       129 -fnDvv~~ReLa~~yEkik~sk----~a~~f~Ka~yr------fI~~~q~~~i~evWeKL~~~--i~dD~D~fl~l~~ki  195 (711)
T COG1747         129 -FNDVVIGRELADKYEKIKKSK----AAEFFGKALYR------FIPRRQNAAIKEVWEKLPEL--IGDDKDFFLRLQKKI  195 (711)
T ss_pred             -chhHHHHHHHHHHHHHhchhh----HHHHHHHHHHH------hcchhhhhhHHHHHHHHHHh--ccccHHHHHHHHHHH
Confidence             355555544444445588888    88888888775      3341      1345555532  145677777777777


Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          200 WPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       200 ~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      .... |.....+   .+.-+-.-|.-..++++|++++..+.+
T Consensus       196 qt~l-g~~~~~V---l~qdv~~~Ys~~eN~~eai~Ilk~il~  233 (711)
T COG1747         196 QTKL-GEGRGSV---LMQDVYKKYSENENWTEAIRILKHILE  233 (711)
T ss_pred             HHhh-ccchHHH---HHHHHHHHhccccCHHHHHHHHHHHhh
Confidence            6543 3233333   566677788889999999999886654

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=92.62  E-value=1.2  Score=39.44  Aligned_cols=109  Identities=14%  Similarity=0.014  Sum_probs=82.7

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchh
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPH  174 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~  174 (246)
                      +.+--+.-+...|+-.+|.++-.+.+-     ||...|..=+.+++..++|++    -+++-+.++           .+.
T Consensus       686 Sl~dTv~~li~~g~~k~a~ql~~~Fki-----pdKr~~wLk~~aLa~~~kwee----LekfAkskk-----------sPI  745 (829)
T KOG2280|consen  686 SLHDTVTTLILIGQNKRAEQLKSDFKI-----PDKRLWWLKLTALADIKKWEE----LEKFAKSKK-----------SPI  745 (829)
T ss_pred             cHHHHHHHHHHccchHHHHHHHHhcCC-----cchhhHHHHHHHHHhhhhHHH----HHHHHhccC-----------CCC
Confidence            344445556667999999988777766     899999999999999999998    554433332           145


Q ss_pred             hHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHH
Q 043380          175 LYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLS  237 (246)
Q Consensus       175 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~  237 (246)
                      -|.-++.+|.+.|+.++|.+++-++...              .-.+.+|.+.|++.+|.++--
T Consensus       746 Gy~PFVe~c~~~~n~~EA~KYiprv~~l--------------~ekv~ay~~~~~~~eAad~A~  794 (829)
T KOG2280|consen  746 GYLPFVEACLKQGNKDEAKKYIPRVGGL--------------QEKVKAYLRVGDVKEAADLAA  794 (829)
T ss_pred             CchhHHHHHHhcccHHHHhhhhhccCCh--------------HHHHHHHHHhccHHHHHHHHH
Confidence            5667999999999999999999887521              136788899999988887643

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.53  E-value=1.4  Score=35.16  Aligned_cols=102  Identities=15%  Similarity=0.219  Sum_probs=72.0

Q ss_pred             cccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCC
Q 043380           11 EHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKG----LEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSS   86 (246)
Q Consensus        11 ~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~----~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~   86 (246)
                      .|.+.++.+-..++..-....++++++..+-.+++.    ..|+. +-.+.++.+.+ -++++++.+...=++-      
T Consensus        58 ~g~~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~-~~~~~irlllk-y~pq~~i~~l~npIqY------  129 (418)
T KOG4570|consen   58 RGLPVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNW-TIHTWIRLLLK-YDPQKAIYTLVNPIQY------  129 (418)
T ss_pred             cCCCcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccc-cHHHHHHHHHc-cChHHHHHHHhCcchh------
Confidence            345556666666677666678889998888777642    12222 22344444444 3467787777777776      


Q ss_pred             CCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHh
Q 043380           87 GGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKS  121 (246)
Q Consensus        87 ~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~  121 (246)
                       |+-||..+++.+|+.+.+.+++.+|.++...|..
T Consensus       130 -GiF~dqf~~c~l~D~flk~~n~~~aa~vvt~~~~  163 (418)
T KOG4570|consen  130 -GIFPDQFTFCLLMDSFLKKENYKDAASVVTEVMM  163 (418)
T ss_pred             -ccccchhhHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence             8999999999999999999999998888777665

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=92.42  E-value=3.2  Score=30.29  Aligned_cols=199  Identities=17%  Similarity=0.056  Sum_probs=140.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHh--CCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHH
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEK--GLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIF   94 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~--~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~   94 (246)
                      ...+......+...+.+..+...+.....  ........+......+...+.+..+.+.+......       ...+ ..
T Consensus        59 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~-~~  130 (291)
T COG0457          59 AGLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEALELLEKALAL-------DPDP-DL  130 (291)
T ss_pred             hHHHHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHhhHHHHHHHHHHHHcC-------CCCc-ch
Confidence            56777888888888999998888877653  34556666777777778888889999999988875       2222 12


Q ss_pred             HHHHHHH-HHHccCCHHHHHHHHHHHHhCCCCCC----CHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCC
Q 043380           95 TYATLLM-GFRHAKDLQSLLEIVFEMKSCCNLIL----DRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGL  169 (246)
Q Consensus        95 ~~~~ll~-~~~~~~~~~~a~~~~~~m~~~~~~~p----~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~  169 (246)
                      ....... .+...|+++.|...+.....   ..|    ....+......+...++.+.    +...+......      .
T Consensus       131 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~----a~~~~~~~~~~------~  197 (291)
T COG0457         131 AEALLALGALYELGDYEEALELYEKALE---LDPELNELAEALLALGALLEALGRYEE----ALELLEKALKL------N  197 (291)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHh---cCCCccchHHHHHHhhhHHHHhcCHHH----HHHHHHHHHhh------C
Confidence            2233333 78889999999999999855   333    24445555555778889999    99999998875      3


Q ss_pred             Cc-chhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          170 WP-KPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       170 ~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                      .. ....+..+-..+...++++.+...+.........  ...    .+..+...+...+..+.+...+......
T Consensus       198 ~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~  265 (291)
T COG0457         198 PDDDAEALLNLGLLYLKLGKYEEALEYYEKALELDPD--NAE----ALYNLALLLLELGRYEEALEALEKALEL  265 (291)
T ss_pred             cccchHHHHHhhHHHHHcccHHHHHHHHHHHHhhCcc--cHH----HHhhHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            33 4677888888888899999999999988754322  011    3444444444777788888888776554

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=92.30  E-value=3.2  Score=34.38  Aligned_cols=169  Identities=11%  Similarity=-0.014  Sum_probs=106.5

Q ss_pred             CCHHHHHHHHH-HHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHH--HccCCHHHHHHHHHHHHhCCCC
Q 043380           49 PDSLSYNILIS-ACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGF--RHAKDLQSLLEIVFEMKSCCNL  125 (246)
Q Consensus        49 ~~~~t~~~li~-~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~--~~~~~~~~a~~~~~~m~~~~~~  125 (246)
                      |...+|-.+-. ++...+++++|.+.=...++.         .+ ...+...+++.  --.++.+.|...|++-..   +
T Consensus       166 pac~~a~~lka~cl~~~~~~~~a~~ea~~ilkl---------d~-~n~~al~vrg~~~yy~~~~~ka~~hf~qal~---l  232 (486)
T KOG0550|consen  166 PACFKAKLLKAECLAFLGDYDEAQSEAIDILKL---------DA-TNAEALYVRGLCLYYNDNADKAINHFQQALR---L  232 (486)
T ss_pred             chhhHHHHhhhhhhhhcccchhHHHHHHHHHhc---------cc-chhHHHHhcccccccccchHHHHHHHhhhhc---c
Confidence            33344443322 334567888888776666654         22 22445555553  356788899999988877   4


Q ss_pred             CCCHHHH-------------HHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHH
Q 043380          126 ILDRSTF-------------TAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIV  192 (246)
Q Consensus       126 ~p~~~~~-------------~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a  192 (246)
                      .|+-..-             ..=-.-..+.|++..    |.+.|.+-...+..  ++.|+...|.....+..+.|+..+|
T Consensus       233 dpdh~~sk~~~~~~k~le~~k~~gN~~fk~G~y~~----A~E~Yteal~idP~--n~~~naklY~nra~v~~rLgrl~ea  306 (486)
T KOG0550|consen  233 DPDHQKSKSASMMPKKLEVKKERGNDAFKNGNYRK----AYECYTEALNIDPS--NKKTNAKLYGNRALVNIRLGRLREA  306 (486)
T ss_pred             ChhhhhHHhHhhhHHHHHHHHhhhhhHhhccchhH----HHHHHHHhhcCCcc--ccchhHHHHHHhHhhhcccCCchhh
Confidence            4553221             111233456788898    99999988776332  5678888888888889999999999


Q ss_pred             hhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          193 KSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                      ..--+.....+...+.      +|-.=..++...+++++|.+-|+...+.
T Consensus       307 isdc~~Al~iD~syik------all~ra~c~l~le~~e~AV~d~~~a~q~  350 (486)
T KOG0550|consen  307 ISDCNEALKIDSSYIK------ALLRRANCHLALEKWEEAVEDYEKAMQL  350 (486)
T ss_pred             hhhhhhhhhcCHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            9888877653321111      2222233445567788888887766543

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=92.24  E-value=10  Score=35.79  Aligned_cols=194  Identities=14%  Similarity=0.067  Sum_probs=102.1

Q ss_pred             cCHHHHHHHHHHHHhcC--CHHHHHHHHHHHHh-C--------------CCCCHHHHHHHHH----------HHHhcCCc
Q 043380           15 LNTIVMNAVIEASREAQ--RIDEAYQILESVEK-G--------------LEPDSLSYNILIS----------ACIKTKKL   67 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g--~~~~a~~~~~~~~~-~--------------~~~~~~t~~~li~----------~~~~~~~~   67 (246)
                      |+ .-.-.+|.+|.+.+  .++.|+......+. .              +.+--..||..+.          |-....++
T Consensus       789 ~~-~~~~~ilTs~vk~~~~~ie~aL~kI~~l~~~~~~~~ad~al~hll~Lvdvn~lfn~ALgtYDl~Lal~VAq~SqkDP  867 (1265)
T KOG1920|consen  789 PD-KFNLFILTSYVKSNPPEIEEALQKIKELQLAQVAVSADEALKHLLFLVDVNELFNSALGTYDLDLALLVAQKSQKDP  867 (1265)
T ss_pred             cc-hhhHHHHHHHHhcCcHHHHHHHHHHHHHHhcccchhHHHHHHHHHhhccHHHHHHhhhcccchHHHHHHHHHhccCh
Confidence            44 45667889999988  77888877766652 1              1111122332222          22345566


Q ss_pred             chHHHHHHHHHhccCCCCCCCCCccHH--HHHHHHHHHHccC--CHHHHHHHHHHHHhCCC--------CCCCHHHH---
Q 043380           68 DVTMPFNEQLKDNGQKCSSGGFHPDIF--TYATLLMGFRHAK--DLQSLLEIVFEMKSCCN--------LILDRSTF---  132 (246)
Q Consensus        68 ~~a~~~~~~m~~~~~~~~~~~~~p~~~--~~~~ll~~~~~~~--~~~~a~~~~~~m~~~~~--------~~p~~~~~---  132 (246)
                      .+-+.++++++..  ......+..|..  -|...+..+.++|  -+++++.+.++    .|        ..||...+   
T Consensus       868 kEyLP~L~el~~m--~~~~rkF~ID~~L~ry~~AL~hLs~~~~~~~~e~~n~I~k----h~Ly~~aL~ly~~~~e~~k~i  941 (1265)
T KOG1920|consen  868 KEYLPFLNELKKM--ETLLRKFKIDDYLKRYEDALSHLSECGETYFPECKNYIKK----HGLYDEALALYKPDSEKQKVI  941 (1265)
T ss_pred             HHHHHHHHHHhhc--hhhhhheeHHHHHHHHHHHHHHHHHcCccccHHHHHHHHh----cccchhhhheeccCHHHHHHH
Confidence            7777777776643  011112333332  4556666666666  45555554332    22        24565544   


Q ss_pred             -HHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchh
Q 043380          133 -TAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEV  211 (246)
Q Consensus       133 -~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~  211 (246)
                       .+....+...+.+++    |--.|+..-+.              ..-+.+|-.+|+|++|..+..++........    
T Consensus       942 ~~~ya~hL~~~~~~~~----Aal~Ye~~Gkl--------------ekAl~a~~~~~dWr~~l~~a~ql~~~~de~~----  999 (1265)
T KOG1920|consen  942 YEAYADHLREELMSDE----AALMYERCGKL--------------EKALKAYKECGDWREALSLAAQLSEGKDELV----  999 (1265)
T ss_pred             HHHHHHHHHHhccccH----HHHHHHHhccH--------------HHHHHHHHHhccHHHHHHHHHhhcCCHHHHH----
Confidence             344445555667777    66666554332              3356677777777777777776653221000    


Q ss_pred             hhHHHHHHHHHHHhcCChhHHHHHHHHH
Q 043380          212 QEEAGHLLMEAALNDGQVDLALDKLSNT  239 (246)
Q Consensus       212 ~~~~~~~li~~~~~~g~~~~a~~~~~~m  239 (246)
                        .+-..|+.-+..+++.-+|-++..+-
T Consensus      1000 --~~a~~L~s~L~e~~kh~eAa~il~e~ 1025 (1265)
T KOG1920|consen 1000 --ILAEELVSRLVEQRKHYEAAKILLEY 1025 (1265)
T ss_pred             --HHHHHHHHHHHHcccchhHHHHHHHH
Confidence              02234555555555555555555443

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=92.18  E-value=4.4  Score=31.33  Aligned_cols=52  Identities=21%  Similarity=0.084  Sum_probs=22.4

Q ss_pred             HHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHH
Q 043380          182 ELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKL  236 (246)
Q Consensus       182 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~  236 (246)
                      -|.+.|.+..|..-+++|.+.-+.....   ....-.|.++|-..|..++|.+.-
T Consensus       176 yY~kr~~~~AA~nR~~~v~e~y~~t~~~---~eaL~~l~eaY~~lgl~~~a~~~~  227 (254)
T COG4105         176 YYLKRGAYVAAINRFEEVLENYPDTSAV---REALARLEEAYYALGLTDEAKKTA  227 (254)
T ss_pred             HHHHhcChHHHHHHHHHHHhccccccch---HHHHHHHHHHHHHhCChHHHHHHH
Confidence            3444555555555555544332111111   113444555555555555554443

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=91.86  E-value=5.3  Score=34.05  Aligned_cols=81  Identities=16%  Similarity=0.203  Sum_probs=58.1

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCC--CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-HHHHH
Q 043380           21 NAVIEASREAQRIDEAYQILESVEKGLEP--DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-IFTYA   97 (246)
Q Consensus        21 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~--~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~~   97 (246)
                      -.+-.++-+.|+.++|.+.|.+|.+..++  +......|+.++...+.+.++..++.+--+.       ..+.+ ...|+
T Consensus       263 rRLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi-------~lpkSAti~YT  335 (539)
T PF04184_consen  263 RRLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDI-------SLPKSATICYT  335 (539)
T ss_pred             HHHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccc-------cCCchHHHHHH
Confidence            34555666789999999999998643333  3456778999999999999999999997543       22222 34788


Q ss_pred             HHHHHHHccCC
Q 043380           98 TLLMGFRHAKD  108 (246)
Q Consensus        98 ~ll~~~~~~~~  108 (246)
                      ..+--+.+.++
T Consensus       336 aALLkaRav~d  346 (539)
T PF04184_consen  336 AALLKARAVGD  346 (539)
T ss_pred             HHHHHHHhhcc
Confidence            87766555544

The molecular function of this protein is uncertain.

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=91.78  E-value=2.7  Score=39.41  Aligned_cols=146  Identities=12%  Similarity=0.077  Sum_probs=97.9

Q ss_pred             HHHHHHHHHHhcC--CHHHHHHHHHHHH------hCCCCCHHHHHHHHHHHH----hcCCcchHHHHHHHHHhccCCCCC
Q 043380           19 VMNAVIEASREAQ--RIDEAYQILESVE------KGLEPDSLSYNILISACI----KTKKLDVTMPFNEQLKDNGQKCSS   86 (246)
Q Consensus        19 ~~~~li~~~~~~g--~~~~a~~~~~~~~------~~~~~~~~t~~~li~~~~----~~~~~~~a~~~~~~m~~~~~~~~~   86 (246)
                      -|...+....+.|  .++++..+.++-.      .-.+|+...+.-...+|+    ....+++|.-+|+..-+.      
T Consensus       895 ry~~AL~hLs~~~~~~~~e~~n~I~kh~Ly~~aL~ly~~~~e~~k~i~~~ya~hL~~~~~~~~Aal~Ye~~Gkl------  968 (1265)
T KOG1920|consen  895 RYEDALSHLSECGETYFPECKNYIKKHGLYDEALALYKPDSEKQKVIYEAYADHLREELMSDEAALMYERCGKL------  968 (1265)
T ss_pred             HHHHHHHHHHHcCccccHHHHHHHHhcccchhhhheeccCHHHHHHHHHHHHHHHHHhccccHHHHHHHHhccH------
Confidence            4555566666666  5666666655421      134677777766665554    467888888877765433      


Q ss_pred             CCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHH--HHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhc
Q 043380           87 GGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRST--FTAMVDALLYSGSIKVVGLYALCIFGEIVKRVC  164 (246)
Q Consensus        87 ~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~--~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~  164 (246)
                                .-.+.+|..+|+|.+|+.+-.++.. .   .|...  --.|+.-+...++.-+    |-++..+..+.  
T Consensus       969 ----------ekAl~a~~~~~dWr~~l~~a~ql~~-~---~de~~~~a~~L~s~L~e~~kh~e----Aa~il~e~~sd-- 1028 (1265)
T KOG1920|consen  969 ----------EKALKAYKECGDWREALSLAAQLSE-G---KDELVILAEELVSRLVEQRKHYE----AAKILLEYLSD-- 1028 (1265)
T ss_pred             ----------HHHHHHHHHhccHHHHHHHHHhhcC-C---HHHHHHHHHHHHHHHHHcccchh----HHHHHHHHhcC--
Confidence                      3567888899999999999888765 1   23222  2567888888888888    88887777654  


Q ss_pred             CCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCC
Q 043380          165 SNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWP  201 (246)
Q Consensus       165 ~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  201 (246)
                                 ..-.+..|++...|++|.++...-..
T Consensus      1029 -----------~~~av~ll~ka~~~~eAlrva~~~~~ 1054 (1265)
T KOG1920|consen 1029 -----------PEEAVALLCKAKEWEEALRVASKAKR 1054 (1265)
T ss_pred             -----------HHHHHHHHhhHhHHHHHHHHHHhccc
Confidence                       23345566777778888877776653

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.35  E-value=1.8  Score=34.54  Aligned_cols=50  Identities=20%  Similarity=0.270  Sum_probs=28.0

Q ss_pred             CHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          108 DLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       108 ~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      +++++..++..-.. .|+.||.+++..+|+.+.+.+++.+    |.++.-.|..+
T Consensus       115 ~pq~~i~~l~npIq-YGiF~dqf~~c~l~D~flk~~n~~~----aa~vvt~~~~q  164 (418)
T KOG4570|consen  115 DPQKAIYTLVNPIQ-YGIFPDQFTFCLLMDSFLKKENYKD----AASVVTEVMMQ  164 (418)
T ss_pred             ChHHHHHHHhCcch-hccccchhhHHHHHHHHHhcccHHH----HHHHHHHHHHH
Confidence            34455555555555 5555666666666666666666555    55555555444

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=91.26  E-value=0.59  Score=24.43  Aligned_cols=28  Identities=25%  Similarity=0.227  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          215 AGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       215 ~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                      +++.|...|...|++++|.+++++...-
T Consensus         4 ~~~~la~~~~~~g~~~~A~~~~~~al~~   31 (42)
T PF13374_consen    4 ALNNLANAYRAQGRYEEALELLEEALEI   31 (42)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhcchhhHHHHHHHHH
Confidence            5677777777777777777777776543

>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=91.23  E-value=4.1  Score=29.12  Aligned_cols=61  Identities=13%  Similarity=0.027  Sum_probs=45.4

Q ss_pred             HHHHHHHH---HHccCCHHHHHHHHHHHHhCCCCCCCHHHHH-HHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           95 TYATLLMG---FRHAKDLQSLLEIVFEMKSCCNLILDRSTFT-AMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        95 ~~~~ll~~---~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~-~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      +.+.|+..   -.+.++.+++..++..+.-   +.|...... .-...+...|+|.+    |.++|+++...
T Consensus         9 iv~gLie~~~~al~~~~~~D~e~lL~ALrv---LRP~~~e~~~~~~~l~i~r~~w~d----A~rlLr~l~~~   73 (160)
T PF09613_consen    9 IVGGLIEVLSVALRLGDPDDAEALLDALRV---LRPEFPELDLFDGWLHIVRGDWDD----ALRLLRELEER   73 (160)
T ss_pred             HHHHHHHHHHHHHccCChHHHHHHHHHHHH---hCCCchHHHHHHHHHHHHhCCHHH----HHHHHHHHhcc
Confidence            44444444   4677899999999999988   677744332 33445778999999    99999998775

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=91.22  E-value=0.64  Score=23.19  Aligned_cols=27  Identities=19%  Similarity=0.148  Sum_probs=17.9

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHh
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKS  121 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~  121 (246)
                      +|..+-.+|...|++++|...|++..+
T Consensus         3 ~~~~~g~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF00515_consen    3 AYYNLGNAYFQLGDYEEALEYYQRALE   29 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHH
Confidence            566666677777777777777776665

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 ....

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=91.05  E-value=5.9  Score=30.59  Aligned_cols=186  Identities=13%  Similarity=0.034  Sum_probs=84.3

Q ss_pred             HHHHHHHHHHHHhCCCCCH----HHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCC
Q 043380           33 IDEAYQILESVEKGLEPDS----LSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKD  108 (246)
Q Consensus        33 ~~~a~~~~~~~~~~~~~~~----~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~  108 (246)
                      ..++.+....-.....||.    ..|.-.-.+|....++++|...+.+..+        +.+-+...|.+       ..-
T Consensus         9 i~ea~e~~a~t~~~wkad~dgaas~yekAAvafRnAk~feKakdcLlkA~~--------~yEnnrslfhA-------AKa   73 (308)
T KOG1585|consen    9 ISEADEMTALTLTRWKADWDGAASLYEKAAVAFRNAKKFEKAKDCLLKASK--------GYENNRSLFHA-------AKA   73 (308)
T ss_pred             HHHHHHHHHHHhhccCCCchhhHHHHHHHHHHHHhhccHHHHHHHHHHHHH--------HHHhcccHHHH-------HHH
Confidence            3444444443332345553    3466666777788888888887777764        23333333222       122


Q ss_pred             HHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhh---------------hhhHHHHHHHHHHHhhcCCCCCCcch
Q 043380          109 LQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKV---------------VGLYALCIFGEIVKRVCSNPGLWPKP  173 (246)
Q Consensus       109 ~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~---------------~~~~a~~~~~~m~~~~~~~~~~~p~~  173 (246)
                      ++.|-.+.++|.+   +.--...|+--...|..+|.++.               .|+.|+++|++-..--......+.-.
T Consensus        74 yEqaamLake~~k---lsEvvdl~eKAs~lY~E~GspdtAAmaleKAak~lenv~Pd~AlqlYqralavve~~dr~~ma~  150 (308)
T KOG1585|consen   74 YEQAAMLAKELSK---LSEVVDLYEKASELYVECGSPDTAAMALEKAAKALENVKPDDALQLYQRALAVVEEDDRDQMAF  150 (308)
T ss_pred             HHHHHHHHHHHHH---hHHHHHHHHHHHHHHHHhCCcchHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHhccchHHHHH
Confidence            3333344444433   11112233344444444444443               01115555554433200000011112


Q ss_pred             hhHHHHHHHHHhcCChhHHhhHHHhhCCCCC--CCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHH
Q 043380          174 HLYVSMMHELAARVDYDIVKSPYRRMWPDST--GTISPEVQEEAGHLLMEAALNDGQVDLALDKLSN  238 (246)
Q Consensus       174 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~--~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  238 (246)
                      ..+...-+.+.+..++++|-..|.+-.....  ...+..  -..|-..|-.+....++..|+++++.
T Consensus       151 el~gk~sr~lVrl~kf~Eaa~a~lKe~~~~~~~~~y~~~--~k~~va~ilv~L~~~Dyv~aekc~r~  215 (308)
T KOG1585|consen  151 ELYGKCSRVLVRLEKFTEAATAFLKEGVAADKCDAYNSQ--CKAYVAAILVYLYAHDYVQAEKCYRD  215 (308)
T ss_pred             HHHHHhhhHhhhhHHhhHHHHHHHHhhhHHHHHhhcccH--HHHHHHHHHHHhhHHHHHHHHHHhcc
Confidence            2344444555555666655544443221000  000100  00355566666677788888888876

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=90.71  E-value=4.3  Score=33.68  Aligned_cols=91  Identities=7%  Similarity=-0.043  Sum_probs=69.4

Q ss_pred             HHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHH
Q 043380           61 CIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDAL  139 (246)
Q Consensus        61 ~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~  139 (246)
                      ..+.|++..|.+.|.+.+..    ...+..|+...|...-....+.|+.++|..--++..+   +.|. ...|..-..++
T Consensus       259 ~fk~G~y~~A~E~Yteal~i----dP~n~~~naklY~nra~v~~rLgrl~eaisdc~~Al~---iD~syikall~ra~c~  331 (486)
T KOG0550|consen  259 AFKNGNYRKAYECYTEALNI----DPSNKKTNAKLYGNRALVNIRLGRLREAISDCNEALK---IDSSYIKALLRRANCH  331 (486)
T ss_pred             HhhccchhHHHHHHHHhhcC----CccccchhHHHHHHhHhhhcccCCchhhhhhhhhhhh---cCHHHHHHHHHHHHHH
Confidence            35789999999999998764    3346677778888888899999999999999988877   3333 23333334456


Q ss_pred             HhcCChhhhhhHHHHHHHHHHHh
Q 043380          140 LYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       140 ~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ...++|++    |.+-|+...+.
T Consensus       332 l~le~~e~----AV~d~~~a~q~  350 (486)
T KOG0550|consen  332 LALEKWEE----AVEDYEKAMQL  350 (486)
T ss_pred             HHHHHHHH----HHHHHHHHHhh
Confidence            66789999    99999987775

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=90.56  E-value=8.9  Score=31.80  Aligned_cols=154  Identities=14%  Similarity=0.078  Sum_probs=89.3

Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCHHH--HHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH-HHHHHHHHHHH
Q 043380           28 REAQRIDEAYQILESVEKGLEPDSLS--YNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI-FTYATLLMGFR  104 (246)
Q Consensus        28 ~~~g~~~~a~~~~~~~~~~~~~~~~t--~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~-~~~~~ll~~~~  104 (246)
                      .-.|+.+.|.+-|+.|..  .|....  ..-|.-.--+.|..+.|..+-+..-..         .|.. -.+.+.+...+
T Consensus       131 l~eG~~~~Ar~kfeAMl~--dPEtRllGLRgLyleAqr~GareaAr~yAe~Aa~~---------Ap~l~WA~~AtLe~r~  199 (531)
T COG3898         131 LLEGDYEDARKKFEAMLD--DPETRLLGLRGLYLEAQRLGAREAARHYAERAAEK---------APQLPWAARATLEARC  199 (531)
T ss_pred             HhcCchHHHHHHHHHHhc--ChHHHHHhHHHHHHHHHhcccHHHHHHHHHHHHhh---------ccCCchHHHHHHHHHH
Confidence            347999999999999963  232221  222333335677777777776666553         3443 36778888888


Q ss_pred             ccCCHHHHHHHHHHHHhCCCCCCCHH--HHHHHHHHHHhc---CChhhhhhHHHHHHHHHHHhhcCCCCCCcchh-hHHH
Q 043380          105 HAKDLQSLLEIVFEMKSCCNLILDRS--TFTAMVDALLYS---GSIKVVGLYALCIFGEIVKRVCSNPGLWPKPH-LYVS  178 (246)
Q Consensus       105 ~~~~~~~a~~~~~~m~~~~~~~p~~~--~~~~li~~~~~~---~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~-~~~~  178 (246)
                      ..|||+.|+++.+.-+...-+.++..  .-..|+.+-+..   .+...    |...-.+-.       ++.||.. .-..
T Consensus       200 ~~gdWd~AlkLvd~~~~~~vie~~~aeR~rAvLLtAkA~s~ldadp~~----Ar~~A~~a~-------KL~pdlvPaav~  268 (531)
T COG3898         200 AAGDWDGALKLVDAQRAAKVIEKDVAERSRAVLLTAKAMSLLDADPAS----ARDDALEAN-------KLAPDLVPAAVV  268 (531)
T ss_pred             hcCChHHHHHHHHHHHHHHhhchhhHHHHHHHHHHHHHHHHhcCChHH----HHHHHHHHh-------hcCCccchHHHH
Confidence            88999999988887766333455532  223343332221   12222    443333322       2334432 1222


Q ss_pred             HHHHHHhcCChhHHhhHHHhhCCCC
Q 043380          179 MMHELAARVDYDIVKSPYRRMWPDS  203 (246)
Q Consensus       179 li~~~~~~g~~~~a~~~~~~~~~~~  203 (246)
                      -..++.+.|+..++-.+++.+.+..
T Consensus       269 AAralf~d~~~rKg~~ilE~aWK~e  293 (531)
T COG3898         269 AARALFRDGNLRKGSKILETAWKAE  293 (531)
T ss_pred             HHHHHHhccchhhhhhHHHHHHhcC
Confidence            3456777788888888888776543

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=90.46  E-value=4.7  Score=28.46  Aligned_cols=52  Identities=13%  Similarity=0.063  Sum_probs=40.0

Q ss_pred             HccCCHHHHHHHHHHHHhCCCCCCCHHHH-HHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          104 RHAKDLQSLLEIVFEMKSCCNLILDRSTF-TAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       104 ~~~~~~~~a~~~~~~m~~~~~~~p~~~~~-~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ...++++++..+++.|.-   +.|+..-. ..-...+..+|+|.+    |.++|+++...
T Consensus        21 L~~~d~~D~e~lLdALrv---LrP~~~e~d~~dg~l~i~rg~w~e----A~rvlr~l~~~   73 (153)
T TIGR02561        21 LRSADPYDAQAMLDALRV---LRPNLKELDMFDGWLLIARGNYDE----AARILRELLSS   73 (153)
T ss_pred             HhcCCHHHHHHHHHHHHH---hCCCccccchhHHHHHHHcCCHHH----HHHHHHhhhcc
Confidence            458899999999999988   66764322 223445678999999    99999999886

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>PF04097 Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic96 is a component of the nuclear pore complex

Probab=90.42  E-value=12  Score=33.26  Aligned_cols=46  Identities=15%  Similarity=0.159  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhc
Q 043380           18 IVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKT   64 (246)
Q Consensus        18 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~   64 (246)
                      .+| ++|--|.|+|++++|.++....+.........|...+..|...
T Consensus       113 p~W-a~Iyy~LR~G~~~~A~~~~~~~~~~~~~~~~~f~~~l~~~~~s  158 (613)
T PF04097_consen  113 PIW-ALIYYCLRCGDYDEALEVANENRNQFQKIERSFPTYLKAYASS  158 (613)
T ss_dssp             EHH-HHHHHHHTTT-HHHHHHHHHHTGGGS-TTTTHHHHHHHHCTTT
T ss_pred             ccH-HHHHHHHhcCCHHHHHHHHHHhhhhhcchhHHHHHHHHHHHhC
Confidence            356 7888899999999999999887777777778888999998775

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.

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=90.37  E-value=0.85  Score=23.78  Aligned_cols=25  Identities=20%  Similarity=0.284  Sum_probs=11.8

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHH
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEM  119 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m  119 (246)
                      +++.|-..|...|++++|..++++.
T Consensus         4 ~~~~la~~~~~~g~~~~A~~~~~~a   28 (42)
T PF13374_consen    4 ALNNLANAYRAQGRYEEALELLEEA   28 (42)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhcchhhHHHHHH
Confidence            4444445555555555555554443

>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=89.82  E-value=0.39  Score=33.52  Aligned_cols=86  Identities=10%  Similarity=0.016  Sum_probs=61.7

Q ss_pred             HHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhH
Q 043380          135 MVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEE  214 (246)
Q Consensus       135 li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~  214 (246)
                      +|..+.+.+.+..    ...+++.+...     +..-+....+.++..|++.++.++..++++....     ..      
T Consensus        13 vi~~~~~~~~~~~----l~~yLe~~~~~-----~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~~~~-----yd------   72 (143)
T PF00637_consen   13 VISAFEERNQPEE----LIEYLEALVKE-----NKENNPDLHTLLLELYIKYDPYEKLLEFLKTSNN-----YD------   72 (143)
T ss_dssp             CHHHCTTTT-GGG----CTCCHHHHHHT-----STC-SHHHHHHHHHHHHCTTTCCHHHHTTTSSSS-----S-------
T ss_pred             HHHHHHhCCCHHH----HHHHHHHHHhc-----ccccCHHHHHHHHHHHHhcCCchHHHHHcccccc-----cC------
Confidence            5677777888888    99999999876     4456678899999999999888888888773321     22      


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          215 AGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       215 ~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                       ...++..|.+.|.+++|.-++.++-.
T Consensus        73 -~~~~~~~c~~~~l~~~a~~Ly~~~~~   98 (143)
T PF00637_consen   73 -LDKALRLCEKHGLYEEAVYLYSKLGN   98 (143)
T ss_dssp             -CTHHHHHHHTTTSHHHHHHHHHCCTT
T ss_pred             -HHHHHHHHHhcchHHHHHHHHHHccc
Confidence             23366677777777777777765543

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.

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=89.81  E-value=0.79  Score=22.46  Aligned_cols=29  Identities=21%  Similarity=0.204  Sum_probs=21.5

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          216 GHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       216 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      +-.+..++.+.|++++|.+.|+++.++-+
T Consensus         3 ~~~~a~~~~~~g~~~~A~~~~~~~~~~~P   31 (33)
T PF13174_consen    3 LYRLARCYYKLGDYDEAIEYFQRLIKRYP   31 (33)
T ss_dssp             HHHHHHHHHHHCHHHHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHHCc
Confidence            33466677778888888888888877654

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=89.41  E-value=5.8  Score=27.92  Aligned_cols=94  Identities=16%  Similarity=0.185  Sum_probs=70.2

Q ss_pred             CCCccH--HHHHHHHHHHHccCCHHHHHHHHHHHHhCCC--C--CCCHHHHHHHHHHHHhcCC-hhhhhhHHHHHHHHHH
Q 043380           88 GFHPDI--FTYATLLMGFRHAKDLQSLLEIVFEMKSCCN--L--ILDRSTFTAMVDALLYSGS-IKVVGLYALCIFGEIV  160 (246)
Q Consensus        88 ~~~p~~--~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~--~--~p~~~~~~~li~~~~~~~~-~~~~~~~a~~~~~~m~  160 (246)
                      +..++.  ...|+++.-....+++.....+++.+..-..  +  ..+...|++++.+.+.... --.    +..+|+-|+
T Consensus        32 ~~~~~~k~~fiN~iL~hl~~~~nf~~~v~~L~~l~~l~~~~~~~~~~~ssf~~if~SlsnSsSaK~~----~~~Lf~~Lk  107 (145)
T PF13762_consen   32 NASQSTKTIFINCILNHLASYQNFSGVVSILEHLHFLNTDNIIGWLDNSSFHIIFKSLSNSSSAKLT----SLTLFNFLK  107 (145)
T ss_pred             ccChhHHHHHHHHHHHHHHHccchHHHHHHHHHHHHhhHHHHhhhcccchHHHHHHHHccChHHHHH----HHHHHHHHH
Confidence            455554  3678888888888999999998888855100  0  1344579999999977776 444    889999999


Q ss_pred             HhhcCCCCCCcchhhHHHHHHHHHhcCChh
Q 043380          161 KRVCSNPGLWPKPHLYVSMMHELAARVDYD  190 (246)
Q Consensus       161 ~~~~~~~~~~p~~~~~~~li~~~~~~g~~~  190 (246)
                      +.     +.+++..-|..||.++.+....+
T Consensus       108 ~~-----~~~~t~~dy~~li~~~l~g~~~~  132 (145)
T PF13762_consen  108 KN-----DIEFTPSDYSCLIKAALRGYFHD  132 (145)
T ss_pred             Hc-----CCCCCHHHHHHHHHHHHcCCCCc
Confidence            86     78999999999999987664333

>PRK11906 transcriptional regulator; Provisional

Probab=89.35  E-value=12  Score=31.64  Aligned_cols=161  Identities=10%  Similarity=0.021  Sum_probs=102.9

Q ss_pred             HHH--HHHHHHHHhc-----CCHHHHHHHHHHHH--hCCCCC-HHHHHHHHHHHHhc---------CCcchHHHHHHHHH
Q 043380           18 IVM--NAVIEASREA-----QRIDEAYQILESVE--KGLEPD-SLSYNILISACIKT---------KKLDVTMPFNEQLK   78 (246)
Q Consensus        18 ~~~--~~li~~~~~~-----g~~~~a~~~~~~~~--~~~~~~-~~t~~~li~~~~~~---------~~~~~a~~~~~~m~   78 (246)
                      ..|  ...+.+....     ...+.|+.+|.+..  +...|+ ...|..+-.++...         ....+|.++-++..
T Consensus       252 ~a~~~d~ylrg~~~~~~~t~~~~~~Al~lf~ra~~~~~ldp~~a~a~~~lA~~h~~~~~~g~~~~~~~~~~a~~~A~rAv  331 (458)
T PRK11906        252 NHYLSDEMLAGKKELYDFTPESIYRAMTIFDRLQNKSDIQTLKTECYCLLAECHMSLALHGKSELELAAQKALELLDYVS  331 (458)
T ss_pred             cchhhHHHHHHHHHhhccCHHHHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHH
Confidence            456  6666665552     23567888898875  334554 44454444443321         23345667777777


Q ss_pred             hccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHH
Q 043380           79 DNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFG  157 (246)
Q Consensus        79 ~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~  157 (246)
                      +.+        +-|......+-.+..-.++.+.|...|++...   +.|| ..+|...-..+..+|+.++    |.+.++
T Consensus       332 eld--------~~Da~a~~~~g~~~~~~~~~~~a~~~f~rA~~---L~Pn~A~~~~~~~~~~~~~G~~~~----a~~~i~  396 (458)
T PRK11906        332 DIT--------TVDGKILAIMGLITGLSGQAKVSHILFEQAKI---HSTDIASLYYYRALVHFHNEKIEE----ARICID  396 (458)
T ss_pred             hcC--------CCCHHHHHHHHHHHHhhcchhhHHHHHHHHhh---cCCccHHHHHHHHHHHHHcCCHHH----HHHHHH
Confidence            652        34666666666666777889999999999988   7788 6667777777788999999    999999


Q ss_pred             HHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHh
Q 043380          158 EIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRR  198 (246)
Q Consensus       158 ~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  198 (246)
                      +-.+.+    ..+.-.......++.|+.. ..+.|.+++-+
T Consensus       397 ~alrLs----P~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~  432 (458)
T PRK11906        397 KSLQLE----PRRRKAVVIKECVDMYVPN-PLKNNIKLYYK  432 (458)
T ss_pred             HHhccC----chhhHHHHHHHHHHHHcCC-chhhhHHHHhh
Confidence            865541    1222223344444566655 56677766654

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=89.34  E-value=1.5  Score=21.64  Aligned_cols=30  Identities=17%  Similarity=0.063  Sum_probs=22.0

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          215 AGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       215 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      .|..+-..+...|++++|++.|++..+..+
T Consensus         3 ~~~~lg~~~~~~~~~~~A~~~~~~al~l~p   32 (34)
T PF07719_consen    3 AWYYLGQAYYQLGNYEEAIEYFEKALELDP   32 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHHCc
Confidence            466777888888888888888888766543

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 ....

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=89.33  E-value=1.4  Score=21.86  Aligned_cols=29  Identities=21%  Similarity=0.039  Sum_probs=21.3

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhhc
Q 043380          215 AGHLLMEAALNDGQVDLALDKLSNTITRW  243 (246)
Q Consensus       215 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g  243 (246)
                      +|..+..+|...|++++|++.|++..+-.
T Consensus         3 ~~~~~g~~~~~~~~~~~A~~~~~~al~~~   31 (34)
T PF00515_consen    3 AYYNLGNAYFQLGDYEEALEYYQRALELD   31 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHHHC
Confidence            57777788888888888888888776543

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 ....

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=89.26  E-value=4.1  Score=30.84  Aligned_cols=80  Identities=10%  Similarity=0.012  Sum_probs=59.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHH
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYAT   98 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~   98 (246)
                      |.+..++.+.+.+.+++|+...++-.+.-+.|..+-+.++..+|-.|++++|..-++-.-+.     +....+-..+|..
T Consensus         3 Tl~~t~seLL~~~sL~dai~~a~~qVkakPtda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l-----~p~~t~~a~lyr~   77 (273)
T COG4455           3 TLRDTISELLDDNSLQDAIGLARDQVKAKPTDAGGRHFLFQLLCVAGDWEKALAQLNLAATL-----SPQDTVGASLYRH   77 (273)
T ss_pred             chHHHHHHHHHhccHHHHHHHHHHHHhcCCccccchhHHHHHHhhcchHHHHHHHHHHHhhc-----CcccchHHHHHHH
Confidence            34566788889999999999986644334668888899999999999999998776655443     1134455668888


Q ss_pred             HHHHH
Q 043380           99 LLMGF  103 (246)
Q Consensus        99 ll~~~  103 (246)
                      +|.+-
T Consensus        78 lir~e   82 (273)
T COG4455          78 LIRCE   82 (273)
T ss_pred             HHHHH
Confidence            88763

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=89.13  E-value=9.8  Score=30.18  Aligned_cols=149  Identities=13%  Similarity=0.096  Sum_probs=99.8

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHH
Q 043380           23 VIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMG  102 (246)
Q Consensus        23 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~  102 (246)
                      -.......|+..+|..+|.....--+-+...--.+..+|...|+.+.|..++..+-..       --.........-|..
T Consensus       140 ~~~~~~~~e~~~~a~~~~~~al~~~~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~-------~~~~~~~~l~a~i~l  212 (304)
T COG3118         140 EAKELIEAEDFGEAAPLLKQALQAAPENSEAKLLLAECLLAAGDVEAAQAILAALPLQ-------AQDKAAHGLQAQIEL  212 (304)
T ss_pred             HhhhhhhccchhhHHHHHHHHHHhCcccchHHHHHHHHHHHcCChHHHHHHHHhCccc-------chhhHHHHHHHHHHH
Confidence            3445677899999999998876434555677778899999999999999999998765       111222222234455


Q ss_pred             HHccCCHHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHH
Q 043380          103 FRHAKDLQSLLEIVFEMKSCCNLIL-DRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMH  181 (246)
Q Consensus       103 ~~~~~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~  181 (246)
                      +.+.....+..++-.+...    .| |...=..+...+...|+.+.    |.+.+=.+..++.   +. -|...-..|+.
T Consensus       213 l~qaa~~~~~~~l~~~~aa----dPdd~~aa~~lA~~~~~~g~~e~----Ale~Ll~~l~~d~---~~-~d~~~Rk~lle  280 (304)
T COG3118         213 LEQAAATPEIQDLQRRLAA----DPDDVEAALALADQLHLVGRNEA----ALEHLLALLRRDR---GF-EDGEARKTLLE  280 (304)
T ss_pred             HHHHhcCCCHHHHHHHHHh----CCCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHhcc---cc-cCcHHHHHHHH
Confidence            5555555555555555554    25 46666678889999999999    8877777666521   33 34455666666


Q ss_pred             HHHhcCChh
Q 043380          182 ELAARVDYD  190 (246)
Q Consensus       182 ~~~~~g~~~  190 (246)
                      .+..-|.-|
T Consensus       281 ~f~~~g~~D  289 (304)
T COG3118         281 LFEAFGPAD  289 (304)
T ss_pred             HHHhcCCCC
Confidence            666666443

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=89.12  E-value=7.3  Score=29.05  Aligned_cols=74  Identities=8%  Similarity=0.048  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChh
Q 043380          111 SLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYD  190 (246)
Q Consensus       111 ~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~  190 (246)
                      .|++.|-.+.. .+..-|+.....|..-|. ..+.++    +..++....+.+.  ++-.+|+..+.+|...+.+.|+++
T Consensus       124 ~A~~~fL~~E~-~~~l~t~elq~aLAtyY~-krD~~K----t~~ll~~~L~l~~--~~~~~n~eil~sLas~~~~~~~~e  195 (203)
T PF11207_consen  124 EALRRFLQLEG-TPELETAELQYALATYYT-KRDPEK----TIQLLLRALELSN--PDDNFNPEILKSLASIYQKLKNYE  195 (203)
T ss_pred             HHHHHHHHHcC-CCCCCCHHHHHHHHHHHH-ccCHHH----HHHHHHHHHHhcC--CCCCCCHHHHHHHHHHHHHhcchh
Confidence            34444444444 333333444444443333 233444    4444444443311  112344444555555555555444


Q ss_pred             HH
Q 043380          191 IV  192 (246)
Q Consensus       191 ~a  192 (246)
                      .|
T Consensus       196 ~A  197 (203)
T PF11207_consen  196 QA  197 (203)
T ss_pred             hh
Confidence            43

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=88.86  E-value=0.53  Score=38.83  Aligned_cols=67  Identities=13%  Similarity=0.052  Sum_probs=43.1

Q ss_pred             hhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHH
Q 043380          174 HLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTI  240 (246)
Q Consensus       174 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  240 (246)
                      ..|..|-..|.-.|+++.|....+.-......+-.....+.+++.|-.+++-.|+++.|.+.|+.-.
T Consensus       196 Ra~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hiflg~fe~A~ehYK~tl  262 (639)
T KOG1130|consen  196 RAYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFLGNFELAIEHYKLTL  262 (639)
T ss_pred             chhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhhcccHhHHHHHHHHH
Confidence            4566666666777889988877664221000001111123378889999999999999999987654

>PRK11906 transcriptional regulator; Provisional

Probab=88.30  E-value=15  Score=31.20  Aligned_cols=160  Identities=11%  Similarity=0.021  Sum_probs=100.2

Q ss_pred             HHH--HHHHHHHHhcC-----CcchHHHHHHHHHhccCCCCCCCCCccH-HHHHHHHHHHHc---------cCCHHHHHH
Q 043380           52 LSY--NILISACIKTK-----KLDVTMPFNEQLKDNGQKCSSGGFHPDI-FTYATLLMGFRH---------AKDLQSLLE  114 (246)
Q Consensus        52 ~t~--~~li~~~~~~~-----~~~~a~~~~~~m~~~~~~~~~~~~~p~~-~~~~~ll~~~~~---------~~~~~~a~~  114 (246)
                      ..|  ..++++.....     ..+.|..+|.+.....      .+.|+- ..|..+-.++..         ..+..+|.+
T Consensus       252 ~a~~~d~ylrg~~~~~~~t~~~~~~Al~lf~ra~~~~------~ldp~~a~a~~~lA~~h~~~~~~g~~~~~~~~~~a~~  325 (458)
T PRK11906        252 NHYLSDEMLAGKKELYDFTPESIYRAMTIFDRLQNKS------DIQTLKTECYCLLAECHMSLALHGKSELELAAQKALE  325 (458)
T ss_pred             cchhhHHHHHHHHHhhccCHHHHHHHHHHHHHHhhcc------cCCcccHHHHHHHHHHHHHHHHhcCCCchHHHHHHHH
Confidence            456  66777666532     3467888999998331      346653 344444333321         223455666


Q ss_pred             HHHHHHhCCCCCC-CHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch-hhHHHHHHHHHhcCChhHH
Q 043380          115 IVFEMKSCCNLIL-DRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP-HLYVSMMHELAARVDYDIV  192 (246)
Q Consensus       115 ~~~~m~~~~~~~p-~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~-~~~~~li~~~~~~g~~~~a  192 (246)
                      +-+...+   +.| |......+..+....++++.    |...|++....       .||. .+|...-..+.-.|+.++|
T Consensus       326 ~A~rAve---ld~~Da~a~~~~g~~~~~~~~~~~----a~~~f~rA~~L-------~Pn~A~~~~~~~~~~~~~G~~~~a  391 (458)
T PRK11906        326 LLDYVSD---ITTVDGKILAIMGLITGLSGQAKV----SHILFEQAKIH-------STDIASLYYYRALVHFHNEKIEEA  391 (458)
T ss_pred             HHHHHHh---cCCCCHHHHHHHHHHHHhhcchhh----HHHHHHHHhhc-------CCccHHHHHHHHHHHHHcCCHHHH
Confidence            6666666   434 47777777777788888999    99999998774       5665 5566666666778999999


Q ss_pred             hhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHH
Q 043380          193 KSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKL  236 (246)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~  236 (246)
                      .+.+++....++....    ...-...++.|+..+ ++.|++++
T Consensus       392 ~~~i~~alrLsP~~~~----~~~~~~~~~~~~~~~-~~~~~~~~  430 (458)
T PRK11906        392 RICIDKSLQLEPRRRK----AVVIKECVDMYVPNP-LKNNIKLY  430 (458)
T ss_pred             HHHHHHHhccCchhhH----HHHHHHHHHHHcCCc-hhhhHHHH
Confidence            9999996544322211    112333444555554 67777665

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=88.13  E-value=1.5  Score=21.56  Aligned_cols=27  Identities=7%  Similarity=0.068  Sum_probs=16.4

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHh
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKS  121 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~  121 (246)
                      .|..+-..+...|++++|.+.|++..+
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            345555666666677777666666655

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 ....

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=87.99  E-value=13  Score=30.13  Aligned_cols=200  Identities=12%  Similarity=0.084  Sum_probs=103.5

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCC-ccHHHHHHHHHH
Q 043380           24 IEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFH-PDIFTYATLLMG  102 (246)
Q Consensus        24 i~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~-p~~~~~~~ll~~  102 (246)
                      ..+.-+.|+++...+....... ..++...|.++...  +.++++++...++.....-..    .+. .....|......
T Consensus         5 ~eaaWrl~~Wd~l~~~~~~~~~-~~~~~~~~~al~~l--~~~~~~~~~~~i~~~r~~~~~----~l~~~~~~s~~~~y~~   77 (352)
T PF02259_consen    5 AEAAWRLGDWDLLEEYLSQSNE-DSPEYSFYRALLAL--RQGDYDEAKKYIEKARQLLLD----ELSALSSESYQRAYPS   77 (352)
T ss_pred             HHHHHhcCChhhHHHHHhhccC-CChhHHHHHHHHHH--hCccHHHHHHHHHHHHHHHHH----HHHHhhhhhHHHHHHH
Confidence            4566778888885555555542 12455555555443  778888888888877664100    000 111233333333


Q ss_pred             HHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHh-----cCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHH
Q 043380          103 FRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLY-----SGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYV  177 (246)
Q Consensus       103 ~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~-----~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~  177 (246)
                      ..+...+.+..++.+-... .  ..+......++.....     ..+++. -...+.+-..+...   -........+|.
T Consensus        78 l~~lq~L~Elee~~~~~~~-~--~~~~~~~~~l~~~W~~Rl~~~~~~~~~-~~~il~~R~~~l~~---~~~~~~~~~~~l  150 (352)
T PF02259_consen   78 LVKLQQLVELEEIIELKSN-L--SQNPQDLKSLLKRWRSRLPNMQDDFSV-WEPILSLRRLVLSL---ILLPEELAETWL  150 (352)
T ss_pred             HHHHhHHHHHHHHHHHHHh-h--cccHHHHHHHHHHHHHHHHHhccchHH-HHHHHHHHHHHHhc---ccchhHHHHHHH
Confidence            3333334444444433322 1  0011112222221111     111111 00011111112210   001234557899


Q ss_pred             HHHHHHHhcCChhHHhhHHHhhCCCCCCC--CCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          178 SMMHELAARVDYDIVKSPYRRMWPDSTGT--ISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       178 ~li~~~~~~g~~~~a~~~~~~~~~~~~~~--~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      .+.+.+.+.|+++.|...+..+...+...  ..|.    ..-.-.+.+-..|+..+|+..+++..+
T Consensus       151 ~~a~~aRk~g~~~~A~~~l~~~~~~~~~~~~~~~~----v~~e~akllw~~g~~~~Ai~~L~~~~~  212 (352)
T PF02259_consen  151 KFAKLARKAGNFQLALSALNRLFQLNPSSESLLPR----VFLEYAKLLWAQGEQEEAIQKLRELLK  212 (352)
T ss_pred             HHHHHHHHCCCcHHHHHHHHHHhccCCcccCCCcc----hHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            99999999999999999999987533111  1333    344456677788999999999988876

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=87.43  E-value=13  Score=29.49  Aligned_cols=117  Identities=10%  Similarity=0.186  Sum_probs=79.9

Q ss_pred             HHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCC--hhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhc
Q 043380          109 LQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGS--IKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAAR  186 (246)
Q Consensus       109 ~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~--~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~  186 (246)
                      +.+|+.+|+....+..+.-|..+...+++......+  ...    -.++.+-+...    .+-.++..+...+|..++..
T Consensus       144 Vv~aL~L~~~~~~~~~Ii~d~evislLL~sMv~~~~~~l~a----lYEvV~~l~~t----~~~~l~~~vi~~Il~~L~~~  215 (292)
T PF13929_consen  144 VVEALKLYDGLNPDESIIFDEEVISLLLKSMVIDENTKLNA----LYEVVDFLVST----FSKSLTRNVIISILEILAES  215 (292)
T ss_pred             HHHHHHHhhccCcccceeeChHHHHHHHHHHHhccccchhh----HHHHHHHHHhc----cccCCChhHHHHHHHHHHhc
Confidence            455666666332212355677778888887776322  233    45555555543    24678889999999999999


Q ss_pred             CChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHH
Q 043380          187 VDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLS  237 (246)
Q Consensus       187 g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~  237 (246)
                      +++.+..++++...........+.    .|..+|+.-...|+..-..++..
T Consensus       216 ~dW~kl~~fW~~~~~~~~~~~D~r----pW~~FI~li~~sgD~~~~~kiI~  262 (292)
T PF13929_consen  216 RDWNKLFQFWEQCIPNSVPGNDPR----PWAEFIKLIVESGDQEVMRKIID  262 (292)
T ss_pred             ccHHHHHHHHHHhcccCCCCCCCc----hHHHHHHHHHHcCCHHHHHHHhh
Confidence            999999999998775522222222    59999999999999877766654

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=87.14  E-value=16  Score=30.27  Aligned_cols=125  Identities=17%  Similarity=0.150  Sum_probs=82.3

Q ss_pred             HHHHHh---cCCHHHHHHHHHH-HHhCCCCCHHHHHHHHHHHHh---------cCCcchHHHHHHHHHhccCCCCCCCCC
Q 043380           24 IEASRE---AQRIDEAYQILES-VEKGLEPDSLSYNILISACIK---------TKKLDVTMPFNEQLKDNGQKCSSGGFH   90 (246)
Q Consensus        24 i~~~~~---~g~~~~a~~~~~~-~~~~~~~~~~t~~~li~~~~~---------~~~~~~a~~~~~~m~~~~~~~~~~~~~   90 (246)
                      .-++-|   .|+-++|++++.. +.+...++..+|..+.+.|-.         ...+++|...|.+.-+.         .
T Consensus       186 afALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~gL~GRIyKD~~~~s~~~d~~~ldkAi~~Y~kgFe~---------~  256 (374)
T PF13281_consen  186 AFALNRRNKPGDREKALQILLPVLESDENPDPDTLGLLGRIYKDLFLESNFTDRESLDKAIEWYRKGFEI---------E  256 (374)
T ss_pred             HHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHHHHHHHHHHHHHHHcCccchHHHHHHHHHHHHHHcC---------C
Confidence            334455   7999999999988 556667888999988877743         22468888888887764         4


Q ss_pred             ccHHHHHHHHHHHHccCC-H---HHHHHHH---HH-HHhCCCC---CCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHH
Q 043380           91 PDIFTYATLLMGFRHAKD-L---QSLLEIV---FE-MKSCCNL---ILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEI  159 (246)
Q Consensus        91 p~~~~~~~ll~~~~~~~~-~---~~a~~~~---~~-m~~~~~~---~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m  159 (246)
                      ||..+=-++...+...|. .   .+..++-   .. ..+ .|.   ..|=+.+.+++.++.-.|+.+.    |.+..+.|
T Consensus       257 ~~~Y~GIN~AtLL~~~g~~~~~~~el~~i~~~l~~llg~-kg~~~~~~dYWd~ATl~Ea~vL~~d~~k----a~~a~e~~  331 (374)
T PF13281_consen  257 PDYYSGINAATLLMLAGHDFETSEELRKIGVKLSSLLGR-KGSLEKMQDYWDVATLLEASVLAGDYEK----AIQAAEKA  331 (374)
T ss_pred             ccccchHHHHHHHHHcCCcccchHHHHHHHHHHHHHHHh-hccccccccHHHHHHHHHHHHHcCCHHH----HHHHHHHH
Confidence            555432222222323332 2   2233332   22 222 332   3456678899999999999999    99999999


Q ss_pred             HHh
Q 043380          160 VKR  162 (246)
Q Consensus       160 ~~~  162 (246)
                      ...
T Consensus       332 ~~l  334 (374)
T PF13281_consen  332 FKL  334 (374)
T ss_pred             hhc
Confidence            875

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=87.07  E-value=1.2  Score=24.14  Aligned_cols=25  Identities=24%  Similarity=0.247  Sum_probs=18.3

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhhc
Q 043380          219 LMEAALNDGQVDLALDKLSNTITRW  243 (246)
Q Consensus       219 li~~~~~~g~~~~a~~~~~~m~~~g  243 (246)
                      |..+|...|+.+.|.++++++...|
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~~~   29 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIEEG   29 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHcC
Confidence            5667777777777777777777544

This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=87.06  E-value=8.4  Score=28.75  Aligned_cols=21  Identities=0%  Similarity=0.029  Sum_probs=10.7

Q ss_pred             CCHHHHHHHHHHHHhcCChhh
Q 043380          127 LDRSTFTAMVDALLYSGSIKV  147 (246)
Q Consensus       127 p~~~~~~~li~~~~~~~~~~~  147 (246)
                      +|+..+.+|...|-+.|+++.
T Consensus       176 ~n~eil~sLas~~~~~~~~e~  196 (203)
T PF11207_consen  176 FNPEILKSLASIYQKLKNYEQ  196 (203)
T ss_pred             CCHHHHHHHHHHHHHhcchhh
Confidence            444445555555555555544

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=86.97  E-value=8.5  Score=33.72  Aligned_cols=29  Identities=21%  Similarity=0.220  Sum_probs=18.7

Q ss_pred             HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHH
Q 043380          129 RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVK  161 (246)
Q Consensus       129 ~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~  161 (246)
                      ..-|..|-++....+++..    |.++|.....
T Consensus       666 ~~Kw~~Lg~~al~~~~l~l----A~EC~~~a~d  694 (794)
T KOG0276|consen  666 EVKWRQLGDAALSAGELPL----ASECFLRARD  694 (794)
T ss_pred             hHHHHHHHHHHhhcccchh----HHHHHHhhcc
Confidence            4556667777777777777    7666665543

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=86.88  E-value=18  Score=30.67  Aligned_cols=200  Identities=12%  Similarity=0.076  Sum_probs=112.6

Q ss_pred             hcCCHHHHHHHHHHHHh---CCCC------------CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           29 EAQRIDEAYQILESVEK---GLEP------------DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        29 ~~g~~~~a~~~~~~~~~---~~~~------------~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      +.++.++|.+.+..-..   +..|            |-..=+....++...|++.++..++++++..   +..+...-+.
T Consensus        91 ~~k~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~---llkrE~~w~~  167 (549)
T PF07079_consen   91 KQKEYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIER---LLKRECEWNS  167 (549)
T ss_pred             HhhhHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHH---HhhhhhcccH
Confidence            56778888888755432   1111            2222356777888999999999999999876   1111223578


Q ss_pred             HHHHHHHHHHHccCC---------------HHHHHHHHHHHHhC-----CCCCCCHHHHHHHHHHHHhcCC--hhhhhhH
Q 043380           94 FTYATLLMGFRHAKD---------------LQSLLEIVFEMKSC-----CNLILDRSTFTAMVDALLYSGS--IKVVGLY  151 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~---------------~~~a~~~~~~m~~~-----~~~~p~~~~~~~li~~~~~~~~--~~~~~~~  151 (246)
                      .+|+.++-.+++.=-               ++.+.-..++|...     ..+.|-......++....-...  ..-    
T Consensus       168 d~yd~~vlmlsrSYfLEl~e~~s~dl~pdyYemilfY~kki~~~d~~~Y~k~~peeeL~s~imqhlfi~p~e~l~~----  243 (549)
T PF07079_consen  168 DMYDRAVLMLSRSYFLELKESMSSDLYPDYYEMILFYLKKIHAFDQRPYEKFIPEEELFSTIMQHLFIVPKERLPP----  243 (549)
T ss_pred             HHHHHHHHHHhHHHHHHHHHhcccccChHHHHHHHHHHHHHHHHhhchHHhhCcHHHHHHHHHHHHHhCCHhhccH----
Confidence            888886666654311               22333333333320     1244555555555554443221  112    


Q ss_pred             HHHHHHHHHHhhcCCCCCCcch-hhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChh
Q 043380          152 ALCIFGEIVKRVCSNPGLWPKP-HLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVD  230 (246)
Q Consensus       152 a~~~~~~m~~~~~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~  230 (246)
                      -.++++.-...     -+.|+. -....|+..+..  +.+++..+.+.+.......+.... ..++..++...++.++..
T Consensus       244 ~mq~l~~We~~-----yv~p~~~LVi~~L~~~f~~--~~e~~~~~ce~ia~~~i~~Lke~l-i~~F~~~Ls~~Vk~~~T~  315 (549)
T PF07079_consen  244 LMQILENWENF-----YVHPNYDLVIEPLKQQFMS--DPEQVGHFCEAIASSKIEKLKEEL-IDRFGNLLSFKVKQVQTE  315 (549)
T ss_pred             HHHHHHHHHhh-----ccCCchhHHHHHHHHHHhc--ChHHHHHHHHHHHHHhHHHHHHHH-HHHHHHHHHHHHHHHhHH
Confidence            33333333443     456765 345556655554  566666666655422111111111 227888999999999999


Q ss_pred             HHHHHHHHHHhhc
Q 043380          231 LALDKLSNTITRW  243 (246)
Q Consensus       231 ~a~~~~~~m~~~g  243 (246)
                      +|.+++.-+.--.
T Consensus       316 ~a~q~l~lL~~ld  328 (549)
T PF07079_consen  316 EAKQYLALLKILD  328 (549)
T ss_pred             HHHHHHHHHHhcC
Confidence            9999988776443

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>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=86.77  E-value=2.4  Score=20.91  Aligned_cols=28  Identities=18%  Similarity=0.040  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          215 AGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       215 ~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                      +|..+-..|...|++++|.+.|++..+-
T Consensus         3 ~~~~lg~~y~~~~~~~~A~~~~~~a~~~   30 (34)
T PF13181_consen    3 AYYNLGKIYEQLGDYEEALEYFEKALEL   30 (34)
T ss_dssp             HHHHHHHHHHHTTSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            5777888888888888888888877653

...

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=86.55  E-value=7.2  Score=34.49  Aligned_cols=114  Identities=11%  Similarity=0.070  Sum_probs=65.7

Q ss_pred             HHHhcCCHHHHHHHHHH-----H----HhCC-CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           26 ASREAQRIDEAYQILES-----V----EKGL-EPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        26 ~~~~~g~~~~a~~~~~~-----~----~~~~-~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      .+..+|+.++|..+..+     |    .+.+ ..+..+...+-..+-+...+..|-++|..|-+.               
T Consensus       712 mLiSaGe~~KAi~i~~d~gW~d~lidI~rkld~~ere~l~~~a~ylk~l~~~gLAaeIF~k~gD~---------------  776 (1081)
T KOG1538|consen  712 MLISAGEHVKAIEICGDHGWVDMLIDIARKLDKAEREPLLLCATYLKKLDSPGLAAEIFLKMGDL---------------  776 (1081)
T ss_pred             HhhcccchhhhhhhhhcccHHHHHHHHHhhcchhhhhHHHHHHHHHhhccccchHHHHHHHhccH---------------
Confidence            34455666666665321     1    1111 233444444444455566777888888887654               


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHH-----------HHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRST-----------FTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~-----------~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                       .+++......++|++|..+-+..-+   +.||...           |.--=.+|-+.|+-.+    |.++++++...
T Consensus       777 -ksiVqlHve~~~W~eAFalAe~hPe---~~~dVy~pyaqwLAE~DrFeEAqkAfhkAGr~~E----A~~vLeQLtnn  846 (1081)
T KOG1538|consen  777 -KSLVQLHVETQRWDEAFALAEKHPE---FKDDVYMPYAQWLAENDRFEEAQKAFHKAGRQRE----AVQVLEQLTNN  846 (1081)
T ss_pred             -HHHhhheeecccchHhHhhhhhCcc---ccccccchHHHHhhhhhhHHHHHHHHHHhcchHH----HHHHHHHhhhh
Confidence             3567777888899999888777655   5555421           2222345555555555    66666555443

>KOG4077 consensus Cytochrome c oxidase, subunit Va/COX6 [Energy production and conversion]

Probab=86.34  E-value=5  Score=27.46  Aligned_cols=49  Identities=18%  Similarity=0.258  Sum_probs=35.3

Q ss_pred             hcccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHH
Q 043380           10 REHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILI   58 (246)
Q Consensus        10 ~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li   58 (246)
                      ...+-|++.+-..-+.+|-+.+++..|.++|+-++..+.+....|-.++
T Consensus        77 ~yDlVP~pkvIEaaLRA~RRvNDfa~aVRilE~iK~K~g~~k~~Y~y~v  125 (149)
T KOG4077|consen   77 DYDLVPSPKVIEAALRACRRVNDFATAVRILEAIKDKCGAQKQVYPYYV  125 (149)
T ss_pred             ccccCCChHHHHHHHHHHHHhccHHHHHHHHHHHHHhcccHHHHHHHHH
Confidence            3347788888888888888888888888888888744444444455443

>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models

Probab=85.89  E-value=1.5  Score=20.50  Aligned_cols=22  Identities=32%  Similarity=0.214  Sum_probs=14.9

Q ss_pred             HHHHHHHHHhcCChhHHHHHHH
Q 043380          216 GHLLMEAALNDGQVDLALDKLS  237 (246)
Q Consensus       216 ~~~li~~~~~~g~~~~a~~~~~  237 (246)
                      ...+...+...|++++|.++++
T Consensus         4 ~~~la~~~~~~G~~~eA~~~l~   25 (26)
T PF07721_consen    4 RLALARALLAQGDPDEAERLLR   25 (26)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHh
Confidence            4456667777777777777665

The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=85.46  E-value=11  Score=26.97  Aligned_cols=113  Identities=19%  Similarity=0.168  Sum_probs=60.7

Q ss_pred             HHHHHHHH---HHhcCCHHHHHHHHHHHHhCCCCC---HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           19 VMNAVIEA---SREAQRIDEAYQILESVEKGLEPD---SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        19 ~~~~li~~---~~~~g~~~~a~~~~~~~~~~~~~~---~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      +.+.||..   -.+.++.+++..++.-++- .+|.   ..++..+  .+...|++++|..+|+++.+.         .|.
T Consensus         9 iv~gLie~~~~al~~~~~~D~e~lL~ALrv-LRP~~~e~~~~~~~--l~i~r~~w~dA~rlLr~l~~~---------~~~   76 (160)
T PF09613_consen    9 IVGGLIEVLSVALRLGDPDDAEALLDALRV-LRPEFPELDLFDGW--LHIVRGDWDDALRLLRELEER---------APG   76 (160)
T ss_pred             HHHHHHHHHHHHHccCChHHHHHHHHHHHH-hCCCchHHHHHHHH--HHHHhCCHHHHHHHHHHHhcc---------CCC
Confidence            34444443   3457888999999988762 2343   3334333  346788999999999998775         344


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhh
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKV  147 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~  147 (246)
                      ...-..|+..|....+-..=...=+++.+ .+-.|+.   ..+++.+....+...
T Consensus        77 ~p~~kALlA~CL~~~~D~~Wr~~A~evle-~~~d~~a---~~Lv~~Ll~~~~~~~  127 (160)
T PF09613_consen   77 FPYAKALLALCLYALGDPSWRRYADEVLE-SGADPDA---RALVRALLARADLEP  127 (160)
T ss_pred             ChHHHHHHHHHHHHcCChHHHHHHHHHHh-cCCChHH---HHHHHHHHHhccccc
Confidence            33334444444433322222233333444 3322332   234555555555444

>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=85.26  E-value=1.8  Score=21.36  Aligned_cols=27  Identities=19%  Similarity=0.149  Sum_probs=18.0

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHh
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKS  121 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~  121 (246)
                      +|..+-..|...|++++|.+.|++..+
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            455666666777777777777766655

...

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=85.25  E-value=17  Score=32.00  Aligned_cols=101  Identities=13%  Similarity=0.065  Sum_probs=72.2

Q ss_pred             HhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHh
Q 043380           62 IKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLY  141 (246)
Q Consensus        62 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~  141 (246)
                      .+.|+++.|.++-.+.             -+..-|..|-++....+++..|.+.|.+...          |..|+-.+..
T Consensus       648 l~lgrl~iA~~la~e~-------------~s~~Kw~~Lg~~al~~~~l~lA~EC~~~a~d----------~~~LlLl~t~  704 (794)
T KOG0276|consen  648 LKLGRLDIAFDLAVEA-------------NSEVKWRQLGDAALSAGELPLASECFLRARD----------LGSLLLLYTS  704 (794)
T ss_pred             hhcCcHHHHHHHHHhh-------------cchHHHHHHHHHHhhcccchhHHHHHHhhcc----------hhhhhhhhhh
Confidence            4567777776655442             3556789999999999999999999888766          6778888888


Q ss_pred             cCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhC
Q 043380          142 SGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMW  200 (246)
Q Consensus       142 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  200 (246)
                      .|+-+.    ...+-..-++.     |.      .|.-..+|-..|+++++.+++.+-.
T Consensus       705 ~g~~~~----l~~la~~~~~~-----g~------~N~AF~~~~l~g~~~~C~~lLi~t~  748 (794)
T KOG0276|consen  705 SGNAEG----LAVLASLAKKQ-----GK------NNLAFLAYFLSGDYEECLELLISTQ  748 (794)
T ss_pred             cCChhH----HHHHHHHHHhh-----cc------cchHHHHHHHcCCHHHHHHHHHhcC
Confidence            888876    44444444443     22      2445556778899999998887753

>KOG4077 consensus Cytochrome c oxidase, subunit Va/COX6 [Energy production and conversion]

Probab=85.16  E-value=9.9  Score=26.07  Aligned_cols=47  Identities=13%  Similarity=0.119  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          111 SLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       111 ~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      +..+-++.+.. ..+.|++.....-+++|.+.+++..    |.++|+-++.+
T Consensus        67 EvrkglN~l~~-yDlVP~pkvIEaaLRA~RRvNDfa~----aVRilE~iK~K  113 (149)
T KOG4077|consen   67 EVRKGLNNLFD-YDLVPSPKVIEAALRACRRVNDFAT----AVRILEAIKDK  113 (149)
T ss_pred             HHHHHHHhhhc-cccCCChHHHHHHHHHHHHhccHHH----HHHHHHHHHHh
Confidence            45566677777 7788888888888888888888888    88888888775

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=84.31  E-value=13  Score=26.86  Aligned_cols=170  Identities=12%  Similarity=0.008  Sum_probs=120.5

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHH-HHHhcCCcchHHHHHHHHHhccCCCCCCCC--
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILIS-ACIKTKKLDVTMPFNEQLKDNGQKCSSGGF--   89 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~-~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~--   89 (246)
                      .......+......+...+..+.+.+.+.........+......... .+...++++.|...+.+....       ..  
T Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~-------~~~~  163 (291)
T COG0457          91 LPNLAEALLNLGLLLEALGKYEEALELLEKALALDPDPDLAEALLALGALYELGDYEEALELYEKALEL-------DPEL  163 (291)
T ss_pred             ccchHHHHHHHHHHHHHHhhHHHHHHHHHHHHcCCCCcchHHHHHHHHHHHHcCCHHHHHHHHHHHHhc-------CCCc
Confidence            34455566667777778888899999998876322222233333333 788999999999999998653       11  


Q ss_pred             CccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC--HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCC
Q 043380           90 HPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD--RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNP  167 (246)
Q Consensus        90 ~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~--~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~  167 (246)
                      ......+......+...++.+.+...+.....   ..++  ...+..+...+...+.++.    |...+......     
T Consensus       164 ~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~----a~~~~~~~~~~-----  231 (291)
T COG0457         164 NELAEALLALGALLEALGRYEEALELLEKALK---LNPDDDAEALLNLGLLYLKLGKYEE----ALEYYEKALEL-----  231 (291)
T ss_pred             cchHHHHHHhhhHHHHhcCHHHHHHHHHHHHh---hCcccchHHHHHhhHHHHHcccHHH----HHHHHHHHHhh-----
Confidence            12344555555557788999999999999988   3333  6778888889999999999    99999998875     


Q ss_pred             CCCcc-hhhHHHHHHHHHhcCChhHHhhHHHhhCCCC
Q 043380          168 GLWPK-PHLYVSMMHELAARVDYDIVKSPYRRMWPDS  203 (246)
Q Consensus       168 ~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  203 (246)
                        .|+ ...+..+...+...+..+.+...+.......
T Consensus       232 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  266 (291)
T COG0457         232 --DPDNAEALYNLALLLLELGRYEEALEALEKALELD  266 (291)
T ss_pred             --CcccHHHHhhHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence              333 4445555555557778999998888876543

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=84.20  E-value=1.5  Score=22.17  Aligned_cols=24  Identities=17%  Similarity=0.069  Sum_probs=19.4

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHH
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAY   37 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~   37 (246)
                      +-|+..|+.+-..|...|++++|+
T Consensus        10 P~n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen   10 PNNAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             CCCHHHHHHHHHHHHHCcCHHhhc
Confidence            457778888888888888888875

>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

Probab=84.19  E-value=5.8  Score=31.45  Aligned_cols=56  Identities=9%  Similarity=-0.021  Sum_probs=29.2

Q ss_pred             HHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHH
Q 043380           56 ILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEM  119 (246)
Q Consensus        56 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m  119 (246)
                      ..-+.|..+|.+.+|.++.+.....        -+.+...|-.|++.+...||--.|...++++
T Consensus       284 kva~~yle~g~~neAi~l~qr~ltl--------dpL~e~~nk~lm~~la~~gD~is~~khyery  339 (361)
T COG3947         284 KVARAYLEAGKPNEAIQLHQRALTL--------DPLSEQDNKGLMASLATLGDEISAIKHYERY  339 (361)
T ss_pred             HHHHHHHHcCChHHHHHHHHHHhhc--------ChhhhHHHHHHHHHHHHhccchhhhhHHHHH
Confidence            3444455555566665555555543        2334445555555555555555555444444

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=84.05  E-value=1.4  Score=22.27  Aligned_cols=21  Identities=10%  Similarity=0.284  Sum_probs=13.4

Q ss_pred             CC-HHHHHHHHHHHHhcCChhh
Q 043380          127 LD-RSTFTAMVDALLYSGSIKV  147 (246)
Q Consensus       127 p~-~~~~~~li~~~~~~~~~~~  147 (246)
                      |+ ...|+.+...|...|++++
T Consensus        10 P~n~~a~~nla~~~~~~g~~~~   31 (34)
T PF13431_consen   10 PNNAEAYNNLANLYLNQGDYEE   31 (34)
T ss_pred             CCCHHHHHHHHHHHHHCcCHHh
Confidence            44 5666666666666666666

>KOG1258 consensus mRNA processing protein [RNA processing and modification]

Probab=84.00  E-value=29  Score=30.41  Aligned_cols=134  Identities=13%  Similarity=0.065  Sum_probs=75.2

Q ss_pred             cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHH-HHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCC
Q 043380           92 DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTF-TAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLW  170 (246)
Q Consensus        92 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~-~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~  170 (246)
                      +-..|+.||.---...+.+.+..+++.+..   -.|-..-| -.....-.+.|..+.    +.++|++-.+      ++.
T Consensus        44 ~f~~wt~li~~~~~~~~~~~~r~~y~~fL~---kyPl~~gyW~kfA~~E~klg~~~~----s~~Vfergv~------aip  110 (577)
T KOG1258|consen   44 DFDAWTTLIQENDSIEDVDALREVYDIFLS---KYPLCYGYWKKFADYEYKLGNAEN----SVKVFERGVQ------AIP  110 (577)
T ss_pred             cccchHHHHhccCchhHHHHHHHHHHHHHh---hCccHHHHHHHHHHHHHHhhhHHH----HHHHHHHHHH------hhh
Confidence            334555555555555555666666666665   34554433 345555556677777    7777777666      355


Q ss_pred             cchhhHHHHHHHHH-hcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          171 PKPHLYVSMMHELA-ARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       171 p~~~~~~~li~~~~-~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      .+...|...+.-++ ..|+.+.....|+..............   .|...|+--..++++....++++++++
T Consensus       111 ~SvdlW~~Y~~f~~n~~~d~~~lr~~fe~A~~~vG~dF~S~~---lWdkyie~en~qks~k~v~~iyeRile  179 (577)
T KOG1258|consen  111 LSVDLWLSYLAFLKNNNGDPETLRDLFERAKSYVGLDFLSDP---LWDKYIEFENGQKSWKRVANIYERILE  179 (577)
T ss_pred             hHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhcccchhccH---HHHHHHHHHhccccHHHHHHHHHHHHh
Confidence            55555555443333 345566666666665432211111111   466677766777777777777766654

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=82.95  E-value=20  Score=27.85  Aligned_cols=88  Identities=11%  Similarity=0.075  Sum_probs=56.9

Q ss_pred             CCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC
Q 043380           49 PDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD  128 (246)
Q Consensus        49 ~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~  128 (246)
                      |-...|+.-+.. .+.|++++|.+.|+.+..+.     .+-+-...+--.++-++-+.++++.|....++.....+-.||
T Consensus        33 p~~~LY~~g~~~-L~~gn~~~A~~~fe~l~~~~-----p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~~n  106 (254)
T COG4105          33 PASELYNEGLTE-LQKGNYEEAIKYFEALDSRH-----PFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTHPN  106 (254)
T ss_pred             CHHHHHHHHHHH-HhcCCHHHHHHHHHHHHHcC-----CCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCCCC
Confidence            334455554444 56788999999999998761     111223446666777788899999999999988883444444


Q ss_pred             HHHHHHHHHHHHhcC
Q 043380          129 RSTFTAMVDALLYSG  143 (246)
Q Consensus       129 ~~~~~~li~~~~~~~  143 (246)
                       ..|...|.+++..-
T Consensus       107 -~dY~~YlkgLs~~~  120 (254)
T COG4105         107 -ADYAYYLKGLSYFF  120 (254)
T ss_pred             -hhHHHHHHHHHHhc
Confidence             33555555555433

>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=82.92  E-value=26  Score=29.23  Aligned_cols=172  Identities=13%  Similarity=0.036  Sum_probs=97.3

Q ss_pred             HHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCC--------
Q 043380           52 LSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCC--------  123 (246)
Q Consensus        52 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~--------  123 (246)
                      ..+.-+-..|..+|+++.|.+.|.+..+-=     ......+..|-.+|..-.-.|+|..+..+..+..+ .        
T Consensus       151 ra~~Dl~dhy~~cG~l~~Alr~YsR~RdYC-----Ts~khvInm~ln~i~VSI~~~nw~hv~sy~~~A~s-t~~~~~~~~  224 (466)
T KOG0686|consen  151 RALEDLGDHYLDCGQLDNALRCYSRARDYC-----TSAKHVINMCLNLILVSIYMGNWGHVLSYISKAES-TPDANENLA  224 (466)
T ss_pred             HHHHHHHHHHHHhccHHHHHhhhhhhhhhh-----cchHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHh-CchhhhhHH
Confidence            446678888899999999999999966530     01123445677778888888999888887777666 2        


Q ss_pred             -CCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCC-CCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCC
Q 043380          124 -NLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSN-PGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWP  201 (246)
Q Consensus       124 -~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~-~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  201 (246)
                       .+.+-...+..+...+.+  .++.    |.+.|=.....-+.. .=+.|...+....+.+++--++-+.-..+.....-
T Consensus       225 q~v~~kl~C~agLa~L~lk--kyk~----aa~~fL~~~~~~~d~~~ivtpsdv~iYggLcALAtfdr~~Lk~~vi~n~~F  298 (466)
T KOG0686|consen  225 QEVPAKLKCAAGLANLLLK--KYKS----AAKYFLLAEFDHCDYPEIVTPSDVAIYGGLCALATFDRQDLKLNVIKNESF  298 (466)
T ss_pred             HhcCcchHHHHHHHHHHHH--HHHH----HHHHHHhCCCCccCccceecchhhHHHHhhHhhccCCHHHHHHHHHcchhh
Confidence             122334444444444433  4555    544443332211111 12456667777777777766655443333332221


Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          202 DSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       202 ~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      ...-...|.    .+..+..-|  ++++...++++++++.
T Consensus       299 k~flel~Pq----lr~il~~fy--~sky~~cl~~L~~~k~  332 (466)
T KOG0686|consen  299 KLFLELEPQ----LREILFKFY--SSKYASCLELLREIKP  332 (466)
T ss_pred             hhHHhcChH----HHHHHHHHh--hhhHHHHHHHHHHhcc
Confidence            111112222    344444444  5667777777777654

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=82.86  E-value=25  Score=28.98  Aligned_cols=211  Identities=12%  Similarity=0.027  Sum_probs=116.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHH-HHHH--hCCCCC---HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           19 VMNAVIEASREAQRIDEAYQIL-ESVE--KGLEPD---SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~-~~~~--~~~~~~---~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      +|..+..+.++.|+.++++..- .+|.  ......   ...|-.+-+++-+..++.+++.+-..-...      .|..|.
T Consensus        45 ~lG~l~~a~s~~g~y~~mL~~a~sqi~~a~~~~ds~~~~ea~lnlar~~e~l~~f~kt~~y~k~~l~l------pgt~~~  118 (518)
T KOG1941|consen   45 VLGCLVTAHSEMGRYKEMLKFAVSQIDTARELEDSDFLLEAYLNLARSNEKLCEFHKTISYCKTCLGL------PGTRAG  118 (518)
T ss_pred             HhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhcC------CCCCcc
Confidence            5666677777777777766542 2332  111111   223334444444444445554444333332      233331


Q ss_pred             ---HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC----HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcC
Q 043380           93 ---IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD----RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCS  165 (246)
Q Consensus        93 ---~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~----~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~  165 (246)
                         ....-++-.+....+.++++++.|+...+...-.-|    ..+|-.|-..|....++++    |.-+.....+... 
T Consensus       119 ~~~gq~~l~~~~Ahlgls~fq~~Lesfe~A~~~A~~~~D~~LElqvcv~Lgslf~~l~D~~K----al~f~~kA~~lv~-  193 (518)
T KOG1941|consen  119 QLGGQVSLSMGNAHLGLSVFQKALESFEKALRYAHNNDDAMLELQVCVSLGSLFAQLKDYEK----ALFFPCKAAELVN-  193 (518)
T ss_pred             cccchhhhhHHHHhhhHHHHHHHHHHHHHHHHHhhccCCceeeeehhhhHHHHHHHHHhhhH----HhhhhHhHHHHHH-
Confidence               123334556666677889999998877662222222    3578889999999999998    6655554333210 


Q ss_pred             CCCCC-----cchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHH
Q 043380          166 NPGLW-----PKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTI  240 (246)
Q Consensus       166 ~~~~~-----p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  240 (246)
                      +.++.     --......|.-++-..|+...|.+.-++..+-....-.........-.+.+.|...|+.+.|+.-|++-.
T Consensus       194 s~~l~d~~~kyr~~~lyhmaValR~~G~LgdA~e~C~Ea~klal~~Gdra~~arc~~~~aDIyR~~gd~e~af~rYe~Am  273 (518)
T KOG1941|consen  194 SYGLKDWSLKYRAMSLYHMAVALRLLGRLGDAMECCEEAMKLALQHGDRALQARCLLCFADIYRSRGDLERAFRRYEQAM  273 (518)
T ss_pred             hcCcCchhHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHhCChHHHHHHHHHHHHHHHhcccHhHHHHHHHHHH
Confidence            00111     1123345566677888888888888776543211111111111234557778889999999988777643

>PF11846 DUF3366: Domain of unknown function (DUF3366); InterPro: IPR021797 This domain is functionally uncharacterised

Probab=82.14  E-value=10  Score=28.05  Aligned_cols=63  Identities=19%  Similarity=0.081  Sum_probs=48.6

Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      +...+.......+.+......+...+.....|+..+|..++..+...|+.++    |.+..+++..-
T Consensus       111 ~~~~l~~~~~~~~~~~l~~~~~~a~~~l~~~P~~~~~~~~a~~l~~~G~~~e----A~~~~~~~~~l  173 (193)
T PF11846_consen  111 YAALLLLARLPPDPEMLEAYIEWAERLLRRRPDPNVYQRYALALALLGDPEE----ARQWLARARRL  173 (193)
T ss_pred             HHHHHHhhcCCCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh
Confidence            3344444456777776666666665544477999999999999999999999    99999998875

This domain is found in bacteria. This presumed domain is about 200 amino acids in length.

>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=81.82  E-value=5.3  Score=24.79  Aligned_cols=49  Identities=14%  Similarity=0.026  Sum_probs=37.3

Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhh
Q 043380           98 TLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKV  147 (246)
Q Consensus        98 ~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~  147 (246)
                      ..+..| ...+-++|+..|....++..-.|+ -.++..++.+|+..|++++
T Consensus        12 ~GlkLY-~~~~~~~Al~~W~~aL~k~~~~~~rf~~lG~l~qA~~e~Gkyr~   61 (80)
T PF10579_consen   12 KGLKLY-HQNETQQALQKWRKALEKITDREDRFRVLGYLIQAHMEWGKYRE   61 (80)
T ss_pred             HHHHHh-ccchHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHHH
Confidence            345555 677889999999998883323344 3568899999999999999

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

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=80.58  E-value=30  Score=31.75  Aligned_cols=88  Identities=18%  Similarity=0.237  Sum_probs=54.0

Q ss_pred             HHHHHHHHHH----hcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHH
Q 043380           19 VMNAVIEASR----EAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIF   94 (246)
Q Consensus        19 ~~~~li~~~~----~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~   94 (246)
                      +-..++..|+    +.|++++|...|-+--.-+.|+.     +|.-|....+..+-..+++.+.+.       |+ .+..
T Consensus       366 ~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~le~s~-----Vi~kfLdaq~IknLt~YLe~L~~~-------gl-a~~d  432 (933)
T KOG2114|consen  366 TLAEIHRKYGDYLYGKGDFDEATDQYIETIGFLEPSE-----VIKKFLDAQRIKNLTSYLEALHKK-------GL-ANSD  432 (933)
T ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHHcccCChHH-----HHHHhcCHHHHHHHHHHHHHHHHc-------cc-ccch
Confidence            3344555444    57999999988855432234432     344455555666666777777776       33 3444


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHH
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEM  119 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m  119 (246)
                      .-+.||.+|.+.++.++-.++.+.-
T Consensus       433 httlLLncYiKlkd~~kL~efI~~~  457 (933)
T KOG2114|consen  433 HTTLLLNCYIKLKDVEKLTEFISKC  457 (933)
T ss_pred             hHHHHHHHHHHhcchHHHHHHHhcC
Confidence            5567888888888776666555443

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=80.30  E-value=17  Score=27.76  Aligned_cols=82  Identities=16%  Similarity=0.106  Sum_probs=57.9

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP  173 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~  173 (246)
                      |.+.-++.+.+.+...+++....+-.+   -+|+ ..+=..++..+|-.|+|++    |..-++..-.-   .+...+-.
T Consensus         3 Tl~~t~seLL~~~sL~dai~~a~~qVk---akPtda~~RhflfqLlcvaGdw~k----Al~Ql~l~a~l---~p~~t~~a   72 (273)
T COG4455           3 TLRDTISELLDDNSLQDAIGLARDQVK---AKPTDAGGRHFLFQLLCVAGDWEK----ALAQLNLAATL---SPQDTVGA   72 (273)
T ss_pred             chHHHHHHHHHhccHHHHHHHHHHHHh---cCCccccchhHHHHHHhhcchHHH----HHHHHHHHhhc---CcccchHH
Confidence            344556677778889998888777666   2354 5556678999999999999    88766665443   34556667


Q ss_pred             hhHHHHHHHHHhc
Q 043380          174 HLYVSMMHELAAR  186 (246)
Q Consensus       174 ~~~~~li~~~~~~  186 (246)
                      .+|..+|.+-...
T Consensus        73 ~lyr~lir~ea~R   85 (273)
T COG4455          73 SLYRHLIRCEAAR   85 (273)
T ss_pred             HHHHHHHHHHHHH
Confidence            8888888775543

>PF11846 DUF3366: Domain of unknown function (DUF3366); InterPro: IPR021797 This domain is functionally uncharacterised

Probab=80.05  E-value=9.6  Score=28.16  Aligned_cols=56  Identities=11%  Similarity=0.036  Sum_probs=41.8

Q ss_pred             hcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC
Q 043380           63 KTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL  127 (246)
Q Consensus        63 ~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p  127 (246)
                      ...+.+......+.+.+.      ....|+..+|..++.++...|+.++|.+...++..   ..|
T Consensus       120 ~~~~~~~l~~~~~~a~~~------l~~~P~~~~~~~~a~~l~~~G~~~eA~~~~~~~~~---lyP  175 (193)
T PF11846_consen  120 LPPDPEMLEAYIEWAERL------LRRRPDPNVYQRYALALALLGDPEEARQWLARARR---LYP  175 (193)
T ss_pred             CCCCHHHHHHHHHHHHHH------HHhCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCC
Confidence            444544444444444333      13479999999999999999999999999999988   556

This domain is found in bacteria. This presumed domain is about 200 amino acids in length.

---

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	246
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	3e-07

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 49.8 bits (117), Expect = 3e-07
 Identities = 18/121 (14%), Positives = 39/121 (32%), Gaps = 12/121 (9%)

Query: 20  MNAVIEASREAQRIDEAYQILES----VEKGLEPDSLSYNILISACIKTKKLDVTMPFNE 75
           + A  +      ++  A+ +L       +K        YN ++    +       +    
Sbjct: 130 LLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLF 189

Query: 76  QLKDNGQKCSSGGFHPDIFTYATLLMGF-RHAKDLQSLLEIVFEMKSCCNLILDRSTFTA 134
            +KD G         PD+ +YA  L    R  +D  ++   + +M      +    T   
Sbjct: 190 MVKDAGLT-------PDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVL 242

Query: 135 M 135
           +
Sbjct: 243 L 243

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	246
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.9
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.89
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.87
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.87
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.79
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.74
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.74
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.74
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.73
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.73
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.72
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.72
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.69
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.68
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.66
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.66
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.66
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.66
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.66
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.65
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.64
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.63
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.63
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.61
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.6
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.59
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.58
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.58
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.57
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.55
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.54
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.52
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.52
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.52
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.51
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.51
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.51
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.5
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.5
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.49
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.49
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.49
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.49
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.48
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.47
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.46
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.44
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.44
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.43
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.43
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.41
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.41
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.39
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.39
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.38
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.36
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.35
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.33
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.31
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.3
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.3
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.29
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.29
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.29
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.27
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.27
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	99.27
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.26
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.22
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.21
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.21
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	99.2
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.18
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.18
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	99.15
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	99.14
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	99.14
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	99.12
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	99.12
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.12
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	99.1
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	99.09
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.08
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	99.08
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.06
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	99.06
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	99.04
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	99.03
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	99.03
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.02
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	99.02
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	99.01
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.01
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	99.01
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.0
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	99.0
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.98
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	98.97
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.96
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.93
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.93
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.92
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	98.92
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.89
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.89
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	98.88
4g1t_A	472	Interferon-induced protein with tetratricopeptide	98.87
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.87
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.87
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.86
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.86
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.86
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	98.84
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.84
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.83
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.81
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.79
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.78
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.78
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.78
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.77
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	98.77
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.77
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.76
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.74
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.74
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.73
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.73
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.72
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.71
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.69
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.68
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.68
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.66
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.63
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	98.63
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.63
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.61
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.61
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.6
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.59
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	98.58
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.57
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.56
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.55
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.55
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.54
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.54
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.53
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.53
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.52
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.52
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.51
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.51
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.5
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	98.49
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.49
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.49
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.48
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.48
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.47
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.44
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.43
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.4
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.38
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	98.38
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.37
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.35
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.3
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.3
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.29
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.28
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.25
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	98.24
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.23
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	98.22
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	98.22
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.22
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.21
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	98.2
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	98.19
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.16
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.13
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	98.12
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	98.1
2l6j_A	111	TPR repeat-containing protein associated with HSP;	98.0
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	97.95
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.95
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	97.94
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	97.91
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.81
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.78
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.77
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	97.75
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	97.68
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.62
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.62
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	97.62
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	97.55
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.54
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.53
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.53
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	97.5
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.45
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	97.45
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.41
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	97.34
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.28
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	97.23
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.16
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	97.09
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	97.09
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.79
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.73
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	96.68
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	96.64
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	96.51
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	96.38
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	96.32
1pc2_A	152	Mitochondria fission protein; unknown function; NM	96.25
1pc2_A	152	Mitochondria fission protein; unknown function; NM	96.15
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	96.1
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	95.66
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	95.6
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	95.55
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	95.14
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	95.0
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	94.87
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	94.58
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	94.54
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	94.02
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	93.83
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	93.82
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	93.46
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	93.43
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	93.41
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	93.25
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	93.25
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	92.75
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	92.62
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	92.61
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	91.18
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	90.22
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	89.02
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	88.37
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	88.14
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	87.03
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	85.93
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	84.01
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	83.33
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	82.6
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	82.51
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	82.47

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=100.00  E-value=3.5e-37  Score=258.78  Aligned_cols=199  Identities=12%  Similarity=0.147  Sum_probs=176.1

Q ss_pred             HHHHhcccCcCH-HHHHHHHHHHHhcCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHHHHhcCC---------cchHHHHH
Q 043380            6 EIVNREHWKLNT-IVMNAVIEASREAQRIDEAYQILESVE-KGLEPDSLSYNILISACIKTKK---------LDVTMPFN   74 (246)
Q Consensus         6 ~~~~~~~~~~~~-~~~~~li~~~~~~g~~~~a~~~~~~~~-~~~~~~~~t~~~li~~~~~~~~---------~~~a~~~~   74 (246)
                      ..+++.+..+++ .+++.+|++|++.|++++|+++|++|. +|+.||..|||+||.+|++.+.         ++.|.++|
T Consensus        14 ~~~~~k~~~~spe~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf   93 (501)
T 4g26_A           14 RKAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIF   93 (501)
T ss_dssp             ----------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHH
T ss_pred             HHHHHhcccCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHH
Confidence            345555655444 468999999999999999999999998 8999999999999999998765         57799999


Q ss_pred             HHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHH
Q 043380           75 EQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALC  154 (246)
Q Consensus        75 ~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~  154 (246)
                      ++|...       |+.||..|||+||.+|++.|++++|.++|++|.+ .|+.||..+|+++|.+|++.|++++    |.+
T Consensus        94 ~~M~~~-------G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~-~g~~Pd~~tyn~lI~~~~~~g~~~~----A~~  161 (501)
T 4g26_A           94 KQMIVD-------KVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKA-FGIQPRLRSYGPALFGFCRKGDADK----AYE  161 (501)
T ss_dssp             HHHHHT-------TCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH-TTCCCCHHHHHHHHHHHHHTTCHHH----HHH
T ss_pred             HHHHHh-------CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-cCCCCccceehHHHHHHHHCCCHHH----HHH
Confidence            999998       8999999999999999999999999999999999 9999999999999999999999999    999


Q ss_pred             HHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhc
Q 043380          155 IFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALND  226 (246)
Q Consensus       155 ~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~  226 (246)
                      +|++|.+.     |+.||..||++||.+|++.|++++|.++|++|...+   ..|+..  ||+.++..|...
T Consensus       162 l~~~M~~~-----G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g---~~ps~~--T~~~l~~~F~s~  223 (501)
T 4g26_A          162 VDAHMVES-----EVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLV---RQVSKS--TFDMIEEWFKSE  223 (501)
T ss_dssp             HHHHHHHT-----TCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT---SSBCHH--HHHHHHHHHHSH
T ss_pred             HHHHHHhc-----CCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhC---CCcCHH--HHHHHHHHHhcC
Confidence            99999999     999999999999999999999999999999998654   444433  999999999864

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=100.00  E-value=4.1e-34  Score=240.18  Aligned_cols=169  Identities=11%  Similarity=0.196  Sum_probs=162.1

Q ss_pred             hhhhHHHHhcccCcCHHHHHHHHHHHHhcCC---------HHHHHHHHHHHH-hCCCCCHHHHHHHHHHHHhcCCcchHH
Q 043380            2 FEENEIVNREHWKLNTIVMNAVIEASREAQR---------IDEAYQILESVE-KGLEPDSLSYNILISACIKTKKLDVTM   71 (246)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~---------~~~a~~~~~~~~-~~~~~~~~t~~~li~~~~~~~~~~~a~   71 (246)
                      ++.+++|++.|++||..+||+||.+|++.+.         +++|.++|++|. .|+.||..|||+||++|++.|++++|.
T Consensus        46 ~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~  125 (501)
T 4g26_A           46 LRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAF  125 (501)
T ss_dssp             HHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHH
Confidence            4578999999999999999999999998665         789999999998 899999999999999999999999999


Q ss_pred             HHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhH
Q 043380           72 PFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLY  151 (246)
Q Consensus        72 ~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~  151 (246)
                      ++|++|.+.       |+.||..||++||.+|++.|++++|.++|++|.+ .|+.||..||++||.+|++.|++++    
T Consensus       126 ~l~~~M~~~-------g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~-~G~~Pd~~ty~~Li~~~~~~g~~d~----  193 (501)
T 4g26_A          126 DMVKQMKAF-------GIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVE-SEVVPEEPELAALLKVSMDTKNADK----  193 (501)
T ss_dssp             HHHHHHHHT-------TCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-TTCCCCHHHHHHHHHHHHHTTCHHH----
T ss_pred             HHHHHHHHc-------CCCCccceehHHHHHHHHCCCHHHHHHHHHHHHh-cCCCCCHHHHHHHHHHHhhCCCHHH----
Confidence            999999998       8999999999999999999999999999999999 9999999999999999999999999    


Q ss_pred             HHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcC
Q 043380          152 ALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARV  187 (246)
Q Consensus       152 a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g  187 (246)
                      |.+++++|.+.     +..|+..||+.++..|+..+
T Consensus       194 A~~ll~~Mr~~-----g~~ps~~T~~~l~~~F~s~~  224 (501)
T 4g26_A          194 VYKTLQRLRDL-----VRQVSKSTFDMIEEWFKSEV  224 (501)
T ss_dssp             HHHHHHHHHHH-----TSSBCHHHHHHHHHHHHSHH
T ss_pred             HHHHHHHHHHh-----CCCcCHHHHHHHHHHHhcCc
Confidence            99999999999     99999999999999998754

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.90  E-value=1.4e-23  Score=183.32  Aligned_cols=161  Identities=12%  Similarity=0.139  Sum_probs=130.9

Q ss_pred             CCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC
Q 043380           49 PDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD  128 (246)
Q Consensus        49 ~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~  128 (246)
                      .-..|||+||++||+.|++++|.++|.+|.+.+    ..|+.||.+|||+||.+||+.|++++|.++|++|.+ .|+.||
T Consensus       125 ~~~~TynaLIdglcK~G~leeA~~Lf~eM~~m~----~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~-~G~~PD  199 (1134)
T 3spa_A          125 GQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQR----QKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKD-AGLTPD  199 (1134)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHSH----HHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH-TTCCCC
T ss_pred             hHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHh----hcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHH-cCCCCc
Confidence            345789999999999999999999998876420    017899999999999999999999999999999999 999999


Q ss_pred             HHHHHHHHHHHHhcCCh-hhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCC
Q 043380          129 RSTFTAMVDALLYSGSI-KVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTI  207 (246)
Q Consensus       129 ~~~~~~li~~~~~~~~~-~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  207 (246)
                      ..|||++|.++|+.|+. ++    |.++|++|.+.     |+.||..+|++++.++.+.+-++.+.++.-.+....    
T Consensus       200 vvTYntLI~glcK~G~~~e~----A~~Ll~EM~~k-----G~~PD~vtY~~ll~~~eR~~vL~~Vrkv~P~f~p~~----  266 (1134)
T 3spa_A          200 LLSYAAALQCMGRQDQDAGT----IERCLEQMSQE-----GLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPP----  266 (1134)
T ss_dssp             HHHHHHHHHHHHHHTCCHHH----HHHHHHHHHHH-----TCCSHHHHHHSCCCHHHHHHHHHHHGGGCCCCCCCC----
T ss_pred             HHHHHHHHHHHHhCCCcHHH----HHHHHHHHHHc-----CCCCChhhcccccChhhHHHHHHHHHHhCcccCCCC----
Confidence            99999999999999985 78    99999999999     999999999999988887766665555544443321    


Q ss_pred             CchhhhHHHHHHHHHHHhcC
Q 043380          208 SPEVQEEAGHLLMEAALNDG  227 (246)
Q Consensus       208 ~~~~~~~~~~~li~~~~~~g  227 (246)
                      ++....++-..|.+.|.+.+
T Consensus       267 ~~~~~~~t~~LL~dl~s~d~  286 (1134)
T 3spa_A          267 QLPPPVNTSKLLRDVYAKDG  286 (1134)
T ss_dssp             CCCCCCCCCTTTHHHHCCCS
T ss_pred             CCcccccchHHHHHHHccCC
Confidence            11111124455666676655

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.89  E-value=1.7e-23  Score=182.70  Aligned_cols=152  Identities=13%  Similarity=0.068  Sum_probs=127.6

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH----hCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCC
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVE----KGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGF   89 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~----~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~   89 (246)
                      .--..|||+||++||+.|++++|.++|++|.    +|+.||++|||+||++||+.|++++|.++|++|.+.       |+
T Consensus       124 ~~~~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~-------G~  196 (1134)
T 3spa_A          124 SGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDA-------GL  196 (1134)
T ss_dssp             CHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHT-------TC
T ss_pred             HhHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHc-------CC
Confidence            3345689999999999999999999998874    489999999999999999999999999999999998       89


Q ss_pred             CccHHHHHHHHHHHHccCC-HHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCC
Q 043380           90 HPDIFTYATLLMGFRHAKD-LQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPG  168 (246)
Q Consensus        90 ~p~~~~~~~ll~~~~~~~~-~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~  168 (246)
                      .||.+|||+||.++++.|+ .++|.++|++|.+ .|+.||..+|++++.++.+.+        +++..+.+.      |+
T Consensus       197 ~PDvvTYntLI~glcK~G~~~e~A~~Ll~EM~~-kG~~PD~vtY~~ll~~~eR~~--------vL~~Vrkv~------P~  261 (1134)
T 3spa_A          197 TPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQ-EGLKLQALFTAVLLSEEDRAT--------VLKAVHKVK------PT  261 (1134)
T ss_dssp             CCCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHH-HTCCSHHHHHHSCCCHHHHHH--------HHHHHGGGC------CC
T ss_pred             CCcHHHHHHHHHHHHhCCCcHHHHHHHHHHHHH-cCCCCChhhcccccChhhHHH--------HHHHHHHhC------cc
Confidence            9999999999999999998 5789999999999 999999999999997655543        333334441      24


Q ss_pred             CCcc------hhhHHHHHHHHHhcC
Q 043380          169 LWPK------PHLYVSMMHELAARV  187 (246)
Q Consensus       169 ~~p~------~~~~~~li~~~~~~g  187 (246)
                      +.|+      ..+...|.+.|.+.+
T Consensus       262 f~p~~~~~~~~~t~~LL~dl~s~d~  286 (1134)
T 3spa_A          262 FSLPPQLPPPVNTSKLLRDVYAKDG  286 (1134)
T ss_dssp             CCCCCCCCCCCCCCTTTHHHHCCCS
T ss_pred             cCCCCCCcccccchHHHHHHHccCC
Confidence            5544      455566667777655

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.87  E-value=1.1e-20  Score=161.82  Aligned_cols=202  Identities=7%  Similarity=0.030  Sum_probs=180.4

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      ++++.+|+.++.+|.+.|++++|.++|+++....+.+..+|+.++.+|.+.|++++|..+++++.+.        .+.+.
T Consensus       302 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--------~~~~~  373 (597)
T 2xpi_A          302 EKSSDLLLCKADTLFVRSRFIDVLAITTKILEIDPYNLDVYPLHLASLHESGEKNKLYLISNDLVDR--------HPEKA  373 (597)
T ss_dssp             GGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHH--------CTTSH
T ss_pred             CchHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhh--------CcccH
Confidence            5899999999999999999999999999987434668899999999999999999999999999975        35678


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK  172 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~  172 (246)
                      .+|+.+..+|.+.|++++|.++|+++.+   ..|+ ..+|+.++..|.+.|++++    |.++|+++.+.      ...+
T Consensus       374 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~~~~l~~~~~~~g~~~~----A~~~~~~~~~~------~~~~  440 (597)
T 2xpi_A          374 VTWLAVGIYYLCVNKISEARRYFSKSST---MDPQFGPAWIGFAHSFAIEGEHDQ----AISAYTTAARL------FQGT  440 (597)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHT------TTTC
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh------Cccc
Confidence            8999999999999999999999999988   3454 8899999999999999999    99999999885      3457


Q ss_pred             hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          173 PHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       173 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                      ..+|..++.+|.+.|++++|.++|+++....+.    +.  .+|+.++..|.+.|++++|.++|+++.+.
T Consensus       441 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~----~~--~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  504 (597)
T 2xpi_A          441 HLPYLFLGMQHMQLGNILLANEYLQSSYALFQY----DP--LLLNELGVVAFNKSDMQTAINHFQNALLL  504 (597)
T ss_dssp             SHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCC----CH--HHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC----Ch--HHHHHHHHHHHHhCCHHHHHHHHHHHHHh
Confidence            899999999999999999999999998754322    22  27999999999999999999999999775

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.87  E-value=4.7e-20  Score=158.02  Aligned_cols=210  Identities=12%  Similarity=0.017  Sum_probs=132.6

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      +.++.+|+.++..|.+.|++++|.++|+++.+..+.+..+|+.++.+|.+.|++++|.++|+++.+.        .+.+.
T Consensus       370 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--------~~~~~  441 (597)
T 2xpi_A          370 PEKAVTWLAVGIYYLCVNKISEARRYFSKSSTMDPQFGPAWIGFAHSFAIEGEHDQAISAYTTAARL--------FQGTH  441 (597)
T ss_dssp             TTSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHT--------TTTCS
T ss_pred             cccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--------Cccch
Confidence            3456666666677777777777777776665323445666777777777777777777777776654        23355


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc-
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK-  172 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~-  172 (246)
                      .+|+.+..+|.+.|++++|.++|+++.+ . .+.+..+|+.++..|.+.|++++    |.++|+++.+.... .+..|+ 
T Consensus       442 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~-~-~~~~~~~~~~l~~~~~~~g~~~~----A~~~~~~~~~~~~~-~~~~p~~  514 (597)
T 2xpi_A          442 LPYLFLGMQHMQLGNILLANEYLQSSYA-L-FQYDPLLLNELGVVAFNKSDMQT----AINHFQNALLLVKK-TQSNEKP  514 (597)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHH-H-CCCCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHHHHH-SCCCSGG
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHH-h-CCCChHHHHHHHHHHHHhCCHHH----HHHHHHHHHHhhhc-cccchhh
Confidence            6667777777777777777777777666 2 12236667777777777777777    77777766554110 023555 


Q ss_pred             -hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          173 -PHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       173 -~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                       ..+|..+..+|.+.|++++|.++|+++...++    ...  .+|..+..+|.+.|++++|.++|+++.+..+
T Consensus       515 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p----~~~--~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~p  581 (597)
T 2xpi_A          515 WAATWANLGHAYRKLKMYDAAIDALNQGLLLST----NDA--NVHTAIALVYLHKKIPGLAITHLHESLAISP  581 (597)
T ss_dssp             GHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSS----CCH--HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC----CCh--HHHHHHHHHHHHhCCHHHHHHHHHHHHhcCC
Confidence             56677777777777777777777777765432    111  1566777777777777777777776665443

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=99.79  E-value=1.9e-16  Score=128.87  Aligned_cols=202  Identities=11%  Similarity=-0.010  Sum_probs=163.1

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc-cH
Q 043380           15 LNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP-DI   93 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p-~~   93 (246)
                      -+..+|+.+..++.+.|++++|...|+++..-.+.+...|..+...+...|++++|...|.+....         .| +.
T Consensus       167 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~---------~p~~~  237 (388)
T 1w3b_A          167 NFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSL---------SPNHA  237 (388)
T ss_dssp             TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHH---------CTTCH
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh---------CcCCH
Confidence            346677777777777777777777777765333445666777777777777778887777777764         34 57


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK  172 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~  172 (246)
                      .++..+..+|...|++++|...|+++.+   ..|+ ..+|..+...+...|++++    |...|+++.+.      .+.+
T Consensus       238 ~~~~~l~~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~~l~~~~~~~g~~~~----A~~~~~~al~~------~p~~  304 (388)
T 1w3b_A          238 VVHGNLACVYYEQGLIDLAIDTYRRAIE---LQPHFPDAYCNLANALKEKGSVAE----AEDCYNTALRL------CPTH  304 (388)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH---TCSSCHHHHHHHHHHHHHHSCHHH----HHHHHHHHHHH------CTTC
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHh---hCCCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHhh------Cccc
Confidence            7899999999999999999999999988   4465 7789999999999999999    99999999886      4567


Q ss_pred             hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          173 PHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       173 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      ..++..+...+...|++++|...++++....+    ...  .++..+...|.+.|++++|.+.|+++.+..+
T Consensus       305 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p----~~~--~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~p  370 (388)
T 1w3b_A          305 ADSLNNLANIKREQGNIEEAVRLYRKALEVFP----EFA--AAHSNLASVLQQQGKLQEALMHYKEAIRISP  370 (388)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCT----TCH--HHHHHHHHHHHTTTCCHHHHHHHHHHHTTCT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC----CcH--HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence            78999999999999999999999999876532    222  2789999999999999999999999876543

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=99.74  E-value=8.7e-16  Score=124.90  Aligned_cols=207  Identities=14%  Similarity=0.055  Sum_probs=111.6

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      .+.++.+|..+..+|.+.|++++|.+.|+++.+-.+.+..+|..+..++...|++++|.+.|.++.+.         .|+
T Consensus        63 ~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~---------~p~  133 (388)
T 1w3b_A           63 NPLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGAVQAYVSALQY---------NPD  133 (388)
T ss_dssp             CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHH---------CTT
T ss_pred             CCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---------CCC
Confidence            34566777777777777777777777777765322344556777777777777777777777766654         232


Q ss_pred             -HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCC---
Q 043380           93 -IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNP---  167 (246)
Q Consensus        93 -~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~---  167 (246)
                       ...+..+...+...|++++|.+.|+++.+   ..|+ ..+|..+...+...|++++    |...|+++.+.+....   
T Consensus       134 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~~l~~~~~~~g~~~~----A~~~~~~al~~~p~~~~~~  206 (388)
T 1w3b_A          134 LYCVRSDLGNLLKALGRLEEAKACYLKAIE---TQPNFAVAWSNLGCVFNAQGEIWL----AIHHFEKAVTLDPNFLDAY  206 (388)
T ss_dssp             CTHHHHHHHHHHHTTSCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHTTTCHHH----HHHHHHHHHHHCTTCHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHhcCCCcHHHH
Confidence             23344444445555555555555555544   2232 3444444444444444444    4444444433210000   


Q ss_pred             ------------------------CCCc-chhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHH
Q 043380          168 ------------------------GLWP-KPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEA  222 (246)
Q Consensus       168 ------------------------~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~  222 (246)
                                              ...| +..++..+..+|...|++++|...|+++....+.  .+    .+|..+...
T Consensus       207 ~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~--~~----~~~~~l~~~  280 (388)
T 1w3b_A          207 INLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQPH--FP----DAYCNLANA  280 (388)
T ss_dssp             HHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSS--CH----HHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC--CH----HHHHHHHHH
Confidence                                    0122 2355555666666666666666666665443211  11    145555666


Q ss_pred             HHhcCChhHHHHHHHHHHh
Q 043380          223 ALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       223 ~~~~g~~~~a~~~~~~m~~  241 (246)
                      +.+.|++++|.++|+++.+
T Consensus       281 ~~~~g~~~~A~~~~~~al~  299 (388)
T 1w3b_A          281 LKEKGSVAEAEDCYNTALR  299 (388)
T ss_dssp             HHHHSCHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHh
Confidence            6666666666666655544

>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=99.74  E-value=5.3e-16  Score=128.31  Aligned_cols=205  Identities=9%  Similarity=-0.045  Sum_probs=174.5

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      .+.++..+..+...+.+.|++++|..+|+.+....+.+..+|..+..++...|++++|...|+++.+.        -+.+
T Consensus        22 ~p~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--------~p~~   93 (450)
T 2y4t_A           22 SMADVEKHLELGKKLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIQL--------KMDF   93 (450)
T ss_dssp             -CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTC
T ss_pred             cHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--------CCCc
Confidence            35677889999999999999999999999987545678999999999999999999999999999986        2345


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCH----HHHHHH------------HHHHHhcCChhhhhhHHHHHH
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDR----STFTAM------------VDALLYSGSIKVVGLYALCIF  156 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~----~~~~~l------------i~~~~~~~~~~~~~~~a~~~~  156 (246)
                      ..++..+..+|.+.|++++|...|+++..   ..|+.    ..+..+            ...+...|++++    |..+|
T Consensus        94 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----A~~~~  166 (450)
T 2y4t_A           94 TAARLQRGHLLLKQGKLDEAEDDFKKVLK---SNPSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTA----AIAFL  166 (450)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHT---SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHH----HHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHh---cCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHH----HHHHH
Confidence            78999999999999999999999999988   45663    555555            444899999999    99999


Q ss_pred             HHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHH
Q 043380          157 GEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKL  236 (246)
Q Consensus       157 ~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~  236 (246)
                      +.+.+.      .+.+..++..+..+|...|++++|..+|+++....+.    ..  .+|..+...|...|++++|.+.|
T Consensus       167 ~~~~~~------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~----~~--~~~~~l~~~~~~~g~~~~A~~~~  234 (450)
T 2y4t_A          167 DKILEV------CVWDAELRELRAECFIKEGEPRKAISDLKAASKLKND----NT--EAFYKISTLYYQLGDHELSLSEV  234 (450)
T ss_dssp             HHHHHH------CTTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHCS----CH--HHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHh------CCCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC----CH--HHHHHHHHHHHHcCCHHHHHHHH
Confidence            999886      3456788999999999999999999999998754321    11  27999999999999999999999


Q ss_pred             HHHHhhcc
Q 043380          237 SNTITRWK  244 (246)
Q Consensus       237 ~~m~~~g~  244 (246)
                      +++.+..+
T Consensus       235 ~~~~~~~p  242 (450)
T 2y4t_A          235 RECLKLDQ  242 (450)
T ss_dssp             HHHHHHCT
T ss_pred             HHHHHhCC
Confidence            99876543

>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=99.74  E-value=2.9e-15  Score=114.41  Aligned_cols=203  Identities=9%  Similarity=-0.074  Sum_probs=175.2

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHH
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTY   96 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~   96 (246)
                      +..|..+...+...|++++|.+.|+.+....+.+...+..+...+...|++++|.+.|+++.+.        .+.+...+
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~--------~~~~~~~~  108 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEIDPSSADAHAALAVVFQTEMEPKLADEEYRKALAS--------DSRNARVL  108 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--------CcCcHHHH
Confidence            6778889999999999999999999886444667889999999999999999999999999986        23467889


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhh
Q 043380           97 ATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHL  175 (246)
Q Consensus        97 ~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~  175 (246)
                      ..+...|...|++++|.++++++.. .+..|+ ...+..+...+...|++++    |...|++..+.      ...+..+
T Consensus       109 ~~la~~~~~~g~~~~A~~~~~~~~~-~~~~~~~~~~~~~la~~~~~~g~~~~----A~~~~~~~~~~------~~~~~~~  177 (252)
T 2ho1_A          109 NNYGGFLYEQKRYEEAYQRLLEASQ-DTLYPERSRVFENLGLVSLQMKKPAQ----AKEYFEKSLRL------NRNQPSV  177 (252)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHTT-CTTCTTHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------CSCCHHH
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHh-CccCcccHHHHHHHHHHHHHcCCHHH----HHHHHHHHHhc------CcccHHH
Confidence            9999999999999999999999987 556665 6778899999999999999    99999999886      2345788


Q ss_pred             HHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          176 YVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       176 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      +..+...+...|++++|...++......+    ....  .+..+...+...|++++|.++++.+.+..+
T Consensus       178 ~~~la~~~~~~g~~~~A~~~~~~~~~~~~----~~~~--~~~~~~~~~~~~g~~~~A~~~~~~~~~~~p  240 (252)
T 2ho1_A          178 ALEMADLLYKEREYVPARQYYDLFAQGGG----QNAR--SLLLGIRLAKVFEDRDTAASYGLQLKRLYP  240 (252)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTTSC----CCHH--HHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCc----CcHH--HHHHHHHHHHHccCHHHHHHHHHHHHHHCC
Confidence            99999999999999999999999876432    2222  688899999999999999999999987654

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.73  E-value=4.4e-16  Score=117.02  Aligned_cols=200  Identities=11%  Similarity=0.018  Sum_probs=160.6

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      ++++..+..+...+.+.|++++|...|+...+--+.+...+..+...+.+.|++++|...|++..+.        -+.+.
T Consensus         2 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~--------~P~~~   73 (217)
T 2pl2_A            2 QTAEQNPLRLGVQLYALGRYDAALTLFERALKENPQDPEALYWLARTQLKLGLVNPALENGKTLVAR--------TPRYL   73 (217)
T ss_dssp             --CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCH
T ss_pred             CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--------CCCcH
Confidence            5777889999999999999999999999987555678899999999999999999999999999986        23356


Q ss_pred             HHHHHHHHHHHcc-----------CCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHH
Q 043380           94 FTYATLLMGFRHA-----------KDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVK  161 (246)
Q Consensus        94 ~~~~~ll~~~~~~-----------~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~  161 (246)
                      ..+..+-.++...           |++++|...|++..+   +.|+ ...+..+...|...|++++    |...|++..+
T Consensus        74 ~a~~~lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~---~~P~~~~~~~~lg~~~~~~g~~~~----A~~~~~~al~  146 (217)
T 2pl2_A           74 GGYMVLSEAYVALYRQAEDRERGKGYLEQALSVLKDAER---VNPRYAPLHLQRGLVYALLGERDK----AEASLKQALA  146 (217)
T ss_dssp             HHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHH---hCcccHHHHHHHHHHHHHcCChHH----HHHHHHHHHh
Confidence            7899999999999           999999999999988   5576 7889999999999999999    9999999999


Q ss_pred             hhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          162 RVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       162 ~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      .     .  .+...+..+..+|...|++++|...|++.....+..    .  .++..+...+...|++++|++.|++...
T Consensus       147 ~-----~--~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~P~~----~--~~~~~la~~~~~~g~~~~A~~~~~~~~~  213 (217)
T 2pl2_A          147 L-----E--DTPEIRSALAELYLSMGRLDEALAQYAKALEQAPKD----L--DLRVRYASALLLKGKAEEAARAAALEHH  213 (217)
T ss_dssp             H-----C--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTC----H--HHHHHHHHHHTC----------------
T ss_pred             c-----c--cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC----h--HHHHHHHHHHHHccCHHHHHHHHHHHhh
Confidence            8     5  678899999999999999999999999987654321    1  2688899999999999999999987643

>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=99.73  E-value=1.5e-15  Score=125.55  Aligned_cols=204  Identities=12%  Similarity=-0.002  Sum_probs=170.5

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      .+.+..+|..+..+|.+.|++++|...|+.+.+..+.+...+..+..+|.+.|++++|.+.|+++.+.         .|+
T Consensus        56 ~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---------~~~  126 (450)
T 2y4t_A           56 DPDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLKMDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKS---------NPS  126 (450)
T ss_dssp             CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS---------CCC
T ss_pred             CCccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc---------CCC
Confidence            45678999999999999999999999999987444667889999999999999999999999999985         343


Q ss_pred             -H---HHHHHHH------------HHHHccCCHHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHhcCChhhhhhHHHHH
Q 043380           93 -I---FTYATLL------------MGFRHAKDLQSLLEIVFEMKSCCNLIL-DRSTFTAMVDALLYSGSIKVVGLYALCI  155 (246)
Q Consensus        93 -~---~~~~~ll------------~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~~~~~~~~~~a~~~  155 (246)
                       .   ..+..+.            ..+...|++++|...|+.+.+   ..| +..++..+...|...|++++    |..+
T Consensus       127 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~~~~l~~~~~~~g~~~~----A~~~  199 (450)
T 2y4t_A          127 ENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILE---VCVWDAELRELRAECFIKEGEPRK----AISD  199 (450)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCGGG----GHHH
T ss_pred             ChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCChHHHHHHHHHHHHCCCHHH----HHHH
Confidence             3   5555554            448899999999999999988   334 58889999999999999999    9999


Q ss_pred             HHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHH------------HHHH
Q 043380          156 FGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLL------------MEAA  223 (246)
Q Consensus       156 ~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~l------------i~~~  223 (246)
                      |+.+.+.      .+.+..++..+..+|...|++++|...|+++....+..    ..  .+..+            ...|
T Consensus       200 ~~~~~~~------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~----~~--~~~~~~~~~~~~~~~~~~~~~  267 (450)
T 2y4t_A          200 LKAASKL------KNDNTEAFYKISTLYYQLGDHELSLSEVRECLKLDQDH----KR--CFAHYKQVKKLNKLIESAEEL  267 (450)
T ss_dssp             HHHHHHH------HCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTC----HH--HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHh------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCh----HH--HHHHHHHHHHHHHHHHHHHHH
Confidence            9999886      24467899999999999999999999999987543221    11  34444            8889


Q ss_pred             HhcCChhHHHHHHHHHHhhcc
Q 043380          224 LNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       224 ~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      .+.|++++|.++|+++.+..+
T Consensus       268 ~~~g~~~~A~~~~~~~l~~~p  288 (450)
T 2y4t_A          268 IRDGRYTDATSKYESVMKTEP  288 (450)
T ss_dssp             HHHTCHHHHHHHHHHHHHHCC
T ss_pred             HHcCCHHHHHHHHHHHHhcCC
Confidence            999999999999999877543

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.72  E-value=5.3e-15  Score=110.64  Aligned_cols=207  Identities=7%  Similarity=-0.108  Sum_probs=175.0

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      +.++..|..+...+...|++++|.+.|+......+.+...+..+...+...|++++|.+.++++.+.        .+.+.
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~--------~~~~~   76 (225)
T 2vq2_A            5 NQVSNIKTQLAMEYMRGQDYRQATASIEDALKSDPKNELAWLVRAEIYQYLKVNDKAQESFRQALSI--------KPDSA   76 (225)
T ss_dssp             CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCH
T ss_pred             cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCChHHHHHHHHHHHHh--------CCCCh
Confidence            3456788899999999999999999999886544667889999999999999999999999999986        24467


Q ss_pred             HHHHHHHHHHHcc-CCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc
Q 043380           94 FTYATLLMGFRHA-KDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP  171 (246)
Q Consensus        94 ~~~~~ll~~~~~~-~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p  171 (246)
                      .++..+...+... |++++|...++.+.+ .+..|+ ...+..+...+...|++++    |...++...+.      .+.
T Consensus        77 ~~~~~l~~~~~~~~~~~~~A~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~----A~~~~~~~~~~------~~~  145 (225)
T 2vq2_A           77 EINNNYGWFLCGRLNRPAESMAYFDKALA-DPTYPTPYIANLNKGICSAKQGQFGL----AEAYLKRSLAA------QPQ  145 (225)
T ss_dssp             HHHHHHHHHHHTTTCCHHHHHHHHHHHHT-STTCSCHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------STT
T ss_pred             HHHHHHHHHHHHhcCcHHHHHHHHHHHHc-CcCCcchHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh------CCC
Confidence            7899999999999 999999999999988 555565 6788899999999999999    99999999886      233


Q ss_pred             chhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          172 KPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       172 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      +...+..+..++...|++++|..+++......+.   ...  ..+..+...+...|+.+.|..+++.+.+..+
T Consensus       146 ~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~---~~~--~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~p  213 (225)
T 2vq2_A          146 FPPAFKELARTKMLAGQLGDADYYFKKYQSRVEV---LQA--DDLLLGWKIAKALGNAQAAYEYEAQLQANFP  213 (225)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCS---CCH--HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             CchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC---CCH--HHHHHHHHHHHhcCcHHHHHHHHHHHHHhCC
Confidence            5788999999999999999999999998754320   111  1577888888999999999999999876544

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.72  E-value=9.5e-16  Score=123.62  Aligned_cols=206  Identities=12%  Similarity=0.027  Sum_probs=166.1

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      +.+..+|..+..+|.+.|++++|.+.|++...-.+.+..+|..+..+|...|++++|...|+++.+.         .|+.
T Consensus        96 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~---------~p~~  166 (365)
T 4eqf_A           96 PGDAEAWQFLGITQAENENEQAAIVALQRCLELQPNNLKALMALAVSYTNTSHQQDACEALKNWIKQ---------NPKY  166 (365)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---------CHHH
T ss_pred             cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHccccHHHHHHHHHHHHHh---------Cccc
Confidence            4678899999999999999999999999886434667889999999999999999999999999875         3432


Q ss_pred             -----------HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           94 -----------FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        94 -----------~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                                 ..+..+...+...|++++|..+|+++.....-.++..++..+...|...|++++    |...|++..+.
T Consensus       167 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~g~~~~----A~~~~~~al~~  242 (365)
T 4eqf_A          167 KYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLGVLFHLSGEFNR----AIDAFNAALTV  242 (365)
T ss_dssp             HCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHH
T ss_pred             hHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHHHHHHHCCCHHH----HHHHHHHHHHh
Confidence                       233445788999999999999999999822111258899999999999999999    99999999886


Q ss_pred             hcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          163 VCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       163 ~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                            .+.+..+|..+..+|...|++++|...|++.....+..    .  .+|..+..+|...|++++|.+.|++..+.
T Consensus       243 ------~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~----~--~~~~~l~~~~~~~g~~~~A~~~~~~al~~  310 (365)
T 4eqf_A          243 ------RPEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQPGF----I--RSRYNLGISCINLGAYREAVSNFLTALSL  310 (365)
T ss_dssp             ------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTC----H--HHHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             ------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCc----h--HHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence                  34467899999999999999999999999987543221    1  27899999999999999999999998775


Q ss_pred             cc
Q 043380          243 WK  244 (246)
Q Consensus       243 g~  244 (246)
                      .+
T Consensus       311 ~~  312 (365)
T 4eqf_A          311 QR  312 (365)
T ss_dssp             HH
T ss_pred             Cc
Confidence            43

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.69  E-value=2.3e-15  Score=114.15  Aligned_cols=206  Identities=11%  Similarity=0.020  Sum_probs=156.7

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      ...+...|..+...+.+.|++++|...|++.....+.+...+..+...+...|++++|...|+++.+.        .+.+
T Consensus        19 ~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~--------~~~~   90 (243)
T 2q7f_A           19 SHMASMTGGQQMGRGSEFGDYEKAAEAFTKAIEENKEDAIPYINFANLLSSVNELERALAFYDKALEL--------DSSA   90 (243)
T ss_dssp             -----------------------CCTTHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTC
T ss_pred             chhHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--------CCcc
Confidence            34566778888889999999999999999987655668889999999999999999999999999986        2346


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK  172 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~  172 (246)
                      ...+..+...|...|++++|...+++..+ . .+.+...+..+...+...|++++    |...+++..+.      ...+
T Consensus        91 ~~~~~~la~~~~~~~~~~~A~~~~~~~~~-~-~~~~~~~~~~~a~~~~~~~~~~~----A~~~~~~~~~~------~~~~  158 (243)
T 2q7f_A           91 ATAYYGAGNVYVVKEMYKEAKDMFEKALR-A-GMENGDLFYMLGTVLVKLEQPKL----ALPYLQRAVEL------NEND  158 (243)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH-H-TCCSHHHHHHHHHHHHHTSCHHH----HHHHHHHHHHH------CTTC
T ss_pred             hHHHHHHHHHHHHhccHHHHHHHHHHHHH-h-CCCCHHHHHHHHHHHHHhccHHH----HHHHHHHHHHh------CCcc
Confidence            78899999999999999999999999988 2 22357889999999999999999    99999999886      3346


Q ss_pred             hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          173 PHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       173 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      ...+..+...+...|++++|...+++.....+.    ..  .++..+...|...|++++|.+.+++..+..+
T Consensus       159 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~----~~--~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p  224 (243)
T 2q7f_A          159 TEARFQFGMCLANEGMLDEALSQFAAVTEQDPG----HA--DAFYNAGVTYAYKENREKALEMLDKAIDIQP  224 (243)
T ss_dssp             HHHHHHHHHHHHHHTCCHHHHHHHHHHHHHCTT----CH--HHHHHHHHHHHHTTCTTHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcc----cH--HHHHHHHHHHHHccCHHHHHHHHHHHHccCc
Confidence            788999999999999999999999998754321    11  2788899999999999999999999877554

>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=99.68  E-value=1.6e-14  Score=114.27  Aligned_cols=209  Identities=9%  Similarity=-0.063  Sum_probs=171.5

Q ss_pred             CcCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           14 KLNTIVMNAVIEASREAQ-RIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g-~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      +.++..|..+...+...| ++++|.+.|+......+.+...|..+...+...|++++|...|+++.+.        .+.+
T Consensus        87 ~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~--------~~~~  158 (330)
T 3hym_B           87 PSNPVSWFAVGCYYLMVGHKNEHARRYLSKATTLEKTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQL--------MKGC  158 (330)
T ss_dssp             TTSTHHHHHHHHHHHHSCSCHHHHHHHHHHHHTTCTTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--------TTTC
T ss_pred             cCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--------cccc
Confidence            446778888899999999 9999999999887544567788999999999999999999999999886        2334


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCC---C
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNP---G  168 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~---~  168 (246)
                      ...+..+...|...|++++|...+++..+   ..|+ ...+..+...+...|++++    |...+++..+......   .
T Consensus       159 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~---~~~~~~~~~~~l~~~~~~~~~~~~----A~~~~~~a~~~~~~~~~~~~  231 (330)
T 3hym_B          159 HLPMLYIGLEYGLTNNSKLAERFFSQALS---IAPEDPFVMHEVGVVAFQNGEWKT----AEKWFLDALEKIKAIGNEVT  231 (330)
T ss_dssp             SHHHHHHHHHHHHTTCHHHHHHHHHHHHT---TCTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHHHTTTSCSCT
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHH---hCCCChHHHHHHHHHHHHcccHHH----HHHHHHHHHHHhhhcccccc
Confidence            56777799999999999999999999988   3344 7889999999999999999    9999999887632111   1


Q ss_pred             CCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhc
Q 043380          169 LWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRW  243 (246)
Q Consensus       169 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  243 (246)
                      ...+..++..+..+|...|++++|...+++.....+..  +    .++..+...|...|++++|.+.|++..+..
T Consensus       232 ~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~--~----~~~~~la~~~~~~g~~~~A~~~~~~al~~~  300 (330)
T 3hym_B          232 VDKWEPLLNNLGHVCRKLKKYAEALDYHRQALVLIPQN--A----STYSAIGYIHSLMGNFENAVDYFHTALGLR  300 (330)
T ss_dssp             TTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTC--S----HHHHHHHHHHHHHTCHHHHHHHHHTTTTTC
T ss_pred             ccHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhhCccc--h----HHHHHHHHHHHHhccHHHHHHHHHHHHccC
Confidence            13345789999999999999999999999987543221  1    278899999999999999999999876644

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.66  E-value=4.1e-15  Score=119.89  Aligned_cols=204  Identities=7%  Similarity=-0.017  Sum_probs=164.2

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      +...|..+...+.+.|++++|.++|+.+....+.+..+|..+...|...|++++|...|+++.+.        .+.+..+
T Consensus        64 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--------~p~~~~~  135 (365)
T 4eqf_A           64 DWPGAFEEGLKRLKEGDLPVTILFMEAAILQDPGDAEAWQFLGITQAENENEQAAIVALQRCLEL--------QPNNLKA  135 (365)
T ss_dssp             TCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHH
T ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--------CCCCHHH
Confidence            44558889999999999999999999987545678899999999999999999999999999986        2345789


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-----------HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhc
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-----------RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVC  164 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-----------~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~  164 (246)
                      |..+..+|...|++++|...|+++.+   ..|+           ...+..+...+...|++++    |..+|+++.+.. 
T Consensus       136 ~~~l~~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~----A~~~~~~al~~~-  207 (365)
T 4eqf_A          136 LMALAVSYTNTSHQQDACEALKNWIK---QNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEG----VKELYLEAAHQN-  207 (365)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH---HCHHHHCC-------------------CCHHHHH----HHHHHHHHHHHS-
T ss_pred             HHHHHHHHHccccHHHHHHHHHHHHH---hCccchHHHhhhccchHHHHHHHHHHhhhhhHHH----HHHHHHHHHHhC-
Confidence            99999999999999999999999988   3344           2233445889999999999    999999999871 


Q ss_pred             CCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          165 SNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       165 ~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                         .-.++..++..+...|...|++++|...|++.....+.    ..  .+|..+..+|...|++++|.+.|++..+..+
T Consensus       208 ---p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~----~~--~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p  278 (365)
T 4eqf_A          208 ---GDMIDPDLQTGLGVLFHLSGEFNRAIDAFNAALTVRPE----DY--SLWNRLGATLANGDRSEEAVEAYTRALEIQP  278 (365)
T ss_dssp             ---CSSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT----CH--HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             ---cCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC----CH--HHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC
Confidence               11125789999999999999999999999998754322    12  2799999999999999999999999887554

>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=99.66  E-value=3.1e-14  Score=114.54  Aligned_cols=202  Identities=12%  Similarity=0.018  Sum_probs=145.4

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHH
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTY   96 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~   96 (246)
                      ...+..+...+.+.|++++|...|+.+....+.+..+|..+..++...|++++|.+.|+++.+.        .+.+..++
T Consensus        64 ~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--------~~~~~~~~  135 (368)
T 1fch_A           64 HPQPFEEGLRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLEL--------KPDNQTAL  135 (368)
T ss_dssp             CSSHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHH
T ss_pred             hHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHhc--------CCCCHHHH
Confidence            3445666777777777777777777765444556667777777777777777777777777765        13356677


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHhCCC-----------------------------------------------CCC--
Q 043380           97 ATLLMGFRHAKDLQSLLEIVFEMKSCCN-----------------------------------------------LIL--  127 (246)
Q Consensus        97 ~~ll~~~~~~~~~~~a~~~~~~m~~~~~-----------------------------------------------~~p--  127 (246)
                      ..+...|...|++++|...++.+.. ..                                               ..|  
T Consensus       136 ~~l~~~~~~~g~~~~A~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~  214 (368)
T 1fch_A          136 MALAVSFTNESLQRQACEILRDWLR-YTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTS  214 (368)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH-TSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTS
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHH-hCcCcHHHHHHHHHHhhhhcccHHHHHHHHHhhcccHHHHHHHHHHHHHhCcCc
Confidence            7777777777777777777766554 11                                               112  


Q ss_pred             -CHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCC
Q 043380          128 -DRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGT  206 (246)
Q Consensus       128 -~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  206 (246)
                       +..++..+...|...|++++    |...|+.....      .+.+..++..+...+...|++++|...+++.....+. 
T Consensus       215 ~~~~~~~~l~~~~~~~g~~~~----A~~~~~~al~~------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~-  283 (368)
T 1fch_A          215 IDPDVQCGLGVLFNLSGEYDK----AVDCFTAALSV------RPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPG-  283 (368)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-
T ss_pred             ccHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh------CcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-
Confidence             46778888888888999999    99999888875      2334678888888889999999999998887654321 


Q ss_pred             CCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhc
Q 043380          207 ISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRW  243 (246)
Q Consensus       207 ~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  243 (246)
                         ..  .++..+...|.+.|++++|.+.|++..+..
T Consensus       284 ---~~--~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  315 (368)
T 1fch_A          284 ---YI--RSRYNLGISCINLGAHREAVEHFLEALNMQ  315 (368)
T ss_dssp             ---CH--HHHHHHHHHHHHHTCHHHHHHHHHHHHHHH
T ss_pred             ---cH--HHHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence               11  268888888999999999999988877644

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.66  E-value=3.3e-14  Score=108.50  Aligned_cols=204  Identities=14%  Similarity=0.056  Sum_probs=170.1

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc----
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD----   92 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~----   92 (246)
                      ...|..+...+...|++++|...|+...+.. .+...|..+..++...|++++|.+.+.+..+..     ....|+    
T Consensus         5 a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-----~~~~~~~~~~   78 (258)
T 3uq3_A            5 ADKEKAEGNKFYKARQFDEAIEHYNKAWELH-KDITYLNNRAAAEYEKGEYETAISTLNDAVEQG-----REMRADYKVI   78 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-----HHTTCCHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhh-ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhC-----cccccchHHH
Confidence            5678889999999999999999999876323 888999999999999999999999999998751     001111    


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCC------------------------CCCC-HHHHHHHHHHHHhcCChhh
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCN------------------------LILD-RSTFTAMVDALLYSGSIKV  147 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~------------------------~~p~-~~~~~~li~~~~~~~~~~~  147 (246)
                      ..+|..+...|...|++++|...|+.... ..                        ..|+ ...+..+...+...|++++
T Consensus        79 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~-~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (258)
T 3uq3_A           79 SKSFARIGNAYHKLGDLKKTIEYYQKSLT-EHRTADILTKLRNAEKELKKAEAEAYVNPEKAEEARLEGKEYFTKSDWPN  157 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHh-cCchhHHHHHHhHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHhcCHHH
Confidence            57899999999999999999999999887 22                        3343 5678889999999999999


Q ss_pred             hhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcC
Q 043380          148 VGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDG  227 (246)
Q Consensus       148 ~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g  227 (246)
                          |...|+.....      .+.+..++..+..+|...|++++|...++......+.    ..  .+|..+...+...|
T Consensus       158 ----A~~~~~~a~~~------~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~----~~--~~~~~l~~~~~~~g  221 (258)
T 3uq3_A          158 ----AVKAYTEMIKR------APEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPN----FV--RAYIRKATAQIAVK  221 (258)
T ss_dssp             ----HHHHHHHHHHH------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT----CH--HHHHHHHHHHHHTT
T ss_pred             ----HHHHHHHHHhc------CcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCHH----HH--HHHHHHHHHHHHHh
Confidence                99999999886      3346788999999999999999999999998754322    11  27888999999999


Q ss_pred             ChhHHHHHHHHHHhhc
Q 043380          228 QVDLALDKLSNTITRW  243 (246)
Q Consensus       228 ~~~~a~~~~~~m~~~g  243 (246)
                      ++++|.+.++...+..
T Consensus       222 ~~~~A~~~~~~a~~~~  237 (258)
T 3uq3_A          222 EYASALETLDAARTKD  237 (258)
T ss_dssp             CHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhC
Confidence            9999999999887654

>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=99.66  E-value=3.7e-14  Score=114.06  Aligned_cols=213  Identities=8%  Similarity=-0.088  Sum_probs=168.3

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCC-----
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSG-----   87 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~-----   87 (246)
                      .+.+..+|..+..++.+.|++++|.+.|+....-.+.+..++..+...+...|++++|.+.|+++....-.....     
T Consensus        94 ~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~  173 (368)
T 1fch_A           94 DPKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAE  173 (368)
T ss_dssp             CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC---
T ss_pred             CCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHH
Confidence            345778888999999999999999999988764346678889999999999999999998888877642100000     


Q ss_pred             -----------------------------------CCCc---cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-
Q 043380           88 -----------------------------------GFHP---DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-  128 (246)
Q Consensus        88 -----------------------------------~~~p---~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-  128 (246)
                                                         ...|   +..++..+...|...|++++|...|++...   ..|+ 
T Consensus       174 ~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~---~~~~~  250 (368)
T 1fch_A          174 EGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALS---VRPND  250 (368)
T ss_dssp             ------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTC
T ss_pred             HHhhhhcccHHHHHHHHHhhcccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCcCC
Confidence                                               0122   477899999999999999999999999988   3454 


Q ss_pred             HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCC
Q 043380          129 RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTIS  208 (246)
Q Consensus       129 ~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  208 (246)
                      ..+|..+...|...|++++    |...|+...+.      .+.+..++..+..+|...|++++|...|++.....+....
T Consensus       251 ~~~~~~l~~~~~~~g~~~~----A~~~~~~al~~------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~  320 (368)
T 1fch_A          251 YLLWNKLGATLANGNQSEE----AVAAYRRALEL------QPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRG  320 (368)
T ss_dssp             HHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC--
T ss_pred             HHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh------CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCC
Confidence            7889999999999999999    99999999886      2345688999999999999999999999987643222111


Q ss_pred             ch-----hhhHHHHHHHHHHHhcCChhHHHHHHHH
Q 043380          209 PE-----VQEEAGHLLMEAALNDGQVDLALDKLSN  238 (246)
Q Consensus       209 ~~-----~~~~~~~~li~~~~~~g~~~~a~~~~~~  238 (246)
                      +.     ....+|..+..+|...|++++|..++++
T Consensus       321 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  355 (368)
T 1fch_A          321 PRGEGGAMSENIWSTLRLALSMLGQSDAYGAADAR  355 (368)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHHTCGGGHHHHHTT
T ss_pred             ccccccchhhHHHHHHHHHHHHhCChHhHHHhHHH
Confidence            10     0123799999999999999999998864

>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=99.66  E-value=6.2e-14  Score=110.83  Aligned_cols=210  Identities=8%  Similarity=0.002  Sum_probs=159.7

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcC-CcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTK-KLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~-~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      +.+...+..+..++.+.|++++|..+++++....+.+...|..+...+...| ++++|...|++..+.        .+.+
T Consensus        53 p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~a~~~--------~~~~  124 (330)
T 3hym_B           53 PFHASCLPVHIGTLVELNKANELFYLSHKLVDLYPSNPVSWFAVGCYYLMVGHKNEHARRYLSKATTL--------EKTY  124 (330)
T ss_dssp             TTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTHHHHHHHHHHHHSCSCHHHHHHHHHHHHTT--------CTTC
T ss_pred             CCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHh--------CCcc
Confidence            3444556667778888888888888888876434556778888888888888 888899988888875        2334


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP  171 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p  171 (246)
                      ...|..+...+...|++++|...|++...   ..|+ ...+..+...|...|++++    |...++...+.      .+.
T Consensus       125 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~---~~~~~~~~~~~l~~~~~~~~~~~~----A~~~~~~al~~------~~~  191 (330)
T 3hym_B          125 GPAWIAYGHSFAVESEHDQAMAAYFTAAQ---LMKGCHLPMLYIGLEYGLTNNSKL----AERFFSQALSI------APE  191 (330)
T ss_dssp             THHHHHHHHHHHHHTCHHHHHHHHHHHHH---HTTTCSHHHHHHHHHHHHTTCHHH----HHHHHHHHHTT------CTT
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHH---hccccHHHHHHHHHHHHHHhhHHH----HHHHHHHHHHh------CCC
Confidence            66788888888899999999999998887   3344 5667778888899999999    99999988775      334


Q ss_pred             chhhHHHHHHHHHhcCChhHHhhHHHhhCCCCC---CCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          172 KPHLYVSMMHELAARVDYDIVKSPYRRMWPDST---GTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       172 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~---~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      +..++..+...+...|++++|...+++......   ....+.....++..+...|...|++++|.+.+++..+..+
T Consensus       192 ~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~  267 (330)
T 3hym_B          192 DPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQALVLIP  267 (330)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST
T ss_pred             ChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhhCc
Confidence            568889999999999999999999988763211   1111111122788899999999999999999998876543

>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=99.65  E-value=2e-14  Score=113.59  Aligned_cols=203  Identities=12%  Similarity=-0.017  Sum_probs=165.8

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      +.+...+..+..++.+.|++++|.+.|++.....+.+..++..+...+...|++++|.+.++++.+.         .|+.
T Consensus        52 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~---------~~~~  122 (327)
T 3cv0_A           52 PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALASLRAWLLS---------QPQY  122 (327)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT---------STTT
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---------CCcc
Confidence            4578889999999999999999999999886444667889999999999999999999999999876         2322


Q ss_pred             -HHHHHH--------------HH-HHHccCCHHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHhcCChhhhhhHHHHHH
Q 043380           94 -FTYATL--------------LM-GFRHAKDLQSLLEIVFEMKSCCNLIL-DRSTFTAMVDALLYSGSIKVVGLYALCIF  156 (246)
Q Consensus        94 -~~~~~l--------------l~-~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~~~~~~~~~~a~~~~  156 (246)
                       ..+..+              .. .+...|++++|...++++.+   ..| +...+..+...|...|++++    |...+
T Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~~~~la~~~~~~~~~~~----A~~~~  195 (327)
T 3cv0_A          123 EQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALE---MNPNDAQLHASLGVLYNLSNNYDS----AAANL  195 (327)
T ss_dssp             TTC--------------------CCTTSHHHHHHHHHHHHHHHH---HSTTCHHHHHHHHHHHHHTTCHHH----HHHHH
T ss_pred             HHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHh---hCCCCHHHHHHHHHHHHHhccHHH----HHHHH
Confidence             222222              22 37788999999999999988   334 58889999999999999999    99999


Q ss_pred             HHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHH
Q 043380          157 GEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKL  236 (246)
Q Consensus       157 ~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~  236 (246)
                      +...+.      .+.+..++..+...+...|++++|...+++.....+.    ..  .++..+...|...|++++|.+.+
T Consensus       196 ~~~~~~------~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~----~~--~~~~~l~~~~~~~g~~~~A~~~~  263 (327)
T 3cv0_A          196 RRAVEL------RPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPG----YV--RVMYNMAVSYSNMSQYDLAAKQL  263 (327)
T ss_dssp             HHHHHH------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT----CH--HHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHh------CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC----CH--HHHHHHHHHHHHhccHHHHHHHH
Confidence            999886      2345688999999999999999999999998654321    11  27889999999999999999999


Q ss_pred             HHHHhhcc
Q 043380          237 SNTITRWK  244 (246)
Q Consensus       237 ~~m~~~g~  244 (246)
                      ++..+..+
T Consensus       264 ~~a~~~~~  271 (327)
T 3cv0_A          264 VRAIYMQV  271 (327)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHhCC
Confidence            98876544

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.64  E-value=1.1e-13  Score=110.57  Aligned_cols=202  Identities=8%  Similarity=-0.043  Sum_probs=171.7

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      |+..+..+...+.+.|++++|...|+.+.+..+.+..++..+...+...|++++|...|+++.+.        .+-+...
T Consensus         2 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~--------~~~~~~~   73 (359)
T 3ieg_A            2 DVEKHLELGKKLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIAL--------KMDFTAA   73 (359)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--------CTTCHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--------CCCcchH
Confidence            46678889999999999999999999986544667889999999999999999999999999986        2336688


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC---C-HHHHHHH------------HHHHHhcCChhhhhhHHHHHHHHH
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL---D-RSTFTAM------------VDALLYSGSIKVVGLYALCIFGEI  159 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p---~-~~~~~~l------------i~~~~~~~~~~~~~~~a~~~~~~m  159 (246)
                      |..+...+...|++++|...|+...+   ..|   + ...+..+            ...+...|++++    |..+++..
T Consensus        74 ~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----A~~~~~~~  146 (359)
T 3ieg_A           74 RLQRGHLLLKQGKLDEAEDDFKKVLK---SNPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTA----AITFLDKI  146 (359)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHT---SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHH----HHHHHHHH
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHHHh---cCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHH----HHHHHHHH
Confidence            99999999999999999999999988   556   4 4445444            588999999999    99999999


Q ss_pred             HHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHH
Q 043380          160 VKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNT  239 (246)
Q Consensus       160 ~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  239 (246)
                      .+.      .+.+..++..+...+...|++++|...++......+.    ..  .++..+...+...|++++|.+.++..
T Consensus       147 ~~~------~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~----~~--~~~~~la~~~~~~~~~~~A~~~~~~a  214 (359)
T 3ieg_A          147 LEV------CVWDAELRELRAECFIKEGEPRKAISDLKAASKLKSD----NT--EAFYKISTLYYQLGDHELSLSEVREC  214 (359)
T ss_dssp             HHH------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCSC----CH--HHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHh------CCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC----CH--HHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            886      3456788999999999999999999999998765422    22  27889999999999999999999988


Q ss_pred             Hhhcc
Q 043380          240 ITRWK  244 (246)
Q Consensus       240 ~~~g~  244 (246)
                      .+..+
T Consensus       215 ~~~~~  219 (359)
T 3ieg_A          215 LKLDQ  219 (359)
T ss_dssp             HHHCT
T ss_pred             HhhCc
Confidence            76543

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.63  E-value=4.2e-14  Score=109.13  Aligned_cols=206  Identities=7%  Similarity=-0.110  Sum_probs=166.2

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHH
Q 043380           15 LNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIF   94 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~   94 (246)
                      .+..+|..+..++...|++++|...|++.....+.+..+|..+...+...|++++|.+.|++..+.        .+.+..
T Consensus        41 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~--------~~~~~~  112 (275)
T 1xnf_A           41 ERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLEL--------DPTYNY  112 (275)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCTH
T ss_pred             hhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHhc--------CccccH
Confidence            357889999999999999999999999986444667899999999999999999999999999986        233578


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchh
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPH  174 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~  174 (246)
                      .+..+..+|...|++++|...|+.+.+   ..|+.......+..+...|++++    |...++.....      ..++..
T Consensus       113 ~~~~la~~~~~~g~~~~A~~~~~~a~~---~~~~~~~~~~~~~~~~~~~~~~~----A~~~~~~~~~~------~~~~~~  179 (275)
T 1xnf_A          113 AHLNRGIALYYGGRDKLAQDDLLAFYQ---DDPNDPFRSLWLYLAEQKLDEKQ----AKEVLKQHFEK------SDKEQW  179 (275)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHCHHH----HHHHHHHHHHH------SCCCST
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHH---hCCCChHHHHHHHHHHHhcCHHH----HHHHHHHHHhc------CCcchH
Confidence            999999999999999999999999988   45665555555566677899999    99999888776      234444


Q ss_pred             hHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          175 LYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       175 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      .+ .+...+...++.++|...+...........+  ....+|..+...|...|++++|.+.|++..+..+
T Consensus       180 ~~-~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p  246 (275)
T 1xnf_A          180 GW-NIVEFYLGNISEQTLMERLKADATDNTSLAE--HLSETNFYLGKYYLSLGDLDSATALFKLAVANNV  246 (275)
T ss_dssp             HH-HHHHHHTTSSCHHHHHHHHHHHCCSHHHHHH--HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCC
T ss_pred             HH-HHHHHHHHhcCHHHHHHHHHHHhcccccccc--cccHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCc
Confidence            44 4777888888999999999988754321100  1123788899999999999999999999877554

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.63  E-value=7.5e-14  Score=109.53  Aligned_cols=200  Identities=13%  Similarity=0.032  Sum_probs=150.6

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH-hCCCC-CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCC
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVE-KGLEP-DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFH   90 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~-~~~~~-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~   90 (246)
                      -+|+..++..+...+...++.++|.+.++++. .+..| +...+..+-..+...|++++|.+.+++             +
T Consensus        61 ~~~~~~a~~~la~~~~~~~~~~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~-------------~  127 (291)
T 3mkr_A           61 SAPELQAVRMFAEYLASHSRRDAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ-------------G  127 (291)
T ss_dssp             SCHHHHHHHHHHHHHHCSTTHHHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT-------------C
T ss_pred             CChhHHHHHHHHHHHcCCCcHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC-------------C
Confidence            45677788888888888888889998888875 44345 455566666888888999998888876             2


Q ss_pred             ccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHH---HHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCC
Q 043380           91 PDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTF---TAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNP  167 (246)
Q Consensus        91 p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~---~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~  167 (246)
                      .+...+..+...|.+.|++++|...|+.+.+   ..|+....   ..++..+...|++++    |..+|+++.+.     
T Consensus       128 ~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~---~~p~~~~~~l~~a~~~l~~~~~~~~e----A~~~~~~~l~~-----  195 (291)
T 3mkr_A          128 DSLECMAMTVQILLKLDRLDLARKELKKMQD---QDEDATLTQLATAWVSLAAGGEKLQD----AYYIFQEMADK-----  195 (291)
T ss_dssp             CSHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHCTTHHHH----HHHHHHHHHHH-----
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh---hCcCcHHHHHHHHHHHHHhCchHHHH----HHHHHHHHHHh-----
Confidence            4566888888899999999999999999988   34663221   223344445688999    99999999886     


Q ss_pred             CCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhH-HHHHHHHHHhhcc
Q 043380          168 GLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDL-ALDKLSNTITRWK  244 (246)
Q Consensus       168 ~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~-a~~~~~~m~~~g~  244 (246)
                       .+.+...++.+..++...|++++|...|++....++.    ...  ++..++..+...|+.++ +.++++++.+..+
T Consensus       196 -~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~p~----~~~--~l~~l~~~~~~~g~~~eaa~~~~~~~~~~~P  266 (291)
T 3mkr_A          196 -CSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKDSG----HPE--TLINLVVLSQHLGKPPEVTNRYLSQLKDAHR  266 (291)
T ss_dssp             -SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT----CHH--HHHHHHHHHHHTTCCHHHHHHHHHHHHHHCT
T ss_pred             -CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC----CHH--HHHHHHHHHHHcCCCHHHHHHHHHHHHHhCC
Confidence             3457788889999999999999999999987754422    111  67888888888898875 5788888776554

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.61  E-value=4.2e-13  Score=107.11  Aligned_cols=204  Identities=12%  Similarity=-0.013  Sum_probs=167.6

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc-
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP-   91 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p-   91 (246)
                      .+.++..+..+..++...|++++|...|+...+..+.+...|..+...+...|++++|...|++..+.         .| 
T Consensus        33 ~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~---------~~~  103 (359)
T 3ieg_A           33 DPDNYIAYYRRATVFLAMGKSKAALPDLTKVIALKMDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKS---------NPS  103 (359)
T ss_dssp             CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTS---------CCC
T ss_pred             CcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHcCChHHHHHHHHHHHhc---------CCc
Confidence            34568899999999999999999999999986434557789999999999999999999999999975         45 


Q ss_pred             ---cHHHHHHH------------HHHHHccCCHHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHhcCChhhhhhHHHHH
Q 043380           92 ---DIFTYATL------------LMGFRHAKDLQSLLEIVFEMKSCCNLIL-DRSTFTAMVDALLYSGSIKVVGLYALCI  155 (246)
Q Consensus        92 ---~~~~~~~l------------l~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~~~~~~~~~~a~~~  155 (246)
                         +...+..+            ...+...|++++|..+++.+.+   ..| +...+..+...+...|++++    |...
T Consensus       104 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~----A~~~  176 (359)
T 3ieg_A          104 EQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILE---VCVWDAELRELRAECFIKEGEPRK----AISD  176 (359)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCHHH----HHHH
T ss_pred             ccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHH---hCCCchHHHHHHHHHHHHCCCHHH----HHHH
Confidence               44455444            5788999999999999999988   334 47889999999999999999    9999


Q ss_pred             HHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHH------------HHHHHH
Q 043380          156 FGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGH------------LLMEAA  223 (246)
Q Consensus       156 ~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~------------~li~~~  223 (246)
                      ++...+.      .+.+..++..+...+...|++++|...++......+...  .    ++.            .+...+
T Consensus       177 ~~~~~~~------~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~--~----~~~~~~~~~~~~~~~~~a~~~  244 (359)
T 3ieg_A          177 LKAASKL------KSDNTEAFYKISTLYYQLGDHELSLSEVRECLKLDQDHK--R----CFAHYKQVKKLNKLIESAEEL  244 (359)
T ss_dssp             HHHHHTT------CSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCH--H----HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHh------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCccch--H----HHHHHHHHHHHHHHHHHHHHH
Confidence            9999875      345678899999999999999999999999875432211  1    222            236678


Q ss_pred             HhcCChhHHHHHHHHHHhhcc
Q 043380          224 LNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       224 ~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      .+.|++++|.+.+++..+..+
T Consensus       245 ~~~~~~~~A~~~~~~~~~~~~  265 (359)
T 3ieg_A          245 IRDGRYTDATSKYESVMKTEP  265 (359)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCC
T ss_pred             HHcCCHHHHHHHHHHHHhcCC
Confidence            999999999999998876543

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.60  E-value=1.1e-13  Score=116.01  Aligned_cols=209  Identities=11%  Similarity=0.006  Sum_probs=169.6

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHH
Q 043380           15 LNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIF   94 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~   94 (246)
                      |+...|..+..++...|++++|.+.|+......+.+...+..+...+...|++++|...|++..+.        .+.+..
T Consensus       268 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--------~~~~~~  339 (514)
T 2gw1_A          268 PRVNSYIYMALIMADRNDSTEYYNYFDKALKLDSNNSSVYYHRGQMNFILQNYDQAGKDFDKAKEL--------DPENIF  339 (514)
T ss_dssp             CCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTCTTCTHHHHHHHHHHHHTTCTTHHHHHHHHHHHT--------CSSCSH
T ss_pred             ccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcCcCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHh--------ChhhHH
Confidence            337888888889999999999999998887545667788999999999999999999999999875        233567


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL-DRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP  173 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~  173 (246)
                      .+..+...|...|++++|...++.+.+   ..| +..++..+...|...|++++    |...++.+.......+...-..
T Consensus       340 ~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~~~~la~~~~~~~~~~~----A~~~~~~a~~~~~~~~~~~~~~  412 (514)
T 2gw1_A          340 PYIQLACLAYRENKFDDCETLFSEAKR---KFPEAPEVPNFFAEILTDKNDFDK----ALKQYDLAIELENKLDGIYVGI  412 (514)
T ss_dssp             HHHHHHHHTTTTTCHHHHHHHHHHHHH---HSTTCSHHHHHHHHHHHHTTCHHH----HHHHHHHHHHHHHTSSSCSSCS
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHH---HcccCHHHHHHHHHHHHHCCCHHH----HHHHHHHHHHhhhccchHHHHH
Confidence            888999999999999999999999888   334 36788899999999999999    9999999887622111111113


Q ss_pred             hhHHHHHHHHHh---cCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          174 HLYVSMMHELAA---RVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       174 ~~~~~li~~~~~---~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      .++..+..++..   .|++++|...++......+.    ..  .++..+...|.+.|++++|.+.|++..+..+
T Consensus       413 ~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~~~----~~--~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~  480 (514)
T 2gw1_A          413 APLVGKATLLTRNPTVENFIEATNLLEKASKLDPR----SE--QAKIGLAQMKLQQEDIDEAITLFEESADLAR  480 (514)
T ss_dssp             HHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHCTT----CH--HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCS
T ss_pred             HHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhCcc----cH--HHHHHHHHHHHHhcCHHHHHHHHHHHHHhcc
Confidence            489999999999   99999999999998754322    11  2788899999999999999999999887654

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.59  E-value=3.2e-13  Score=113.19  Aligned_cols=213  Identities=9%  Similarity=-0.113  Sum_probs=141.5

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCC---------
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKC---------   84 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~---------   84 (246)
                      .|++..|..+..+|.+.|++++|.+.|+.+.+..+.+..+|..+..++...|++++|...|+++....-..         
T Consensus        36 ~p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~  115 (514)
T 2gw1_A           36 KEDPVFYSNLSACYVSVGDLKKVVEMSTKALELKPDYSKVLLRRASANEGLGKFADAMFDLSVLSLNGDFNDASIEPMLE  115 (514)
T ss_dssp             CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSSSCCGGGTHHHHH
T ss_pred             CccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccChHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCccchHHHHHH
Confidence            47999999999999999999999999998864346677899999999999999999999999887652000         


Q ss_pred             -------------------------------------CCCCC-------------------------CccHHHHHHHHHH
Q 043380           85 -------------------------------------SSGGF-------------------------HPDIFTYATLLMG  102 (246)
Q Consensus        85 -------------------------------------~~~~~-------------------------~p~~~~~~~ll~~  102 (246)
                                                           .....                         +.+...+..+...
T Consensus       116 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  195 (514)
T 2gw1_A          116 RNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSVTSMASFFGIFKPELTFANYDESNEADKELMNGLS  195 (514)
T ss_dssp             HHHHHHHHHHHTTC---------------------------CCCCHHHHHHHHTTSCCCCCCSSCCSSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchhHHHHHHHhhcCHHHHHHHhcCCcHHHHHHHHHHH
Confidence                                                 00000                         0112233333333


Q ss_pred             HH---ccCCHHHHHHHHHHHHh-----CCCC-------CCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCC
Q 043380          103 FR---HAKDLQSLLEIVFEMKS-----CCNL-------ILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNP  167 (246)
Q Consensus       103 ~~---~~~~~~~a~~~~~~m~~-----~~~~-------~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~  167 (246)
                      +.   +.|++++|..+|+++..     ....       ..+..++..+...+...|++++    |..+|+...+.     
T Consensus       196 ~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----A~~~~~~~l~~-----  266 (514)
T 2gw1_A          196 NLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTGIFKFLKNDPLG----AHEDIKKAIEL-----  266 (514)
T ss_dssp             HHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHHHHHHHSSCHHH----HHHHHHHHHHH-----
T ss_pred             HHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHHHHHHHCCCHHH----HHHHHHHHHhh-----
Confidence            33   26777777777777665     1111       1124566677777777777777    77777777665     


Q ss_pred             CCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhc
Q 043380          168 GLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRW  243 (246)
Q Consensus       168 ~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  243 (246)
                        .|+..++..+..++...|++++|...++......+..  +    .+|..+...|...|++++|.+.+++..+..
T Consensus       267 --~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~--~----~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~  334 (514)
T 2gw1_A          267 --FPRVNSYIYMALIMADRNDSTEYYNYFDKALKLDSNN--S----SVYYHRGQMNFILQNYDQAGKDFDKAKELD  334 (514)
T ss_dssp             --CCCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTCTTC--T----HHHHHHHHHHHHTTCTTHHHHHHHHHHHTC
T ss_pred             --CccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcCcCC--H----HHHHHHHHHHHHhCCHHHHHHHHHHHHHhC
Confidence              2336666677777777777777777777765443221  1    156666667777777777777776665543

>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=99.58  E-value=1.4e-13  Score=116.26  Aligned_cols=211  Identities=8%  Similarity=-0.010  Sum_probs=169.4

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      ..|+...|..+...+...|++++|.+.|+......+.+..+|..+...+...|++++|...|++..+.        .+.+
T Consensus       272 ~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~--------~~~~  343 (537)
T 3fp2_A          272 LHPTPNSYIFLALTLADKENSQEFFKFFQKAVDLNPEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSL--------NPEN  343 (537)
T ss_dssp             HCCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTC
T ss_pred             cCCCchHHHHHHHHHHHhcCHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh--------CCCC
Confidence            45668888889999999999999999998876444667888999999999999999999999999886        1334


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP  171 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p  171 (246)
                      ...|..+...|...|++++|...+++..+   ..|+ ...+..+...+...|++++    |...|+...+.....+....
T Consensus       344 ~~~~~~la~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~~~~l~~~~~~~g~~~~----A~~~~~~a~~~~~~~~~~~~  416 (537)
T 3fp2_A          344 VYPYIQLACLLYKQGKFTESEAFFNETKL---KFPTLPEVPTFFAEILTDRGDFDT----AIKQYDIAKRLEEVQEKIHV  416 (537)
T ss_dssp             SHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCTHHHHHHHHHHHHTTCHHH----HHHHHHHHHHHHHHCSSCSS
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCChHHHHHHHHHHHHhCCHHH----HHHHHHHHHHcCCcchhhHH
Confidence            67889999999999999999999999988   3344 6788899999999999999    99999998876322222222


Q ss_pred             chhhHHHHHHHHHhc----------CChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          172 KPHLYVSMMHELAAR----------VDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       172 ~~~~~~~li~~~~~~----------g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      ....+.....++...          |++++|...|++.....+..    .  .++..+...|...|++++|.+.|++..+
T Consensus       417 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~----~--~~~~~l~~~~~~~g~~~~A~~~~~~al~  490 (537)
T 3fp2_A          417 GIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELDPRS----E--QAKIGLAQLKLQMEKIDEAIELFEDSAI  490 (537)
T ss_dssp             TTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHCTTC----H--HHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhCCCC----H--HHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            233355556777787          99999999999987543221    1  2789999999999999999999999877


Q ss_pred             hcc
Q 043380          242 RWK  244 (246)
Q Consensus       242 ~g~  244 (246)
                      ..+
T Consensus       491 ~~~  493 (537)
T 3fp2_A          491 LAR  493 (537)
T ss_dssp             HC-
T ss_pred             hCC
Confidence            544

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=99.58  E-value=1.6e-13  Score=108.27  Aligned_cols=202  Identities=11%  Similarity=-0.026  Sum_probs=164.1

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      +...+..+...+.+.|++++|..+|+++.+..+.+...+..+..++...|++++|...|+++.+.        .+.+..+
T Consensus        20 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~--------~~~~~~~   91 (327)
T 3cv0_A           20 YHENPMEEGLSMLKLANLAEAALAFEAVCQAAPEREEAWRSLGLTQAENEKDGLAIIALNHARML--------DPKDIAV   91 (327)
T ss_dssp             GSSCHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHH
T ss_pred             hhHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--------CcCCHHH
Confidence            44456678889999999999999999986544668889999999999999999999999999986        2446789


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCH-HHHHHH--------------HH-HHHhcCChhhhhhHHHHHHHHH
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDR-STFTAM--------------VD-ALLYSGSIKVVGLYALCIFGEI  159 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~-~~~~~l--------------i~-~~~~~~~~~~~~~~a~~~~~~m  159 (246)
                      +..+...|...|++++|...++....   ..|+. ..+..+              .. .+...|++++    |..+++..
T Consensus        92 ~~~la~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----A~~~~~~~  164 (327)
T 3cv0_A           92 HAALAVSHTNEHNANAALASLRAWLL---SQPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRE----CRTLLHAA  164 (327)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH---TSTTTTTC--------------------CCTTSHHHHHH----HHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH---hCCccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHH----HHHHHHHH
Confidence            99999999999999999999999988   33442 223222              22 3778889999    99999999


Q ss_pred             HHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHH
Q 043380          160 VKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNT  239 (246)
Q Consensus       160 ~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  239 (246)
                      .+.      .+.+..++..+...|...|++++|...+++.....+.    ..  .+|..+...+...|++++|.+.+++.
T Consensus       165 ~~~------~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~----~~--~~~~~l~~~~~~~~~~~~A~~~~~~a  232 (327)
T 3cv0_A          165 LEM------NPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPD----DA--QLWNKLGATLANGNRPQEALDAYNRA  232 (327)
T ss_dssp             HHH------STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT----CH--HHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             Hhh------CCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCC----cH--HHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            886      2346788999999999999999999999998754321    11  27889999999999999999999998


Q ss_pred             Hhhcc
Q 043380          240 ITRWK  244 (246)
Q Consensus       240 ~~~g~  244 (246)
                      .+..+
T Consensus       233 ~~~~~  237 (327)
T 3cv0_A          233 LDINP  237 (327)
T ss_dssp             HHHCT
T ss_pred             HHcCC
Confidence            76543

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.57  E-value=9.9e-14  Score=108.85  Aligned_cols=192  Identities=8%  Similarity=0.002  Sum_probs=155.3

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-HHHHH
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-IFTYA   97 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~~   97 (246)
                      ..-.+..+|...|+++.|...++.   .-+|+..++..+...+...++.++|.+.++++...       +..|+ ...+.
T Consensus        36 ~~~~l~r~yi~~g~~~~al~~~~~---~~~~~~~a~~~la~~~~~~~~~~~A~~~l~~ll~~-------~~~P~~~~~~~  105 (291)
T 3mkr_A           36 RDVFLYRAYLAQRKYGVVLDEIKP---SSAPELQAVRMFAEYLASHSRRDAIVAELDREMSR-------SVDVTNTTFLL  105 (291)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHSCT---TSCHHHHHHHHHHHHHHCSTTHHHHHHHHHHHHHS-------CCCCSCHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHhcc---cCChhHHHHHHHHHHHcCCCcHHHHHHHHHHHHhc-------ccCCCCHHHHH
Confidence            445678899999999999986654   24678889999999999999999999999999876       44564 55667


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhh--
Q 043380           98 TLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHL--  175 (246)
Q Consensus        98 ~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~--  175 (246)
                      .+-..+...|++++|.+.+++       ..+...+..+...|.+.|++++    |.+.|+.+.+.       .|+...  
T Consensus       106 ~la~~~~~~g~~~~Al~~l~~-------~~~~~~~~~l~~~~~~~g~~~~----A~~~l~~~~~~-------~p~~~~~~  167 (291)
T 3mkr_A          106 MAASIYFYDQNPDAALRTLHQ-------GDSLECMAMTVQILLKLDRLDL----ARKELKKMQDQ-------DEDATLTQ  167 (291)
T ss_dssp             HHHHHHHHTTCHHHHHHHHTT-------CCSHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-------CTTCHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHhC-------CCCHHHHHHHHHHHHHCCCHHH----HHHHHHHHHhh-------CcCcHHHH
Confidence            777889999999999999987       2568889999999999999999    99999999886       355321  


Q ss_pred             -HHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          176 -YVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       176 -~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                       ....+..+...|++++|..+|+++....+    .+..  +|+.+..++.+.|++++|.+.|++..+..+
T Consensus       168 l~~a~~~l~~~~~~~~eA~~~~~~~l~~~p----~~~~--~~~~la~~~~~~g~~~eA~~~l~~al~~~p  231 (291)
T 3mkr_A          168 LATAWVSLAAGGEKLQDAYYIFQEMADKCS----PTLL--LLNGQAACHMAQGRWEAAEGVLQEALDKDS  231 (291)
T ss_dssp             HHHHHHHHHHCTTHHHHHHHHHHHHHHHSC----CCHH--HHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHhCchHHHHHHHHHHHHHHhCC----CcHH--HHHHHHHHHHHcCCHHHHHHHHHHHHHhCC
Confidence             12233444556999999999999986532    2222  789999999999999999999999877654

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.55  E-value=2.7e-13  Score=106.21  Aligned_cols=226  Identities=8%  Similarity=-0.019  Sum_probs=169.3

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh--------CCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCC
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEK--------GLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKC   84 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~--------~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~   84 (246)
                      .+.+..++..+...+...|++++|..+|++...        ..+.....+..+...|...|++++|...+++......+.
T Consensus        23 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~  102 (311)
T 3nf1_A           23 IPARLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKT  102 (311)
T ss_dssp             SCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            445677889999999999999999999988753        233356778899999999999999999999988641000


Q ss_pred             CCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCC-----CCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHH
Q 043380           85 SSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCC-----NLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGE  158 (246)
Q Consensus        85 ~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~-----~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~  158 (246)
                      ..........++..+...|...|++++|...+++..+..     +-.|+ ...+..+...|...|++++    |.++++.
T Consensus       103 ~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~----A~~~~~~  178 (311)
T 3nf1_A          103 LGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEE----VEYYYQR  178 (311)
T ss_dssp             HCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHH----HHHHHHH
T ss_pred             hCCCChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHH----HHHHHHH
Confidence            000123346689999999999999999999999887721     22343 5678899999999999999    9999999


Q ss_pred             HHHhhcCCC-CCCc-chhhHHHHHHHHHhcCChhHHhhHHHhhCCCCC--------------------------------
Q 043380          159 IVKRVCSNP-GLWP-KPHLYVSMMHELAARVDYDIVKSPYRRMWPDST--------------------------------  204 (246)
Q Consensus       159 m~~~~~~~~-~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~--------------------------------  204 (246)
                      ..+...... +..| ...++..+..+|...|++++|...+++......                                
T Consensus       179 a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  258 (311)
T 3nf1_A          179 ALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEEREECKGKQKDGT  258 (311)
T ss_dssp             HHHHHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHHHC-------C
T ss_pred             HHHHHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHhcCchhhHH
Confidence            877421110 1123 346788999999999999999999988763100                                


Q ss_pred             ------------CCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhc
Q 043380          205 ------------GTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRW  243 (246)
Q Consensus       205 ------------~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  243 (246)
                                  ....| ....++..+..+|.+.|++++|.++|++..+..
T Consensus       259 ~~~~a~~~~~~~~~~~~-~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l~  308 (311)
T 3nf1_A          259 SFGEYGGWYKACKVDSP-TVTTTLKNLGALYRRQGKFEAAETLEEAAMRSR  308 (311)
T ss_dssp             CSCCCC---------CH-HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhcCCCCc-hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence                        00111 123378889999999999999999999887654

>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=2.7e-12  Score=93.27  Aligned_cols=167  Identities=10%  Similarity=-0.038  Sum_probs=134.7

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHH
Q 043380           15 LNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIF   94 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~   94 (246)
                      -++.+|..+-..|.+.|++++|++.|++..+--+-+...|..+..+|.+.|++++|...+......        .+-+..
T Consensus         3 e~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~--------~~~~~~   74 (184)
T 3vtx_A            3 ETTTIYMDIGDKKRTKGDFDGAIRAYKKVLKADPNNVETLLKLGKTYMDIGLPNDAIESLKKFVVL--------DTTSAE   74 (184)
T ss_dssp             -CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CCCCHH
T ss_pred             cHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--------CchhHH
Confidence            367788889999999999999999998875433557788888888999999999999999888875        234566


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP  173 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~  173 (246)
                      .+..+...+...++++.|...+.....   ..|+ ...+..+...|...|++++    |++.|++..+.      -+.+.
T Consensus        75 ~~~~~~~~~~~~~~~~~a~~~~~~a~~---~~~~~~~~~~~lg~~~~~~g~~~~----A~~~~~~~l~~------~p~~~  141 (184)
T 3vtx_A           75 AYYILGSANFMIDEKQAAIDALQRAIA---LNTVYADAYYKLGLVYDSMGEHDK----AIEAYEKTISI------KPGFI  141 (184)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------CTTCH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHH---hCccchHHHHHHHHHHHHhCCchh----HHHHHHHHHHh------cchhh
Confidence            777777888888999999999988877   3454 7778888889999999999    99999988876      23356


Q ss_pred             hhHHHHHHHHHhcCChhHHhhHHHhhCCC
Q 043380          174 HLYVSMMHELAARVDYDIVKSPYRRMWPD  202 (246)
Q Consensus       174 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~  202 (246)
                      .+|..+..+|...|++++|.+.|++..+.
T Consensus       142 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~  170 (184)
T 3vtx_A          142 RAYQSIGLAYEGKGLRDEAVKYFKKALEK  170 (184)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHCCCHHHHHHHHHHHHhC
Confidence            78888888999999999999999887643

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.52  E-value=1.6e-12  Score=100.13  Aligned_cols=208  Identities=11%  Similarity=-0.015  Sum_probs=161.0

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCH----HHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCC
Q 043380           15 LNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDS----LSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFH   90 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~----~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~   90 (246)
                      .+...+..+..+|.+.|++++|.+.|+.... .+++.    ..|..+...+...|++++|.+.|++..+.        .+
T Consensus        35 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~-~~~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~a~~~--------~~  105 (272)
T 3u4t_A           35 NSPYIYNRRAVCYYELAKYDLAQKDIETYFS-KVNATKAKSADFEYYGKILMKKGQDSLAIQQYQAAVDR--------DT  105 (272)
T ss_dssp             CCSTTHHHHHHHHHHTTCHHHHHHHHHHHHT-TSCTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------ST
T ss_pred             CcHHHHHHHHHHHHHHhhHHHHHHHHHHHHh-ccCchhHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhc--------Cc
Confidence            3455788889999999999999999998764 22333    34889999999999999999999999986        23


Q ss_pred             ccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCC
Q 043380           91 PDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGL  169 (246)
Q Consensus        91 p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~  169 (246)
                      .+..+|..+...|...|++++|...|++..+   ..|+ ...+..+...+...+++++    |...|+...+.      .
T Consensus       106 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~---~~~~~~~~~~~l~~~~~~~~~~~~----A~~~~~~a~~~------~  172 (272)
T 3u4t_A          106 TRLDMYGQIGSYFYNKGNFPLAIQYMEKQIR---PTTTDPKVFYELGQAYYYNKEYVK----ADSSFVKVLEL------K  172 (272)
T ss_dssp             TCTHHHHHHHHHHHHTTCHHHHHHHHGGGCC---SSCCCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------S
T ss_pred             ccHHHHHHHHHHHHHccCHHHHHHHHHHHhh---cCCCcHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHh------C
Confidence            3567899999999999999999999999988   3555 6677777734445569999    99999999886      2


Q ss_pred             CcchhhHHHHHHHHHhcCC---hhHHhhHHHhhCCCCCCCCC--chhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          170 WPKPHLYVSMMHELAARVD---YDIVKSPYRRMWPDSTGTIS--PEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       170 ~p~~~~~~~li~~~~~~g~---~~~a~~~~~~~~~~~~~~~~--~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      +.+...+..+..++...|+   +++|...+++..........  ......+|..+...|...|++++|.+.|++..+..+
T Consensus       173 p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p  252 (272)
T 3u4t_A          173 PNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKYKDELIEANEYIAYYYTINRDKVKADAAWKNILALDP  252 (272)
T ss_dssp             TTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             ccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCc
Confidence            3346778888888888888   88888888876532111011  111123788899999999999999999999876544

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.52  E-value=2.3e-12  Score=93.68  Aligned_cols=168  Identities=10%  Similarity=-0.000  Sum_probs=143.2

Q ss_pred             CCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC
Q 043380           49 PDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD  128 (246)
Q Consensus        49 ~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~  128 (246)
                      -+...|..+-..|...|++++|.+.|++..+.        -+-+..+|..+..+|.+.|++++|...+.....   ..|+
T Consensus         3 e~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~--------~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~---~~~~   71 (184)
T 3vtx_A            3 ETTTIYMDIGDKKRTKGDFDGAIRAYKKVLKA--------DPNNVETLLKLGKTYMDIGLPNDAIESLKKFVV---LDTT   71 (184)
T ss_dssp             -CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCCC
T ss_pred             cHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--------CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh---cCch
Confidence            35678999999999999999999999999986        133577899999999999999999999999988   3444


Q ss_pred             -HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCC
Q 043380          129 -RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTI  207 (246)
Q Consensus       129 -~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  207 (246)
                       ...+..+...+...++++.    |...+......      .+-+...+..+..+|...|++++|.+.|++....++.. 
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~----a~~~~~~a~~~------~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p~~-  140 (184)
T 3vtx_A           72 SAEAYYILGSANFMIDEKQA----AIDALQRAIAL------NTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKPGF-  140 (184)
T ss_dssp             CHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTC-
T ss_pred             hHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh------CccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcchh-
Confidence             7778888899999999999    99999998886      33456888999999999999999999999987654321 


Q ss_pred             CchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhc
Q 043380          208 SPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRW  243 (246)
Q Consensus       208 ~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  243 (246)
                         .  .+|..+..+|.+.|++++|++.|++..+..
T Consensus       141 ---~--~~~~~lg~~~~~~g~~~~A~~~~~~al~~~  171 (184)
T 3vtx_A          141 ---I--RAYQSIGLAYEGKGLRDEAVKYFKKALEKE  171 (184)
T ss_dssp             ---H--HHHHHHHHHHHHTTCHHHHHHHHHHHHHTT
T ss_pred             ---h--hHHHHHHHHHHHCCCHHHHHHHHHHHHhCC
Confidence               1  278999999999999999999999887643

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.52  E-value=7.8e-12  Score=98.70  Aligned_cols=209  Identities=15%  Similarity=0.092  Sum_probs=165.4

Q ss_pred             cCcCHHHHHHHHHHHHh-------cCCH-------HHHHHHHHHHHhCCCC-CHHHHHHHHHHHHhcCCcchHHHHHHHH
Q 043380           13 WKLNTIVMNAVIEASRE-------AQRI-------DEAYQILESVEKGLEP-DSLSYNILISACIKTKKLDVTMPFNEQL   77 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~-------~g~~-------~~a~~~~~~~~~~~~~-~~~t~~~li~~~~~~~~~~~a~~~~~~m   77 (246)
                      .+-++..|..+...+..       .|++       ++|..+|++....+.| +...|..+...+.+.|++++|.++|++.
T Consensus        46 ~p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~a  125 (308)
T 2ond_A           46 LGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRL  125 (308)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence            45678888888888764       4885       8999999998764445 5668999999999999999999999999


Q ss_pred             HhccCCCCCCCCCcc-HH-HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHH-hcCChhhhhhHHHH
Q 043380           78 KDNGQKCSSGGFHPD-IF-TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALL-YSGSIKVVGLYALC  154 (246)
Q Consensus        78 ~~~~~~~~~~~~~p~-~~-~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~-~~~~~~~~~~~a~~  154 (246)
                      .+.         .|+ .. .|..+...+.+.|++++|..+|++..+ .. +++...|........ ..|++++    |..
T Consensus       126 l~~---------~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~-~~-p~~~~~~~~~a~~~~~~~~~~~~----A~~  190 (308)
T 2ond_A          126 LAI---------EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKARE-DA-RTRHHVYVTAALMEYYCSKDKSV----AFK  190 (308)
T ss_dssp             HTS---------SSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHT-ST-TCCTHHHHHHHHHHHHTSCCHHH----HHH
T ss_pred             Hhc---------cccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHh-cC-CCCHHHHHHHHHHHHHHcCCHHH----HHH
Confidence            985         453 33 899999999999999999999999988 32 223455544433322 3699999    999


Q ss_pred             HHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHH
Q 043380          155 IFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALD  234 (246)
Q Consensus       155 ~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~  234 (246)
                      +|+...+.      .+-+...|..++..+.+.|++++|..+|++......  .+|......|..++..+.+.|+.+.|..
T Consensus       191 ~~~~al~~------~p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~--l~p~~~~~l~~~~~~~~~~~g~~~~a~~  262 (308)
T 2ond_A          191 IFELGLKK------YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGS--LPPEKSGEIWARFLAFESNIGDLASILK  262 (308)
T ss_dssp             HHHHHHHH------HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSS--SCGGGCHHHHHHHHHHHHHHSCHHHHHH
T ss_pred             HHHHHHHh------CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccC--CCHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            99999886      223568899999999999999999999999875421  2333223378899999999999999999


Q ss_pred             HHHHHHhhcc
Q 043380          235 KLSNTITRWK  244 (246)
Q Consensus       235 ~~~~m~~~g~  244 (246)
                      ++++..+..+
T Consensus       263 ~~~~a~~~~p  272 (308)
T 2ond_A          263 VEKRRFTAFR  272 (308)
T ss_dssp             HHHHHHHHTT
T ss_pred             HHHHHHHHcc
Confidence            9999887654

>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=99.51  E-value=5.2e-12  Score=96.23  Aligned_cols=170  Identities=10%  Similarity=-0.094  Sum_probs=147.0

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc-c
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP-D   92 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p-~   92 (246)
                      +.+...+..+..+|.+.|++++|.+.|++.....+.+...+..+...|...|++++|.++|+++...       +..| +
T Consensus        68 ~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~-------~~~~~~  140 (252)
T 2ho1_A           68 PSSADAHAALAVVFQTEMEPKLADEEYRKALASDSRNARVLNNYGGFLYEQKRYEEAYQRLLEASQD-------TLYPER  140 (252)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTC-------TTCTTH
T ss_pred             CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHHhHHHHHHHHHHHHHhC-------ccCccc
Confidence            4578889999999999999999999999876434567889999999999999999999999999873       2345 5


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP  171 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p  171 (246)
                      ...+..+...+...|++++|...|++..+   ..|+ ...+..+...|...|++++    |...++...+.      ...
T Consensus       141 ~~~~~~la~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~~~~la~~~~~~g~~~~----A~~~~~~~~~~------~~~  207 (252)
T 2ho1_A          141 SRVFENLGLVSLQMKKPAQAKEYFEKSLR---LNRNQPSVALEMADLLYKEREYVP----ARQYYDLFAQG------GGQ  207 (252)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCSCCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHTT------SCC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHh---cCcccHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh------CcC
Confidence            67889999999999999999999999988   3344 7889999999999999999    99999998775      345


Q ss_pred             chhhHHHHHHHHHhcCChhHHhhHHHhhCCCC
Q 043380          172 KPHLYVSMMHELAARVDYDIVKSPYRRMWPDS  203 (246)
Q Consensus       172 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  203 (246)
                      +...+..+...+...|++++|.++++.+....
T Consensus       208 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~  239 (252)
T 2ho1_A          208 NARSLLLGIRLAKVFEDRDTAASYGLQLKRLY  239 (252)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC
Confidence            66788899999999999999999999987543

>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=99.51  E-value=1.8e-12  Score=109.44  Aligned_cols=206  Identities=14%  Similarity=0.019  Sum_probs=165.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHH
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTY   96 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~   96 (246)
                      ..++..+...+...|++++|...|+.... ..|+...|..+...+...|++++|.+.|+++.+.        .+.+..+|
T Consensus       243 ~~~~~~~g~~~~~~~~~~~A~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--------~~~~~~~~  313 (537)
T 3fp2_A          243 ALALCYTGIFHFLKNNLLDAQVLLQESIN-LHPTPNSYIFLALTLADKENSQEFFKFFQKAVDL--------NPEYPPTY  313 (537)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HCCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHH--------CTTCHHHH
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHh-cCCCchHHHHHHHHHHHhcCHHHHHHHHHHHhcc--------CCCCHHHH
Confidence            33577777888999999999999998763 2566888999999999999999999999999986        24467789


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhh
Q 043380           97 ATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHL  175 (246)
Q Consensus        97 ~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~  175 (246)
                      ..+...+...|++++|...|+...+   ..|+ ...+..+...|...|++++    |..+++...+.      .+.+..+
T Consensus       314 ~~l~~~~~~~~~~~~A~~~~~~a~~---~~~~~~~~~~~la~~~~~~g~~~~----A~~~~~~~~~~------~~~~~~~  380 (537)
T 3fp2_A          314 YHRGQMYFILQDYKNAKEDFQKAQS---LNPENVYPYIQLACLLYKQGKFTE----SEAFFNETKLK------FPTLPEV  380 (537)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCSHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------CTTCTHH
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh------CCCChHH
Confidence            9999999999999999999999988   3354 6788999999999999999    99999999886      2345678


Q ss_pred             HHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhc----------CChhHHHHHHHHHHhhcc
Q 043380          176 YVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALND----------GQVDLALDKLSNTITRWK  244 (246)
Q Consensus       176 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~----------g~~~~a~~~~~~m~~~g~  244 (246)
                      +..+...+...|++++|...+++.....+...........+..+...+...          |++++|...|+...+..+
T Consensus       381 ~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p  459 (537)
T 3fp2_A          381 PTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELDP  459 (537)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHcCCcchhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhCC
Confidence            999999999999999999999987633211111111111244455677777          999999999999877544

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.51  E-value=3.1e-13  Score=113.10  Aligned_cols=198  Identities=12%  Similarity=-0.002  Sum_probs=171.2

Q ss_pred             cCcCHHHHHHHHHHHHhcCCH-HHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc
Q 043380           13 WKLNTIVMNAVIEASREAQRI-DEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP   91 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~-~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p   91 (246)
                      .+.+...+..+-.++...|++ ++|++.|++..+-.+.+...|..+..+|...|++++|.+.|++..+.         .|
T Consensus        98 ~~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~---------~p  168 (474)
T 4abn_A           98 AQVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLEPELVEAWNQLGEVYWKKGDVTSAHTCFSGALTH---------CK  168 (474)
T ss_dssp             CCCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTT---------CC
T ss_pred             CchhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh---------CC
Confidence            345788899999999999999 99999999876433556889999999999999999999999999986         57


Q ss_pred             cHHHHHHHHHHHHcc---------CCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhc--------CChhhhhhHHH
Q 043380           92 DIFTYATLLMGFRHA---------KDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYS--------GSIKVVGLYAL  153 (246)
Q Consensus        92 ~~~~~~~ll~~~~~~---------~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~--------~~~~~~~~~a~  153 (246)
                      +...+..+-..|...         |++++|...|++..+   +.|+ ...|..+..+|...        |++++    |.
T Consensus       169 ~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~~lg~~~~~~~~~~~~~~g~~~~----A~  241 (474)
T 4abn_A          169 NKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQ---MDVLDGRSWYILGNAYLSLYFNTGQNPKISQQ----AL  241 (474)
T ss_dssp             CHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHHHHTTCCHHHHHH----HH
T ss_pred             CHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHHHHhhccccchHHH----HH
Confidence            788999999999999         999999999999988   4565 88899999999998        99999    99


Q ss_pred             HHHHHHHHhhcCCCCCCc----chhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCCh
Q 043380          154 CIFGEIVKRVCSNPGLWP----KPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQV  229 (246)
Q Consensus       154 ~~~~~m~~~~~~~~~~~p----~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~  229 (246)
                      ..|++..+.       .|    +...|..+..+|...|++++|...|++.....+..  +    .++..+...+...|++
T Consensus       242 ~~~~~al~~-------~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~--~----~a~~~l~~~~~~lg~~  308 (474)
T 4abn_A          242 SAYAQAEKV-------DRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALDPAW--P----EPQQREQQLLEFLSRL  308 (474)
T ss_dssp             HHHHHHHHH-------CGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTC--H----HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHh-------CCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC--H----HHHHHHHHHHHHHHHH
Confidence            999999886       34    67899999999999999999999999987544322  1    2688899999999999


Q ss_pred             hHHHHHHHHH
Q 043380          230 DLALDKLSNT  239 (246)
Q Consensus       230 ~~a~~~~~~m  239 (246)
                      ++|.+.+..+
T Consensus       309 ~eAi~~~~~~  318 (474)
T 4abn_A          309 TSLLESKGKT  318 (474)
T ss_dssp             HHHHHHTTTC
T ss_pred             HHHHHHhccc
Confidence            9999876554

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.50  E-value=7e-12  Score=94.75  Aligned_cols=169  Identities=9%  Similarity=-0.036  Sum_probs=148.1

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      +.+...+..+..++.+.|++++|.+.|+......+.+...+..+...+...|++++|.++++++.+.        .+.+.
T Consensus        54 ~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~--------~~~~~  125 (243)
T 2q7f_A           54 KEDAIPYINFANLLSSVNELERALAFYDKALELDSSAATAYYGAGNVYVVKEMYKEAKDMFEKALRA--------GMENG  125 (243)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------TCCSH
T ss_pred             cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHhccHHHHHHHHHHHHHh--------CCCCH
Confidence            4568889999999999999999999999886444567889999999999999999999999999986        24467


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL-DRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK  172 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~  172 (246)
                      ..+..+...+...|++++|...+++..+   ..| +...+..+...+...|++++    |...|+...+.      ...+
T Consensus       126 ~~~~~~a~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~~~~l~~~~~~~~~~~~----A~~~~~~~~~~------~~~~  192 (243)
T 2q7f_A          126 DLFYMLGTVLVKLEQPKLALPYLQRAVE---LNENDTEARFQFGMCLANEGMLDE----ALSQFAAVTEQ------DPGH  192 (243)
T ss_dssp             HHHHHHHHHHHHTSCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHTCCHH----HHHHHHHHHHH------CTTC
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHH---hCCccHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh------Cccc
Confidence            7899999999999999999999999988   334 47889999999999999999    99999999886      2345


Q ss_pred             hhhHHHHHHHHHhcCChhHHhhHHHhhCCCC
Q 043380          173 PHLYVSMMHELAARVDYDIVKSPYRRMWPDS  203 (246)
Q Consensus       173 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  203 (246)
                      ..++..+..+|...|++++|...+++.....
T Consensus       193 ~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  223 (243)
T 2q7f_A          193 ADAFYNAGVTYAYKENREKALEMLDKAIDIQ  223 (243)
T ss_dssp             HHHHHHHHHHHHHTTCTTHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHccC
Confidence            7889999999999999999999999987543

>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=99.50  E-value=1.3e-14  Score=118.23  Aligned_cols=145  Identities=12%  Similarity=0.151  Sum_probs=25.5

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHH
Q 043380           15 LNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIF   94 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~   94 (246)
                      +++.+|..|..++.+.|++++|++.|..     .+|..+|..++.++...|++++|..+++..++.         .++..
T Consensus        30 ~~~~vWs~La~A~l~~g~~~eAIdsfik-----a~D~~~y~~V~~~ae~~g~~EeAi~yl~~ark~---------~~~~~   95 (449)
T 1b89_A           30 NEPAVWSQLAKAQLQKGMVKEAIDSYIK-----ADDPSSYMEVVQAANTSGNWEELVKYLQMARKK---------ARESY   95 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CChHHHHHHHHHHHHcCCHHHHHHHHHc-----CCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHh---------Cccch
Confidence            4445888888888888888888888854     356668888888888888888888866666553         34455


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchh
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPH  174 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~  174 (246)
                      +.+.|+.+|.+.|+++++.++++        .|+..+|..+...|...|++++    |..+|..+              .
T Consensus        96 i~~~Li~~Y~Klg~l~e~e~f~~--------~pn~~a~~~IGd~~~~~g~yee----A~~~Y~~a--------------~  149 (449)
T 1b89_A           96 VETELIFALAKTNRLAELEEFIN--------GPNNAHIQQVGDRCYDEKMYDA----AKLLYNNV--------------S  149 (449)
T ss_dssp             -------------CHHHHTTTTT--------CC----------------CTTT----HHHHHHHT--------------T
T ss_pred             hHHHHHHHHHHhCCHHHHHHHHc--------CCcHHHHHHHHHHHHHcCCHHH----HHHHHHHh--------------h
Confidence            66666667777776666665553        1444566666666666666666    66666543              1


Q ss_pred             hHHHHHHHHHhcCChhHHhhHHHhh
Q 043380          175 LYVSMMHELAARVDYDIVKSPYRRM  199 (246)
Q Consensus       175 ~~~~li~~~~~~g~~~~a~~~~~~~  199 (246)
                      .|..+..++.+.|++++|.+.+.+.
T Consensus       150 n~~~LA~~L~~Lg~yq~AVea~~KA  174 (449)
T 1b89_A          150 NFGRLASTLVHLGEYQAAVDGARKA  174 (449)
T ss_dssp             CHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHhccHHHHHHHHHHc
Confidence            3444444444444444444444444

>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=99.49  E-value=7.4e-12  Score=90.34  Aligned_cols=165  Identities=12%  Similarity=0.007  Sum_probs=122.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHH
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTY   96 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~   96 (246)
                      ...|..+...+...|++++|.+.|+.+....+.+...+..+...+...|++++|...++++.+.        .+.+...+
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--------~~~~~~~~   79 (186)
T 3as5_A            8 QVYYRDKGISHAKAGRYSQAVMLLEQVYDADAFDVDVALHLGIAYVKTGAVDRGTELLERSLAD--------APDNVKVA   79 (186)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHTTTCCTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHH
T ss_pred             hHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--------CCCCHHHH
Confidence            3456667777888888888888888776444556777888888888888888888888888775        23456677


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhH
Q 043380           97 ATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLY  176 (246)
Q Consensus        97 ~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~  176 (246)
                      ..+...+...|++++|.+.++.... . .+.+...+..+...+...|++++    |...++...+.      ...+..++
T Consensus        80 ~~~a~~~~~~~~~~~A~~~~~~~~~-~-~~~~~~~~~~~a~~~~~~~~~~~----A~~~~~~~~~~------~~~~~~~~  147 (186)
T 3as5_A           80 TVLGLTYVQVQKYDLAVPLLIKVAE-A-NPINFNVRFRLGVALDNLGRFDE----AIDSFKIALGL------RPNEGKVH  147 (186)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHH-H-CTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------CTTCHHHH
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHHh-c-CcHhHHHHHHHHHHHHHcCcHHH----HHHHHHHHHhc------CccchHHH
Confidence            7788888888888888888888777 2 22346677778888888888888    88888887775      23345677


Q ss_pred             HHHHHHHHhcCChhHHhhHHHhhCC
Q 043380          177 VSMMHELAARVDYDIVKSPYRRMWP  201 (246)
Q Consensus       177 ~~li~~~~~~g~~~~a~~~~~~~~~  201 (246)
                      ..+...+...|++++|...++....
T Consensus       148 ~~la~~~~~~~~~~~A~~~~~~~~~  172 (186)
T 3as5_A          148 RAIAFSYEQMGRHEEALPHFKKANE  172 (186)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            7788888888888888888877653

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.49  E-value=3.2e-12  Score=95.78  Aligned_cols=166  Identities=8%  Similarity=-0.015  Sum_probs=133.1

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhc-----------CCcchHHHHHHHHHhcc
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKT-----------KKLDVTMPFNEQLKDNG   81 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~-----------~~~~~a~~~~~~m~~~~   81 (246)
                      .+.++..|..+..++.+.|++++|...|++..+--+.+...+..+...+...           |++++|...|++..+. 
T Consensus        35 ~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~-  113 (217)
T 2pl2_A           35 NPQDPEALYWLARTQLKLGLVNPALENGKTLVARTPRYLGGYMVLSEAYVALYRQAEDRERGKGYLEQALSVLKDAERV-  113 (217)
T ss_dssp             SSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHH-
T ss_pred             CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHh-
Confidence            4567888999999999999999999999987643466788899999999999           9999999999999986 


Q ss_pred             CCCCCCCCCc-cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHH
Q 043380           82 QKCSSGGFHP-DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIV  160 (246)
Q Consensus        82 ~~~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~  160 (246)
                              .| +...|..+-.+|...|++++|...|++..+ ..  .+...+..+...|...|++++    |...|+...
T Consensus       114 --------~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~-~~--~~~~~~~~la~~~~~~g~~~~----A~~~~~~al  178 (217)
T 2pl2_A          114 --------NPRYAPLHLQRGLVYALLGERDKAEASLKQALA-LE--DTPEIRSALAELYLSMGRLDE----ALAQYAKAL  178 (217)
T ss_dssp             --------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HC--CCHHHHHHHHHHHHHHTCHHH----HHHHHHHHH
T ss_pred             --------CcccHHHHHHHHHHHHHcCChHHHHHHHHHHHh-cc--cchHHHHHHHHHHHHcCCHHH----HHHHHHHHH
Confidence                    44 567899999999999999999999999998 55  678899999999999999999    999999998


Q ss_pred             HhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhC
Q 043380          161 KRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMW  200 (246)
Q Consensus       161 ~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  200 (246)
                      +.      -+.+...+..+..++...|++++|...+++..
T Consensus       179 ~~------~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~~  212 (217)
T 2pl2_A          179 EQ------APKDLDLRVRYASALLLKGKAEEAARAAALEH  212 (217)
T ss_dssp             HH------STTCHHHHHHHHHHHTC---------------
T ss_pred             Hh------CCCChHHHHHHHHHHHHccCHHHHHHHHHHHh
Confidence            86      23356788999999999999999999988753

>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=99.49  E-value=5.2e-11  Score=92.01  Aligned_cols=194  Identities=9%  Similarity=-0.003  Sum_probs=135.1

Q ss_pred             cCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHh----cCCcchHHHHHHHHHhccCCCCC
Q 043380           15 LNTIVMNAVIEASRE----AQRIDEAYQILESVEKGLEPDSLSYNILISACIK----TKKLDVTMPFNEQLKDNGQKCSS   86 (246)
Q Consensus        15 ~~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~~~~   86 (246)
                      -++..+..+...|..    .+++++|.+.|++...  ..+...+..+-..|..    .+++++|..+|++..+.      
T Consensus        36 ~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~--~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~------  107 (273)
T 1ouv_A           36 KENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACD--LNYSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACDL------  107 (273)
T ss_dssp             TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHH--TTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT------
T ss_pred             CCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHH--CCCHHHHHHHHHHHhCCCCcccCHHHHHHHHHHHHHc------
Confidence            345566677777777    7777777777776642  1266677777777777    77777777777777765      


Q ss_pred             CCCCccHHHHHHHHHHHHc----cCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHh----cCChhhhhhHHHHHHHH
Q 043380           87 GGFHPDIFTYATLLMGFRH----AKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLY----SGSIKVVGLYALCIFGE  158 (246)
Q Consensus        87 ~~~~p~~~~~~~ll~~~~~----~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~----~~~~~~~~~~a~~~~~~  158 (246)
                       +   +...+..+-..|..    .+++++|...|++..+ .+   +...+..+...|..    .+++++    |...|+.
T Consensus       108 -~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~-~~---~~~a~~~lg~~~~~~~~~~~~~~~----A~~~~~~  175 (273)
T 1ouv_A          108 -K---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACD-LN---DGDGCTILGSLYDAGRGTPKDLKK----ALASYDK  175 (273)
T ss_dssp             -T---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHH-TT---CHHHHHHHHHHHHHTSSSCCCHHH----HHHHHHH
T ss_pred             -C---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHh-cC---cHHHHHHHHHHHHcCCCCCCCHHH----HHHHHHH
Confidence             2   55667777777777    7778888887777777 43   45566667777776    777777    8877777


Q ss_pred             HHHhhcCCCCCCcchhhHHHHHHHHHh----cCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHh----cCChh
Q 043380          159 IVKRVCSNPGLWPKPHLYVSMMHELAA----RVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALN----DGQVD  230 (246)
Q Consensus       159 m~~~~~~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~  230 (246)
                      ..+.     +   +...+..+-..|..    .+++++|...|++....+.    +.    ++..+...|..    .++++
T Consensus       176 a~~~-----~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~----~~----a~~~l~~~~~~g~~~~~~~~  239 (273)
T 1ouv_A          176 ACDL-----K---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELEN----GG----GCFNLGAMQYNGEGVTRNEK  239 (273)
T ss_dssp             HHHT-----T---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTTC----HH----HHHHHHHHHHTTSSSSCCST
T ss_pred             HHHC-----C---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCCC----HH----HHHHHHHHHHcCCCcccCHH
Confidence            7664     2   34566677777777    7788888888877654421    11    56667777777    77888


Q ss_pred             HHHHHHHHHHhhcc
Q 043380          231 LALDKLSNTITRWK  244 (246)
Q Consensus       231 ~a~~~~~~m~~~g~  244 (246)
                      +|.++|+...+.|+
T Consensus       240 ~A~~~~~~a~~~~~  253 (273)
T 1ouv_A          240 QAIENFKKGCKLGA  253 (273)
T ss_dssp             THHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHcCC
Confidence            88888877776654

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.49  E-value=1.2e-11  Score=92.24  Aligned_cols=169  Identities=8%  Similarity=-0.071  Sum_probs=145.7

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhc-CCcchHHHHHHHHHhccCCCCCCCCCc-
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKT-KKLDVTMPFNEQLKDNGQKCSSGGFHP-   91 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~-~~~~~a~~~~~~m~~~~~~~~~~~~~p-   91 (246)
                      +.+...|..+..+|...|++++|.+.|+....-.+.+..++..+...+... |++++|...++++.+.       ...| 
T Consensus        39 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~-------~~~~~  111 (225)
T 2vq2_A           39 PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIKPDSAEINNNYGWFLCGRLNRPAESMAYFDKALAD-------PTYPT  111 (225)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTS-------TTCSC
T ss_pred             ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhcCcHHHHHHHHHHHHcC-------cCCcc
Confidence            456888999999999999999999999988644466788999999999999 9999999999999883       2234 


Q ss_pred             cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCC
Q 043380           92 DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLW  170 (246)
Q Consensus        92 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~  170 (246)
                      +...+..+..++...|++++|...++++.+   ..|+ ...+..+...+...|++++    |..+++...+.      .+
T Consensus       112 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~~~~la~~~~~~~~~~~----A~~~~~~~~~~------~~  178 (225)
T 2vq2_A          112 PYIANLNKGICSAKQGQFGLAEAYLKRSLA---AQPQFPPAFKELARTKMLAGQLGD----ADYYFKKYQSR------VE  178 (225)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HSTTCHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHH------HC
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCCchHHHHHHHHHHHcCCHHH----HHHHHHHHHHh------CC
Confidence            467899999999999999999999999988   3454 7889999999999999999    99999999886      22


Q ss_pred             -cchhhHHHHHHHHHhcCChhHHhhHHHhhCCC
Q 043380          171 -PKPHLYVSMMHELAARVDYDIVKSPYRRMWPD  202 (246)
Q Consensus       171 -p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  202 (246)
                       .+...+..+...+...|+.+.+..+++.+...
T Consensus       179 ~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  211 (225)
T 2vq2_A          179 VLQADDLLLGWKIAKALGNAQAAYEYEAQLQAN  211 (225)
T ss_dssp             SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHh
Confidence             46677888888899999999999999998643

>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=99.48  E-value=9.1e-14  Score=113.19  Aligned_cols=188  Identities=12%  Similarity=0.054  Sum_probs=90.8

Q ss_pred             hhHHHHhcc-cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccC
Q 043380            4 ENEIVNREH-WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQ   82 (246)
Q Consensus         4 ~~~~~~~~~-~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~   82 (246)
                      .++++++.+ -.+|..+|..++.++...|++++|+..++..++. .+++.+.+.++.+|.+.|+++++.++++       
T Consensus        47 ~~~eAIdsfika~D~~~y~~V~~~ae~~g~~EeAi~yl~~ark~-~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------  118 (449)
T 1b89_A           47 MVKEAIDSYIKADDPSSYMEVVQAANTSGNWEELVKYLQMARKK-ARESYVETELIFALAKTNRLAELEEFIN-------  118 (449)
T ss_dssp             ---------------------------------------------------------------CHHHHTTTTT-------
T ss_pred             CHHHHHHHHHcCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHh-CccchhHHHHHHHHHHhCCHHHHHHHHc-------
Confidence            445555555 3578889999999999999999999977776653 5668889999999999999999887763       


Q ss_pred             CCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           83 KCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        83 ~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                             .|+..+|+.+...|...|++++|...|..+.          .|..+..++.+.|++++    |.+.+....  
T Consensus       119 -------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a~----------n~~~LA~~L~~Lg~yq~----AVea~~KA~--  175 (449)
T 1b89_A          119 -------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNVS----------NFGRLASTLVHLGEYQA----AVDGARKAN--  175 (449)
T ss_dssp             -------CC----------------CTTTHHHHHHHTT----------CHHHHHHHHHTTTCHHH----HHHHHHHHT--
T ss_pred             -------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHhh----------hHHHHHHHHHHhccHHH----HHHHHHHcC--
Confidence                   2677799999999999999999999999763          49999999999999999    999998771  


Q ss_pred             hcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          163 VCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       163 ~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                               ++.+|..++.+|...|+++.|......+.      ..|+.    ...++..|.+.|++++|..+++.-..
T Consensus       176 ---------~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~------~~ad~----l~~lv~~Yek~G~~eEai~lLe~aL~  235 (449)
T 1b89_A          176 ---------STRTWKEVCFACVDGKEFRLAQMCGLHIV------VHADE----LEELINYYQDRGYFEELITMLEAALG  235 (449)
T ss_dssp             ---------CHHHHHHHHHHHHHTTCHHHHHHTTTTTT------TCHHH----HHHHHHHHHHTTCHHHHHHHHHHHTT
T ss_pred             ---------CchhHHHHHHHHHHcCcHHHHHHHHHHHH------hCHhh----HHHHHHHHHHCCCHHHHHHHHHHHhC
Confidence                     57899999999999999999976666543      33332    34588999999999999999987653

>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=99.47  E-value=1.1e-10  Score=90.10  Aligned_cols=193  Identities=10%  Similarity=-0.035  Sum_probs=166.5

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHh----cCCcchHHHHHHHHHhccCCCCCCCCC
Q 043380           15 LNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIK----TKKLDVTMPFNEQLKDNGQKCSSGGFH   90 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~~~~~~~~   90 (246)
                      -++..+..+-..|.+.|++++|.+.|++...  +.+...+..+...|..    .+++++|..+|++..+.       +  
T Consensus         4 ~~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~--~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~-------~--   72 (273)
T 1ouv_A            4 QDPKELVGLGAKSYKEKDFTQAKKYFEKACD--LKENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDL-------N--   72 (273)
T ss_dssp             -CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--TTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT-------T--
T ss_pred             CChHHHHHHHHHHHhCCCHHHHHHHHHHHHH--CCCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHC-------C--
Confidence            3567788889999999999999999998765  4566788889999999    99999999999999986       3  


Q ss_pred             ccHHHHHHHHHHHHc----cCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHh----cCChhhhhhHHHHHHHHHHHh
Q 043380           91 PDIFTYATLLMGFRH----AKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLY----SGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        91 p~~~~~~~ll~~~~~----~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~----~~~~~~~~~~a~~~~~~m~~~  162 (246)
                       +...+..+-..|..    .+++++|...|++..+ .+   +...+..+...|..    .+++++    |...|+...+.
T Consensus        73 -~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~-~~---~~~a~~~lg~~~~~~~~~~~~~~~----A~~~~~~a~~~  143 (273)
T 1ouv_A           73 -YSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACD-LK---YAEGCASLGGIYHDGKVVTRDFKK----AVEYFTKACDL  143 (273)
T ss_dssp             -CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHH-TT---CHHHHHHHHHHHHHCSSSCCCHHH----HHHHHHHHHHT
T ss_pred             -CHHHHHHHHHHHhCCCCcccCHHHHHHHHHHHHH-cC---CccHHHHHHHHHHcCCCcccCHHH----HHHHHHHHHhc
Confidence             67788899999999    9999999999999998 54   67889999999999    999999    99999999886


Q ss_pred             hcCCCCCCcchhhHHHHHHHHHh----cCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHh----cCChhHHHH
Q 043380          163 VCSNPGLWPKPHLYVSMMHELAA----RVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALN----DGQVDLALD  234 (246)
Q Consensus       163 ~~~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~a~~  234 (246)
                           +   +...+..+-..|..    .+++++|...|++....+    .+.    ++..+...|..    .+++++|.+
T Consensus       144 -----~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~----~~~----a~~~lg~~~~~g~~~~~~~~~A~~  207 (273)
T 1ouv_A          144 -----N---DGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLK----DSP----GCFNAGNMYHHGEGATKNFKEALA  207 (273)
T ss_dssp             -----T---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT----CHH----HHHHHHHHHHHTCSSCCCHHHHHH
T ss_pred             -----C---cHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC----CHH----HHHHHHHHHHcCCCCCccHHHHHH
Confidence                 4   56677888888888    999999999999987553    222    67889999999    999999999


Q ss_pred             HHHHHHhhc
Q 043380          235 KLSNTITRW  243 (246)
Q Consensus       235 ~~~~m~~~g  243 (246)
                      +|+...+.+
T Consensus       208 ~~~~a~~~~  216 (273)
T 1ouv_A          208 RYSKACELE  216 (273)
T ss_dssp             HHHHHHHTT
T ss_pred             HHHHHHhCC
Confidence            999887655

>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=5.8e-12  Score=90.88  Aligned_cols=167  Identities=10%  Similarity=-0.028  Sum_probs=141.6

Q ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC-CH
Q 043380           51 SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL-DR  129 (246)
Q Consensus        51 ~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~  129 (246)
                      ...|..+...+...|++++|...++++.+.        .+.+...+..+...+...|++++|...++...+   ..| +.
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~---~~~~~~   76 (186)
T 3as5_A            8 QVYYRDKGISHAKAGRYSQAVMLLEQVYDA--------DAFDVDVALHLGIAYVKTGAVDRGTELLERSLA---DAPDNV   76 (186)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHTTTCCT--------TSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCH
T ss_pred             hHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--------CccChHHHHHHHHHHHHcCCHHHHHHHHHHHHh---cCCCCH
Confidence            355777888899999999999999998875        344678899999999999999999999999988   334 47


Q ss_pred             HHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCc
Q 043380          130 STFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISP  209 (246)
Q Consensus       130 ~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  209 (246)
                      ..+..+...+...|++++    |.+.++...+.      .+.+...+..+...+...|++++|...+++.....+.    
T Consensus        77 ~~~~~~a~~~~~~~~~~~----A~~~~~~~~~~------~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~----  142 (186)
T 3as5_A           77 KVATVLGLTYVQVQKYDL----AVPLLIKVAEA------NPINFNVRFRLGVALDNLGRFDEAIDSFKIALGLRPN----  142 (186)
T ss_dssp             HHHHHHHHHHHHHTCHHH----HHHHHHHHHHH------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT----
T ss_pred             HHHHHHHHHHHHhcCHHH----HHHHHHHHHhc------CcHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcCcc----
Confidence            888999999999999999    99999999886      3456788899999999999999999999998754322    


Q ss_pred             hhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          210 EVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       210 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      ..  .++..+...+...|++++|.+++++..+..+
T Consensus       143 ~~--~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~  175 (186)
T 3as5_A          143 EG--KVHRAIAFSYEQMGRHEEALPHFKKANELDE  175 (186)
T ss_dssp             CH--HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             ch--HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC
Confidence            11  2788999999999999999999999876543

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.44  E-value=1.9e-11  Score=93.05  Aligned_cols=183  Identities=14%  Similarity=0.064  Sum_probs=147.0

Q ss_pred             hhHHHHhcccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh---CCCCC----HHHHHHHHHHHHhcCCcchHHHHHHH
Q 043380            4 ENEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVEK---GLEPD----SLSYNILISACIKTKKLDVTMPFNEQ   76 (246)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~---~~~~~----~~t~~~li~~~~~~~~~~~a~~~~~~   76 (246)
                      .++.+.+..  .++..|..+..++...|++++|.+.|+....   ...|+    ..+|..+...+...|++++|...|++
T Consensus        27 ~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~  104 (258)
T 3uq3_A           27 HYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFARIGNAYHKLGDLKKTIEYYQK  104 (258)
T ss_dssp             HHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHHHHHHcccHHHHHHHHHH
Confidence            344555555  7888999999999999999999999988642   12222    57889999999999999999999999


Q ss_pred             HHhccCCCC-----------------CCCCCc-cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC-CHHHHHHHHH
Q 043380           77 LKDNGQKCS-----------------SGGFHP-DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL-DRSTFTAMVD  137 (246)
Q Consensus        77 m~~~~~~~~-----------------~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~  137 (246)
                      .....-...                 .....| +...|..+...+...|++++|...|+....   ..| +..+|..+..
T Consensus       105 a~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~---~~~~~~~~~~~l~~  181 (258)
T 3uq3_A          105 SLTEHRTADILTKLRNAEKELKKAEAEAYVNPEKAEEARLEGKEYFTKSDWPNAVKAYTEMIK---RAPEDARGYSNRAA  181 (258)
T ss_dssp             HHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHH
T ss_pred             HHhcCchhHHHHHHhHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHhcCHHHHHHHHHHHHh---cCcccHHHHHHHHH
Confidence            987310000                 000233 355788899999999999999999999988   334 4788999999


Q ss_pred             HHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCC
Q 043380          138 ALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWP  201 (246)
Q Consensus       138 ~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  201 (246)
                      .|...|++++    |...|+...+.      .+.+..++..+..++...|++++|...++....
T Consensus       182 ~~~~~~~~~~----A~~~~~~al~~------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~  235 (258)
T 3uq3_A          182 ALAKLMSFPE----AIADCNKAIEK------DPNFVRAYIRKATAQIAVKEYASALETLDAART  235 (258)
T ss_dssp             HHHHTTCHHH----HHHHHHHHHHH------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhCCHHH----HHHHHHHHHHh------CHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            9999999999    99999999886      234578899999999999999999999998764

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.44  E-value=7.9e-12  Score=96.24  Aligned_cols=201  Identities=9%  Similarity=-0.003  Sum_probs=157.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHH
Q 043380           18 IVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYA   97 (246)
Q Consensus        18 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~   97 (246)
                      ..+......+.+.|++++|+..|+...+..+.+...+..+..+|...|++++|.+.+++..+..     .........|.
T Consensus         4 ~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-----~~~~~~~~~~~   78 (272)
T 3u4t_A            4 DVEFRYADFLFKNNNYAEAIEVFNKLEAKKYNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKV-----NATKAKSADFE   78 (272)
T ss_dssp             -CHHHHHHHHHTTTCHHHHHHHHHHHHHTTCCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTS-----CTTTCCHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcc-----CchhHHHHHHH
Confidence            3455677888999999999999999865445566689999999999999999999999999851     01122345689


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhH
Q 043380           98 TLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLY  176 (246)
Q Consensus        98 ~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~  176 (246)
                      .+...|...|++++|...|+...+   ..|+ ..++..+...|...|++++    |...|++..+.      .+.+..++
T Consensus        79 ~lg~~~~~~~~~~~A~~~~~~a~~---~~~~~~~~~~~l~~~~~~~~~~~~----A~~~~~~al~~------~~~~~~~~  145 (272)
T 3u4t_A           79 YYGKILMKKGQDSLAIQQYQAAVD---RDTTRLDMYGQIGSYFYNKGNFPL----AIQYMEKQIRP------TTTDPKVF  145 (272)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHH---HSTTCTHHHHHHHHHHHHTTCHHH----HHHHHGGGCCS------SCCCHHHH
T ss_pred             HHHHHHHHcccHHHHHHHHHHHHh---cCcccHHHHHHHHHHHHHccCHHH----HHHHHHHHhhc------CCCcHHHH
Confidence            999999999999999999999988   3444 6789999999999999999    99999988764      22345667


Q ss_pred             HHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCC---hhHHHHHHHHHHhh
Q 043380          177 VSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQ---VDLALDKLSNTITR  242 (246)
Q Consensus       177 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~---~~~a~~~~~~m~~~  242 (246)
                      ..+...+...+++++|...|++.....+..    .  ..+..+...+...|+   +++|...+++..+.
T Consensus       146 ~~l~~~~~~~~~~~~A~~~~~~a~~~~p~~----~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~  208 (272)
T 3u4t_A          146 YELGQAYYYNKEYVKADSSFVKVLELKPNI----Y--IGYLWRARANAAQDPDTKQGLAKPYYEKLIEV  208 (272)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHSTTC----H--HHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhCccc----h--HHHHHHHHHHHHcCcchhhHHHHHHHHHHHHH
Confidence            777734445669999999999987654322    1  167778888888888   88888888877654

>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=99.43  E-value=3.2e-11  Score=98.01  Aligned_cols=199  Identities=11%  Similarity=0.005  Sum_probs=162.1

Q ss_pred             CcCHHHHHHHHHHHHhcCC-HHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           14 KLNTIVMNAVIEASREAQR-IDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~-~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      +-+...|+.+..++.+.|+ +++|+..|++...--+.+...|+.+-.++...|++++|+..|+++++.        -+-+
T Consensus       128 P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P~~~~a~~~~g~~~~~~g~~~eAl~~~~kal~l--------dP~~  199 (382)
T 2h6f_A          128 AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLVEWLRDPSQELEFIADILNQ--------DAKN  199 (382)
T ss_dssp             TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHH--------CTTC
T ss_pred             ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--------CccC
Confidence            4567889999999999997 999999999876444668889999999999999999999999999986        2346


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHh-cCChhhhhhHH-----HHHHHHHHHhhcC
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLY-SGSIKVVGLYA-----LCIFGEIVKRVCS  165 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~-~~~~~~~~~~a-----~~~~~~m~~~~~~  165 (246)
                      ...|..+-.++.+.|++++|+..|+++.+   +.|+ ...|+.+...+.. .|..++    |     +..|+.....   
T Consensus       200 ~~a~~~lg~~~~~~g~~~eAl~~~~~al~---l~P~~~~a~~~lg~~l~~l~~~~~e----A~~~~el~~~~~Al~l---  269 (382)
T 2h6f_A          200 YHAWQHRQWVIQEFKLWDNELQYVDQLLK---EDVRNNSVWNQRYFVISNTTGYNDR----AVLEREVQYTLEMIKL---  269 (382)
T ss_dssp             HHHHHHHHHHHHHHTCCTTHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCSCSH----HHHHHHHHHHHHHHHH---
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHhcCcchH----HHHHHHHHHHHHHHHH---
Confidence            77999999999999999999999999998   5565 7889999999999 666577    7     5888888776   


Q ss_pred             CCCCCc-chhhHHHHHHHHHhcC--ChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcC---------ChhHHH
Q 043380          166 NPGLWP-KPHLYVSMMHELAARV--DYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDG---------QVDLAL  233 (246)
Q Consensus       166 ~~~~~p-~~~~~~~li~~~~~~g--~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g---------~~~~a~  233 (246)
                          .| +...|..+..++...|  ++++|.+.+.++ +..+    ...  .++..+...|.+.|         .+++|.
T Consensus       270 ----~P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~~~p----~~~--~al~~La~~~~~~~~~~~~~~~~~~~~A~  338 (382)
T 2h6f_A          270 ----VPHNESAWNYLKGILQDRGLSKYPNLLNQLLDL-QPSH----SSP--YLIAFLVDIYEDMLENQCDNKEDILNKAL  338 (382)
T ss_dssp             ----STTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-TTTC----CCH--HHHHHHHHHHHHHHHTTCSSHHHHHHHHH
T ss_pred             ----CCCCHHHHHHHHHHHHccCccchHHHHHHHHHh-ccCC----CCH--HHHHHHHHHHHHHhcccccchHHHHHHHH
Confidence                34 4578888888999988  689999999988 3322    111  26788888888864         358999


Q ss_pred             HHHHHH-Hh
Q 043380          234 DKLSNT-IT  241 (246)
Q Consensus       234 ~~~~~m-~~  241 (246)
                      ++|+++ .+
T Consensus       339 ~~~~~l~~~  347 (382)
T 2h6f_A          339 ELCEILAKE  347 (382)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHHH
Confidence            999998 44

>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=99.43  E-value=1.5e-11  Score=99.98  Aligned_cols=197  Identities=10%  Similarity=0.002  Sum_probs=164.8

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCC-cchHHHHHHHHHhccCCCCCCCCCccHH
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKK-LDVTMPFNEQLKDNGQKCSSGGFHPDIF   94 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~-~~~a~~~~~~m~~~~~~~~~~~~~p~~~   94 (246)
                      +...|+.+-..+.+.|++++|++.|++...--+-+...|+.+..++...|+ +++|+..|++.+..        -+-+..
T Consensus        96 ~~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l--------~P~~~~  167 (382)
T 2h6f_A           96 FRDVYDYFRAVLQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEE--------QPKNYQ  167 (382)
T ss_dssp             HHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH--------CTTCHH
T ss_pred             hHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHH--------CCCCHH
Confidence            356788888899999999999999998764346678899999999999997 99999999999986        233677


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP  173 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~  173 (246)
                      .|+.+-.++...|++++|+..|++..+   +.|+ ...|..+..++...|++++    |+..|+.+.+.      -.-+.
T Consensus       168 a~~~~g~~~~~~g~~~eAl~~~~kal~---ldP~~~~a~~~lg~~~~~~g~~~e----Al~~~~~al~l------~P~~~  234 (382)
T 2h6f_A          168 VWHHRRVLVEWLRDPSQELEFIADILN---QDAKNYHAWQHRQWVIQEFKLWDN----ELQYVDQLLKE------DVRNN  234 (382)
T ss_dssp             HHHHHHHHHHHHTCCTTHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHTCCTT----HHHHHHHHHHH------CTTCH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHH---hCccCHHHHHHHHHHHHHcCChHH----HHHHHHHHHHh------CCCCH
Confidence            999999999999999999999999998   5565 8889999999999999999    99999999987      23356


Q ss_pred             hhHHHHHHHHHh-cCChhHH-----hhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcC--ChhHHHHHHHHH
Q 043380          174 HLYVSMMHELAA-RVDYDIV-----KSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDG--QVDLALDKLSNT  239 (246)
Q Consensus       174 ~~~~~li~~~~~-~g~~~~a-----~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g--~~~~a~~~~~~m  239 (246)
                      ..|+.+..++.. .|..++|     ...+++....++..      ..+|..+...+...|  ++++|++.+.++
T Consensus       235 ~a~~~lg~~l~~l~~~~~eA~~~~el~~~~~Al~l~P~~------~~a~~~l~~ll~~~g~~~~~~a~~~~~~~  302 (382)
T 2h6f_A          235 SVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKLVPHN------ESAWNYLKGILQDRGLSKYPNLLNQLLDL  302 (382)
T ss_dssp             HHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHHSTTC------HHHHHHHHHHHTTTCGGGCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHCCCC------HHHHHHHHHHHHccCccchHHHHHHHHHh
Confidence            889999999999 6665777     47777766543221      127888888898888  689999988876

>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=99.41  E-value=1.9e-11  Score=94.17  Aligned_cols=219  Identities=12%  Similarity=0.007  Sum_probs=150.6

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-------CC-CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCC
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEK-------GL-EPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCS   85 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~-------~~-~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~   85 (246)
                      +....++..+...|...|++++|...|++...       +- +....++..+...|...|++++|.+.|.+......+..
T Consensus        40 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~  119 (283)
T 3edt_B           40 PDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVL  119 (283)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHc
Confidence            44577889999999999999999999988642       11 23456789999999999999999999999886410000


Q ss_pred             CCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCC------CCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHH
Q 043380           86 SGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCC------NLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGE  158 (246)
Q Consensus        86 ~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~------~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~  158 (246)
                      ....+....++..+...|...|++++|...+++... .      +-.|+ ..++..+...|...|++++    |..++++
T Consensus       120 ~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~-~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~----A~~~~~~  194 (283)
T 3edt_B          120 GKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALE-IYATRLGPDDPNVAKTKNNLASCYLKQGKYQD----AETLYKE  194 (283)
T ss_dssp             CTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHH-HHHHHSCTTCHHHHHHHHHHHHHHHHHTCHHH----HHHHHHH
T ss_pred             CCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-HHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHH----HHHHHHH
Confidence            001233466899999999999999999999999877 2      11343 5678899999999999999    9999999


Q ss_pred             HHHhhcC--CCCCCcch-hhHHHHHHHHHhcCChhHH------hhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCCh
Q 043380          159 IVKRVCS--NPGLWPKP-HLYVSMMHELAARVDYDIV------KSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQV  229 (246)
Q Consensus       159 m~~~~~~--~~~~~p~~-~~~~~li~~~~~~g~~~~a------~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~  229 (246)
                      ..+....  .....|.. ..+..+...+...+....+      ...+.....     ..+. ...++..+...|...|++
T Consensus       195 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~-~~~~~~~la~~~~~~g~~  268 (283)
T 3edt_B          195 ILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKV-----DSPT-VNTTLRSLGALYRRQGKL  268 (283)
T ss_dssp             HHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC------------CCCC-----CCHH-HHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCC-----CCHH-HHHHHHHHHHHHHHcCCH
Confidence            8764110  00123333 3333333343333333322      222222211     1122 233788899999999999


Q ss_pred             hHHHHHHHHHHhhc
Q 043380          230 DLALDKLSNTITRW  243 (246)
Q Consensus       230 ~~a~~~~~~m~~~g  243 (246)
                      ++|.++|++..+..
T Consensus       269 ~~A~~~~~~al~~~  282 (283)
T 3edt_B          269 EAAHTLEDCASRNR  282 (283)
T ss_dssp             HHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhh
Confidence            99999999887654

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.41  E-value=1.5e-11  Score=102.93  Aligned_cols=188  Identities=9%  Similarity=-0.081  Sum_probs=156.2

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCc-chHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHH
Q 043380           33 IDEAYQILESVEKGLEPDSLSYNILISACIKTKKL-DVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQS  111 (246)
Q Consensus        33 ~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~-~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~  111 (246)
                      ++++...++......+.+...+..+-..+...|++ ++|.+.|++..+.        -+-+...|..+-.+|...|++++
T Consensus        84 ~~~al~~l~~~~~~~~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~--------~p~~~~a~~~lg~~~~~~g~~~~  155 (474)
T 4abn_A           84 MEKTLQQMEEVLGSAQVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKL--------EPELVEAWNQLGEVYWKKGDVTS  155 (474)
T ss_dssp             HHHHHHHHHHHHTTCCCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHHHHHHHHhccCchhHHHHHHHHHHHHhccccHHHHHHHHHHHHhh--------CCCCHHHHHHHHHHHHHcCCHHH
Confidence            55666667666544455788899999999999999 9999999999986        13347899999999999999999


Q ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHHHHHhc---------CChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHH
Q 043380          112 LLEIVFEMKSCCNLILDRSTFTAMVDALLYS---------GSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHE  182 (246)
Q Consensus       112 a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~---------~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~  182 (246)
                      |...|++..+   +.|+...+..+...|...         |++++    |...|++..+.      -.-+...|..+..+
T Consensus       156 A~~~~~~al~---~~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~----A~~~~~~al~~------~p~~~~~~~~lg~~  222 (474)
T 4abn_A          156 AHTCFSGALT---HCKNKVSLQNLSMVLRQLQTDSGDEHSRHVMD----SVRQAKLAVQM------DVLDGRSWYILGNA  222 (474)
T ss_dssp             HHHHHHHHHT---TCCCHHHHHHHHHHHTTCCCSCHHHHHHHHHH----HHHHHHHHHHH------CTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHh---hCCCHHHHHHHHHHHHHhccCChhhhhhhHHH----HHHHHHHHHHh------CCCCHHHHHHHHHH
Confidence            9999999998   568888899999999999         99999    99999999886      23456889999999


Q ss_pred             HHhc--------CChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          183 LAAR--------VDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       183 ~~~~--------g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      |...        |++++|...|++....++. .+..  ..+|..+..+|...|++++|.+.|++..+..+
T Consensus       223 ~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~--~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p  289 (474)
T 4abn_A          223 YLSLYFNTGQNPKISQQALSAYAQAEKVDRK-ASSN--PDLHLNRATLHKYEESYGEALEGFSQAAALDP  289 (474)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHHHHHCGG-GGGC--HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHhhccccchHHHHHHHHHHHHHhCCC-cccC--HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC
Confidence            9999        9999999999998754320 0012  22789999999999999999999999876544

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.39  E-value=7.9e-12  Score=96.25  Aligned_cols=195  Identities=12%  Similarity=-0.082  Sum_probs=148.8

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      +.+..+|..+..+|...|++++|.+.|+......+.+...+..+...|...|++++|...|+++.+.         .|+.
T Consensus        74 ~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~---------~~~~  144 (275)
T 1xnf_A           74 PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD---------DPND  144 (275)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---------CTTC
T ss_pred             CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCccccHHHHHHHHHHHHhccHHHHHHHHHHHHHh---------CCCC
Confidence            4568899999999999999999999999987544567889999999999999999999999999986         4555


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc-c
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP-K  172 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p-~  172 (246)
                      ..+...+..+...|++++|...++.... . ..++...+ .++..+...++.++    |...++.......   ...| +
T Consensus       145 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~-~-~~~~~~~~-~~~~~~~~~~~~~~----a~~~~~~~~~~~~---~~~~~~  214 (275)
T 1xnf_A          145 PFRSLWLYLAEQKLDEKQAKEVLKQHFE-K-SDKEQWGW-NIVEFYLGNISEQT----LMERLKADATDNT---SLAEHL  214 (275)
T ss_dssp             HHHHHHHHHHHHHHCHHHHHHHHHHHHH-H-SCCCSTHH-HHHHHHTTSSCHHH----HHHHHHHHCCSHH---HHHHHH
T ss_pred             hHHHHHHHHHHHhcCHHHHHHHHHHHHh-c-CCcchHHH-HHHHHHHHhcCHHH----HHHHHHHHhcccc---cccccc
Confidence            5555566666778999999999988777 2 22334444 47777888888888    9999988755310   1111 2


Q ss_pred             hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHH
Q 043380          173 PHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKL  236 (246)
Q Consensus       173 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~  236 (246)
                      ..++..+...|...|++++|...|++....++.         .+.....++...|++++|++.+
T Consensus       215 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~---------~~~~~~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          215 SETNFYLGKYYLSLGDLDSATALFKLAVANNVH---------NFVEHRYALLELSLLGQDQDDL  269 (275)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCT---------TCHHHHHHHHHHHHHHHC----
T ss_pred             cHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCch---------hHHHHHHHHHHHHHHHhhHHHH
Confidence            578899999999999999999999998765422         1333456777888999888776

>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=99.39  E-value=3.7e-11  Score=105.04  Aligned_cols=163  Identities=16%  Similarity=0.173  Sum_probs=144.5

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc-cH
Q 043380           15 LNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP-DI   93 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p-~~   93 (246)
                      -++..|+.|-..|.+.|++++|++.|++..+-.+-+...|+.+-.+|.+.|++++|.+.|++.++.         .| +.
T Consensus         7 ~~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l---------~P~~~   77 (723)
T 4gyw_A            7 THADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI---------SPTFA   77 (723)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---------CTTCH
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---------CCCCH
Confidence            346789999999999999999999999876433556889999999999999999999999999986         45 47


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc-
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP-  171 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p-  171 (246)
                      ..|+.+-.+|...|++++|.+.|++..+   +.|+ ...|+.+...|...|++++    |++.|++..+.       .| 
T Consensus        78 ~a~~nLg~~l~~~g~~~~A~~~~~kAl~---l~P~~~~a~~~Lg~~~~~~g~~~e----Ai~~~~~Al~l-------~P~  143 (723)
T 4gyw_A           78 DAYSNMGNTLKEMQDVQGALQCYTRAIQ---INPAFADAHSNLASIHKDSGNIPE----AIASYRTALKL-------KPD  143 (723)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-------CSC
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh-------CCC
Confidence            7999999999999999999999999988   5676 7889999999999999999    99999999886       34 


Q ss_pred             chhhHHHHHHHHHhcCChhHHhhHHHhhC
Q 043380          172 KPHLYVSMMHELAARVDYDIVKSPYRRMW  200 (246)
Q Consensus       172 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~  200 (246)
                      +...+..+..++...|++++|.+.+++..
T Consensus       144 ~~~a~~~L~~~l~~~g~~~~A~~~~~kal  172 (723)
T 4gyw_A          144 FPDAYCNLAHCLQIVCDWTDYDERMKKLV  172 (723)
T ss_dssp             CHHHHHHHHHHHHHTTCCTTHHHHHHHHH
T ss_pred             ChHHHhhhhhHHHhcccHHHHHHHHHHHH
Confidence            45889999999999999999998888754

>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=2e-11  Score=106.70  Aligned_cols=164  Identities=11%  Similarity=0.016  Sum_probs=144.7

Q ss_pred             CCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc-cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC
Q 043380           49 PDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP-DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL  127 (246)
Q Consensus        49 ~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p  127 (246)
                      -+...|+.|-..|.+.|++++|++.|++.++.         .| +..+|+.|-.+|.+.|++++|...|++..+   +.|
T Consensus         7 ~~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l---------~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~---l~P   74 (723)
T 4gyw_A            7 THADSLNNLANIKREQGNIEEAVRLYRKALEV---------FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIR---ISP   74 (723)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---------CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCT
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCC
Confidence            35678999999999999999999999999986         45 477999999999999999999999999988   567


Q ss_pred             C-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc-chhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCC
Q 043380          128 D-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP-KPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTG  205 (246)
Q Consensus       128 ~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  205 (246)
                      + ...|..+...|...|++++    |++.|++..+.       .| +..+|..+..+|...|++++|...|++..+.++.
T Consensus        75 ~~~~a~~nLg~~l~~~g~~~~----A~~~~~kAl~l-------~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~  143 (723)
T 4gyw_A           75 TFADAYSNMGNTLKEMQDVQG----ALQCYTRAIQI-------NPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPD  143 (723)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSC
T ss_pred             CCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh-------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC
Confidence            7 8899999999999999999    99999999886       34 4688999999999999999999999998765432


Q ss_pred             CCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          206 TISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       206 ~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      .    .  .+|..+..+|...|++++|.+.+++..+
T Consensus       144 ~----~--~a~~~L~~~l~~~g~~~~A~~~~~kal~  173 (723)
T 4gyw_A          144 F----P--DAYCNLAHCLQIVCDWTDYDERMKKLVS  173 (723)
T ss_dssp             C----H--HHHHHHHHHHHHTTCCTTHHHHHHHHHH
T ss_pred             C----h--HHHhhhhhHHHhcccHHHHHHHHHHHHH
Confidence            2    1  2789999999999999999999988765

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.36  E-value=4.3e-10  Score=95.24  Aligned_cols=206  Identities=15%  Similarity=0.103  Sum_probs=162.8

Q ss_pred             cCcCHHHHHHHHHHHHh-------cCCHH-------HHHHHHHHHHhCC-CCCHHHHHHHHHHHHhcCCcchHHHHHHHH
Q 043380           13 WKLNTIVMNAVIEASRE-------AQRID-------EAYQILESVEKGL-EPDSLSYNILISACIKTKKLDVTMPFNEQL   77 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~-------~g~~~-------~a~~~~~~~~~~~-~~~~~t~~~li~~~~~~~~~~~a~~~~~~m   77 (246)
                      .+-++..|..+...+.+       .|+++       +|..+|++..+.+ +.+...|..+...+.+.|++++|..+|+++
T Consensus       268 ~p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~a  347 (530)
T 2ooe_A          268 LGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRL  347 (530)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence            34578888888888876       68977       8999999987533 446888999999999999999999999999


Q ss_pred             HhccCCCCCCCCCcc--HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHH-HHHhcCChhhhhhHHH
Q 043380           78 KDNGQKCSSGGFHPD--IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVD-ALLYSGSIKVVGLYAL  153 (246)
Q Consensus        78 ~~~~~~~~~~~~~p~--~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~-~~~~~~~~~~~~~~a~  153 (246)
                      .+.         .|+  ...|..+...+.+.|++++|.++|++..+ .  .|+ ...|..... .+...|++++    |.
T Consensus       348 l~~---------~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~-~--~~~~~~~~~~~a~~~~~~~~~~~~----A~  411 (530)
T 2ooe_A          348 LAI---------EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKARE-D--ARTRHHVYVTAALMEYYCSKDKSV----AF  411 (530)
T ss_dssp             HHS---------SSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-C--TTCCTHHHHHHHHHHHHHTCCHHH----HH
T ss_pred             hCc---------cccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHh-c--cCCchHHHHHHHHHHHHHcCChhH----HH
Confidence            985         453  35899999999999999999999999988 3  333 333332222 2346899999    99


Q ss_pred             HHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHH
Q 043380          154 CIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLAL  233 (246)
Q Consensus       154 ~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~  233 (246)
                      .+|+...+.      .+-+...|..++..+.+.|+.++|..+|++.....+  .+|......|...+......|+.+.+.
T Consensus       412 ~~~e~al~~------~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~--~~~~~~~~lw~~~~~~e~~~G~~~~~~  483 (530)
T 2ooe_A          412 KIFELGLKK------YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGS--LPPEKSGEIWARFLAFESNIGDLASIL  483 (530)
T ss_dssp             HHHHHHHHH------HTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCC--SCGGGCHHHHHHHHHHHHHSSCHHHHH
T ss_pred             HHHHHHHHH------CCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccC--CCHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            999998886      223568899999999999999999999999875432  334322336888888888999999999


Q ss_pred             HHHHHHHhh
Q 043380          234 DKLSNTITR  242 (246)
Q Consensus       234 ~~~~~m~~~  242 (246)
                      ++++++.+.
T Consensus       484 ~~~~r~~~~  492 (530)
T 2ooe_A          484 KVEKRRFTA  492 (530)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999887653

>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=99.35  E-value=1.6e-10  Score=86.85  Aligned_cols=173  Identities=12%  Similarity=0.009  Sum_probs=138.8

Q ss_pred             CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC
Q 043380           48 EPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL  127 (246)
Q Consensus        48 ~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p  127 (246)
                      ..|+..+......+...|++++|...|++..+.       ...++...+..+..++...|++++|...|++..+   ..|
T Consensus         4 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~-------~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~---~~p   73 (228)
T 4i17_A            4 TTDPNQLKNEGNDALNAKNYAVAFEKYSEYLKL-------TNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIK---KNY   73 (228)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-------TTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---TTC
T ss_pred             ccCHHHHHHHHHHHHHccCHHHHHHHHHHHHhc-------cCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHH---hCc
Confidence            346678888888999999999999999999986       2226777887899999999999999999999988   556


Q ss_pred             C-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch-------hhHHHHHHHHHhcCChhHHhhHHHhh
Q 043380          128 D-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP-------HLYVSMMHELAARVDYDIVKSPYRRM  199 (246)
Q Consensus       128 ~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~-------~~~~~li~~~~~~g~~~~a~~~~~~~  199 (246)
                      + ...|..+...|...|++++    |...+++..+.      .+.+.       ..|..+-..+...|++++|...|++.
T Consensus        74 ~~~~~~~~l~~~~~~~~~~~~----A~~~~~~al~~------~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~a  143 (228)
T 4i17_A           74 NLANAYIGKSAAYRDMKNNQE----YIATLTEGIKA------VPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHA  143 (228)
T ss_dssp             SHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------STTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHcccHHH----HHHHHHHHHHH------CCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHH
Confidence            6 6778899999999999999    99999999886      12233       45788888899999999999999998


Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhcCCh---------------------------hHHHHHHHHHHhhcc
Q 043380          200 WPDSTGTISPEVQEEAGHLLMEAALNDGQV---------------------------DLALDKLSNTITRWK  244 (246)
Q Consensus       200 ~~~~~~~~~~~~~~~~~~~li~~~~~~g~~---------------------------~~a~~~~~~m~~~g~  244 (246)
                      ...+    |.+....+|..+..+|...|+.                           ++|...|++..+..+
T Consensus       144 l~~~----p~~~~~~~~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~l~p  211 (228)
T 4i17_A          144 TDVT----SKKWKTDALYSLGVLFYNNGADVLRKATPLASSNKEKYASEKAKADAAFKKAVDYLGEAVTLSP  211 (228)
T ss_dssp             TTSS----CHHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HhcC----CCcccHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Confidence            7643    2200122688888888888887                           889999888776544

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.33  E-value=2e-10  Score=90.51  Aligned_cols=199  Identities=9%  Similarity=-0.017  Sum_probs=154.0

Q ss_pred             HHHHHHHHHHHHhc----CCH----HHHHHHHHHHHhCCCCCHHHHHHHHHHHHh-------cCCc-------chHHHHH
Q 043380           17 TIVMNAVIEASREA----QRI----DEAYQILESVEKGLEPDSLSYNILISACIK-------TKKL-------DVTMPFN   74 (246)
Q Consensus        17 ~~~~~~li~~~~~~----g~~----~~a~~~~~~~~~~~~~~~~t~~~li~~~~~-------~~~~-------~~a~~~~   74 (246)
                      ...|...+...-+.    ++.    ++|..+|++.....+.+...|..+...+..       .|++       ++|..+|
T Consensus         8 ~~~W~~yi~~E~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~   87 (308)
T 2ond_A            8 VDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLVLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIY   87 (308)
T ss_dssp             HHHHHHHHHHHHTCTTCCCCHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcccCCchHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHH
Confidence            45666666665443    233    788899988764446788889888888763       5886       8999999


Q ss_pred             HHHHhccCCCCCCCCCc-cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HH-HHHHHHHHHHhcCChhhhhhH
Q 043380           75 EQLKDNGQKCSSGGFHP-DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RS-TFTAMVDALLYSGSIKVVGLY  151 (246)
Q Consensus        75 ~~m~~~~~~~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~-~~~~li~~~~~~~~~~~~~~~  151 (246)
                      ++....        +.| +...|..+...+.+.|++++|..+|++..+   +.|+ .. .|..+...+.+.|++++    
T Consensus        88 ~rAl~~--------~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~---~~p~~~~~~~~~~~~~~~~~~~~~~----  152 (308)
T 2ond_A           88 ERAIST--------LLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLA---IEDIDPTLVYIQYMKFARRAEGIKS----  152 (308)
T ss_dssp             HHHHTT--------TTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT---SSSSCTHHHHHHHHHHHHHHHCHHH----
T ss_pred             HHHHHH--------hCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHHh---ccccCccHHHHHHHHHHHHhcCHHH----
Confidence            999983        355 456899999999999999999999999998   5565 33 89999999999999999    


Q ss_pred             HHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHH-hcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChh
Q 043380          152 ALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELA-ARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVD  230 (246)
Q Consensus       152 a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~-~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~  230 (246)
                      |..+|++..+.      -.++...|........ ..|++++|..+|+......+.    ..  ..|..++..+.+.|+++
T Consensus       153 A~~~~~~a~~~------~p~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~p~----~~--~~~~~~~~~~~~~g~~~  220 (308)
T 2ond_A          153 GRMIFKKARED------ARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGD----IP--EYVLAYIDYLSHLNEDN  220 (308)
T ss_dssp             HHHHHHHHHTS------TTCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHTT----CH--HHHHHHHHHHHTTCCHH
T ss_pred             HHHHHHHHHhc------CCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC----cH--HHHHHHHHHHHHCCCHH
Confidence            99999999875      1233455554443322 379999999999998754322    12  27899999999999999


Q ss_pred             HHHHHHHHHHhh
Q 043380          231 LALDKLSNTITR  242 (246)
Q Consensus       231 ~a~~~~~~m~~~  242 (246)
                      +|..+|++....
T Consensus       221 ~A~~~~~~al~~  232 (308)
T 2ond_A          221 NTRVLFERVLTS  232 (308)
T ss_dssp             HHHHHHHHHHHS
T ss_pred             HHHHHHHHHHhc
Confidence            999999998874

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.31  E-value=3.9e-11  Score=97.94  Aligned_cols=219  Identities=10%  Similarity=-0.012  Sum_probs=157.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCH----HHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPDS----LSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~----~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      ...+..+...+...|++++|...|++...-.+.+.    ..|..+...|...|++++|...|++..+.....  ......
T Consensus        48 ~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~--~~~~~~  125 (411)
T 4a1s_A           48 CLELALEGERLCNAGDCRAGVAFFQAAIQAGTEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSM--NDRLGE  125 (411)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHT--TCHHHH
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHc--cCchHH
Confidence            34455566788899999999999998763223333    478889999999999999999999987641000  011234


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhC---CCCCCC-HHHHHHHHHHHHhcCC-----------------hhhhhhH
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSC---CNLILD-RSTFTAMVDALLYSGS-----------------IKVVGLY  151 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~---~~~~p~-~~~~~~li~~~~~~~~-----------------~~~~~~~  151 (246)
                      ..++..+...|...|++++|...+++....   .+-.|. ..++..+...|...|+                 +++    
T Consensus       126 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~----  201 (411)
T 4a1s_A          126 AKSSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTR----  201 (411)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHH----
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHH----
Confidence            568889999999999999999999987661   111233 5578889999999999                 999    


Q ss_pred             HHHHHHHHHHhhcCCCCCCc-chhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChh
Q 043380          152 ALCIFGEIVKRVCSNPGLWP-KPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVD  230 (246)
Q Consensus       152 a~~~~~~m~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~  230 (246)
                      |.+.+++..+..... +-.| ...++..+...|...|++++|...+++..........+.....++..+...|...|+++
T Consensus       202 A~~~~~~al~~~~~~-~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~  280 (411)
T 4a1s_A          202 AVEFYQENLKLMRDL-GDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFE  280 (411)
T ss_dssp             HHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHH
T ss_pred             HHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHH
Confidence            999988865531100 1112 23578888999999999999999999876322111111222236788899999999999


Q ss_pred             HHHHHHHHHHhh
Q 043380          231 LALDKLSNTITR  242 (246)
Q Consensus       231 ~a~~~~~~m~~~  242 (246)
                      +|.+++++..+.
T Consensus       281 ~A~~~~~~al~~  292 (411)
T 4a1s_A          281 DAAEHYKRTLAL  292 (411)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999887653

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.30  E-value=8e-11  Score=95.53  Aligned_cols=221  Identities=10%  Similarity=0.005  Sum_probs=161.0

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC----HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCC
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPD----SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGG   88 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~----~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~   88 (246)
                      ..+....+...-..+.+.|++++|...|++...-.+.+    ...|..+...+...|++++|...+++.......   .+
T Consensus         5 ~~~~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~---~~   81 (406)
T 3sf4_A            5 MEASCLELALEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLART---IG   81 (406)
T ss_dssp             CCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH---TT
T ss_pred             HHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHh---cc
Confidence            34566777788889999999999999999876322333    357888999999999999999999987653100   01


Q ss_pred             CCc-cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC----HHHHHHHHHHHHhcCC-------------------
Q 043380           89 FHP-DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD----RSTFTAMVDALLYSGS-------------------  144 (246)
Q Consensus        89 ~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~----~~~~~~li~~~~~~~~-------------------  144 (246)
                      -.| ...++..+...|...|++++|...+++......-.++    ..++..+...|...|+                   
T Consensus        82 ~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~  161 (406)
T 3sf4_A           82 DQLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRD  161 (406)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHH
Confidence            122 3557888999999999999999999987661111112    4478889999999999                   


Q ss_pred             -hhhhhhHHHHHHHHHHHhhcCCCCCCc-chhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHH
Q 043380          145 -IKVVGLYALCIFGEIVKRVCSNPGLWP-KPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEA  222 (246)
Q Consensus       145 -~~~~~~~a~~~~~~m~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~  222 (246)
                       +++    |...++......... +-.| ...++..+...|...|++++|...+++..........+.....++..+...
T Consensus       162 ~~~~----A~~~~~~al~~~~~~-~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~  236 (406)
T 3sf4_A          162 ALQA----AVDFYEENLSLVTAL-GDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNA  236 (406)
T ss_dssp             HHHH----HHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHH----HHHHHHHHHHHHHhc-cCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHH
Confidence             999    999998865531111 1112 235788889999999999999999998763221112222223368888999


Q ss_pred             HHhcCChhHHHHHHHHHHh
Q 043380          223 ALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       223 ~~~~g~~~~a~~~~~~m~~  241 (246)
                      |...|++++|.+++++..+
T Consensus       237 ~~~~g~~~~A~~~~~~al~  255 (406)
T 3sf4_A          237 YIFLGEFETASEYYKKTLL  255 (406)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHcCChHHHHHHHHHHHH
Confidence            9999999999999988764

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=99.30  E-value=3.3e-10  Score=88.65  Aligned_cols=208  Identities=11%  Similarity=-0.003  Sum_probs=149.3

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHh-----CCCCC-HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCC-
Q 043380           18 IVMNAVIEASREAQRIDEAYQILESVEK-----GLEPD-SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFH-   90 (246)
Q Consensus        18 ~~~~~li~~~~~~g~~~~a~~~~~~~~~-----~~~~~-~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~-   90 (246)
                      ..|+.....|...|++++|.+.|++...     +-+++ ..+|+.+..+|...|++++|...|++..+.....   |-. 
T Consensus        38 ~~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~---g~~~  114 (292)
T 1qqe_A           38 DLCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHR---GQFR  114 (292)
T ss_dssp             HHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT---TCHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHc---CCHH
Confidence            3677788889999999999999987531     22222 5689999999999999999999999988641000   101 


Q ss_pred             ccHHHHHHHHHHHHcc-CCHHHHHHHHHHHHhCCCCCCC-------HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           91 PDIFTYATLLMGFRHA-KDLQSLLEIVFEMKSCCNLILD-------RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        91 p~~~~~~~ll~~~~~~-~~~~~a~~~~~~m~~~~~~~p~-------~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      .-..+|+.+-..|... |++++|...|++..+   +.|+       ..++..+...|...|++++    |...|++....
T Consensus       115 ~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~---~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~----A~~~~~~al~~  187 (292)
T 1qqe_A          115 RGANFKFELGEILENDLHDYAKAIDCYELAGE---WYAQDQSVALSNKCFIKCADLKALDGQYIE----ASDIYSKLIKS  187 (292)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH---HHHHTTCHHHHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHH---HHHhCCChHHHHHHHHHHHHHHHHhCCHHH----HHHHHHHHHHH
Confidence            1145888999999996 999999999998876   2221       3568889999999999999    99999999886


Q ss_pred             hcCCCCCCcch-----hhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHH--hcCChhHHHHH
Q 043380          163 VCSNPGLWPKP-----HLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAAL--NDGQVDLALDK  235 (246)
Q Consensus       163 ~~~~~~~~p~~-----~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~--~~g~~~~a~~~  235 (246)
                      ..   .. +..     ..|..+..++...|++++|...|++.....+...... ....+..++.+|.  ..+++++|++.
T Consensus       188 ~~---~~-~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~-~~~~l~~l~~~~~~~~~~~~~~A~~~  262 (292)
T 1qqe_A          188 SM---GN-RLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSR-ESNFLKSLIDAVNEGDSEQLSEHCKE  262 (292)
T ss_dssp             TS---SC-TTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC----------HHHHHHHHHHHHTTCTTTHHHHHHH
T ss_pred             Hh---cC-CcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcH-HHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            11   11 111     2577888899999999999999999876544332211 1113445666664  45678888888


Q ss_pred             HHHHH
Q 043380          236 LSNTI  240 (246)
Q Consensus       236 ~~~m~  240 (246)
                      |+.+.
T Consensus       263 ~~~~~  267 (292)
T 1qqe_A          263 FDNFM  267 (292)
T ss_dssp             HTTSS
T ss_pred             hccCC
Confidence            86653

>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=99.29  E-value=5e-10  Score=76.11  Aligned_cols=130  Identities=11%  Similarity=0.031  Sum_probs=112.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHH
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYAT   98 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~   98 (246)
                      .|..+...+...|++++|.++|+.+.+..+.+...+..+...+...|++++|..+++++...        .+.+...+..
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~--------~~~~~~~~~~   74 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALEL--------DPRSAEAWYN   74 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--------CTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcCCcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHH--------CCCchHHHHH
Confidence            57788999999999999999999886434567888999999999999999999999999886        2446778899


Q ss_pred             HHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           99 LLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        99 ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      +...+...|++++|...++++.. . .+.+...+..+...+...|++++    |...++.+...
T Consensus        75 l~~~~~~~~~~~~A~~~~~~~~~-~-~~~~~~~~~~la~~~~~~~~~~~----A~~~~~~~~~~  132 (136)
T 2fo7_A           75 LGNAYYKQGDYDEAIEYYQKALE-L-DPRSAEAWYNLGNAYYKQGDYDE----AIEYYQKALEL  132 (136)
T ss_dssp             HHHHHHTTTCHHHHHHHHHHHHH-H-CTTCHHHHHHHHHHHHTTTCHHH----HHHHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHH-h-CCCChHHHHHHHHHHHHHccHHH----HHHHHHHHHcc
Confidence            99999999999999999999988 3 22347788899999999999999    99999998775

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.29  E-value=3.3e-11  Score=98.35  Aligned_cols=223  Identities=13%  Similarity=-0.014  Sum_probs=159.5

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-----C-CCCCHHHHHHHHHHHHhcCC-----------------cchH
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEK-----G-LEPDSLSYNILISACIKTKK-----------------LDVT   70 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~-----~-~~~~~~t~~~li~~~~~~~~-----------------~~~a   70 (246)
                      +....++..+...|...|++++|...|++...     + .+....++..+...|...|+                 +++|
T Consensus       123 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A  202 (411)
T 4a1s_A          123 LGEAKSSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRA  202 (411)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHH
Confidence            34456788888889999999999999887532     1 12234578888889999999                 9999


Q ss_pred             HHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC----HHHHHHHHHHHHhcCChh
Q 043380           71 MPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD----RSTFTAMVDALLYSGSIK  146 (246)
Q Consensus        71 ~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~----~~~~~~li~~~~~~~~~~  146 (246)
                      .+.+.+..+.....  ........++..+...|...|++++|...+++..+...-.++    ..++..+...|...|+++
T Consensus       203 ~~~~~~al~~~~~~--~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~  280 (411)
T 4a1s_A          203 VEFYQENLKLMRDL--GDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFE  280 (411)
T ss_dssp             HHHHHHHHHHHHHH--TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHH
T ss_pred             HHHHHHHHHHHHHc--CCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHH
Confidence            99988876531000  011123458888999999999999999999988761100112    237888999999999999


Q ss_pred             hhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhc
Q 043380          147 VVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALND  226 (246)
Q Consensus       147 ~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~  226 (246)
                      +    |...+++................++..+...|...|++++|...+++..........+.....++..+...|...
T Consensus       281 ~----A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~  356 (411)
T 4a1s_A          281 D----AAEHYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAI  356 (411)
T ss_dssp             H----HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHT
T ss_pred             H----HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHh
Confidence            9    999999887752111011122577888999999999999999999987632111111122233788899999999


Q ss_pred             CChhHHHHHHHHHHhh
Q 043380          227 GQVDLALDKLSNTITR  242 (246)
Q Consensus       227 g~~~~a~~~~~~m~~~  242 (246)
                      |++++|.+++++..+-
T Consensus       357 g~~~~A~~~~~~al~~  372 (411)
T 4a1s_A          357 GGHERALKYAEQHLQL  372 (411)
T ss_dssp             TCHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHH
Confidence            9999999999987653

>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=99.29  E-value=4.3e-10  Score=84.42  Aligned_cols=153  Identities=11%  Similarity=-0.023  Sum_probs=129.7

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC-CCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           15 LNTIVMNAVIEASREAQRIDEAYQILESVEKGLE-PDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      .|+..+......+.+.|++++|...|+....-.+ ++...+..+..++...|++++|...|++..+.        -+-+.
T Consensus         5 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--------~p~~~   76 (228)
T 4i17_A            5 TDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKK--------NYNLA   76 (228)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--------TCSHH
T ss_pred             cCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHh--------CcchH
Confidence            4678888999999999999999999998764334 78888888999999999999999999999986        23356


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-H-------HHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcC
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-R-------STFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCS  165 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~-------~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~  165 (246)
                      ..|..+..+|...|++++|...|++..+   ..|+ .       ..|..+...+...|++++    |.+.|+...+.   
T Consensus        77 ~~~~~l~~~~~~~~~~~~A~~~~~~al~---~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~----A~~~~~~al~~---  146 (228)
T 4i17_A           77 NAYIGKSAAYRDMKNNQEYIATLTEGIK---AVPGNATIEKLYAIYYLKEGQKFQQAGNIEK----AEENYKHATDV---  146 (228)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH---HSTTCHHHHHHHHHHHHHHHHHHHHTTCHHH----HHHHHHHHTTS---
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHH---HCCCcHHHHHHHHHHHHHHhHHHHHhccHHH----HHHHHHHHHhc---
Confidence            7899999999999999999999999988   4455 4       458888889999999999    99999998764   


Q ss_pred             CCCCCcc---hhhHHHHHHHHHhcCCh
Q 043380          166 NPGLWPK---PHLYVSMMHELAARVDY  189 (246)
Q Consensus       166 ~~~~~p~---~~~~~~li~~~~~~g~~  189 (246)
                          .|+   ...+..+..+|...|+.
T Consensus       147 ----~p~~~~~~~~~~l~~~~~~~~~~  169 (228)
T 4i17_A          147 ----TSKKWKTDALYSLGVLFYNNGAD  169 (228)
T ss_dssp             ----SCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ----CCCcccHHHHHHHHHHHHHHHHH
Confidence                565   57788888888887776

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.27  E-value=7.7e-11  Score=95.63  Aligned_cols=220  Identities=9%  Similarity=-0.021  Sum_probs=158.5

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHh-----CCCC-CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCC
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEK-----GLEP-DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFH   90 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~-----~~~~-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~   90 (246)
                      ..+|..+...|...|++++|...|++...     +..| ...++..+...|...|++++|...+.+..+...+.  ....
T Consensus        47 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~--~~~~  124 (406)
T 3sf4_A           47 SAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISREL--NDKV  124 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH--TCHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhc--cccc
Confidence            46788899999999999999999987531     1112 25568888899999999999999999887641000  0001


Q ss_pred             ccHHHHHHHHHHHHccCC--------------------HHHHHHHHHHHHhC---CCCCCC-HHHHHHHHHHHHhcCChh
Q 043380           91 PDIFTYATLLMGFRHAKD--------------------LQSLLEIVFEMKSC---CNLILD-RSTFTAMVDALLYSGSIK  146 (246)
Q Consensus        91 p~~~~~~~ll~~~~~~~~--------------------~~~a~~~~~~m~~~---~~~~p~-~~~~~~li~~~~~~~~~~  146 (246)
                      ....++..+...|...|+                    +++|...+++....   .+-.|. ..++..+...|...|+++
T Consensus       125 ~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~  204 (406)
T 3sf4_A          125 GEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFR  204 (406)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHH
T ss_pred             chHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHH
Confidence            124488889999999999                    99999998876541   222222 457888999999999999


Q ss_pred             hhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhc
Q 043380          147 VVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALND  226 (246)
Q Consensus       147 ~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~  226 (246)
                      +    |...+++..+.....+.......++..+...|...|++++|...+++..........+.....++..+...|...
T Consensus       205 ~----A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~  280 (406)
T 3sf4_A          205 D----AVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLL  280 (406)
T ss_dssp             H----HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             H----HHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHh
Confidence            9    999999987652111111112347888999999999999999999986532111112222233788899999999


Q ss_pred             CChhHHHHHHHHHHhh
Q 043380          227 GQVDLALDKLSNTITR  242 (246)
Q Consensus       227 g~~~~a~~~~~~m~~~  242 (246)
                      |++++|.+.+++..+.
T Consensus       281 g~~~~A~~~~~~a~~~  296 (406)
T 3sf4_A          281 QDYEKAIDYHLKHLAI  296 (406)
T ss_dssp             TCHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHH
Confidence            9999999999887653

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.27  E-value=7.8e-11  Score=92.78  Aligned_cols=217  Identities=10%  Similarity=0.014  Sum_probs=154.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC----HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCC-c
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPD----SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFH-P   91 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~----~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~-p   91 (246)
                      ...+......+...|++++|...|++..+-.+.+    ...+..+...+...|++++|.+.+++........   +.. .
T Consensus         5 ~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~---~~~~~   81 (338)
T 3ro2_A            5 CLELALEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTI---GDQLG   81 (338)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH---TCHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcc---cccHH
Confidence            3445566778889999999999999876322333    4678889999999999999999999876531000   112 2


Q ss_pred             cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC----HHHHHHHHHHHHhcCC--------------------hhh
Q 043380           92 DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD----RSTFTAMVDALLYSGS--------------------IKV  147 (246)
Q Consensus        92 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~----~~~~~~li~~~~~~~~--------------------~~~  147 (246)
                      ...++..+...|...|++++|...+++..+...-.++    ..++..+...|...|+                    +++
T Consensus        82 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~  161 (338)
T 3ro2_A           82 EAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQA  161 (338)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHH
Confidence            3557888999999999999999999987651111122    3478889999999999                    899


Q ss_pred             hhhHHHHHHHHHHHhhcCCCCCCc-chhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhc
Q 043380          148 VGLYALCIFGEIVKRVCSNPGLWP-KPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALND  226 (246)
Q Consensus       148 ~~~~a~~~~~~m~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~  226 (246)
                          |.+.+++........ +..| ...++..+...+...|++++|...+++..........+.....++..+...+...
T Consensus       162 ----A~~~~~~a~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~  236 (338)
T 3ro2_A          162 ----AVDLYEENLSLVTAL-GDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFL  236 (338)
T ss_dssp             ----HHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHH
T ss_pred             ----HHHHHHHHHHHHHhc-CCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHc
Confidence                999988765431100 1112 2357888889999999999999999986532111112222223678888899999


Q ss_pred             CChhHHHHHHHHHHh
Q 043380          227 GQVDLALDKLSNTIT  241 (246)
Q Consensus       227 g~~~~a~~~~~~m~~  241 (246)
                      |++++|.+++++..+
T Consensus       237 g~~~~A~~~~~~al~  251 (338)
T 3ro2_A          237 GEFETASEYYKKTLL  251 (338)
T ss_dssp             TCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHH
Confidence            999999999987764

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=99.27  E-value=4.2e-10  Score=86.38  Aligned_cols=201  Identities=10%  Similarity=-0.066  Sum_probs=146.5

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC---HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCC
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPD---SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGF   89 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~---~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~   89 (246)
                      -+.++..+-.+...+.+.|++++|...|+.+....+.+   ...+..+..+|.+.|++++|...|++..+..     .+.
T Consensus        11 ~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~-----p~~   85 (261)
T 3qky_A           11 RHSSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYGRTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIY-----QID   85 (261)
T ss_dssp             CCSSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGCSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-----TTC
T ss_pred             CCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHC-----CCC
Confidence            34566777788889999999999999999987533434   6778889999999999999999999999861     001


Q ss_pred             CccHHHHHHHHHHHHc--------cCCHHHHHHHHHHHHhCCCCCCC-HHHH-----------------HHHHHHHHhcC
Q 043380           90 HPDIFTYATLLMGFRH--------AKDLQSLLEIVFEMKSCCNLILD-RSTF-----------------TAMVDALLYSG  143 (246)
Q Consensus        90 ~p~~~~~~~ll~~~~~--------~~~~~~a~~~~~~m~~~~~~~p~-~~~~-----------------~~li~~~~~~~  143 (246)
                      +.....+..+..++..        .|++++|...|++..+   ..|+ ....                 ..+...|...|
T Consensus        86 ~~~~~a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~---~~p~~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g  162 (261)
T 3qky_A           86 PRVPQAEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFID---RYPNHELVDDATQKIRELRAKLARKQYEAARLYERRE  162 (261)
T ss_dssp             TTHHHHHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHH---HCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             chhHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHH---HCcCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            1224567778888888        9999999999999988   3344 2223                 55688899999


Q ss_pred             ChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhc----------CChhHHhhHHHhhCCCCCCCCCchhhh
Q 043380          144 SIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAAR----------VDYDIVKSPYRRMWPDSTGTISPEVQE  213 (246)
Q Consensus       144 ~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~----------g~~~~a~~~~~~~~~~~~~~~~~~~~~  213 (246)
                      ++++    |...|+...+..   |.-......+..+..+|...          |++++|...++.+....+.....   .
T Consensus       163 ~~~~----A~~~~~~~l~~~---p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~---~  232 (261)
T 3qky_A          163 LYEA----AAVTYEAVFDAY---PDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQIFPDSPLL---R  232 (261)
T ss_dssp             CHHH----HHHHHHHHHHHC---TTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHHCTTCTHH---H
T ss_pred             CHHH----HHHHHHHHHHHC---CCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHHCCCChHH---H
Confidence            9999    999999998861   11112346778888888876          88999999999987654322111   1


Q ss_pred             HHHHHHHHHHHhcCChhH
Q 043380          214 EAGHLLMEAALNDGQVDL  231 (246)
Q Consensus       214 ~~~~~li~~~~~~g~~~~  231 (246)
                      .+...+-..+...+++++
T Consensus       233 ~a~~~l~~~~~~~~~~~~  250 (261)
T 3qky_A          233 TAEELYTRARQRLTELEG  250 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHhhh
Confidence            144445555555554443

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.26  E-value=4.4e-11  Score=94.23  Aligned_cols=221  Identities=11%  Similarity=-0.026  Sum_probs=151.8

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHh--CCCCC----HHHHHHHHHHHHhcCC--------------------cchH
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEK--GLEPD----SLSYNILISACIKTKK--------------------LDVT   70 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~--~~~~~----~~t~~~li~~~~~~~~--------------------~~~a   70 (246)
                      ..++..+...|...|++++|...|++...  .-.++    ..++..+...+...|+                    +++|
T Consensus        83 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A  162 (338)
T 3ro2_A           83 AKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAA  162 (338)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHH
Confidence            55677777778888888888888776431  01122    3367777788888888                    8888


Q ss_pred             HHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC----HHHHHHHHHHHHhcCChh
Q 043380           71 MPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD----RSTFTAMVDALLYSGSIK  146 (246)
Q Consensus        71 ~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~----~~~~~~li~~~~~~~~~~  146 (246)
                      .+.+++........  ........++..+...+...|++++|...+++..+...-.++    ..++..+...+...|+++
T Consensus       163 ~~~~~~a~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  240 (338)
T 3ro2_A          163 VDLYEENLSLVTAL--GDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFE  240 (338)
T ss_dssp             HHHHHHHHHHHHHH--TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHHHHHHHHhc--CCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHH
Confidence            88887765420000  011122447888889999999999999999987651111112    347888999999999999


Q ss_pred             hhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhc
Q 043380          147 VVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALND  226 (246)
Q Consensus       147 ~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~  226 (246)
                      +    |...+++................++..+...|...|++++|...+++..........+.....++..+...|...
T Consensus       241 ~----A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~  316 (338)
T 3ro2_A          241 T----ASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTAL  316 (338)
T ss_dssp             H----HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHH
T ss_pred             H----HHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHc
Confidence            9    999999887652111011111467888999999999999999999987532111111222233688899999999


Q ss_pred             CChhHHHHHHHHHHhhc
Q 043380          227 GQVDLALDKLSNTITRW  243 (246)
Q Consensus       227 g~~~~a~~~~~~m~~~g  243 (246)
                      |++++|.+++++..+-.
T Consensus       317 g~~~~A~~~~~~a~~~~  333 (338)
T 3ro2_A          317 GNHDQAMHFAEKHLEIS  333 (338)
T ss_dssp             TCHHHHHHHHHHHHHC-
T ss_pred             CChHHHHHHHHHHHHHH
Confidence            99999999999887644

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.22  E-value=1.1e-09  Score=88.85  Aligned_cols=215  Identities=6%  Similarity=-0.087  Sum_probs=158.1

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHh---CCC----CCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCC
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEK---GLE----PDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGG   88 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~---~~~----~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~   88 (246)
                      ...+|..+..+|...|++++|...+++...   ...    ....+++.+...|...|++++|.+.|.+..+...+.  ..
T Consensus       142 ~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~--~~  219 (383)
T 3ulq_A          142 KAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAE--KQ  219 (383)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT--TC
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHc--CC
Confidence            356888899999999999999999987532   111    124578888999999999999999999988641000  00


Q ss_pred             CCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhC---CCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhc
Q 043380           89 FHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSC---CNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVC  164 (246)
Q Consensus        89 ~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~---~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~  164 (246)
                      ......++..+-.+|...|++++|...|++..+.   .+..|+ ..++..+...|...|++++    |...+++......
T Consensus       220 ~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~----A~~~~~~al~~~~  295 (383)
T 3ulq_A          220 PQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLITQIHYKLGKIDK----AHEYHSKGMAYSQ  295 (383)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHCCCHHH----HHHHHHHHHHHHH
Confidence            1112348889999999999999999999987651   133244 6778999999999999999    9999998766411


Q ss_pred             CCCCCCcchhhHHHHHHHHHhcCC---hhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          165 SNPGLWPKPHLYVSMMHELAARVD---YDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       165 ~~~~~~p~~~~~~~li~~~~~~g~---~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      .. +-......+..+-..|...|+   +++|..++++..      ..+.. ..++..+...|...|++++|.++++...+
T Consensus       296 ~~-~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~~------~~~~~-~~~~~~la~~y~~~g~~~~A~~~~~~al~  367 (383)
T 3ulq_A          296 KA-GDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESKM------LYADL-EDFAIDVAKYYHERKNFQKASAYFLKVEQ  367 (383)
T ss_dssp             HH-TCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHTT------CHHHH-HHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             Hc-CCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCc------CHHHH-HHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            00 111122346678888888898   888888888773      12221 23678899999999999999999998876


Q ss_pred             hcc
Q 043380          242 RWK  244 (246)
Q Consensus       242 ~g~  244 (246)
                      -.+
T Consensus       368 ~~~  370 (383)
T 3ulq_A          368 VRQ  370 (383)
T ss_dssp             HHT
T ss_pred             HHH
Confidence            543

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.21  E-value=3.5e-10  Score=88.37  Aligned_cols=183  Identities=11%  Similarity=0.028  Sum_probs=138.3

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-------CC-CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCC
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEK-------GL-EPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKC   84 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~-------~~-~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~   84 (246)
                      .+....++..+...|...|++++|...|++...       +- +....++..+...|...|++++|...|++..+...+.
T Consensus        65 ~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~  144 (311)
T 3nf1_A           65 HPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKV  144 (311)
T ss_dssp             SHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHh
Confidence            344567788899999999999999999987642       11 2345678899999999999999999999998741000


Q ss_pred             CCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCC------CCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHH
Q 043380           85 SSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCC------NLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFG  157 (246)
Q Consensus        85 ~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~------~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~  157 (246)
                      ...........+..+...|...|++++|.+++++... .      +-.|+ ..++..+...|...|++++    |...++
T Consensus       145 ~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~-~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~----A~~~~~  219 (311)
T 3nf1_A          145 LGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALE-IYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQ----AETLYK  219 (311)
T ss_dssp             HCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHH-HHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHH----HHHHHH
T ss_pred             cCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-HHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHH----HHHHHH
Confidence            0001233456788999999999999999999999877 2      22344 5678899999999999999    999999


Q ss_pred             HHHHhhcC----------------------------------------C--CCCCc-chhhHHHHHHHHHhcCChhHHhh
Q 043380          158 EIVKRVCS----------------------------------------N--PGLWP-KPHLYVSMMHELAARVDYDIVKS  194 (246)
Q Consensus       158 ~m~~~~~~----------------------------------------~--~~~~p-~~~~~~~li~~~~~~g~~~~a~~  194 (246)
                      +..+....                                        .  ....| +..++..+..+|...|++++|.+
T Consensus       220 ~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  299 (311)
T 3nf1_A          220 EILTRAHEREFGSVDDENKPIWMHAEEREECKGKQKDGTSFGEYGGWYKACKVDSPTVTTTLKNLGALYRRQGKFEAAET  299 (311)
T ss_dssp             HHHHHHHHHHHC------CCHHHHHHHHHHC-------CCSCCCC---------CHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHhcCCCCCcchHHHHHHHHHHHHhcCchhhHHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHCCCHHHHHH
Confidence            98763100                                        0  00122 34778899999999999999999


Q ss_pred             HHHhhC
Q 043380          195 PYRRMW  200 (246)
Q Consensus       195 ~~~~~~  200 (246)
                      +|++..
T Consensus       300 ~~~~al  305 (311)
T 3nf1_A          300 LEEAAM  305 (311)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            998764

>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=99.21  E-value=1e-09  Score=74.50  Aligned_cols=126  Identities=11%  Similarity=0.091  Sum_probs=60.5

Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHH
Q 043380           54 YNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFT  133 (246)
Q Consensus        54 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~  133 (246)
                      |..+...+...|++++|..+++++.+.        .+.+...+..+...+...|++++|..+++++.. .+ +.+...+.
T Consensus         4 ~~~l~~~~~~~~~~~~A~~~~~~~~~~--------~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~-~~-~~~~~~~~   73 (136)
T 2fo7_A            4 WYNLGNAYYKQGDYDEAIEYYQKALEL--------DPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALE-LD-PRSAEAWY   73 (136)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH-HC-TTCHHHHH
T ss_pred             HHHHHHHHHHcCcHHHHHHHHHHHHHc--------CCcchhHHHHHHHHHHHhcCHHHHHHHHHHHHH-HC-CCchHHHH
Confidence            444445555555555555555555443        122344445555555555555555555555544 11 11244444


Q ss_pred             HHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhh
Q 043380          134 AMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRM  199 (246)
Q Consensus       134 ~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~  199 (246)
                      .+...+...|++++    |.+.++.+.+.      .+.+..++..+...+...|++++|...++++
T Consensus        74 ~l~~~~~~~~~~~~----A~~~~~~~~~~------~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~  129 (136)
T 2fo7_A           74 NLGNAYYKQGDYDE----AIEYYQKALEL------DPRSAEAWYNLGNAYYKQGDYDEAIEYYQKA  129 (136)
T ss_dssp             HHHHHHHTTTCHHH----HHHHHHHHHHH------CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCHHH----HHHHHHHHHHh------CCCChHHHHHHHHHHHHHccHHHHHHHHHHH
Confidence            55555555555555    55555555443      1123344444445555555555555554443

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=99.20  E-value=2.6e-09  Score=81.95  Aligned_cols=174  Identities=9%  Similarity=0.003  Sum_probs=135.9

Q ss_pred             CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc----HHHHHHHHHHHHccCCHHHHHHHHHHHHhCC
Q 043380           48 EPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD----IFTYATLLMGFRHAKDLQSLLEIVFEMKSCC  123 (246)
Q Consensus        48 ~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~  123 (246)
                      +.+...+-.+...+.+.|++++|...|+++.+.         .|+    ...+..+..+|.+.|++++|...|+...+..
T Consensus        12 ~~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~---------~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~   82 (261)
T 3qky_A           12 HSSPQEAFERAMEFYNQGKYDRAIEYFKAVFTY---------GRTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIY   82 (261)
T ss_dssp             CSSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGG---------CSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHh---------CCCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHC
Confidence            345677777888899999999999999999986         343    6788899999999999999999999998822


Q ss_pred             CCCCC-HHHHHHHHHHHHh--------cCChhhhhhHHHHHHHHHHHhhcCCCCCCcc-hhhH-----------------
Q 043380          124 NLILD-RSTFTAMVDALLY--------SGSIKVVGLYALCIFGEIVKRVCSNPGLWPK-PHLY-----------------  176 (246)
Q Consensus       124 ~~~p~-~~~~~~li~~~~~--------~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~-~~~~-----------------  176 (246)
                      .-.|. ...+..+..++..        .|++++    |...|++..+.       .|+ ....                 
T Consensus        83 p~~~~~~~a~~~lg~~~~~~~~~~~~~~~~~~~----A~~~~~~~l~~-------~p~~~~~~~a~~~~~~~~~~~~~~~  151 (261)
T 3qky_A           83 QIDPRVPQAEYERAMCYYKLSPPYELDQTDTRK----AIEAFQLFIDR-------YPNHELVDDATQKIRELRAKLARKQ  151 (261)
T ss_dssp             TTCTTHHHHHHHHHHHHHHHCCCTTSCCHHHHH----HHHHHHHHHHH-------CTTCTTHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCchhHHHHHHHHHHHHHhcccccccchhHHH----HHHHHHHHHHH-------CcCchhHHHHHHHHHHHHHHHHHHH
Confidence            11223 4567778888888        999999    99999999987       232 2333                 


Q ss_pred             HHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhc----------CChhHHHHHHHHHHhhcc
Q 043380          177 VSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALND----------GQVDLALDKLSNTITRWK  244 (246)
Q Consensus       177 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~----------g~~~~a~~~~~~m~~~g~  244 (246)
                      ..+...|...|++++|...|+.+....+.... .  ..++..+..+|...          |++++|.+.|+.+.+.-+
T Consensus       152 ~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~-~--~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~~p  226 (261)
T 3qky_A          152 YEAARLYERRELYEAAAVTYEAVFDAYPDTPW-A--DDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQIFP  226 (261)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTT-H--HHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHCCCCch-H--HHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHHCC
Confidence            55678899999999999999998765433221 1  12677788888866          889999999999887544

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.18  E-value=1.7e-08  Score=81.29  Aligned_cols=214  Identities=8%  Similarity=-0.071  Sum_probs=148.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHh--CCCCCH----HHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCC--
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVEK--GLEPDS----LSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFH--   90 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~~--~~~~~~----~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~--   90 (246)
                      .++.+...+...|++++|...+++...  .-.++.    .+++.+...+...|++++|...+++..+.....   +..  
T Consensus        55 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~---~~~~~  131 (373)
T 1hz4_A           55 ATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQ---HLEQL  131 (373)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT---TCTTS
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHh---ccccC
Confidence            566777888899999999999987532  111222    335677788899999999999999987641100   111  


Q ss_pred             c-cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCC-C-CC-CHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCC
Q 043380           91 P-DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCN-L-IL-DRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSN  166 (246)
Q Consensus        91 p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~-~-~p-~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~  166 (246)
                      | ....+..+-..+...|++++|...+++...... . .+ ...++..+...+...|++++    |...+++....... 
T Consensus       132 ~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~----A~~~l~~a~~~~~~-  206 (373)
T 1hz4_A          132 PMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDN----ARSQLNRLENLLGN-  206 (373)
T ss_dssp             THHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHHHTT-
T ss_pred             cHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHHHhc-
Confidence            3 345677788889999999999999998766111 1 11 24678888999999999999    99999998765110 


Q ss_pred             CCCCcchhhH--HHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          167 PGLWPKPHLY--VSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       167 ~~~~p~~~~~--~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                      ++..+.....  ...+..+...|++++|...++.......+.  +......+..+...+...|++++|.+.+++....
T Consensus       207 ~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~--~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~  282 (373)
T 1hz4_A          207 GKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFAN--NHFLQGQWRNIARAQILLGEFEPAEIVLEELNEN  282 (373)
T ss_dssp             SCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTT--CGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCc--chhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            0111111111  123345779999999999999987544321  1111124677888999999999999999887543

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.18  E-value=5.2e-09  Score=86.89  Aligned_cols=212  Identities=9%  Similarity=-0.058  Sum_probs=147.1

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh---------CCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCC
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEK---------GLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKC   84 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~---------~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~   84 (246)
                      +.....||.|-..+...|+.++|++.|++...         ..+....+|+.+-.+|...|++++|...+++..+...+.
T Consensus        48 ~~~a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~  127 (472)
T 4g1t_A           48 EFKATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKF  127 (472)
T ss_dssp             --CCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHS
T ss_pred             hhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhc
Confidence            44467899999999999999999999976421         123356789999999999999999999999887532111


Q ss_pred             CCCCCCccHHHHHHHHHHHHc--cCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHH---HHhcCChhhhhhHHHHHHHH
Q 043380           85 SSGGFHPDIFTYATLLMGFRH--AKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDA---LLYSGSIKVVGLYALCIFGE  158 (246)
Q Consensus        85 ~~~~~~p~~~~~~~ll~~~~~--~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~---~~~~~~~~~~~~~a~~~~~~  158 (246)
                      ..........+++.+-.++..  .+++++|.+.|++..+   +.|+ ...+..+...   +...++.++    |++.+++
T Consensus       128 ~~~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~---~~p~~~~~~~~~~~~~~~l~~~~~~~~----al~~~~~  200 (472)
T 4g1t_A          128 SSPYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALE---KKPKNPEFTSGLAIASYRLDNWPPSQN----AIDPLRQ  200 (472)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHH---HSTTCHHHHHHHHHHHHHHHHSCCCCC----THHHHHH
T ss_pred             ccccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHhcCchHHHH----HHHHHHH
Confidence            111111234566666555544  4579999999999988   5576 5555555444   445677888    9999998


Q ss_pred             HHHhhcCCCCCCcchhhHHHHHHHHHh----cCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHH
Q 043380          159 IVKRVCSNPGLWPKPHLYVSMMHELAA----RVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALD  234 (246)
Q Consensus       159 m~~~~~~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~  234 (246)
                      ..+.      -+.+..++..+...+..    .|++++|.+++++.....+.  .  .  .++..+...|...|++++|.+
T Consensus       201 al~l------~p~~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~~~--~--~--~~~~~lg~~~~~~~~~~~A~~  268 (472)
T 4g1t_A          201 AIRL------NPDNQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKAPG--V--T--DVLRSAAKFYRRKDEPDKAIE  268 (472)
T ss_dssp             HHHH------CSSCHHHHHHHHHHHHHCC------CHHHHHHHHHHHHCSS--C--H--HHHHHHHHHHHHTTCHHHHHH
T ss_pred             Hhhc------CCcchHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhCcc--H--H--HHHHHHHHHHHHcCchHHHHH
Confidence            8776      12344556555555544    46778999999987654321  1  1  168889999999999999999


Q ss_pred             HHHHHHhhcc
Q 043380          235 KLSNTITRWK  244 (246)
Q Consensus       235 ~~~~m~~~g~  244 (246)
                      .+++..+..+
T Consensus       269 ~~~~al~~~p  278 (472)
T 4g1t_A          269 LLKKALEYIP  278 (472)
T ss_dssp             HHHHHHHHST
T ss_pred             HHHHHHHhCC
Confidence            9998876543

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=99.15  E-value=2.8e-09  Score=83.20  Aligned_cols=168  Identities=7%  Similarity=-0.093  Sum_probs=119.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc-cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCC
Q 043380           48 EPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP-DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLI  126 (246)
Q Consensus        48 ~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~  126 (246)
                      +.+...+..+-..+...|++++|...|++..+.         .| +...+..+...+.+.|++++|...+++...   ..
T Consensus       114 p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~---------~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~---~~  181 (287)
T 3qou_A          114 PREEELXAQQAMQLMQESNYTDALPLLXDAWQL---------SNQNGEIGLLLAETLIALNRSEDAEAVLXTIPL---QD  181 (287)
T ss_dssp             CCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---------TTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCG---GG
T ss_pred             CCchhhHHHHHHHHHhCCCHHHHHHHHHHHHHh---------CCcchhHHHHHHHHHHHCCCHHHHHHHHHhCch---hh
Confidence            445566677777778888888888888888775         34 456777788888888888888888887766   44


Q ss_pred             CCHHHHH-HHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCC
Q 043380          127 LDRSTFT-AMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTG  205 (246)
Q Consensus       127 p~~~~~~-~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  205 (246)
                      |+..... .....+...++.+.    |...+++....      -+.+...+..+...+...|++++|...|.++...+++
T Consensus       182 p~~~~~~~~~~~~l~~~~~~~~----a~~~l~~al~~------~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~  251 (287)
T 3qou_A          182 QDTRYQGLVAQIELLXQAADTP----EIQQLQQQVAE------NPEDAALATQLALQLHQVGRNEEALELLFGHLRXDLT  251 (287)
T ss_dssp             CSHHHHHHHHHHHHHHHHTSCH----HHHHHHHHHHH------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             cchHHHHHHHHHHHHhhcccCc----cHHHHHHHHhc------CCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccc
Confidence            6643332 33334666777777    88888877775      2334577788888888888888888888887766543


Q ss_pred             CCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          206 TISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       206 ~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      ...+.    ++..+...|...|+.++|...+++-..
T Consensus       252 ~~~~~----a~~~l~~~~~~~g~~~~a~~~~r~al~  283 (287)
T 3qou_A          252 AADGQ----TRXTFQEILAALGTGDALASXYRRQLY  283 (287)
T ss_dssp             GGGGH----HHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             cccch----HHHHHHHHHHHcCCCCcHHHHHHHHHH
Confidence            32222    678888888888888888888776553

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=99.14  E-value=4.2e-09  Score=82.27  Aligned_cols=184  Identities=10%  Similarity=0.028  Sum_probs=131.8

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCC-CccHHHHHHHHHHHHccCCHHHHHH
Q 043380           36 AYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGF-HPDIFTYATLLMGFRHAKDLQSLLE  114 (246)
Q Consensus        36 a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~-~p~~~~~~~ll~~~~~~~~~~~a~~  114 (246)
                      |+..|++....-.++..++..+..++...|++++|++++.+.+..       +- .-+...+..++..+.+.|+.+.|.+
T Consensus        85 a~~~l~~l~~~~~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~-------~~~~~~lea~~l~vqi~L~~~r~d~A~k  157 (310)
T 3mv2_B           85 NIEELENLLKDKQNSPYELYLLATAQAILGDLDKSLETCVEGIDN-------DEAEGTTELLLLAIEVALLNNNVSTAST  157 (310)
T ss_dssp             CCHHHHHTTTTSCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTS-------SCSTTHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhcc-------CCCcCcHHHHHHHHHHHHHCCCHHHHHH
Confidence            566666654322566677778889999999999999999998765       22 2367788899999999999999999


Q ss_pred             HHHHHHhCCCCCC-----CHHHHHHHHHH--HHhcC--ChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHh
Q 043380          115 IVFEMKSCCNLIL-----DRSTFTAMVDA--LLYSG--SIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAA  185 (246)
Q Consensus       115 ~~~~m~~~~~~~p-----~~~~~~~li~~--~~~~~--~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~  185 (246)
                      .++.|.+   ..|     +..+...+..+  ....|  +...    |..+|+++.+.       .|+..+-..++.++.+
T Consensus       158 ~l~~~~~---~~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~----A~~~f~El~~~-------~p~~~~~~lLln~~~~  223 (310)
T 3mv2_B          158 IFDNYTN---AIEDTVSGDNEMILNLAESYIKFATNKETATS----NFYYYEELSQT-------FPTWKTQLGLLNLHLQ  223 (310)
T ss_dssp             HHHHHHH---HSCHHHHHHHHHHHHHHHHHHHHHHTCSTTTH----HHHHHHHHHTT-------SCSHHHHHHHHHHHHH
T ss_pred             HHHHHHh---cCccccccchHHHHHHHHHHHHHHhCCccHHH----HHHHHHHHHHh-------CCCcccHHHHHHHHHH
Confidence            9999988   567     35555556655  33334  8999    99999998765       4553344455558999


Q ss_pred             cCChhHHhhHHHhhCCCCCCC------CCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          186 RVDYDIVKSPYRRMWPDSTGT------ISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       186 ~g~~~~a~~~~~~~~~~~~~~------~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      .|++++|++.++.+....+..      -+.+..  +...+|......|+  +|.++++++++..+
T Consensus       224 ~g~~~eAe~~L~~l~~~~p~~~~k~~~~p~~~~--~LaN~i~l~~~lgk--~a~~l~~qL~~~~P  284 (310)
T 3mv2_B          224 QRNIAEAQGIVELLLSDYYSVEQKENAVLYKPT--FLANQITLALMQGL--DTEDLTNQLVKLDH  284 (310)
T ss_dssp             HTCHHHHHHHHHHHHSHHHHTTTCHHHHSSHHH--HHHHHHHHHHHTTC--TTHHHHHHHHHTTC
T ss_pred             cCCHHHHHHHHHHHHHhcccccccccCCCCCHH--HHHHHHHHHHHhCh--HHHHHHHHHHHhCC
Confidence            999999999999765431000      022222  55455555555676  88999998887543

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=99.14  E-value=2.3e-09  Score=80.51  Aligned_cols=172  Identities=13%  Similarity=0.041  Sum_probs=124.2

Q ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc-cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCH
Q 043380           51 SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP-DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDR  129 (246)
Q Consensus        51 ~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~  129 (246)
                      ...+..+...+.+.|++++|...|+++.+..      .-.| ....+..+..+|.+.|++++|...|++..+   ..|+.
T Consensus         4 ~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~------p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~---~~P~~   74 (225)
T 2yhc_A            4 PNEIYATAQQKLQDGNWRQAITQLEALDNRY------PFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIR---LNPTH   74 (225)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC------TTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC------CCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH---HCcCC
Confidence            3455566677888899999999999988751      0011 235777888889999999999999999887   33432


Q ss_pred             ----HHHHHHHHHHHh------------------cCChhhhhhHHHHHHHHHHHhhcCCCCCCcch-hhH----------
Q 043380          130 ----STFTAMVDALLY------------------SGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP-HLY----------  176 (246)
Q Consensus       130 ----~~~~~li~~~~~------------------~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~-~~~----------  176 (246)
                          ..+..+..++..                  .|++++    |...|+.+.+.       -|+. .++          
T Consensus        75 ~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----A~~~~~~~l~~-------~P~~~~a~~a~~~l~~~~  143 (225)
T 2yhc_A           75 PNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQQARA----AFSDFSKLVRG-------YPNSQYTTDATKRLVFLK  143 (225)
T ss_dssp             TTHHHHHHHHHHHHHHHHC--------------CCHHHHH----HHHHHHHHHTT-------CTTCTTHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHhhhhhhhhhhhccchhhcCcHHHHH----HHHHHHHHHHH-------CcCChhHHHHHHHHHHHH
Confidence                234444444443                  578899    99999999886       2333 222          


Q ss_pred             -------HHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhccC
Q 043380          177 -------VSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWKG  245 (246)
Q Consensus       177 -------~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~  245 (246)
                             ..+...|...|++++|...|+.+....+..  + ....++..+..+|.+.|++++|.+.++.+...++.
T Consensus       144 ~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~--~-~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~~~  216 (225)
T 2yhc_A          144 DRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDT--Q-ATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSN  216 (225)
T ss_dssp             HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTS--H-HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCCSC
T ss_pred             HHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHCcCC--C-ccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCC
Confidence                   245567889999999999999987654332  1 11226888999999999999999999999887653

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=99.12  E-value=5.2e-09  Score=81.66  Aligned_cols=175  Identities=10%  Similarity=-0.036  Sum_probs=139.9

Q ss_pred             hHHHHhcccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCC
Q 043380            5 NEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKC   84 (246)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~   84 (246)
                      +........+.+...+..+...+.+.|++++|...|++....-+-+...+..+...+...|++++|...+++....    
T Consensus       105 l~~~l~~~lp~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~----  180 (287)
T 3qou_A          105 IRALLDXVLPREEELXAQQAMQLMQESNYTDALPLLXDAWQLSNQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQ----  180 (287)
T ss_dssp             HHHHHHHHSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGG----
T ss_pred             HHHHHHHHcCCchhhHHHHHHHHHhCCCHHHHHHHHHHHHHhCCcchhHHHHHHHHHHHCCCHHHHHHHHHhCchh----
Confidence            3444444456667778888889999999999999999986444667888999999999999999999999998875    


Q ss_pred             CCCCCCccHHHHHH-HHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           85 SSGGFHPDIFTYAT-LLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        85 ~~~~~~p~~~~~~~-ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                           .|+...... ....+...++.++|...+++...   ..|+ ...+..+...+...|++++    |...|.+..+.
T Consensus       181 -----~p~~~~~~~~~~~~l~~~~~~~~a~~~l~~al~---~~P~~~~~~~~la~~l~~~g~~~~----A~~~l~~~l~~  248 (287)
T 3qou_A          181 -----DQDTRYQGLVAQIELLXQAADTPEIQQLQQQVA---ENPEDAALATQLALQLHQVGRNEE----ALELLFGHLRX  248 (287)
T ss_dssp             -----GCSHHHHHHHHHHHHHHHHTSCHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH
T ss_pred             -----hcchHHHHHHHHHHHHhhcccCccHHHHHHHHh---cCCccHHHHHHHHHHHHHcccHHH----HHHHHHHHHhc
Confidence                 465543333 23336677888889999999888   4465 7889999999999999999    99999999987


Q ss_pred             hcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhh
Q 043380          163 VCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRM  199 (246)
Q Consensus       163 ~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~  199 (246)
                      .   | -..+...+..+...+...|+.++|...+++.
T Consensus       249 ~---p-~~~~~~a~~~l~~~~~~~g~~~~a~~~~r~a  281 (287)
T 3qou_A          249 D---L-TAADGQTRXTFQEILAALGTGDALASXYRRQ  281 (287)
T ss_dssp             C---T-TGGGGHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             c---c-ccccchHHHHHHHHHHHcCCCCcHHHHHHHH
Confidence            1   1 1123678999999999999999999888764

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=99.12  E-value=5.6e-09  Score=78.38  Aligned_cols=173  Identities=9%  Similarity=0.008  Sum_probs=128.9

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC---HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPD---SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~---~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      ++..+..+...+.+.|++++|...|+.+....+.+   ...+..+..+|.+.|++++|...|+++.+.         .|+
T Consensus         3 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~---------~P~   73 (225)
T 2yhc_A            3 PPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRL---------NPT   73 (225)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---------CTT
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH---------CcC
Confidence            45566677888999999999999999986422222   356788889999999999999999999986         333


Q ss_pred             H----HHHHHHHHHHH------------------ccCCHHHHHHHHHHHHhCCCCCCCH-HHH-----------------
Q 043380           93 I----FTYATLLMGFR------------------HAKDLQSLLEIVFEMKSCCNLILDR-STF-----------------  132 (246)
Q Consensus        93 ~----~~~~~ll~~~~------------------~~~~~~~a~~~~~~m~~~~~~~p~~-~~~-----------------  132 (246)
                      .    ..+..+..++.                  ..|++++|...|+++.+   ..|+. ..+                 
T Consensus        74 ~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~---~~P~~~~a~~a~~~l~~~~~~~~~~~  150 (225)
T 2yhc_A           74 HPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVR---GYPNSQYTTDATKRLVFLKDRLAKYE  150 (225)
T ss_dssp             CTTHHHHHHHHHHHHHHHHC--------------CCHHHHHHHHHHHHHHT---TCTTCTTHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHH---HCcCChhHHHHHHHHHHHHHHHHHHH
Confidence            2    23444444443                  36789999999999988   34552 222                 


Q ss_pred             HHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCC
Q 043380          133 TAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTI  207 (246)
Q Consensus       133 ~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  207 (246)
                      ..+...|.+.|+++.    |...|+.+.+..   |+-......+..+..+|.+.|+.++|.+.++.+....+...
T Consensus       151 ~~~a~~~~~~~~~~~----A~~~~~~~l~~~---p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~~~~~  218 (225)
T 2yhc_A          151 YSVAEYYTERGAWVA----VVNRVEGMLRDY---PDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNTL  218 (225)
T ss_dssp             HHHHHHHHHHTCHHH----HHHHHHHHHHHS---TTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCCSCCC
T ss_pred             HHHHHHHHHcCcHHH----HHHHHHHHHHHC---cCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCCch
Confidence            245667889999999    999999999871   11111236788999999999999999999999876654433

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.12  E-value=1.4e-08  Score=85.95  Aligned_cols=199  Identities=8%  Similarity=-0.031  Sum_probs=150.5

Q ss_pred             HHHHHHHHHHHhc----CCH----HHHHHHHHHHHhCCCCCHHHHHHHHHHHHh-------cCCcc-------hHHHHHH
Q 043380           18 IVMNAVIEASREA----QRI----DEAYQILESVEKGLEPDSLSYNILISACIK-------TKKLD-------VTMPFNE   75 (246)
Q Consensus        18 ~~~~~li~~~~~~----g~~----~~a~~~~~~~~~~~~~~~~t~~~li~~~~~-------~~~~~-------~a~~~~~   75 (246)
                      ..|...+...-..    ++.    ++|..+|++.....+.+...|..+...+.+       .|+++       +|..+|+
T Consensus       231 ~~w~~~~~~e~~~~~~~~~~~~~~~~a~~~y~~al~~~p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~  310 (530)
T 2ooe_A          231 DMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLVLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYE  310 (530)
T ss_dssp             HHHHHHHHHHHHCSSCCSCSHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCccCCcchhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHH
Confidence            5666666443332    222    477888988764446678889888888876       68887       8999999


Q ss_pred             HHHhccCCCCCCCCCc-cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-H-HHHHHHHHHHHhcCChhhhhhHH
Q 043380           76 QLKDNGQKCSSGGFHP-DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-R-STFTAMVDALLYSGSIKVVGLYA  152 (246)
Q Consensus        76 ~m~~~~~~~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~-~~~~~li~~~~~~~~~~~~~~~a  152 (246)
                      +..+.        +.| +...|..+...+.+.|++++|..+|+...+   +.|+ . ..|..++..+.+.|++++    |
T Consensus       311 ~Al~~--------~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~~~~~~~~~~~~~~~~----A  375 (530)
T 2ooe_A          311 RAIST--------LLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLA---IEDIDPTLVYIQYMKFARRAEGIKS----G  375 (530)
T ss_dssp             HHTTT--------TCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---SSSSCHHHHHHHHHHHHHHHHHHHH----H
T ss_pred             HHHHH--------hCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhC---ccccCchHHHHHHHHHHHHhcCHHH----H
Confidence            99862        244 578999999999999999999999999998   5565 3 579999999999999999    9


Q ss_pred             HHHHHHHHHhhcCCCCCCcchhhHHHHHHH-HHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhH
Q 043380          153 LCIFGEIVKRVCSNPGLWPKPHLYVSMMHE-LAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDL  231 (246)
Q Consensus       153 ~~~~~~m~~~~~~~~~~~p~~~~~~~li~~-~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~  231 (246)
                      ..+|+...+.      ...+...|...... +...|+.++|..+|+...+..+    ...  ..|..++..+.+.|+.++
T Consensus       376 ~~~~~~Al~~------~~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~~p----~~~--~~~~~~~~~~~~~g~~~~  443 (530)
T 2ooe_A          376 RMIFKKARED------ARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYG----DIP--EYVLAYIDYLSHLNEDNN  443 (530)
T ss_dssp             HHHHHHHHTC------TTCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHT----TCH--HHHHHHHHHHTTTTCHHH
T ss_pred             HHHHHHHHhc------cCCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHHCC----CCH--HHHHHHHHHHHhCCCHhh
Confidence            9999998875      11223333332222 3468999999999998765432    112  278999999999999999


Q ss_pred             HHHHHHHHHhhc
Q 043380          232 ALDKLSNTITRW  243 (246)
Q Consensus       232 a~~~~~~m~~~g  243 (246)
                      |..+|++.....
T Consensus       444 Ar~~~~~al~~~  455 (530)
T 2ooe_A          444 TRVLFERVLTSG  455 (530)
T ss_dssp             HHHHHHHHHHSC
T ss_pred             HHHHHHHHHhcc
Confidence            999999987753

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=99.10  E-value=1.9e-08  Score=78.61  Aligned_cols=169  Identities=9%  Similarity=-0.007  Sum_probs=128.6

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH-hCC-CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVE-KGL-EPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP   91 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~-~~~-~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p   91 (246)
                      .++..++..+..++...|++++|++++.+.. .+- .-+...+..++..+.+.|+.+.|.+.+++|.+.         .|
T Consensus        97 ~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~~~---------~~  167 (310)
T 3mv2_B           97 QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYTNA---------IE  167 (310)
T ss_dssp             CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---------SC
T ss_pred             CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc---------Cc
Confidence            4666666788899999999999999998864 321 246778889999999999999999999999875         67


Q ss_pred             -----cHHHHHHHHHHH--HccC--CHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           92 -----DIFTYATLLMGF--RHAK--DLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        92 -----~~~~~~~ll~~~--~~~~--~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                           +..+...|..++  ...|  +..+|..+|+++..   -.|+..+-..++.++...|++++    |.+.++.+.+.
T Consensus       168 d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~---~~p~~~~~~lLln~~~~~g~~~e----Ae~~L~~l~~~  240 (310)
T 3mv2_B          168 DTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQ---TFPTWKTQLGLLNLHLQQRNIAE----AQGIVELLLSD  240 (310)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHT---TSCSHHHHHHHHHHHHHHTCHHH----HHHHHHHHHSH
T ss_pred             cccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHH---hCCCcccHHHHHHHHHHcCCHHH----HHHHHHHHHHh
Confidence                 356666777663  3334  89999999999977   34663344445558999999999    99999977653


Q ss_pred             hcCCCCC-------CcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCC
Q 043380          163 VCSNPGL-------WPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDS  203 (246)
Q Consensus       163 ~~~~~~~-------~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  203 (246)
                      .   |.+       .-|+.++..+|......|+  +|.++++++....
T Consensus       241 ~---p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~~~  283 (310)
T 3mv2_B          241 Y---YSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVKLD  283 (310)
T ss_dssp             H---HHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHHTT
T ss_pred             c---ccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHHhC
Confidence            1   011       3356777677777777787  8899999998654

>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=99.09  E-value=4.9e-09  Score=75.56  Aligned_cols=163  Identities=10%  Similarity=0.010  Sum_probs=115.8

Q ss_pred             HHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHH
Q 043380           53 SYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTF  132 (246)
Q Consensus        53 t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~  132 (246)
                      .+..+...+...|++++|...|++..+.        -+-+...+..+...+...|++++|...|+....   ..|+...+
T Consensus         8 ~~~~~a~~~~~~g~~~~A~~~~~~al~~--------~P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~---~~p~~~~~   76 (176)
T 2r5s_A            8 QLLKQVSELLQQGEHAQALNVIQTLSDE--------LQSRGDVKLAKADCLLETKQFELAQELLATIPL---EYQDNSYK   76 (176)
T ss_dssp             THHHHHHHHHHTTCHHHHHHHHHTSCHH--------HHTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCG---GGCCHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH--------CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhh---ccCChHHH
Confidence            3455566778888999999999888765        133566788888888899999999999888776   33444333


Q ss_pred             HHHHHH-HHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc-chhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCch
Q 043380          133 TAMVDA-LLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP-KPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPE  210 (246)
Q Consensus       133 ~~li~~-~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  210 (246)
                      ..+... +...+....    |...++...+.       .| +...+..+..++...|++++|...|+++....+....+.
T Consensus        77 ~~~~~~~~~~~~~~~~----a~~~~~~al~~-------~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~  145 (176)
T 2r5s_A           77 SLIAKLELHQQAAESP----ELKRLEQELAA-------NPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGE  145 (176)
T ss_dssp             HHHHHHHHHHHHTSCH----HHHHHHHHHHH-------STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTH
T ss_pred             HHHHHHHHHhhcccch----HHHHHHHHHHh-------CCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHH
Confidence            222211 222233455    78888887775       34 467888888889999999999999998876543322222


Q ss_pred             hhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          211 VQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       211 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                          .+..+...+...|+.++|...|++...
T Consensus       146 ----a~~~l~~~~~~~g~~~~A~~~y~~al~  172 (176)
T 2r5s_A          146 ----VKKTFMDILSALGQGNAIASKYRRQLY  172 (176)
T ss_dssp             ----HHHHHHHHHHHHCSSCHHHHHHHHHHH
T ss_pred             ----HHHHHHHHHHHhCCCCcHHHHHHHHHH
Confidence                577888889999999999998887654

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.08  E-value=3e-09  Score=86.22  Aligned_cols=209  Identities=9%  Similarity=-0.054  Sum_probs=149.9

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHh---CCCC---CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCC-CCccHHH
Q 043380           23 VIEASREAQRIDEAYQILESVEK---GLEP---DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGG-FHPDIFT   95 (246)
Q Consensus        23 li~~~~~~g~~~~a~~~~~~~~~---~~~~---~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~-~~p~~~~   95 (246)
                      ....+...|++++|...|++...   ..+.   ...++..+...|...|++++|...+.+..+.-.+.  .+ ......+
T Consensus       109 ~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~--~~~~~~~~~~  186 (383)
T 3ulq_A          109 RGMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEH--EAYNIRLLQC  186 (383)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTC--STTHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhC--ccchHHHHHH
Confidence            44567788999999999988753   1221   34678889999999999999999999987641000  01 1122458


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhC---CCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCC-C
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSC---CNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGL-W  170 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~---~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~-~  170 (246)
                      ++.+-..|...|++++|...|++..+.   .+-.+. ..++..+...|...|++++    |.+.+++..+..... +. .
T Consensus       187 ~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~----A~~~~~~al~~~~~~-~~~~  261 (383)
T 3ulq_A          187 HSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYED----AIPYFKRAIAVFEES-NILP  261 (383)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHHHHHT-TCGG
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHH----HHHHHHHHHHHHHhh-ccch
Confidence            889999999999999999999987651   111111 3478899999999999999    999999987731100 12 2


Q ss_pred             cchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCC---hhHHHHHHHHH
Q 043380          171 PKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQ---VDLALDKLSNT  239 (246)
Q Consensus       171 p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~---~~~a~~~~~~m  239 (246)
                      ....++..+..+|...|++++|...+++........-.+.. ...+..+...|...|+   +++|..++++.
T Consensus       262 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~~al~~~~~~  332 (383)
T 3ulq_A          262 SLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIY-LSEFEFLKSLYLSGPDEEAIQGFFDFLESK  332 (383)
T ss_dssp             GHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHH-HHHHHHHHHHHTSSCCHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHH-HHHHHHHHHHHhCCCcHHHHHHHHHHHHHC
Confidence            33578899999999999999999999986632111111221 1236678888888998   78888887765

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=99.08  E-value=8.4e-09  Score=76.49  Aligned_cols=164  Identities=10%  Similarity=-0.038  Sum_probs=121.3

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHH----------------HHHHHHhcCCcchHHHHHHHHHhcc
Q 043380           18 IVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNI----------------LISACIKTKKLDVTMPFNEQLKDNG   81 (246)
Q Consensus        18 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~----------------li~~~~~~~~~~~a~~~~~~m~~~~   81 (246)
                      ..+-.....+.+.|++++|...|+......+-+...|..                +..+|.+.|++++|...|++..+. 
T Consensus         5 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~-   83 (208)
T 3urz_A            5 DEMLQKVSAAIEAGQNGQAVSYFRQTIALNIDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQK-   83 (208)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH-
Confidence            334445567788999999999999876422334556666                888999999999999999999986 


Q ss_pred             CCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCCh--hhhhhHHHHHHHH
Q 043380           82 QKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSI--KVVGLYALCIFGE  158 (246)
Q Consensus        82 ~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~--~~~~~~a~~~~~~  158 (246)
                             -+-+...|..+-.+|...|++++|...|++..+   +.|+ ..++..+...|...|+.  ..    +...++.
T Consensus        84 -------~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~---~~P~~~~a~~~lg~~~~~~~~~~~~~----~~~~~~~  149 (208)
T 3urz_A           84 -------APNNVDCLEACAEMQVCRGQEKDALRMYEKILQ---LEADNLAANIFLGNYYYLTAEQEKKK----LETDYKK  149 (208)
T ss_dssp             -------CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHHHHHHHH----HHHHHC-
T ss_pred             -------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---cCCCCHHHHHHHHHHHHHHhHHHHHH----HHHHHHH
Confidence                   233577899999999999999999999999988   5576 77888888887666543  33    4555544


Q ss_pred             HHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCC
Q 043380          159 IVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDS  203 (246)
Q Consensus       159 m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  203 (246)
                      ...       ..|....+...-.++...|++++|...|++.....
T Consensus       150 ~~~-------~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~l~  187 (208)
T 3urz_A          150 LSS-------PTKMQYARYRDGLSKLFTTRYEKARNSLQKVILRF  187 (208)
T ss_dssp             --C-------CCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTTTS
T ss_pred             HhC-------CCchhHHHHHHHHHHHHccCHHHHHHHHHHHHHhC
Confidence            422       23434445556666777899999999999987654

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.06  E-value=4e-08  Score=79.49  Aligned_cols=212  Identities=10%  Similarity=-0.001  Sum_probs=155.3

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHH---hCCC---C-CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCC
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVE---KGLE---P-DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGG   88 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~---~~~~---~-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~   88 (246)
                      ...++..+..+|...|+++.|...+++..   ....   + ...+++.+...|...|++++|.+.|.+..+...+   .+
T Consensus       140 ~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~---~~  216 (378)
T 3q15_A          140 KAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMD---IQ  216 (378)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH---TT
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH---cC
Confidence            35678888999999999999999998753   1111   1 2557888999999999999999999998764100   01


Q ss_pred             CC-ccHHHHHHHHHHHHccCCHHHHHHHHHHHHhC---CCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhc
Q 043380           89 FH-PDIFTYATLLMGFRHAKDLQSLLEIVFEMKSC---CNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVC  164 (246)
Q Consensus        89 ~~-p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~---~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~  164 (246)
                      -. ....+++.+-.+|...|++++|...|++....   .+.+....++..+...|.+.|++++    |...+++..+...
T Consensus       217 ~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~----A~~~~~~al~~~~  292 (378)
T 3q15_A          217 NDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQK----AFQFIEEGLDHIT  292 (378)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHHCC
T ss_pred             CHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHHHHHHHCCCHHH----HHHHHHHHHHHHH
Confidence            11 12457888999999999999999999987651   1222236778899999999999999    9999999888621


Q ss_pred             CCCCCCcchhhHHHHHHHHHhcCC---hhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          165 SNPGLWPKPHLYVSMMHELAARVD---YDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       165 ~~~~~~p~~~~~~~li~~~~~~g~---~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      .. +-......+..+-..+...++   +.+|..+++...      ..+.. ...+..+...|...|++++|.+.|+...+
T Consensus       293 ~~-~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~~------~~~~~-~~~~~~la~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          293 AR-SHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKKN------LHAYI-EACARSAAAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             TT-CCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHTT------CHHHH-HHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             Hc-CCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhCC------ChhHH-HHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            10 111223456666677777888   788888888742      12222 22677899999999999999999998865


Q ss_pred             h
Q 043380          242 R  242 (246)
Q Consensus       242 ~  242 (246)
                      -
T Consensus       365 ~  365 (378)
T 3q15_A          365 A  365 (378)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=99.06  E-value=5.6e-09  Score=89.18  Aligned_cols=132  Identities=7%  Similarity=-0.094  Sum_probs=80.5

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      +...|..+...+.+.|++++|.+.|++..+-.+.+...+..+..+|...|++++|.+.|++..+.        -+.+...
T Consensus        22 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--------~p~~~~~   93 (568)
T 2vsy_A           22 DFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRVRWTQQRHAEAAVLLQQASDA--------APEHPGI   93 (568)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--------CCCCHHH
Confidence            35566666666666666666666666655333445566666666666666666666666666654        1223456


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhc---CChhhhhhHHHHHHHHHHHh
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYS---GSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~---~~~~~~~~~a~~~~~~m~~~  162 (246)
                      +..+..+|...|++++|.+.|++..+   ..|+ ...+..+...+...   |+.++    |.+.+++..+.
T Consensus        94 ~~~la~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~~l~~~~~~~~~~g~~~~----A~~~~~~al~~  157 (568)
T 2vsy_A           94 ALWLGHALEDAGQAEAAAAAYTRAHQ---LLPEEPYITAQLLNWRRRLCDWRALDV----LSAQVRAAVAQ  157 (568)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCCTTHHH----HHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHhhccccHHH----HHHHHHHHHhc
Confidence            66666666666666666666666655   2333 55566666666666   66666    66666666554

>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=99.04  E-value=2.6e-08  Score=78.43  Aligned_cols=206  Identities=10%  Similarity=0.026  Sum_probs=144.8

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHh---CC-CC--CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCC-
Q 043380           18 IVMNAVIEASREAQRIDEAYQILESVEK---GL-EP--DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFH-   90 (246)
Q Consensus        18 ~~~~~li~~~~~~g~~~~a~~~~~~~~~---~~-~~--~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~-   90 (246)
                      ..|+.....|...|++++|.+.|.+...   .. .+  -..+|+.+...|...|++++|...|++..+....   .|-. 
T Consensus        37 ~~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~---~g~~~  113 (307)
T 2ifu_A           37 SEYAKAAVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVE---NGTPD  113 (307)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHT---TTCHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHH---cCCHH
Confidence            3688888889999999999999987531   11 11  1457888999999999999999999988754100   0111 


Q ss_pred             ccHHHHHHHHHHHHccCCHHHHHHHHHHHHhC---CCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCC
Q 043380           91 PDIFTYATLLMGFRHAKDLQSLLEIVFEMKSC---CNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSN  166 (246)
Q Consensus        91 p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~---~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~  166 (246)
                      .-..+++.+-..|.. |++++|...|++....   .+-.+. ..+++.+...|...|++++    |...|++........
T Consensus       114 ~~a~~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~----A~~~~~~al~~~~~~  188 (307)
T 2ifu_A          114 TAAMALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDE----AAASLQKEKSMYKEM  188 (307)
T ss_dssp             HHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHHHHHc
Confidence            124688889999988 9999999999987661   111111 4678889999999999999    999999987752111


Q ss_pred             CCCCcc-hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHH
Q 043380          167 PGLWPK-PHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDK  235 (246)
Q Consensus       167 ~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~  235 (246)
                       +..+. ..++..+..++...|++++|...|++.. ..+...... .......++.++ ..|+.+.+.++
T Consensus       189 -~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~al-~~p~~~~~~-e~~~l~~l~~~~-~~~d~~~~~~~  254 (307)
T 2ifu_A          189 -ENYPTCYKKCIAQVLVQLHRADYVAAQKCVRESY-SIPGFSGSE-DCAALEDLLQAY-DEQDEEQLLRV  254 (307)
T ss_dssp             -TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT-TSTTSTTSH-HHHHHHHHHHHH-HTTCHHHHHHH
T ss_pred             -CChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh-CCCCCCCCH-HHHHHHHHHHHH-HhcCHHHHHHH
Confidence             11122 2367777788888899999999999987 554433222 112345566666 56777666553

>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=99.03  E-value=7.1e-09  Score=88.53  Aligned_cols=155  Identities=10%  Similarity=-0.041  Sum_probs=113.9

Q ss_pred             cCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhc
Q 043380           64 TKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYS  142 (246)
Q Consensus        64 ~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~  142 (246)
                      .|++++|.+.|++..+.        -+-+...|..+...|...|++++|.+.|++..+   ..|+ ...+..+...|...
T Consensus         2 ~g~~~~A~~~~~~al~~--------~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~~lg~~~~~~   70 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRH--------RPQDFVAWLMLADAELGMGDTTAGEMAVQRGLA---LHPGHPEAVARLGRVRWTQ   70 (568)
T ss_dssp             ---------------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHT---TSTTCHHHHHHHHHHHHHT
T ss_pred             CccHHHHHHHHHHHHHh--------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHC
Confidence            46789999999998875        233577899999999999999999999999988   4565 78889999999999


Q ss_pred             CChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHH
Q 043380          143 GSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEA  222 (246)
Q Consensus       143 ~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~  222 (246)
                      |++++    |.+.+++..+.      -..+...+..+..+|...|++++|.+.+++.....+..    .  .++..+...
T Consensus        71 g~~~~----A~~~~~~al~~------~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~----~--~~~~~l~~~  134 (568)
T 2vsy_A           71 QRHAE----AAVLLQQASDA------APEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEE----P--YITAQLLNW  134 (568)
T ss_dssp             TCHHH----HHHHHHHHHHH------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTC----H--HHHHHHHHH
T ss_pred             CCHHH----HHHHHHHHHhc------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC----H--HHHHHHHHH
Confidence            99999    99999999886      23356788999999999999999999999987543221    1  268889999


Q ss_pred             HHhc---CChhHHHHHHHHHHhhccC
Q 043380          223 ALND---GQVDLALDKLSNTITRWKG  245 (246)
Q Consensus       223 ~~~~---g~~~~a~~~~~~m~~~g~~  245 (246)
                      +...   |+.++|.+.+++..+.++.
T Consensus       135 ~~~~~~~g~~~~A~~~~~~al~~~p~  160 (568)
T 2vsy_A          135 RRRLCDWRALDVLSAQVRAAVAQGVG  160 (568)
T ss_dssp             HHHTTCCTTHHHHHHHHHHHHHHTCC
T ss_pred             HHHhhccccHHHHHHHHHHHHhcCCc
Confidence            9999   9999999999998876653

>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=99.03  E-value=3.6e-09  Score=74.33  Aligned_cols=142  Identities=10%  Similarity=0.059  Sum_probs=111.2

Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHH
Q 043380           25 EASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFR  104 (246)
Q Consensus        25 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~  104 (246)
                      ..+...|++++|++.++......+-+...+-.+-..|.+.|++++|.+.|++..+.        -+-+..+|..+-.+|.
T Consensus         5 ~~~~~~~~~e~ai~~~~~a~~~~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~--------~p~~~~a~~~lg~~~~   76 (150)
T 4ga2_A            5 SMRRSKADVERYIASVQGSTPSPRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINV--------QERDPKAHRFLGLLYE   76 (150)
T ss_dssp             --CCCHHHHHHHHHHHHHHSCSHHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHH
T ss_pred             HHHHHcChHHHHHHHHHHhcccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--------CCCCHHHHHHHHHHHH
Confidence            34556788999999998875322334556777889999999999999999999986        2336789999999999


Q ss_pred             ccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHH-HHHHHhhcCCCCCCc-chhhHHHHHH
Q 043380          105 HAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIF-GEIVKRVCSNPGLWP-KPHLYVSMMH  181 (246)
Q Consensus       105 ~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~-~~m~~~~~~~~~~~p-~~~~~~~li~  181 (246)
                      ..|++++|...|+...+   +.|+ ..+|..+...|...|++++    |.+.| +...+.       .| ++.+|.....
T Consensus        77 ~~~~~~~A~~~~~~al~---~~p~~~~~~~~la~~~~~~~~~~~----aa~~~~~~al~l-------~P~~~~~~~l~~~  142 (150)
T 4ga2_A           77 LEENTDKAVECYRRSVE---LNPTQKDLVLKIAELLCKNDVTDG----RAKYWVERAAKL-------FPGSPAVYKLKEQ  142 (150)
T ss_dssp             HTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHCSSSS----HHHHHHHHHHHH-------STTCHHHHHHHHH
T ss_pred             HcCchHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcCChHH----HHHHHHHHHHHh-------CcCCHHHHHHHHH
Confidence            99999999999999988   5676 7889999999999999988    77664 777665       34 4466766666


Q ss_pred             HHHhcCC
Q 043380          182 ELAARVD  188 (246)
Q Consensus       182 ~~~~~g~  188 (246)
                      .+...|+
T Consensus       143 ll~~~G~  149 (150)
T 4ga2_A          143 LLDCEGE  149 (150)
T ss_dssp             HHHTCCC
T ss_pred             HHHHhCc
Confidence            6666654

>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=99.02  E-value=3.2e-09  Score=81.56  Aligned_cols=176  Identities=13%  Similarity=0.019  Sum_probs=127.6

Q ss_pred             HhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCC-----CCCCC-HHHHHHH
Q 043380           62 IKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCC-----NLILD-RSTFTAM  135 (246)
Q Consensus        62 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~-----~~~p~-~~~~~~l  135 (246)
                      ...|++++|..+|++..+.-.+......+....++..+...|...|++++|...+++..+..     +-.|. ..++..+
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            45678888888888877631100001223346689999999999999999999999987621     22333 6678999


Q ss_pred             HHHHHhcCChhhhhhHHHHHHHHHHHhhcCC--CCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCC---CCCCCch
Q 043380          136 VDALLYSGSIKVVGLYALCIFGEIVKRVCSN--PGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDS---TGTISPE  210 (246)
Q Consensus       136 i~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~--~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~---~~~~~~~  210 (246)
                      ...|...|++++    |...|++........  +.-.....++..+...|...|++++|..++++.....   .+...|.
T Consensus        92 ~~~~~~~g~~~~----A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  167 (283)
T 3edt_B           92 AVLYGKRGKYKE----AEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPN  167 (283)
T ss_dssp             HHHHHTTTCHHH----HHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHH
T ss_pred             HHHHHHhccHHH----HHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHH
Confidence            999999999999    999999987651100  0112345788999999999999999999999876430   0111222


Q ss_pred             hhhHHHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          211 VQEEAGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       211 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                       ...++..+...|...|++++|.+++++..+.
T Consensus       168 -~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~  198 (283)
T 3edt_B          168 -VAKTKNNLASCYLKQGKYQDAETLYKEILTR  198 (283)
T ss_dssp             -HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             -HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence             2237888999999999999999999988764

>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=99.02  E-value=8.1e-09  Score=90.16  Aligned_cols=183  Identities=8%  Similarity=-0.081  Sum_probs=142.5

Q ss_pred             HhcCCHHHHHHHHHHHH--------hCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHH
Q 043380           28 REAQRIDEAYQILESVE--------KGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATL   99 (246)
Q Consensus        28 ~~~g~~~~a~~~~~~~~--------~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~l   99 (246)
                      ...|++++|++.|++..        ...+.+...+..+..++...|++++|.+.|++..+.        -+-+...|..+
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~--------~p~~~~a~~~l  473 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAER--------VGWRWRLVWYR  473 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--------HCCCHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhcc--------CcchHHHHHHH
Confidence            67899999999999876        444556788999999999999999999999999986        23467789999


Q ss_pred             HHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHH
Q 043380          100 LMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVS  178 (246)
Q Consensus       100 l~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~  178 (246)
                      -.+|...|++++|...|++..+   +.|+ ...|..+...|...|++++     ...|++..+.      -.-+...|..
T Consensus       474 g~~~~~~g~~~~A~~~~~~al~---l~P~~~~~~~~lg~~~~~~g~~~~-----~~~~~~al~~------~P~~~~a~~~  539 (681)
T 2pzi_A          474 AVAELLTGDYDSATKHFTEVLD---TFPGELAPKLALAATAELAGNTDE-----HKFYQTVWST------NDGVISAAFG  539 (681)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHH---HSTTCSHHHHHHHHHHHHHTCCCT-----TCHHHHHHHH------CTTCHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHH---hCCCChHHHHHHHHHHHHcCChHH-----HHHHHHHHHh------CCchHHHHHH
Confidence            9999999999999999999988   5565 7788899999999999876     4556666664      1235578999


Q ss_pred             HHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCC--------hhHHHHHHHH
Q 043380          179 MMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQ--------VDLALDKLSN  238 (246)
Q Consensus       179 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~--------~~~a~~~~~~  238 (246)
                      +..++...|++++|...|++....++.    ..  .+|..+..++...++        +++|.+.+..
T Consensus       540 lg~~~~~~g~~~~A~~~~~~al~l~P~----~~--~a~~~~~~~~~~~~~~~~~~~~~~~~A~~~l~~  601 (681)
T 2pzi_A          540 LARARSAEGDRVGAVRTLDEVPPTSRH----FT--TARLTSAVTLLSGRSTSEVTEEQIRDAARRVEA  601 (681)
T ss_dssp             HHHHHHHTTCHHHHHHHHHTSCTTSTT----HH--HHHHHHHHHTC-------CCHHHHHHHHHHHHT
T ss_pred             HHHHHHHcCCHHHHHHHHHhhcccCcc----cH--HHHHHHHHHHHccCCCCCCCHHHHHHHHHHHhh
Confidence            999999999999999999998765422    12  267777777766554        4555555543

>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=99.01  E-value=5.9e-09  Score=75.14  Aligned_cols=157  Identities=12%  Similarity=0.041  Sum_probs=123.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHH
Q 043380           20 MNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATL   99 (246)
Q Consensus        20 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~l   99 (246)
                      +..+...+.+.|++++|...|++..+.-+.+...+..+...+...|++++|...|++....         .|+...+..+
T Consensus         9 ~~~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~---------~p~~~~~~~~   79 (176)
T 2r5s_A            9 LLKQVSELLQQGEHAQALNVIQTLSDELQSRGDVKLAKADCLLETKQFELAQELLATIPLE---------YQDNSYKSLI   79 (176)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHTSCHHHHTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGG---------GCCHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhc---------cCChHHHHHH
Confidence            4456678889999999999999865333567888999999999999999999999998875         3444333322


Q ss_pred             HHH-HHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc---hh
Q 043380          100 LMG-FRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK---PH  174 (246)
Q Consensus       100 l~~-~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~---~~  174 (246)
                      ... +...++..+|...+++..+   ..|+ ...+..+...+...|++++    |...|+...+.       .|+   ..
T Consensus        80 ~~~~~~~~~~~~~a~~~~~~al~---~~P~~~~~~~~la~~~~~~g~~~~----A~~~~~~~l~~-------~p~~~~~~  145 (176)
T 2r5s_A           80 AKLELHQQAAESPELKRLEQELA---ANPDNFELACELAVQYNQVGRDEE----ALELLWNILKV-------NLGAQDGE  145 (176)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHH---HSTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHTT-------CTTTTTTH
T ss_pred             HHHHHHhhcccchHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcccHHH----HHHHHHHHHHh-------CcccChHH
Confidence            211 2222333457888888887   5565 7889999999999999999    99999998875       343   56


Q ss_pred             hHHHHHHHHHhcCChhHHhhHHHhh
Q 043380          175 LYVSMMHELAARVDYDIVKSPYRRM  199 (246)
Q Consensus       175 ~~~~li~~~~~~g~~~~a~~~~~~~  199 (246)
                      .+..+..++...|+.++|...|++.
T Consensus       146 a~~~l~~~~~~~g~~~~A~~~y~~a  170 (176)
T 2r5s_A          146 VKKTFMDILSALGQGNAIASKYRRQ  170 (176)
T ss_dssp             HHHHHHHHHHHHCSSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCcHHHHHHHH
Confidence            8899999999999999999998865

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.01  E-value=4.1e-07  Score=76.13  Aligned_cols=113  Identities=8%  Similarity=-0.045  Sum_probs=54.1

Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHh----cCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHH
Q 043380          106 AKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLY----SGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMH  181 (246)
Q Consensus       106 ~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~----~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~  181 (246)
                      .+++++|.+.|++..+ .|   +...+..+...|..    .++.++    |.+.|+...+.     +   +..++..+..
T Consensus       164 ~~d~~~A~~~~~~a~~-~~---~~~a~~~Lg~~y~~g~g~~~~~~~----A~~~~~~a~~~-----~---~~~a~~~lg~  227 (490)
T 2xm6_A          164 TRDYVMAREWYSKAAE-QG---NVWSCNQLGYMYSRGLGVERNDAI----SAQWYRKSATS-----G---DELGQLHLAD  227 (490)
T ss_dssp             CCCHHHHHHHHHHHHH-TT---CHHHHHHHHHHHHHTSSSCCCHHH----HHHHHHHHHHT-----T---CHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHH-CC---CHHHHHHHHHHHhcCCCCCcCHHH----HHHHHHHHHHC-----C---CHHHHHHHHH
Confidence            4445555555554444 22   34444444444444    455555    55555554443     1   2334444444


Q ss_pred             HHHh----cCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHh----cCChhHHHHHHHHHHhh
Q 043380          182 ELAA----RVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALN----DGQVDLALDKLSNTITR  242 (246)
Q Consensus       182 ~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~  242 (246)
                      .|..    .+++++|...|++....+    .+.    ++..|-..|..    .+++++|.++|+...+.
T Consensus       228 ~y~~g~g~~~~~~~A~~~~~~a~~~~----~~~----a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~  288 (490)
T 2xm6_A          228 MYYFGIGVTQDYTQSRVLFSQSAEQG----NSI----AQFRLGYILEQGLAGAKEPLKALEWYRKSAEQ  288 (490)
T ss_dssp             HHHHTSSSCCCHHHHHHHHHHHHTTT----CHH----HHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTT
T ss_pred             HHHcCCCCCCCHHHHHHHHHHHHHCC----CHH----HHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHc
Confidence            4443    455555555555544321    111    34445555555    56666666666655443

>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=99.01  E-value=4e-08  Score=76.68  Aligned_cols=175  Identities=10%  Similarity=-0.032  Sum_probs=127.7

Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHH----HHHHHHHHHHccCCHHHHHHHHHHHHhCCCC-CCC
Q 043380           54 YNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIF----TYATLLMGFRHAKDLQSLLEIVFEMKSCCNL-ILD  128 (246)
Q Consensus        54 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~----~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~-~p~  128 (246)
                      +...+..+...+++++|..++++..+..      ...|+..    .+..+...+...+++++|...|+.... ... .++
T Consensus        78 l~~~i~~~~~~~~y~~a~~~~~~~l~~~------~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~-~~~~~~~  150 (293)
T 3u3w_A           78 FKDQVIMLCKQKRYKEIYNKVWNELKKE------EYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLN-QQLTGID  150 (293)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTTC------CCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHH-TCCCCSC
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHhccc------cCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHH-Hhccccc
Confidence            3344777889999999999999998751      2334422    344577777888899999999999987 322 233


Q ss_pred             ----HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch-hhHHHHHHHHHhcCChhHHhhHHHhhCCCC
Q 043380          129 ----RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP-HLYVSMMHELAARVDYDIVKSPYRRMWPDS  203 (246)
Q Consensus       129 ----~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  203 (246)
                          ..+|+.+...|...|+++.    |...|++..+.....++..|.. .++..+...|...|++++|...+++.....
T Consensus       151 ~~~~~~~~~~lg~~y~~~g~~~~----A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~  226 (293)
T 3u3w_A          151 VYQNLYIENAIANIYAENGYLKK----GIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEIS  226 (293)
T ss_dssp             TTHHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence                3469999999999999999    9999999886422111222332 588999999999999999999999765211


Q ss_pred             --CCCCCchhhhHHHHHHHHHHHhcCC-hhHHHHHHHHHHh
Q 043380          204 --TGTISPEVQEEAGHLLMEAALNDGQ-VDLALDKLSNTIT  241 (246)
Q Consensus       204 --~~~~~~~~~~~~~~~li~~~~~~g~-~~~a~~~~~~m~~  241 (246)
                        .+.....  ..+|..+..+|.+.|+ +++|.+.+++...
T Consensus       227 ~~~~~~~~~--~~~~~~lg~~~~~~g~~~~~A~~~~~~Al~  265 (293)
T 3u3w_A          227 CRINSMALI--GQLYYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHTTBCTTH--HHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHcCcHHHH--HHHHHHHHHHHHHhCCcHHHHHHHHHHHHH
Confidence              1111111  2278899999999995 6999999987654

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.00  E-value=6.6e-07  Score=74.89  Aligned_cols=191  Identities=7%  Similarity=0.038  Sum_probs=104.3

Q ss_pred             HHHHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHh----cCCcchHHHHHHHHHhccCCCCCCC
Q 043380           17 TIVMNAVIEASRE----AQRIDEAYQILESVEKGLEPDSLSYNILISACIK----TKKLDVTMPFNEQLKDNGQKCSSGG   88 (246)
Q Consensus        17 ~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~~~~~~   88 (246)
                      +..+..|-..|..    .+++++|.+.|+....  .-+...+..+-..|..    .+++++|.++|++..+.        
T Consensus       111 ~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~--~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~--------  180 (490)
T 2xm6_A          111 PQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAE--QGRDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQ--------  180 (490)
T ss_dssp             HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHH--TTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT--------
T ss_pred             HHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHH--CCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHC--------
Confidence            3344444444444    4455555555544431  1233444444444444    44555555555555543        


Q ss_pred             CCccHHHHHHHHHHHHc----cCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHh----cCChhhhhhHHHHHHHHHH
Q 043380           89 FHPDIFTYATLLMGFRH----AKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLY----SGSIKVVGLYALCIFGEIV  160 (246)
Q Consensus        89 ~~p~~~~~~~ll~~~~~----~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~----~~~~~~~~~~a~~~~~~m~  160 (246)
                        -+...+..|-..|..    .++.++|...|+...+ .|   +...+..+...|..    .+++++    |...|+...
T Consensus       181 --~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~-~~---~~~a~~~lg~~y~~g~g~~~~~~~----A~~~~~~a~  250 (490)
T 2xm6_A          181 --GNVWSCNQLGYMYSRGLGVERNDAISAQWYRKSAT-SG---DELGQLHLADMYYFGIGVTQDYTQ----SRVLFSQSA  250 (490)
T ss_dssp             --TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHH-TT---CHHHHHHHHHHHHHTSSSCCCHHH----HHHHHHHHH
T ss_pred             --CCHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHH-CC---CHHHHHHHHHHHHcCCCCCCCHHH----HHHHHHHHH
Confidence              134455556666655    6667777777776666 32   34555556666655    566666    776666665


Q ss_pred             HhhcCCCCCCcchhhHHHHHHHHHh----cCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhc-----CChhH
Q 043380          161 KRVCSNPGLWPKPHLYVSMMHELAA----RVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALND-----GQVDL  231 (246)
Q Consensus       161 ~~~~~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~-----g~~~~  231 (246)
                      +.     +   +...+..+-..|..    .++.++|...|++....+    .+.    ++..|...|...     +++++
T Consensus       251 ~~-----~---~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~----~~~----a~~~Lg~~y~~~~~g~~~~~~~  314 (490)
T 2xm6_A          251 EQ-----G---NSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQG----NSD----GQYYLAHLYDKGAEGVAKNREQ  314 (490)
T ss_dssp             TT-----T---CHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTT----CHH----HHHHHHHHHHHCBTTBCCCHHH
T ss_pred             HC-----C---CHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcC----CHH----HHHHHHHHHHcCCCCCcCCHHH
Confidence            53     2   33455555555555    666777777776654331    111    455566666665     66777


Q ss_pred             HHHHHHHHHhhc
Q 043380          232 ALDKLSNTITRW  243 (246)
Q Consensus       232 a~~~~~~m~~~g  243 (246)
                      |.++|+...+.|
T Consensus       315 A~~~~~~a~~~~  326 (490)
T 2xm6_A          315 AISWYTKSAEQG  326 (490)
T ss_dssp             HHHHHHHHHHTT
T ss_pred             HHHHHHHHHhcC
Confidence            777776665543

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=99.00  E-value=4.1e-08  Score=72.77  Aligned_cols=163  Identities=13%  Similarity=0.090  Sum_probs=122.8

Q ss_pred             HHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-HHHHHH----------------HHHHHHccCCHHHHHHH
Q 043380           53 SYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-IFTYAT----------------LLMGFRHAKDLQSLLEI  115 (246)
Q Consensus        53 t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~~~----------------ll~~~~~~~~~~~a~~~  115 (246)
                      .+-.....+...|++++|...|++..+.         .|+ ...|..                +-.+|.+.|++++|...
T Consensus         6 ~~~~~g~~~~~~g~~~~A~~~~~~al~~---------~p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~   76 (208)
T 3urz_A            6 EMLQKVSAAIEAGQNGQAVSYFRQTIAL---------NIDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLF   76 (208)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH---------CHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHh---------CCCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHH
Confidence            3344455677899999999999999986         454 446666                88899999999999999


Q ss_pred             HHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCC--hhHH
Q 043380          116 VFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVD--YDIV  192 (246)
Q Consensus       116 ~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~--~~~a  192 (246)
                      |++..+   +.|+ ...+..+...|...|++++    |...|++..+.      -+-+..++..+..+|...|+  ...+
T Consensus        77 ~~~al~---~~p~~~~~~~~lg~~~~~~g~~~~----A~~~~~~al~~------~P~~~~a~~~lg~~~~~~~~~~~~~~  143 (208)
T 3urz_A           77 YKELLQ---KAPNNVDCLEACAEMQVCRGQEKD----ALRMYEKILQL------EADNLAANIFLGNYYYLTAEQEKKKL  143 (208)
T ss_dssp             HHHHHH---HCTTCHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHH------CTTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHH---HCCCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHc------CCCCHHHHHHHHHHHHHHhHHHHHHH
Confidence            999988   5565 7889999999999999999    99999999986      22345788888888776654  3455


Q ss_pred             hhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          193 KSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      ...+.....     .+|.  ...+..+-.++...|++++|...|++..+..+
T Consensus       144 ~~~~~~~~~-----~~~~--~~a~~~~g~~~~~~~~~~~A~~~~~~al~l~P  188 (208)
T 3urz_A          144 ETDYKKLSS-----PTKM--QYARYRDGLSKLFTTRYEKARNSLQKVILRFP  188 (208)
T ss_dssp             HHHHC---C-----CCHH--HHHHHHHHHHHHHHHTHHHHHHHHHHHTTTSC
T ss_pred             HHHHHHHhC-----CCch--hHHHHHHHHHHHHccCHHHHHHHHHHHHHhCC
Confidence            666665532     1221  22445556677778999999999998876543

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.98  E-value=2.8e-08  Score=77.64  Aligned_cols=188  Identities=11%  Similarity=0.005  Sum_probs=135.4

Q ss_pred             CHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-HHHHHHHHHHHHccCCHH
Q 043380           32 RIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-IFTYATLLMGFRHAKDLQ  110 (246)
Q Consensus        32 ~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~~~ll~~~~~~~~~~  110 (246)
                      ++++|.+.|++.              ...|...|++++|.+.|.+..+...+   .+-.++ ..+|+.+-.+|...|+++
T Consensus        32 ~~~~A~~~~~~a--------------~~~~~~~g~~~~A~~~~~~al~~~~~---~~~~~~~a~~~~~lg~~~~~~g~~~   94 (292)
T 1qqe_A           32 KFEEAADLCVQA--------------ATIYRLRKELNLAGDSFLKAADYQKK---AGNEDEAGNTYVEAYKCFKSGGNSV   94 (292)
T ss_dssp             HHHHHHHHHHHH--------------HHHHHHTTCTHHHHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             cHHHHHHHHHHH--------------HHHHHHcCCHHHHHHHHHHHHHHHHH---hCCHHHHHHHHHHHHHHHHHCCCHH
Confidence            477777777665              44677899999999999988764100   011222 568999999999999999


Q ss_pred             HHHHHHHHHHhC---CCCCCC-HHHHHHHHHHHHhc-CChhhhhhHHHHHHHHHHHhhcCCCCCCcc-hhhHHHHHHHHH
Q 043380          111 SLLEIVFEMKSC---CNLILD-RSTFTAMVDALLYS-GSIKVVGLYALCIFGEIVKRVCSNPGLWPK-PHLYVSMMHELA  184 (246)
Q Consensus       111 ~a~~~~~~m~~~---~~~~p~-~~~~~~li~~~~~~-~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~-~~~~~~li~~~~  184 (246)
                      +|...|++....   .|-.+. ..+++.+...|... |++++    |+..|++..+..... +-.+. ..++..+...+.
T Consensus        95 ~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~----A~~~~~~Al~~~~~~-~~~~~~~~~~~~lg~~~~  169 (292)
T 1qqe_A           95 NAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAK----AIDCYELAGEWYAQD-QSVALSNKCFIKCADLKA  169 (292)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHH----HHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHH----HHHHHHHHHHHHHhC-CChHHHHHHHHHHHHHHH
Confidence            999999987661   111111 45788999999996 99999    999999987752100 00011 357888999999


Q ss_pred             hcCChhHHhhHHHhhCCCCCCCCCch-hhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          185 ARVDYDIVKSPYRRMWPDSTGTISPE-VQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       185 ~~g~~~~a~~~~~~~~~~~~~~~~~~-~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      ..|++++|...|++.....+...... ....+|..+..++...|++++|.+.|++..+
T Consensus       170 ~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  227 (292)
T 1qqe_A          170 LDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQS  227 (292)
T ss_dssp             HTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGC
T ss_pred             HhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            99999999999999875443221110 1111567788889999999999999987654

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=98.97  E-value=5.5e-08  Score=78.30  Aligned_cols=214  Identities=10%  Similarity=-0.044  Sum_probs=146.2

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHh-----CCC--C-CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCC
Q 043380           18 IVMNAVIEASREAQRIDEAYQILESVEK-----GLE--P-DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGF   89 (246)
Q Consensus        18 ~~~~~li~~~~~~g~~~~a~~~~~~~~~-----~~~--~-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~   89 (246)
                      .+++.+...+...|++++|...+++...     +..  | ....+..+...+...|++++|...+++.....-..   +.
T Consensus        94 ~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~---~~  170 (373)
T 1hz4_A           94 WSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSY---QP  170 (373)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTS---CG
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcc---Cc
Confidence            3466778889999999999999987531     221  2 23456778888999999999999999988652110   11


Q ss_pred             CccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHH----HHHHHHHhcCChhhhhhHHHHHHHHHHHhhc
Q 043380           90 HPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFT----AMVDALLYSGSIKVVGLYALCIFGEIVKRVC  164 (246)
Q Consensus        90 ~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~----~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~  164 (246)
                      .....+|..+...+...|++++|...+++......-..+ .....    ..+..+...|++++    |...++...... 
T Consensus       171 ~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~----A~~~~~~a~~~~-  245 (373)
T 1hz4_A          171 QQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAA----AANWLRHTAKPE-  245 (373)
T ss_dssp             GGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHH----HHHHHHHSCCCC-
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHH----HHHHHHhCCCCC-
Confidence            113457888889999999999999999988651111111 11111    23345779999999    999998876531 


Q ss_pred             CCCCC-CcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          165 SNPGL-WPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       165 ~~~~~-~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                        ++. ......+..+...+...|++++|...++.........-.+.....++..+..++...|+.++|.+.+++...
T Consensus       246 --~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~  321 (373)
T 1hz4_A          246 --FANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  321 (373)
T ss_dssp             --CTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             --CCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence              110 111235677888999999999999999987532111011111112566778889999999999999988764

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=98.96  E-value=7.1e-09  Score=81.65  Aligned_cols=202  Identities=10%  Similarity=0.009  Sum_probs=140.0

Q ss_pred             cCCHHHHHHHHHHHHh-------CCCCCH----HHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCC-ccHHHHH
Q 043380           30 AQRIDEAYQILESVEK-------GLEPDS----LSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFH-PDIFTYA   97 (246)
Q Consensus        30 ~g~~~~a~~~~~~~~~-------~~~~~~----~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~-p~~~~~~   97 (246)
                      .|++++|.+++++..+       +..++.    ..|+.....|...|++++|...|.+..+...+.   +-. .-..+|+
T Consensus         4 ~~~~~eA~~~~~~a~k~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~---~~~~~~a~~~~   80 (307)
T 2ifu_A            4 AQKISEAHEHIAKAEKYLKTSFMKWKPDYDSAASEYAKAAVAFKNAKQLEQAKDAYLQEAEAHANN---RSLFHAAKAFE   80 (307)
T ss_dssp             HHHHHHHHHHHHHHHHHHCCCSSSCSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT---TCHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHccccccCCCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHc---CCHHHHHHHHH
Confidence            4667788888776532       112332    256777788889999999999999887641000   111 1245899


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHhC---CCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc-c
Q 043380           98 TLLMGFRHAKDLQSLLEIVFEMKSC---CNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP-K  172 (246)
Q Consensus        98 ~ll~~~~~~~~~~~a~~~~~~m~~~---~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p-~  172 (246)
                      .+...|...|++++|...|++..+.   .|-... ..+++.+...|.. |++++    |+..|++........ +-.+ .
T Consensus        81 ~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~----A~~~~~~Al~~~~~~-~~~~~~  154 (307)
T 2ifu_A           81 QAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSK----AVHLYQQAAAVFENE-ERLRQA  154 (307)
T ss_dssp             HHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHH----HHHHHHHHHHHHHHT-TCHHHH
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHH----HHHHHHHHHHHHHhC-CChhHH
Confidence            9999999999999999999976551   121111 4578888889988 99999    999999887652100 1111 1


Q ss_pred             hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHH
Q 043380          173 PHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTI  240 (246)
Q Consensus       173 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  240 (246)
                      ..++..+...|...|++++|...|++................++..+..++...|++++|.+.|++..
T Consensus       155 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~al  222 (307)
T 2ifu_A          155 AELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRESY  222 (307)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            46788899999999999999999998764211111111112256677778888899999999999875

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.93  E-value=6.6e-08  Score=64.50  Aligned_cols=114  Identities=11%  Similarity=0.008  Sum_probs=94.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHH
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTY   96 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~   96 (246)
                      ...|..+...+.+.|++++|.+.|+++.+..+.+..++..+...+...|++++|..+|+++...        .+.+..++
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~--------~~~~~~~~   80 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALEL--------DPNNAEAW   80 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHh--------CCccHHHH
Confidence            6778889999999999999999999886434567888999999999999999999999999885        24467788


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHh
Q 043380           97 ATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLY  141 (246)
Q Consensus        97 ~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~  141 (246)
                      ..+...|...|++++|...|+++..   ..|+ ...+..+...+..
T Consensus        81 ~~la~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~~~~l~~~~~~  123 (125)
T 1na0_A           81 YNLGNAYYKQGDYDEAIEYYQKALE---LDPNNAEAKQNLGNAKQK  123 (125)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHHH---hCCCcHHHHHHHHHHHHh
Confidence            9999999999999999999999988   3354 5556555555544

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.93  E-value=2.5e-08  Score=72.99  Aligned_cols=167  Identities=11%  Similarity=-0.024  Sum_probs=118.3

Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc-cHHHHHHHHHHHHc
Q 043380           27 SREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP-DIFTYATLLMGFRH  105 (246)
Q Consensus        27 ~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p-~~~~~~~ll~~~~~  105 (246)
                      ....|++++|.++++.+..........+..+-..+...|++++|...+++..+....   .+..| ...++..+-..|..
T Consensus         2 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~---~~~~~~~~~~~~~l~~~~~~   78 (203)
T 3gw4_A            2 AFEAHDYALAERQAQALLAHPATASGARFMLGYVYAFMDRFDEARASFQALQQQAQK---SGDHTAEHRALHQVGMVERM   78 (203)
T ss_dssp             -----CHHHHHHHHHHHHTSTTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHT---TCCHHHHHHHHHHHHHHHHH
T ss_pred             ccccccHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHH---cCCcHHHHHHHHHHHHHHHH
Confidence            356799999999666665322345678899999999999999999999998873100   01222 34578889999999


Q ss_pred             cCCHHHHHHHHHHHHhC---CCCCC-C-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHH
Q 043380          106 AKDLQSLLEIVFEMKSC---CNLIL-D-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMM  180 (246)
Q Consensus       106 ~~~~~~a~~~~~~m~~~---~~~~p-~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li  180 (246)
                      .|++++|...+++....   .+-.| . ...+..+...+...|++++    |...+++.............-..++..+.
T Consensus        79 ~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~----A~~~~~~al~~~~~~~~~~~~~~~~~~la  154 (203)
T 3gw4_A           79 AGNWDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAG----ARQEYEKSLVYAQQADDQVAIACAFRGLG  154 (203)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHH----HHHHHHHHHHHHHhccchHHHHHHHHHHH
Confidence            99999999999987662   12122 1 4567888999999999999    99999987654110001111234567888


Q ss_pred             HHHHhcCChhHHhhHHHhhC
Q 043380          181 HELAARVDYDIVKSPYRRMW  200 (246)
Q Consensus       181 ~~~~~~g~~~~a~~~~~~~~  200 (246)
                      .++...|++++|...+++..
T Consensus       155 ~~~~~~g~~~~A~~~~~~al  174 (203)
T 3gw4_A          155 DLAQQEKNLLEAQQHWLRAR  174 (203)
T ss_dssp             HHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHCcCHHHHHHHHHHHH
Confidence            89999999999999888765

>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=98.92  E-value=2e-07  Score=68.77  Aligned_cols=130  Identities=9%  Similarity=-0.077  Sum_probs=110.1

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHH
Q 043380           18 IVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYA   97 (246)
Q Consensus        18 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~   97 (246)
                      ..+..+...+...|++++|...|++..   .|+...|..+...|...|++++|.+.|++....        .+.+...|.
T Consensus         7 ~~~~~~g~~~~~~~~~~~A~~~~~~a~---~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--------~~~~~~~~~   75 (213)
T 1hh8_A            7 ISLWNEGVLAADKKDWKGALDAFSAVQ---DPHSRICFNIGCMYTILKNMTEAEKAFTRSINR--------DKHLAVAYF   75 (213)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHTSS---SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHc---CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--------CccchHHHH
Confidence            345677788889999999999998774   678899999999999999999999999999986        244677899


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHhCCC-------------CCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           98 TLLMGFRHAKDLQSLLEIVFEMKSCCN-------------LILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        98 ~ll~~~~~~~~~~~a~~~~~~m~~~~~-------------~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      .+..+|...|++++|...|+...+...             ..|+ ...+..+...|...|++++    |...|+...+.
T Consensus        76 ~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~----A~~~~~~al~~  150 (213)
T 1hh8_A           76 QRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKK----AEEQLALATSM  150 (213)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHTT
T ss_pred             HHHHHHHHcccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHH----HHHHHHHHHHc
Confidence            999999999999999999999988211             1122 3778899999999999999    99999998875

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=98.92  E-value=1.7e-07  Score=75.76  Aligned_cols=208  Identities=13%  Similarity=-0.049  Sum_probs=147.2

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhC--CCCC----HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc-cHHH
Q 043380           23 VIEASREAQRIDEAYQILESVEKG--LEPD----SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP-DIFT   95 (246)
Q Consensus        23 li~~~~~~g~~~~a~~~~~~~~~~--~~~~----~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p-~~~~   95 (246)
                      .-..+...|++++|...|++...-  ..++    ..++..+...|...|+++.|...+.+..+...+.  .+..+ ...+
T Consensus       107 ~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~--~~~~~~~~~~  184 (378)
T 3q15_A          107 RGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNH--PLYSIRTIQS  184 (378)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTS--TTCHHHHHHH
T ss_pred             HHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhC--CCchhhHHHH
Confidence            344567889999999999887521  1233    4568888999999999999999999987641000  01122 2458


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhC---CCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSC---CNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP  171 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~---~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p  171 (246)
                      ++.+-.+|...|++++|.+.|++..+.   .+-.+. ..+++.+...|...|++++    |.+.|++........ +.+.
T Consensus       185 ~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~----A~~~~~~al~~~~~~-~~~~  259 (378)
T 3q15_A          185 LFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQM----AVEHFQKAAKVSREK-VPDL  259 (378)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHHHHHH-CGGG
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHH----HHHHHHHHHHHHHhh-CChh
Confidence            889999999999999999999887651   111111 4578889999999999999    999999987721000 1122


Q ss_pred             chhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCC---hhHHHHHHHH
Q 043380          172 KPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQ---VDLALDKLSN  238 (246)
Q Consensus       172 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~---~~~a~~~~~~  238 (246)
                      ...++..+..+|.+.|++++|...+++........-.+.. ...+..+-..|...|+   +++|..+++.
T Consensus       260 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~-~~~~~~l~~ly~~~~~~~~~~~al~~~~~  328 (378)
T 3q15_A          260 LPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFY-KELFLFLQAVYKETVDERKIHDLLSYFEK  328 (378)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCH-HHHHHHHHHHHSSSCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHH-HHHHHHHHHHHhCCCcHHHHHHHHHHHHh
Confidence            3578889999999999999999999986642211111111 1246677777778888   7888887765

>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=98.89  E-value=5e-07  Score=70.40  Aligned_cols=173  Identities=9%  Similarity=0.014  Sum_probs=123.5

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCC--CCCH----HHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           22 AVIEASREAQRIDEAYQILESVEKGL--EPDS----LSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        22 ~li~~~~~~g~~~~a~~~~~~~~~~~--~~~~----~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      ..+..+.+.|++++|.++++......  .|+.    ..+..+...+...+++++|...|.+......+.  ....-...+
T Consensus        80 ~~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~--~~~~~~~~~  157 (293)
T 3u3w_A           80 DQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTG--IDVYQNLYI  157 (293)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCC--SCTTHHHHH
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhccc--ccHHHHHHH
Confidence            34678889999999999999876422  2231    123346666777789999999999998741100  000011347


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhC---C-CCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCC
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSC---C-NLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLW  170 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~---~-~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~  170 (246)
                      |+.+...|...|++++|...|++..+.   . +..+. ..+|..+...|...|++++    |...+++..+.........
T Consensus       158 ~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~----A~~~~~~al~~~~~~~~~~  233 (293)
T 3u3w_A          158 ENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEE----SLYQVNKAIEISCRINSMA  233 (293)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHHHHHTTBCT
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHH----HHHHHHHHHHHHHHcCcHH
Confidence            999999999999999999999988731   1 22233 3478899999999999999    9999998776421111111


Q ss_pred             cchhhHHHHHHHHHhcCC-hhHHhhHHHhhC
Q 043380          171 PKPHLYVSMMHELAARVD-YDIVKSPYRRMW  200 (246)
Q Consensus       171 p~~~~~~~li~~~~~~g~-~~~a~~~~~~~~  200 (246)
                      .-..+|..+-.+|.+.|+ +++|.+.+++..
T Consensus       234 ~~~~~~~~lg~~~~~~g~~~~~A~~~~~~Al  264 (293)
T 3u3w_A          234 LIGQLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             THHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCcHHHHHHHHHHHH
Confidence            225788999999999995 688888887654

>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=1.2e-07  Score=69.92  Aligned_cols=136  Identities=10%  Similarity=-0.077  Sum_probs=107.6

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP  173 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~  173 (246)
                      ..+..+...+...|++++|...|++..     .|+...|..+...|...|++++    |...|+...+.      ...+.
T Consensus         7 ~~~~~~g~~~~~~~~~~~A~~~~~~a~-----~~~~~~~~~lg~~~~~~g~~~~----A~~~~~~al~~------~~~~~   71 (213)
T 1hh8_A            7 ISLWNEGVLAADKKDWKGALDAFSAVQ-----DPHSRICFNIGCMYTILKNMTE----AEKAFTRSINR------DKHLA   71 (213)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHTSS-----SCCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------CTTCH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHc-----CCChHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh------Cccch
Confidence            345667777889999999999998764     3678899999999999999999    99999998886      23456


Q ss_pred             hhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCC----------CchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhc
Q 043380          174 HLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTI----------SPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRW  243 (246)
Q Consensus       174 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~----------~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  243 (246)
                      ..+..+..+|...|++++|...|++.....+...          .......++..+..+|...|++++|.+.|+...+..
T Consensus        72 ~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  151 (213)
T 1hh8_A           72 VAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMK  151 (213)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHcC
Confidence            7889999999999999999999998775433211          000111368889999999999999999999887654


Q ss_pred             c
Q 043380          244 K  244 (246)
Q Consensus       244 ~  244 (246)
                      +
T Consensus       152 p  152 (213)
T 1hh8_A          152 S  152 (213)
T ss_dssp             C
T ss_pred             c
Confidence            4

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=98.88  E-value=6.7e-07  Score=77.65  Aligned_cols=216  Identities=9%  Similarity=-0.024  Sum_probs=158.8

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHH-HHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCC--CCC
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAY-QILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSS--GGF   89 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~-~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~--~~~   89 (246)
                      .+-+...|-.....+.+.|+.++|. ++|+.....++.+...|-..+...-+.|+++.|.++|+++.+.......  ..-
T Consensus       339 ~p~~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~~~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~  418 (679)
T 4e6h_A          339 VCFAPEIWFNMANYQGEKNTDSTVITKYLKLGQQCIPNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMED  418 (679)
T ss_dssp             TTTCHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhc
Confidence            3457778888888888899999996 9999876556667777888888888999999999999999874000000  000


Q ss_pred             Cc------------cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCC-C-CCCCHHHHHHHHHHHHhcCChhhhhhHHHHH
Q 043380           90 HP------------DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCC-N-LILDRSTFTAMVDALLYSGSIKVVGLYALCI  155 (246)
Q Consensus        90 ~p------------~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~-~-~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~  155 (246)
                      .|            ....|...+....+.|+.+.|..+|..... . + ..+......+.+...+ .++.+.    |..+
T Consensus       419 ~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A~~-~~~~~~~~lyi~~A~lE~~~-~~d~e~----Ar~i  492 (679)
T 4e6h_A          419 DPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCRR-LKKLVTPDIYLENAYIEYHI-SKDTKT----ACKV  492 (679)
T ss_dssp             STTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHH-TGGGSCTHHHHHHHHHHHTT-TSCCHH----HHHH
T ss_pred             cCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-hcCCCChHHHHHHHHHHHHh-CCCHHH----HHHH
Confidence            13            234688888888899999999999999988 4 2 2233333334443222 345899    9999


Q ss_pred             HHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHH
Q 043380          156 FGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDK  235 (246)
Q Consensus       156 ~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~  235 (246)
                      |+...+.      ..-+...|...+......|+.+.|..+|+........   +.-....|...+..-.+.|+.+.+.++
T Consensus       493 fe~~Lk~------~p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~~~~---~~~~~~lw~~~~~fE~~~G~~~~~~~v  563 (679)
T 4e6h_A          493 LELGLKY------FATDGEYINKYLDFLIYVNEESQVKSLFESSIDKISD---SHLLKMIFQKVIFFESKVGSLNSVRTL  563 (679)
T ss_dssp             HHHHHHH------HTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTTSSS---TTHHHHHHHHHHHHHHHTCCSHHHHHH
T ss_pred             HHHHHHH------CCCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCC---HHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            9999886      3335566778888888899999999999998765321   111223799999999999999999999


Q ss_pred             HHHHHhhc
Q 043380          236 LSNTITRW  243 (246)
Q Consensus       236 ~~~m~~~g  243 (246)
                      .+++.+.-
T Consensus       564 ~~R~~~~~  571 (679)
T 4e6h_A          564 EKRFFEKF  571 (679)
T ss_dssp             HHHHHHHS
T ss_pred             HHHHHHhC
Confidence            99998654

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=98.87  E-value=5.9e-07  Score=74.41  Aligned_cols=132  Identities=7%  Similarity=-0.106  Sum_probs=90.6

Q ss_pred             CHHHHHHHHHHHHhc--CCHHHHHHHHHHHHhCCCCCHHHHHHHHHH---HHhcCCcchHHHHHHHHHhccCCCCCCCCC
Q 043380           16 NTIVMNAVIEASREA--QRIDEAYQILESVEKGLEPDSLSYNILISA---CIKTKKLDVTMPFNEQLKDNGQKCSSGGFH   90 (246)
Q Consensus        16 ~~~~~~~li~~~~~~--g~~~~a~~~~~~~~~~~~~~~~t~~~li~~---~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~   90 (246)
                      .+.+++.+-.++.+.  +++++|.+.|++...--+-+...+..+..+   +...++.++|.+.+++..+.        -+
T Consensus       135 ~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l--------~p  206 (472)
T 4g1t_A          135 SPELDCEEGWTRLKCGGNQNERAKVCFEKALEKKPKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRL--------NP  206 (472)
T ss_dssp             CHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHH--------CS
T ss_pred             hHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhc--------CC
Confidence            355666666666654  468999999998753223445555554444   34567888999999988875        13


Q ss_pred             ccHHHHHHHHHHHHc----cCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           91 PDIFTYATLLMGFRH----AKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        91 p~~~~~~~ll~~~~~----~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      .+..++..+...+..    .+++++|.+++++...   ..|+ ..++..+...|...|++++    |...+++..+.
T Consensus       207 ~~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~---~~~~~~~~~~~lg~~~~~~~~~~~----A~~~~~~al~~  276 (472)
T 4g1t_A          207 DNQYLKVLLALKLHKMREEGEEEGEGEKLVEEALE---KAPGVTDVLRSAAKFYRRKDEPDK----AIELLKKALEY  276 (472)
T ss_dssp             SCHHHHHHHHHHHHHCC------CHHHHHHHHHHH---HCSSCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH---hCccHHHHHHHHHHHHHHcCchHH----HHHHHHHHHHh
Confidence            345566555555443    4677889999998877   3454 7788889999999999999    99999887765

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.87  E-value=9.9e-08  Score=64.19  Aligned_cols=121  Identities=7%  Similarity=-0.085  Sum_probs=102.0

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      +.+...+..+...+...|++++|...|+......+.+...+..+...+...|++++|...+.+....        .+.+.
T Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~--------~~~~~   80 (131)
T 2vyi_A            9 SAEAERLKTEGNEQMKVENFEAAVHFYGKAIELNPANAVYFCNRAAAYSKLGNYAGAVQDCERAICI--------DPAYS   80 (131)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCH
T ss_pred             hhhhHHHHHHHHHHHHccCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhc--------CccCH
Confidence            3456788888999999999999999999876434567888999999999999999999999999986        23457


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHhcCCh
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL-DRSTFTAMVDALLYSGSI  145 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~~~~  145 (246)
                      ..+..+...+...|++++|...|++..+   ..| +...+..+...+...|++
T Consensus        81 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~---~~p~~~~~~~~l~~~~~~~~~~  130 (131)
T 2vyi_A           81 KAYGRMGLALSSLNKHVEAVAYYKKALE---LDPDNETYKSNLKIAELKLREA  130 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH---HSTTCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHh---cCccchHHHHHHHHHHHHHhcC
Confidence            7899999999999999999999999988   345 467788888888877765

>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=98.87  E-value=1.5e-07  Score=66.28  Aligned_cols=131  Identities=7%  Similarity=-0.056  Sum_probs=107.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHH
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTY   96 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~   96 (246)
                      ...+..+...+...|++++|...|+......+.+...+..+...+...|++++|...+.+....        .+.+...|
T Consensus        13 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--------~~~~~~~~   84 (166)
T 1a17_A           13 AEELKTQANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIEL--------DKKYIKGY   84 (166)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--------CcccHHHH
Confidence            4567788889999999999999999876444667889999999999999999999999999986        24467789


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHH--HHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           97 ATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTF--TAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        97 ~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~--~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ..+..++...|++++|...|++...   ..|+ ...+  ..+...+...|++++    |...+......
T Consensus        85 ~~~a~~~~~~~~~~~A~~~~~~a~~---~~p~~~~~~~~~~~~~~~~~~~~~~~----A~~~~~~~~~~  146 (166)
T 1a17_A           85 YRRAASNMALGKFRAALRDYETVVK---VKPHDKDAKMKYQECNKIVKQKAFER----AIAGDEHKRSV  146 (166)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH---HSTTCHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHH
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHHHHHHHHH----HHHcccchHHH
Confidence            9999999999999999999999988   3343 4444  344445778899999    99999876553

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.86  E-value=2.2e-07  Score=72.43  Aligned_cols=177  Identities=9%  Similarity=-0.040  Sum_probs=126.4

Q ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc----HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCC--
Q 043380           51 SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD----IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCN--  124 (246)
Q Consensus        51 ~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~--  124 (246)
                      ...+...+..+...|++++|.+.+.+..+..      ...++    ...+..+...+...|++++|...++.......  
T Consensus        75 ~~~l~~~~~~~~~~~~y~~A~~~~~~~l~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~  148 (293)
T 2qfc_A           75 KKQFKDQVIMLCKQKRYKEIYNKVWNELKKE------EYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTG  148 (293)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC------CCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCS
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHhccc------cCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcC
Confidence            3456667888899999999999999888751      11111    12344566677889999999999999875111  


Q ss_pred             CCCC--HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc--chhhHHHHHHHHHhcCChhHHhhHHHhhC
Q 043380          125 LILD--RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP--KPHLYVSMMHELAARVDYDIVKSPYRRMW  200 (246)
Q Consensus       125 ~~p~--~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p--~~~~~~~li~~~~~~g~~~~a~~~~~~~~  200 (246)
                      ..+.  ..+|+.+...|...|++++    |...|++..+..... +..+  ...++..+..+|...|++++|...+++..
T Consensus       149 ~~~~~~~~~~~~lg~~y~~~~~~~~----A~~~~~kal~~~~~~-~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal  223 (293)
T 2qfc_A          149 IDVYQNLYIENAIANIYAENGYLKK----GIDLFEQILKQLEAL-HDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAI  223 (293)
T ss_dssp             SCTTHHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHHHHHS-CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHHHHhc-CccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHH
Confidence            1122  4588999999999999999    999999987431101 1111  22688999999999999999999999865


Q ss_pred             CCC--CCCCCchhhhHHHHHHHHHHHhcCChhHH-HHHHHHHH
Q 043380          201 PDS--TGTISPEVQEEAGHLLMEAALNDGQVDLA-LDKLSNTI  240 (246)
Q Consensus       201 ~~~--~~~~~~~~~~~~~~~li~~~~~~g~~~~a-~~~~~~m~  240 (246)
                      ...  .+....  ...+|..+...|.+.|++++| ...++...
T Consensus       224 ~~~~~~~~~~~--~~~~~~~lg~~y~~~g~~~~Ai~~~~~~Al  264 (293)
T 2qfc_A          224 EISCRINSMAL--IGQLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             HHHHHTTBCSS--HHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHhcCcHHH--HHHHHHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence            321  111111  123788899999999999999 77777654

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.86  E-value=5.8e-08  Score=70.97  Aligned_cols=167  Identities=8%  Similarity=-0.102  Sum_probs=119.0

Q ss_pred             HhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhC---CCCCCC-HHHHHHHHH
Q 043380           62 IKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSC---CNLILD-RSTFTAMVD  137 (246)
Q Consensus        62 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~---~~~~p~-~~~~~~li~  137 (246)
                      ...|++++|.++++.+...        ......++..+-..+...|++++|...+++....   .+..|. ..++..+..
T Consensus         3 ~~~g~~~~A~~~~~~~~~~--------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~   74 (203)
T 3gw4_A            3 FEAHDYALAERQAQALLAH--------PATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGM   74 (203)
T ss_dssp             ----CHHHHHHHHHHHHTS--------TTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             cccccHHHHHHHHHHhcCC--------hHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence            4678999999966555442        2345678999999999999999999999876551   223333 567888999


Q ss_pred             HHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc--chhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHH
Q 043380          138 ALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP--KPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEA  215 (246)
Q Consensus       138 ~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p--~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~  215 (246)
                      .|...|++++    |.+.+++........ +-.|  ...++..+...+...|++++|...+++........-.+.....+
T Consensus        75 ~~~~~g~~~~----A~~~~~~al~~~~~~-~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~  149 (203)
T 3gw4_A           75 VERMAGNWDA----ARRCFLEERELLASL-PEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACA  149 (203)
T ss_dssp             HHHHTTCHHH----HHHHHHHHHHHHHHS-CCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHcCCHHH----HHHHHHHHHHHHHHc-CccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHH
Confidence            9999999999    999999876642110 1112  23568888899999999999999999865321111122222235


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          216 GHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       216 ~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      +..+...+...|++++|.+.+++..+
T Consensus       150 ~~~la~~~~~~g~~~~A~~~~~~al~  175 (203)
T 3gw4_A          150 FRGLGDLAQQEKNLLEAQQHWLRARD  175 (203)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            78888999999999999999988765

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.86  E-value=5e-07  Score=70.40  Aligned_cols=175  Identities=10%  Similarity=0.048  Sum_probs=125.2

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCH------HHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc
Q 043380           18 IVMNAVIEASREAQRIDEAYQILESVEKGLEPDS------LSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP   91 (246)
Q Consensus        18 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~------~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p   91 (246)
                      ..+...+..+...|++++|.+.++......+...      ..+..+...+...|++++|...+.+......+    ...+
T Consensus        76 ~~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~----~~~~  151 (293)
T 2qfc_A           76 KQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLT----GIDV  151 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCC----SSCT
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhc----CCch
Confidence            3445667788899999999999987653222222      22344556677888999999999998764110    1122


Q ss_pred             c--HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-----HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhc
Q 043380           92 D--IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-----RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVC  164 (246)
Q Consensus        92 ~--~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-----~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~  164 (246)
                      .  ..+|+.+-..|...|++++|...|++........|+     ..+|+.+...|...|++++    |...+++..+...
T Consensus       152 ~~~~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~----Al~~~~kal~~~~  227 (293)
T 2qfc_A          152 YQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEE----SLYQVNKAIEISC  227 (293)
T ss_dssp             THHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHH----HHHHHHHHHHHHH
Confidence            2  458999999999999999999999988731011222     2588999999999999999    9999999876521


Q ss_pred             CCCCCCcchhhHHHHHHHHHhcCChhHH-hhHHHhhC
Q 043380          165 SNPGLWPKPHLYVSMMHELAARVDYDIV-KSPYRRMW  200 (246)
Q Consensus       165 ~~~~~~p~~~~~~~li~~~~~~g~~~~a-~~~~~~~~  200 (246)
                      .......-..+|..+..+|...|++++| ...+++..
T Consensus       228 ~~~~~~~~~~~~~~lg~~y~~~g~~~~Ai~~~~~~Al  264 (293)
T 2qfc_A          228 RINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             HTTBCSSHHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             hcCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence            0001111257889999999999999999 77677643

>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=98.84  E-value=5.8e-07  Score=82.35  Aligned_cols=181  Identities=12%  Similarity=0.168  Sum_probs=119.1

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHH
Q 043380           15 LNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIF   94 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~   94 (246)
                      -++.+|..+-.++...|++++|.+-|...     .|...|..++.+|.+.|++++|.+++...++.         .++..
T Consensus      1103 n~p~vWsqLAKAql~~G~~kEAIdsYiKA-----dD~say~eVa~~~~~lGkyEEAIeyL~mArk~---------~~e~~ 1168 (1630)
T 1xi4_A         1103 NEPAVWSQLAKAQLQKGMVKEAIDSYIKA-----DDPSSYMEVVQAANTSGNWEELVKYLQMARKK---------ARESY 1168 (1630)
T ss_pred             CCHHHHHHHHHHHHhCCCHHHHHHHHHhc-----CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhh---------ccccc
Confidence            34677888889999999999999888553     56677888899999999999999988877765         23333


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchh
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPH  174 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~  174 (246)
                      ..+.+..+|++.+++++...+.   ..     |+...|..+...|-..|++++    |..+|....              
T Consensus      1169 Idt~LafaYAKl~rleele~fI---~~-----~n~ad~~~iGd~le~eg~Yee----A~~~Y~kA~-------------- 1222 (1630)
T 1xi4_A         1169 VETELIFALAKTNRLAELEEFI---NG-----PNNAHIQQVGDRCYDEKMYDA----AKLLYNNVS-------------- 1222 (1630)
T ss_pred             ccHHHHHHHHhhcCHHHHHHHH---hC-----CCHHHHHHHHHHHHhcCCHHH----HHHHHHhhh--------------
Confidence            3334777777777776533332   11     344555566666777777777    776666641              


Q ss_pred             hHHHHHHHHHhcCChhHHhhHHHhhCCCCC--------------------C---CCCchhhhHHHHHHHHHHHhcCChhH
Q 043380          175 LYVSMMHELAARVDYDIVKSPYRRMWPDST--------------------G---TISPEVQEEAGHLLMEAALNDGQVDL  231 (246)
Q Consensus       175 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~--------------------~---~~~~~~~~~~~~~li~~~~~~g~~~~  231 (246)
                      .|..+..+|.+.|++++|.+.+++......                    +   ...++    .+..++..|.+.|.+++
T Consensus      1223 ny~rLA~tLvkLge~q~AIEaarKA~n~~aWkev~~acve~~Ef~LA~~cgl~Iiv~~d----eLeeli~yYe~~G~feE 1298 (1630)
T 1xi4_A         1223 NFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHAD----ELEELINYYQDRGYFEE 1298 (1630)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHhCCHHHHHHHHHHHhhhhHHHHHHHHHHhhhcCHH----HHHHHHHHHHHcCCHHH
Confidence            456666666666666666666665532210                    0   00111    35567777788888888


Q ss_pred             HHHHHHHH
Q 043380          232 ALDKLSNT  239 (246)
Q Consensus       232 a~~~~~~m  239 (246)
                      |+++++.-
T Consensus      1299 AI~LlE~a 1306 (1630)
T 1xi4_A         1299 LITMLEAA 1306 (1630)
T ss_pred             HHHHHHHH
Confidence            88887654

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=98.84  E-value=1.1e-08  Score=71.87  Aligned_cols=141  Identities=10%  Similarity=-0.026  Sum_probs=108.6

Q ss_pred             HHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHH
Q 043380           59 SACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMV  136 (246)
Q Consensus        59 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li  136 (246)
                      ..+...|++++|.+.+......         .|+ ...+..+-..|.+.|++++|.+.|++..+   +.|+ ..+|..+.
T Consensus         5 ~~~~~~~~~e~ai~~~~~a~~~---------~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~---~~p~~~~a~~~lg   72 (150)
T 4ga2_A            5 SMRRSKADVERYIASVQGSTPS---------PRQKSIKGFYFAKLYYEAKEYDLAKKYICTYIN---VQERDPKAHRFLG   72 (150)
T ss_dssp             --CCCHHHHHHHHHHHHHHSCS---------HHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHH
T ss_pred             HHHHHcChHHHHHHHHHHhccc---------CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCCHHHHHHHH
Confidence            3445567889999998887764         444 44677888999999999999999999988   5576 88899999


Q ss_pred             HHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc-chhhHHHHHHHHHhcCChhHHhhH-HHhhCCCCCCCCCchhhhH
Q 043380          137 DALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP-KPHLYVSMMHELAARVDYDIVKSP-YRRMWPDSTGTISPEVQEE  214 (246)
Q Consensus       137 ~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~-~~~~~~~~~~~~~~~~~~~  214 (246)
                      ..|...|++++    |...|+...+.       .| +..++..+...|...|++++|.+. +++..+.++..  +.    
T Consensus        73 ~~~~~~~~~~~----A~~~~~~al~~-------~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~P~~--~~----  135 (150)
T 4ga2_A           73 LLYELEENTDK----AVECYRRSVEL-------NPTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKLFPGS--PA----  135 (150)
T ss_dssp             HHHHHTTCHHH----HHHHHHHHHHH-------CTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHSTTC--HH----
T ss_pred             HHHHHcCchHH----HHHHHHHHHHh-------CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhCcCC--HH----
Confidence            99999999999    99999999886       34 467899999999999999876654 56655433221  11    


Q ss_pred             HHHHHHHHHHhcCC
Q 043380          215 AGHLLMEAALNDGQ  228 (246)
Q Consensus       215 ~~~~li~~~~~~g~  228 (246)
                      +|......+...|+
T Consensus       136 ~~~l~~~ll~~~G~  149 (150)
T 4ga2_A          136 VYKLKEQLLDCEGE  149 (150)
T ss_dssp             HHHHHHHHHHTCCC
T ss_pred             HHHHHHHHHHHhCc
Confidence            57766666666664

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=98.83  E-value=3.2e-08  Score=86.42  Aligned_cols=161  Identities=12%  Similarity=0.073  Sum_probs=129.4

Q ss_pred             HhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHH
Q 043380           62 IKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALL  140 (246)
Q Consensus        62 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~  140 (246)
                      ...+++++|.+.+++..+..........+.+...+..+..+|...|++++|...|++..+   ..|+ ...|..+...|.
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~---~~p~~~~a~~~lg~~~~  478 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAE---RVGWRWRLVWYRAVAEL  478 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHH---HHCCCHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhc---cCcchHHHHHHHHHHHH
Confidence            678999999999999982100000001234567888999999999999999999999988   4565 788999999999


Q ss_pred             hcCChhhhhhHHHHHHHHHHHhhcCCCCCCc-chhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHH
Q 043380          141 YSGSIKVVGLYALCIFGEIVKRVCSNPGLWP-KPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLL  219 (246)
Q Consensus       141 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~l  219 (246)
                      ..|++++    |...|++..+.       .| +...+..+..+|...|++++ ...|++....++..    .  .+|..+
T Consensus       479 ~~g~~~~----A~~~~~~al~l-------~P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~P~~----~--~a~~~l  540 (681)
T 2pzi_A          479 LTGDYDS----ATKHFTEVLDT-------FPGELAPKLALAATAELAGNTDE-HKFYQTVWSTNDGV----I--SAAFGL  540 (681)
T ss_dssp             HHTCHHH----HHHHHHHHHHH-------STTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHCTTC----H--HHHHHH
T ss_pred             HcCCHHH----HHHHHHHHHHh-------CCCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhCCch----H--HHHHHH
Confidence            9999999    99999999886       34 45788999999999999999 99999987654322    1  278899


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhhc
Q 043380          220 MEAALNDGQVDLALDKLSNTITRW  243 (246)
Q Consensus       220 i~~~~~~g~~~~a~~~~~~m~~~g  243 (246)
                      ..++.+.|++++|.+.|++..+..
T Consensus       541 g~~~~~~g~~~~A~~~~~~al~l~  564 (681)
T 2pzi_A          541 ARARSAEGDRVGAVRTLDEVPPTS  564 (681)
T ss_dssp             HHHHHHTTCHHHHHHHHHTSCTTS
T ss_pred             HHHHHHcCCHHHHHHHHHhhcccC
Confidence            999999999999999999876543

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.81  E-value=1.7e-07  Score=63.38  Aligned_cols=120  Identities=9%  Similarity=-0.007  Sum_probs=97.1

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      .+.++..|..+...+.+.|++++|...|+......+.+...+..+...+...|++++|...+++..+.        .+.+
T Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~--------~~~~   83 (133)
T 2lni_A           12 NPDLALMVKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRAACYTKLLEFQLALKDCEECIQL--------EPTF   83 (133)
T ss_dssp             SSCHHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTCTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHH--------CTTC
T ss_pred             CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHh--------CCCc
Confidence            45677888889999999999999999999876544557888999999999999999999999999885        2345


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcC
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSG  143 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~  143 (246)
                      ...+..+..++...|++++|.+.|++..+   ..|+ ...+..+...+...|
T Consensus        84 ~~~~~~la~~~~~~~~~~~A~~~~~~~~~---~~p~~~~~~~~l~~~~~~~~  132 (133)
T 2lni_A           84 IKGYTRKAAALEAMKDYTKAMDVYQKALD---LDSSCKEAADGYQRCMMAQY  132 (133)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCGGGTHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHhhHHHHHHHHHHHHH---hCCCchHHHHHHHHHHHHhc
Confidence            77888899999999999999999999887   3344 455666666665544

>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=98.79  E-value=1e-06  Score=65.42  Aligned_cols=175  Identities=10%  Similarity=-0.032  Sum_probs=103.8

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccC----CHHH
Q 043380           36 AYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAK----DLQS  111 (246)
Q Consensus        36 a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~----~~~~  111 (246)
                      |.+.|+..-.  .-+...+..+-..|...+++++|..+|++..+.       +   +...+..|-..|.. +    ++++
T Consensus         5 A~~~~~~aa~--~g~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~-------g---~~~a~~~lg~~y~~-~g~~~~~~~   71 (212)
T 3rjv_A            5 PGSQYQQQAE--AGDRRAQYYLADTWVSSGDYQKAEYWAQKAAAQ-------G---DGDALALLAQLKIR-NPQQADYPQ   71 (212)
T ss_dssp             TTHHHHHHHH--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHT-------T---CHHHHHHHHHHTTS-STTSCCHHH
T ss_pred             HHHHHHHHHH--CCCHHHHHHHHHHHhcCCCHHHHHHHHHHHHHc-------C---CHHHHHHHHHHHHc-CCCCCCHHH
Confidence            4555555432  245566666666666677777777777776664       2   34455556666655 5    6777


Q ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHHHHHh----cCChhhhhhHHHHHHHHHHHhhcCCCCCC-cchhhHHHHHHHHHh-
Q 043380          112 LLEIVFEMKSCCNLILDRSTFTAMVDALLY----SGSIKVVGLYALCIFGEIVKRVCSNPGLW-PKPHLYVSMMHELAA-  185 (246)
Q Consensus       112 a~~~~~~m~~~~~~~p~~~~~~~li~~~~~----~~~~~~~~~~a~~~~~~m~~~~~~~~~~~-p~~~~~~~li~~~~~-  185 (246)
                      |.+.|+...+ .|   +...+..|-..|..    .+++++    |...|+...+.     +.. .+...+..|-..|.. 
T Consensus        72 A~~~~~~A~~-~g---~~~a~~~Lg~~y~~g~g~~~d~~~----A~~~~~~A~~~-----~~~~~~~~a~~~Lg~~y~~g  138 (212)
T 3rjv_A           72 ARQLAEKAVE-AG---SKSGEIVLARVLVNRQAGATDVAH----AITLLQDAARD-----SESDAAVDAQMLLGLIYASG  138 (212)
T ss_dssp             HHHHHHHHHH-TT---CHHHHHHHHHHHTCGGGSSCCHHH----HHHHHHHHTSS-----TTSHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHH-CC---CHHHHHHHHHHHHcCCCCccCHHH----HHHHHHHHHHc-----CCCcchHHHHHHHHHHHHcC
Confidence            7777777666 33   45556666666665    666777    77777766554     211 014566666666666 


Q ss_pred             ---cCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhc-C-----ChhHHHHHHHHHHhhc
Q 043380          186 ---RVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALND-G-----QVDLALDKLSNTITRW  243 (246)
Q Consensus       186 ---~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~-g-----~~~~a~~~~~~m~~~g  243 (246)
                         .+++++|...|++..... + . +.    ++..|-..|... |     ++++|.++|+.-.+.|
T Consensus       139 ~g~~~d~~~A~~~~~~A~~~~-~-~-~~----a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g  198 (212)
T 3rjv_A          139 VHGPEDDVKASEYFKGSSSLS-R-T-GY----AEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEG  198 (212)
T ss_dssp             SSSSCCHHHHHHHHHHHHHTS-C-T-TH----HHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHT
T ss_pred             CCCCCCHHHHHHHHHHHHHcC-C-C-HH----HHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcC
Confidence               666777777777764331 1 1 11    345555555543 2     6777777777666554

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.78  E-value=5.6e-07  Score=60.74  Aligned_cols=119  Identities=12%  Similarity=-0.001  Sum_probs=98.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC
Q 043380           48 EPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL  127 (246)
Q Consensus        48 ~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p  127 (246)
                      +.+...|..+...+...|++++|...|++..+.        .+.+...+..+..+|...|++++|...+++..+   ..|
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--------~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~---~~~   81 (133)
T 2lni_A           13 PDLALMVKNKGNECFQKGDYPQAMKHYTEAIKR--------NPKDAKLYSNRAACYTKLLEFQLALKDCEECIQ---LEP   81 (133)
T ss_dssp             SCHHHHHHHHHHHHHHTTCSHHHHHHHHHHHTT--------CTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHH---HCT
T ss_pred             cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--------CCCcHHHHHHHHHHHHHhccHHHHHHHHHHHHH---hCC
Confidence            456677889999999999999999999999875        234678899999999999999999999999988   334


Q ss_pred             C-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcC
Q 043380          128 D-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARV  187 (246)
Q Consensus       128 ~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g  187 (246)
                      + ...+..+...+...|++++    |.+.|++..+.      ..-+...+..+..++...|
T Consensus        82 ~~~~~~~~la~~~~~~~~~~~----A~~~~~~~~~~------~p~~~~~~~~l~~~~~~~~  132 (133)
T 2lni_A           82 TFIKGYTRKAAALEAMKDYTK----AMDVYQKALDL------DSSCKEAADGYQRCMMAQY  132 (133)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------CGGGTHHHHHHHHHHHHHT
T ss_pred             CchHHHHHHHHHHHHHhhHHH----HHHHHHHHHHh------CCCchHHHHHHHHHHHHhc
Confidence            4 7889999999999999999    99999999886      1223456666666666554

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.78  E-value=4.7e-07  Score=60.25  Aligned_cols=115  Identities=9%  Similarity=0.014  Sum_probs=93.6

Q ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHH
Q 043380           51 SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRS  130 (246)
Q Consensus        51 ~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~  130 (246)
                      ...|..+...+...|++++|.++|+++...        .+.+..++..+...+...|++++|...++++.. . .+.+..
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--------~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~-~-~~~~~~   78 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALEL--------DPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALE-L-DPNNAE   78 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-H-CTTCHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--------CcCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHH-h-CCccHH
Confidence            567888899999999999999999999886        234677899999999999999999999999988 3 223578


Q ss_pred             HHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHh
Q 043380          131 TFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAA  185 (246)
Q Consensus       131 ~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~  185 (246)
                      ++..+...|...|++++    |...|+...+.      .+.+...+..+...+..
T Consensus        79 ~~~~la~~~~~~~~~~~----A~~~~~~~~~~------~~~~~~~~~~l~~~~~~  123 (125)
T 1na0_A           79 AWYNLGNAYYKQGDYDE----AIEYYQKALEL------DPNNAEAKQNLGNAKQK  123 (125)
T ss_dssp             HHHHHHHHHHHTTCHHH----HHHHHHHHHHH------CTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHH----HHHHHHHHHHh------CCCcHHHHHHHHHHHHh
Confidence            88999999999999999    99999999886      12334555555555443

>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=98.78  E-value=4.9e-07  Score=63.63  Aligned_cols=127  Identities=9%  Similarity=0.038  Sum_probs=93.7

Q ss_pred             HHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HH
Q 043380           52 LSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RS  130 (246)
Q Consensus        52 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~  130 (246)
                      ..+..+...+...|++++|...|.+..+.        .+.+..++..+..++...|++++|...+++...   ..|+ ..
T Consensus        14 ~~~~~~a~~~~~~~~~~~A~~~~~~al~~--------~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~---~~~~~~~   82 (166)
T 1a17_A           14 EELKTQANDYFKAKDYENAIKFYSQAIEL--------NPSNAIYYGNRSLAYLRTECYGYALGDATRAIE---LDKKYIK   82 (166)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHh--------CCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCcccHH
Confidence            45667777788888888888888888875        233577788888888888888888888888877   3343 67


Q ss_pred             HHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhH--HHHHHHHHhcCChhHHhhHHHhh
Q 043380          131 TFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLY--VSMMHELAARVDYDIVKSPYRRM  199 (246)
Q Consensus       131 ~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~--~~li~~~~~~g~~~~a~~~~~~~  199 (246)
                      .+..+...+...|++++    |...|++..+.      ...+...+  ..+...+...|++++|...+...
T Consensus        83 ~~~~~a~~~~~~~~~~~----A~~~~~~a~~~------~p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~  143 (166)
T 1a17_A           83 GYYRRAASNMALGKFRA----ALRDYETVVKV------KPHDKDAKMKYQECNKIVKQKAFERAIAGDEHK  143 (166)
T ss_dssp             HHHHHHHHHHHTTCHHH----HHHHHHHHHHH------STTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHH----HHHHHHHHHHh------CCCCHHHHHHHHHHHHHHHHHHHHHHHHcccch
Confidence            78888888888888888    88888888775      11233333  33444467778888888777754

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.77  E-value=4e-07  Score=61.78  Aligned_cols=108  Identities=6%  Similarity=-0.107  Sum_probs=89.0

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHH
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTY   96 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~   96 (246)
                      ...+...-..|.+.|++++|++.|++..+-.+.+...|..+..+|.+.|++++|...|++.++.        -+.+...|
T Consensus        13 a~~~~~~G~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--------~p~~~~a~   84 (126)
T 4gco_A           13 AQEEKNKGNEYFKKGDYPTAMRHYNEAVKRDPENAILYSNRAACLTKLMEFQRALDDCDTCIRL--------DSKFIKGY   84 (126)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHh--------hhhhhHHH
Confidence            3567778889999999999999998875434667888999999999999999999999999885        23457789


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHH
Q 043380           97 ATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAM  135 (246)
Q Consensus        97 ~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~l  135 (246)
                      ..+-.+|...|++++|.+.|+...+   +.|+ ...+..+
T Consensus        85 ~~lg~~~~~~~~~~~A~~~~~~al~---l~P~~~~a~~~l  121 (126)
T 4gco_A           85 IRKAACLVAMREWSKAQRAYEDALQ---VDPSNEEAREGV  121 (126)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHH---HCcCCHHHHHHH
Confidence            9999999999999999999999988   5676 4444444

>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=98.77  E-value=9.1e-07  Score=81.11  Aligned_cols=165  Identities=13%  Similarity=0.103  Sum_probs=136.1

Q ss_pred             HHHH-hcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHH
Q 043380           25 EASR-EAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGF  103 (246)
Q Consensus        25 ~~~~-~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~  103 (246)
                      ..+. ..+++++|.++.++..     +..+|..+-.++...|++++|.+.|.+.             -|...|..++.+|
T Consensus      1083 ~VLie~i~nldrAiE~Aervn-----~p~vWsqLAKAql~~G~~kEAIdsYiKA-------------dD~say~eVa~~~ 1144 (1630)
T 1xi4_A         1083 QVLIEHIGNLDRAYEFAERCN-----EPAVWSQLAKAQLQKGMVKEAIDSYIKA-------------DDPSSYMEVVQAA 1144 (1630)
T ss_pred             HHHHHHHhhHHHHHHHHHhcC-----CHHHHHHHHHHHHhCCCHHHHHHHHHhc-------------CChHHHHHHHHHH
Confidence            3344 7789999999998663     3678999999999999999999999553             4566888899999


Q ss_pred             HccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHH
Q 043380          104 RHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHEL  183 (246)
Q Consensus       104 ~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~  183 (246)
                      .+.|++++|.+.+...++ .  .+++...+.++.+|++.+++++    ...+.    +        .|+...|..+-..|
T Consensus      1145 ~~lGkyEEAIeyL~mArk-~--~~e~~Idt~LafaYAKl~rlee----le~fI----~--------~~n~ad~~~iGd~l 1205 (1630)
T 1xi4_A         1145 NTSGNWEELVKYLQMARK-K--ARESYVETELIFALAKTNRLAE----LEEFI----N--------GPNNAHIQQVGDRC 1205 (1630)
T ss_pred             HHcCCHHHHHHHHHHHHh-h--cccccccHHHHHHHHhhcCHHH----HHHHH----h--------CCCHHHHHHHHHHH
Confidence            999999999999998877 3  3555555569999999988877    55442    2        24566777899999


Q ss_pred             HhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHH
Q 043380          184 AARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTI  240 (246)
Q Consensus       184 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  240 (246)
                      ...|++++|..+|....              .|..+..+|++.|++++|.+.++.-.
T Consensus      1206 e~eg~YeeA~~~Y~kA~--------------ny~rLA~tLvkLge~q~AIEaarKA~ 1248 (1630)
T 1xi4_A         1206 YDEKMYDAAKLLYNNVS--------------NFGRLASTLVHLGEYQAAVDGARKAN 1248 (1630)
T ss_pred             HhcCCHHHHHHHHHhhh--------------HHHHHHHHHHHhCCHHHHHHHHHHhC
Confidence            99999999999999962              58999999999999999999987653

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.77  E-value=1.5e-07  Score=66.17  Aligned_cols=104  Identities=9%  Similarity=-0.227  Sum_probs=79.5

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      +...+..+-..+.+.|++++|...|+....--+.+...|..+-.+|...|++++|...|++....        -+-+...
T Consensus        35 ~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l--------~P~~~~~  106 (151)
T 3gyz_A           35 MMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFAL--------GKNDYTP  106 (151)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------SSSCCHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhh--------CCCCcHH
Confidence            44566677778888888888888888876433557778888888888888888888888888875        1234567


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHH
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRS  130 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~  130 (246)
                      |..+-.+|...|++++|...|+...+   +.|+..
T Consensus       107 ~~~lg~~~~~lg~~~eA~~~~~~al~---l~~~~~  138 (151)
T 3gyz_A          107 VFHTGQCQLRLKAPLKAKECFELVIQ---HSNDEK  138 (151)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH---HCCCHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCHH
Confidence            88888888888888888888888887   456654

>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=98.76  E-value=4.7e-08  Score=75.99  Aligned_cols=195  Identities=8%  Similarity=-0.049  Sum_probs=129.0

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHH
Q 043380           15 LNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIF   94 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~   94 (246)
                      .+...+..+...+.+.|++++|...|+......+.+...|..+..+|.+.|++++|...+++..+.        -+-+..
T Consensus         2 ~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~--------~p~~~~   73 (281)
T 2c2l_A            2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALEL--------DGQSVK   73 (281)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--------CTTCHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--------CCCCHH
Confidence            456778888999999999999999999876433557888999999999999999999999999875        234577


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCH-HHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDR-STFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP  173 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~-~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~  173 (246)
                      .+..+..+|...|++++|...|+...+   +.|+. ..+...+....+   ...    + .-+......     ....+.
T Consensus        74 ~~~~lg~~~~~~g~~~~A~~~~~~al~---l~p~~~~~~~~~~~~~~~---~~~----~-~~~~~~~~~-----~~~~~~  137 (281)
T 2c2l_A           74 AHFFLGQCQLEMESYDEAIANLQRAYS---LAKEQRLNFGDDIPSALR---IAK----K-KRWNSIEER-----RIHQES  137 (281)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHH---HHHHTTCCCCSHHHHHHH---HHH----H-HHHHHHHHT-----CCCCCC
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHH---hCccchhhHHHHHHHHHH---HHH----H-HHHHHHHHH-----HHhhhH
Confidence            899999999999999999999998877   22321 111111211111   111    1 112222232     233343


Q ss_pred             hhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhc-CChhHHHHHHHHHHh
Q 043380          174 HLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALND-GQVDLALDKLSNTIT  241 (246)
Q Consensus       174 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~-g~~~~a~~~~~~m~~  241 (246)
                      .....+ ..+ ..|+.++|.+.++......++    +.  .....+-..+.+. +.+++|.++|....+
T Consensus       138 ~i~~~l-~~l-~~~~~~~A~~~~~~al~~~p~----~~--~~~~~l~~~~~~~~~~~~~a~~~f~~a~~  198 (281)
T 2c2l_A          138 ELHSYL-TRL-IAAERERELEECQRNHEGHED----DG--HIRAQQACIEAKHDKYMADMDELFSQVDE  198 (281)
T ss_dssp             HHHHHH-HHH-HHHHHHHHHTTTSGGGTTTSC----HH--HHTHHHHHHHHHHHHHHHHHHHHHHHSSC
T ss_pred             HHHHHH-HHH-HHHHHHHHHHHHHhhhccccc----hh--hhhhHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            333333 333 368889999888887654321    11  1333444444444 668889999887654

>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=98.74  E-value=8e-06  Score=60.49  Aligned_cols=161  Identities=6%  Similarity=-0.123  Sum_probs=130.0

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcC----CcchHHHHHHHHHhccCCCCCCCCC
Q 043380           15 LNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTK----KLDVTMPFNEQLKDNGQKCSSGGFH   90 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~----~~~~a~~~~~~m~~~~~~~~~~~~~   90 (246)
                      -++..+..|-..|...+++++|.+.|+..-.  .-+...+..|-..|.. +    ++++|..+|++..+.          
T Consensus        16 g~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~--~g~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~~----------   82 (212)
T 3rjv_A           16 GDRRAQYYLADTWVSSGDYQKAEYWAQKAAA--QGDGDALALLAQLKIR-NPQQADYPQARQLAEKAVEA----------   82 (212)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH--TTCHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHHT----------
T ss_pred             CCHHHHHHHHHHHhcCCCHHHHHHHHHHHHH--cCCHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHC----------
Confidence            5777888999999999999999999998753  2466777788888877 6    899999999999875          


Q ss_pred             ccHHHHHHHHHHHHc----cCCHHHHHHHHHHHHhCCCCCCC---HHHHHHHHHHHHh----cCChhhhhhHHHHHHHHH
Q 043380           91 PDIFTYATLLMGFRH----AKDLQSLLEIVFEMKSCCNLILD---RSTFTAMVDALLY----SGSIKVVGLYALCIFGEI  159 (246)
Q Consensus        91 p~~~~~~~ll~~~~~----~~~~~~a~~~~~~m~~~~~~~p~---~~~~~~li~~~~~----~~~~~~~~~~a~~~~~~m  159 (246)
                      -+...+..|-..|..    .+++++|.+.|++..+ .|  |+   ...+..|-..|..    .+++++    |...|+..
T Consensus        83 g~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~-~~--~~~~~~~a~~~Lg~~y~~g~g~~~d~~~----A~~~~~~A  155 (212)
T 3rjv_A           83 GSKSGEIVLARVLVNRQAGATDVAHAITLLQDAAR-DS--ESDAAVDAQMLLGLIYASGVHGPEDDVK----ASEYFKGS  155 (212)
T ss_dssp             TCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTS-ST--TSHHHHHHHHHHHHHHHHTSSSSCCHHH----HHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHH-cC--CCcchHHHHHHHHHHHHcCCCCCCCHHH----HHHHHHHH
Confidence            256677888888877    8899999999999988 44  43   6778888888988    888999    99999998


Q ss_pred             HHhhcCCCCCCcchhhHHHHHHHHHhc-C-----ChhHHhhHHHhhCCC
Q 043380          160 VKRVCSNPGLWPKPHLYVSMMHELAAR-V-----DYDIVKSPYRRMWPD  202 (246)
Q Consensus       160 ~~~~~~~~~~~p~~~~~~~li~~~~~~-g-----~~~~a~~~~~~~~~~  202 (246)
                      .+.       .++...+..|-..|... |     +.++|...|+.....
T Consensus       156 ~~~-------~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~  197 (212)
T 3rjv_A          156 SSL-------SRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLE  197 (212)
T ss_dssp             HHT-------SCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHH
T ss_pred             HHc-------CCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHc
Confidence            774       23455677777777653 3     889999999887543

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.74  E-value=6.1e-07  Score=60.19  Aligned_cols=117  Identities=5%  Similarity=-0.041  Sum_probs=65.4

Q ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-H
Q 043380           51 SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-R  129 (246)
Q Consensus        51 ~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~  129 (246)
                      ...+..+...+...|++++|...|++....        .+.+...+..+...+...|++++|...++....   ..|+ .
T Consensus        12 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--------~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~---~~~~~~   80 (131)
T 2vyi_A           12 AERLKTEGNEQMKVENFEAAVHFYGKAIEL--------NPANAVYFCNRAAAYSKLGNYAGAVQDCERAIC---IDPAYS   80 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCH
T ss_pred             hHHHHHHHHHHHHccCHHHHHHHHHHHHHc--------CCCCHHHHHHHHHHHHHhhchHHHHHHHHHHHh---cCccCH
Confidence            344555555666666666666666666553        122445556666666666666666666666555   2233 5


Q ss_pred             HHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCC
Q 043380          130 STFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVD  188 (246)
Q Consensus       130 ~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~  188 (246)
                      ..+..+...|...|++++    |...|+...+.      .+.+...+..+..++...|+
T Consensus        81 ~~~~~~~~~~~~~~~~~~----A~~~~~~~~~~------~p~~~~~~~~l~~~~~~~~~  129 (131)
T 2vyi_A           81 KAYGRMGLALSSLNKHVE----AVAYYKKALEL------DPDNETYKSNLKIAELKLRE  129 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------STTCHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhCCHHH----HHHHHHHHHhc------CccchHHHHHHHHHHHHHhc
Confidence            555566666666666666    66666665554      11233445555555555444

>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=98.73  E-value=3e-07  Score=61.83  Aligned_cols=116  Identities=7%  Similarity=0.008  Sum_probs=93.1

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc----
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD----   92 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~----   92 (246)
                      ...|..+...+...|++++|...|+......+.+...+..+...+...|++++|...+++.....     ....++    
T Consensus         4 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-----~~~~~~~~~~   78 (131)
T 1elr_A            4 ALKEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVG-----RENREDYRQI   78 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-----HHSTTCHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhc-----cccchhHHHH
Confidence            46788889999999999999999998764446678889999999999999999999999998761     000111    


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHH
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALL  140 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~  140 (246)
                      ..+|..+..++...|++++|.+.|+...+   ..|+......+.....
T Consensus        79 ~~~~~~la~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~~~l~~~~~  123 (131)
T 1elr_A           79 AKAYARIGNSYFKEEKYKDAIHFYNKSLA---EHRTPDVLKKCQQAEK  123 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHH---hCCCHHHHHHHHHHHH
Confidence            67889999999999999999999999988   4467665555544433

>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=98.73  E-value=1.9e-07  Score=67.01  Aligned_cols=119  Identities=10%  Similarity=0.072  Sum_probs=63.8

Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHH-HHccC
Q 043380           29 EAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMG-FRHAK  107 (246)
Q Consensus        29 ~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~-~~~~~  107 (246)
                      ..|++++|...|+......+.+...|..+...|...|++++|...|++..+.        .+.+...+..+..+ +...|
T Consensus        22 ~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--------~p~~~~~~~~la~~l~~~~~   93 (177)
T 2e2e_A           22 SQQNPEAQLQALQDKIRANPQNSEQWALLGEYYLWQNDYSNSLLAYRQALQL--------RGENAELYAALATVLYYQAS   93 (177)
T ss_dssp             -----CCCCHHHHHHHHHCCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------HCSCHHHHHHHHHHHHHHTT
T ss_pred             hccCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--------CCCCHHHHHHHHHHHHHhcC
Confidence            3455556666665543222445555666666666666666666666666554        12234455555555 55556


Q ss_pred             CH--HHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          108 DL--QSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       108 ~~--~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ++  ++|...|+....   ..|+ ...+..+...|...|++++    |...|+...+.
T Consensus        94 ~~~~~~A~~~~~~al~---~~p~~~~~~~~la~~~~~~g~~~~----A~~~~~~al~~  144 (177)
T 2e2e_A           94 QHMTAQTRAMIDKALA---LDSNEITALMLLASDAFMQANYAQ----AIELWQKVMDL  144 (177)
T ss_dssp             TCCCHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHT
T ss_pred             CcchHHHHHHHHHHHH---hCCCcHHHHHHHHHHHHHcccHHH----HHHHHHHHHhh
Confidence            65  666666666555   2233 4555556666666666666    66666665553

>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=5.1e-07  Score=71.97  Aligned_cols=132  Identities=8%  Similarity=-0.031  Sum_probs=111.2

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC---------------HHHHHHHHHHHHhcCCcchHHHHHHHHHhc
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPD---------------SLSYNILISACIKTKKLDVTMPFNEQLKDN   80 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~---------------~~t~~~li~~~~~~~~~~~a~~~~~~m~~~   80 (246)
                      +...|..+-..|.+.|++++|...|++...-.+.+               ...|..+..+|.+.|++++|...|++.++.
T Consensus       146 ~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  225 (336)
T 1p5q_A          146 QSTIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALEL  225 (336)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            46678889999999999999999999875322333               588999999999999999999999999986


Q ss_pred             cCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHH-HHHHHH
Q 043380           81 GQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYA-LCIFGE  158 (246)
Q Consensus        81 ~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a-~~~~~~  158 (246)
                              -+.+...|..+-.+|...|++++|...|++..+   +.|+ ...+..+...+...|+.++    | ...|+.
T Consensus       226 --------~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~---l~P~~~~a~~~l~~~~~~~~~~~~----a~~~~~~~  290 (336)
T 1p5q_A          226 --------DSNNEKGLSRRGEAHLAVNDFELARADFQKVLQ---LYPNNKAAKTQLAVCQQRIRRQLA----REKKLYAN  290 (336)
T ss_dssp             --------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCSSCHHHHHHHHHHHHHHHHHHH----HHHHHHHH
T ss_pred             --------CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHH---HCCCCHHHHHHHHHHHHHHHHHHH----HHHHHHHH
Confidence                    234678999999999999999999999999988   5565 7788899999999999998    7 456666


Q ss_pred             HHHh
Q 043380          159 IVKR  162 (246)
Q Consensus       159 m~~~  162 (246)
                      |...
T Consensus       291 ~~~~  294 (336)
T 1p5q_A          291 MFER  294 (336)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6554

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.71  E-value=1.3e-06  Score=71.60  Aligned_cols=208  Identities=8%  Similarity=-0.062  Sum_probs=145.9

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCC-----------------HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCC
Q 043380           24 IEASREAQRIDEAYQILESVEKGLEPD-----------------SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSS   86 (246)
Q Consensus        24 i~~~~~~g~~~~a~~~~~~~~~~~~~~-----------------~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~   86 (246)
                      ...+.+.|++++|++.|..+.+..+.+                 ...+..+...|...|++++|.+++.++...-     
T Consensus        11 a~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~-----   85 (434)
T 4b4t_Q           11 ARRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYM-----   85 (434)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHH-----
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH-----
Confidence            456788999999999998875311111                 1247789999999999999999999887641     


Q ss_pred             CCCCccH----HHHHHHHHHHHccCCHHHHHHHHHHHHhC---CCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHH
Q 043380           87 GGFHPDI----FTYATLLMGFRHAKDLQSLLEIVFEMKSC---CNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGE  158 (246)
Q Consensus        87 ~~~~p~~----~~~~~ll~~~~~~~~~~~a~~~~~~m~~~---~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~  158 (246)
                       +-.++.    .+.+.+-..+...|+.+.|..++......   .+..+. ..++..+...|...|++++    |..++++
T Consensus        86 -~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~----A~~~l~~  160 (434)
T 4b4t_Q           86 -MQFAKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKD----SLALIND  160 (434)
T ss_dssp             -HTSCHHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHH----HHHHHHH
T ss_pred             -HHccchHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHH----HHHHHHH
Confidence             111222    23334444455678999999998876431   233344 5678899999999999999    9999999


Q ss_pred             HHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCC-CCCchhhhHHHHHHHHHHHhcCChhHHHHHHH
Q 043380          159 IVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTG-TISPEVQEEAGHLLMEAALNDGQVDLALDKLS  237 (246)
Q Consensus       159 m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~  237 (246)
                      ..........-.....++..++..|...|++++|..++++....... ..++......+..+...+...|++++|...|.
T Consensus       161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~  240 (434)
T 4b4t_Q          161 LLREFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFF  240 (434)
T ss_dssp             HHHHHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHH
T ss_pred             HHHHHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence            87652211111122467899999999999999999999876532111 12333333467778888889999999999887


Q ss_pred             HHHh
Q 043380          238 NTIT  241 (246)
Q Consensus       238 ~m~~  241 (246)
                      +..+
T Consensus       241 ~a~~  244 (434)
T 4b4t_Q          241 ESFE  244 (434)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7653

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=98.69  E-value=1.6e-06  Score=57.02  Aligned_cols=109  Identities=10%  Similarity=-0.074  Sum_probs=90.4

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      ++..+..+...+...|++++|...|+......+.+...+..+...+...|++++|...+++..+.        .+.+...
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~--------~~~~~~~   74 (118)
T 1elw_A            3 QVNELKEKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDL--------KPDWGKG   74 (118)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--------CTTCHHH
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHh--------CcccHHH
Confidence            45678888999999999999999999876444567888999999999999999999999999886        2335778


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHH
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAM  135 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~l  135 (246)
                      +..+..++...|++++|.+.++...+   ..|+ ...+..+
T Consensus        75 ~~~~a~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~~~~l  112 (118)
T 1elw_A           75 YSRKAAALEFLNRFEEAKRTYEEGLK---HEANNPQLKEGL  112 (118)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHT---TCTTCHHHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHH---cCCCCHHHHHHH
Confidence            89999999999999999999999988   4455 4444443

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.68  E-value=1.9e-06  Score=66.43  Aligned_cols=198  Identities=7%  Similarity=-0.132  Sum_probs=140.8

Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCHHHHHHH-------HHHHHhcCCcchHHHHHHHHHhccCCCC------C-CC----CC
Q 043380           29 EAQRIDEAYQILESVEKGLEPDSLSYNIL-------ISACIKTKKLDVTMPFNEQLKDNGQKCS------S-GG----FH   90 (246)
Q Consensus        29 ~~g~~~~a~~~~~~~~~~~~~~~~t~~~l-------i~~~~~~~~~~~a~~~~~~m~~~~~~~~------~-~~----~~   90 (246)
                      +.++.+.|.+.|.+...--+-....|..+       ...+.+.++..++...+..-.+.  .+.      . .|    +.
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 LPMSEARSLDLFTEITNYDESACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQI--SMSTLNARIAIGGLYGDIT   95 (282)
T ss_dssp             TTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTTC--CGGGGCCEEECCTTTCCCE
T ss_pred             cCCCHHHHHHHHHHHHHhChhhhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhcC--ChhhhhhhhccCCcccccc
Confidence            68999999999999864445667888877       56666666666776666665542  110      0 11    11


Q ss_pred             c----cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCC
Q 043380           91 P----DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSN  166 (246)
Q Consensus        91 p----~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~  166 (246)
                      +    -...+-.+...+...|++++|.++|+.+.. .  .|+......+...+.+.+++++    |+..|+.....    
T Consensus        96 ~~v~~r~dl~LayA~~L~~~g~y~eA~~~l~~~~~-~--~p~~~~~~~~a~l~~~~~r~~d----A~~~l~~a~~~----  164 (282)
T 4f3v_A           96 YPVTSPLAITMGFAACEAAQGNYADAMEALEAAPV-A--GSEHLVAWMKAVVYGAAERWTD----VIDQVKSAGKW----  164 (282)
T ss_dssp             EECSSHHHHHHHHHHHHHHHTCHHHHHHHHTSSCC-T--TCHHHHHHHHHHHHHHTTCHHH----HHHHHTTGGGC----
T ss_pred             cccCCHhHHHHHHHHHHHHCCCHHHHHHHHHHHHh-c--CCchHHHHHHHHHHHHcCCHHH----HHHHHHHhhcc----
Confidence            0    122445567778889999999999999887 3  3764466677779999999999    99999844332    


Q ss_pred             CCCCcc--hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          167 PGLWPK--PHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       167 ~~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                       . .|.  ...+..+-.++...|++++|...|++.....   ..|............++.+.|+.++|..+|+++....+
T Consensus       165 -~-d~~~~~~a~~~LG~al~~LG~~~eAl~~l~~a~~g~---~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~P  239 (282)
T 4f3v_A          165 -P-DKFLAGAAGVAHGVAAANLALFTEAERRLTEANDSP---AGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTHP  239 (282)
T ss_dssp             -S-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTST---TTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSC
T ss_pred             -C-CcccHHHHHHHHHHHHHHCCCHHHHHHHHHHHhcCC---CCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC
Confidence             1 121  2467888899999999999999999986322   21221122566788889999999999999999987654

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.68  E-value=1.6e-07  Score=65.59  Aligned_cols=147  Identities=10%  Similarity=-0.028  Sum_probs=106.7

Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC----HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCC
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD----RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPG  168 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~----~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~  168 (246)
                      ..++..+-..|...|++++|...+++......-.++    ..++..+...+...|++++    |.+.++...........
T Consensus         9 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~----A~~~~~~a~~~~~~~~~   84 (164)
T 3ro3_A            9 GRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFET----ASEYYKKTLLLARQLKD   84 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHHHHHhCC
Confidence            457888888999999999999999987761111112    2478889999999999999    99999997765211111


Q ss_pred             CCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhc
Q 043380          169 LWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRW  243 (246)
Q Consensus       169 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  243 (246)
                      ......++..+...+...|++++|...+++........-.+.....++..+...+...|++++|.+.+++..+..
T Consensus        85 ~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~  159 (164)
T 3ro3_A           85 RAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEIS  159 (164)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHH
Confidence            111246788888999999999999999988653211111122223368889999999999999999999877643

>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=98.66  E-value=5e-07  Score=72.02  Aligned_cols=129  Identities=11%  Similarity=-0.005  Sum_probs=109.8

Q ss_pred             CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc----------------HHHHHHHHHHHHccCCHHHHH
Q 043380           50 DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD----------------IFTYATLLMGFRHAKDLQSLL  113 (246)
Q Consensus        50 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~----------------~~~~~~ll~~~~~~~~~~~a~  113 (246)
                      +...|..+-..|.+.|++++|...|++....         .|+                ...|..+-.+|.+.|++++|.
T Consensus       146 ~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~---------~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~  216 (336)
T 1p5q_A          146 QSTIVKERGTVYFKEGKYKQALLQYKKIVSW---------LEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAI  216 (336)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---------TTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH---------hhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            4667888999999999999999999999986         333                479999999999999999999


Q ss_pred             HHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHH
Q 043380          114 EIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIV  192 (246)
Q Consensus       114 ~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a  192 (246)
                      ..|++..+   +.|+ ...|..+..+|...|++++    |...|+...+.      -+-+..++..+..++...|+.++|
T Consensus       217 ~~~~~al~---~~p~~~~a~~~lg~~~~~~g~~~~----A~~~~~~al~l------~P~~~~a~~~l~~~~~~~~~~~~a  283 (336)
T 1p5q_A          217 ESCNKALE---LDSNNEKGLSRRGEAHLAVNDFEL----ARADFQKVLQL------YPNNKAAKTQLAVCQQRIRRQLAR  283 (336)
T ss_dssp             HHHHHHHH---HCTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------CSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHH---hCCCcHHHHHHHHHHHHHCCCHHH----HHHHHHHHHHH------CCCCHHHHHHHHHHHHHHHHHHHH
Confidence            99999998   4455 8889999999999999999    99999999886      233567888999999999999988


Q ss_pred             -hhHHHhhC
Q 043380          193 -KSPYRRMW  200 (246)
Q Consensus       193 -~~~~~~~~  200 (246)
                       ..++..|.
T Consensus       284 ~~~~~~~~~  292 (336)
T 1p5q_A          284 EKKLYANMF  292 (336)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence             44555543

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.63  E-value=1.7e-06  Score=58.62  Aligned_cols=97  Identities=8%  Similarity=-0.014  Sum_probs=86.7

Q ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-H
Q 043380           51 SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-R  129 (246)
Q Consensus        51 ~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~  129 (246)
                      ...+......|.+.|++++|.+.|++.++.        -+.+...|..+-.+|.+.|++++|...|+...+   +.|+ .
T Consensus        13 a~~~~~~G~~~~~~g~~~~A~~~~~~al~~--------~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~---~~p~~~   81 (126)
T 4gco_A           13 AQEEKNKGNEYFKKGDYPTAMRHYNEAVKR--------DPENAILYSNRAACLTKLMEFQRALDDCDTCIR---LDSKFI   81 (126)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--------CCCCHHHHHHHhhHHHhhccHHHHHHHHHHHHH---hhhhhh
Confidence            356778889999999999999999999986        244678999999999999999999999999988   5566 7


Q ss_pred             HHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          130 STFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       130 ~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ..|..+..+|...|++++    |.+.|+...+.
T Consensus        82 ~a~~~lg~~~~~~~~~~~----A~~~~~~al~l  110 (126)
T 4gco_A           82 KGYIRKAACLVAMREWSK----AQRAYEDALQV  110 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHH----HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHH----HHHHHHHHHHH
Confidence            889999999999999999    99999999886

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=98.63  E-value=3e-05  Score=60.81  Aligned_cols=206  Identities=7%  Similarity=-0.072  Sum_probs=156.6

Q ss_pred             CcCHHHHHHHHHHHHhcC--CHHHHHHHHHHHHhCCCCCHHHHHHHHHHH----Hhc---CCcchHHHHHHHHHhccCCC
Q 043380           14 KLNTIVMNAVIEASREAQ--RIDEAYQILESVEKGLEPDSLSYNILISAC----IKT---KKLDVTMPFNEQLKDNGQKC   84 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g--~~~~a~~~~~~~~~~~~~~~~t~~~li~~~----~~~---~~~~~a~~~~~~m~~~~~~~   84 (246)
                      +-+...||.--.++...|  +++++++.++.+....+-+...|+.--..+    ...   +++++++++++++.+.    
T Consensus        64 P~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nPk~y~aW~~R~~iL~~~~~~l~~~~~~~~EL~~~~~~l~~----  139 (306)
T 3dra_A           64 ASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDNEKNYQIWNYRQLIIGQIMELNNNDFDPYREFDILEAMLSS----  139 (306)
T ss_dssp             TTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHHHTTTCCCTHHHHHHHHHHHHH----
T ss_pred             cHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHCcccHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHh----
Confidence            345567888777888888  999999999988654466777887655555    555   7899999999999986    


Q ss_pred             CCCCCCccHHHHHHHHHHHHccCCHH--HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCC------hhhhhhHHHHHH
Q 043380           85 SSGGFHPDIFTYATLLMGFRHAKDLQ--SLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGS------IKVVGLYALCIF  156 (246)
Q Consensus        85 ~~~~~~p~~~~~~~ll~~~~~~~~~~--~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~------~~~~~~~a~~~~  156 (246)
                          -+-|..+|+.---.+.+.|+++  ++++.++.+.+ ... -|-..|+.-...+...+.      +++    +++.+
T Consensus       140 ----~pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~-~d~-~N~sAW~~R~~ll~~l~~~~~~~~~~e----El~~~  209 (306)
T 3dra_A          140 ----DPKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVID-TDL-KNNSAWSHRFFLLFSKKHLATDNTIDE----ELNYV  209 (306)
T ss_dssp             ----CTTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHH-HCT-TCHHHHHHHHHHHHSSGGGCCHHHHHH----HHHHH
T ss_pred             ----CCCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHH-hCC-CCHHHHHHHHHHHHhccccchhhhHHH----HHHHH
Confidence                3457788888888888888888  99999999998 322 346777766666666666      788    99999


Q ss_pred             HHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChh-HHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHH
Q 043380          157 GEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYD-IVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDK  235 (246)
Q Consensus       157 ~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~-~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~  235 (246)
                      +.....      -.-|...|+-+-..+.+.|+.. .+..+..++...+.....   ...++..+.+.|.+.|+.++|.++
T Consensus       210 ~~aI~~------~p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~---s~~al~~la~~~~~~~~~~~A~~~  280 (306)
T 3dra_A          210 KDKIVK------CPQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVT---SSFALETLAKIYTQQKKYNESRTV  280 (306)
T ss_dssp             HHHHHH------CSSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEES---CHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHh------CCCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCC---CHHHHHHHHHHHHccCCHHHHHHH
Confidence            999887      3456788999988998888854 455677776543211111   122788899999999999999999


Q ss_pred             HHHHHhh
Q 043380          236 LSNTITR  242 (246)
Q Consensus       236 ~~~m~~~  242 (246)
                      ++.+.++
T Consensus       281 ~~~l~~~  287 (306)
T 3dra_A          281 YDLLKSK  287 (306)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHhc
Confidence            9998763

>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=98.63  E-value=1.7e-06  Score=58.25  Aligned_cols=98  Identities=11%  Similarity=-0.021  Sum_probs=83.9

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      +...|..+-..+.+.|++++|...|++..+-.+.+...|..+..++.+.|++++|...|++..+.        -+.+...
T Consensus         3 ~a~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~--------~p~~~~~   74 (126)
T 3upv_A            3 KAEEARLEGKEYFTKSDWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEK--------DPNFVRA   74 (126)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHH
T ss_pred             hHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--------CCCcHHH
Confidence            35567788889999999999999998876434667888999999999999999999999999986        2335778


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHh
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKS  121 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~  121 (246)
                      |..+-.++...|++++|...|++..+
T Consensus        75 ~~~lg~~~~~~~~~~~A~~~~~~al~  100 (126)
T 3upv_A           75 YIRKATAQIAVKEYASALETLDAART  100 (126)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCHHHHHHHHHHHHH
Confidence            89999999999999999999999887

>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=98.61  E-value=9e-07  Score=63.38  Aligned_cols=123  Identities=6%  Similarity=-0.009  Sum_probs=99.1

Q ss_pred             HhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC-CHHHHHHHHHH-H
Q 043380           62 IKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL-DRSTFTAMVDA-L  139 (246)
Q Consensus        62 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~-~  139 (246)
                      ...|++++|...+++..+.        .+.+...|..+...|...|++++|...|+....   ..| +...+..+... +
T Consensus        21 ~~~~~~~~A~~~~~~al~~--------~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~---~~p~~~~~~~~la~~l~   89 (177)
T 2e2e_A           21 ASQQNPEAQLQALQDKIRA--------NPQNSEQWALLGEYYLWQNDYSNSLLAYRQALQ---LRGENAELYAALATVLY   89 (177)
T ss_dssp             C-----CCCCHHHHHHHHH--------CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HHCSCHHHHHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHh--------CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---cCCCCHHHHHHHHHHHH
Confidence            4568899999999998876        244678999999999999999999999999988   445 46778888888 7


Q ss_pred             HhcCCh--hhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCC
Q 043380          140 LYSGSI--KVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTG  205 (246)
Q Consensus       140 ~~~~~~--~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  205 (246)
                      ...|++  ++    |...++...+.      -+.+...+..+...|...|++++|...|+......+.
T Consensus        90 ~~~~~~~~~~----A~~~~~~al~~------~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~  147 (177)
T 2e2e_A           90 YQASQHMTAQ----TRAMIDKALAL------DSNEITALMLLASDAFMQANYAQAIELWQKVMDLNSP  147 (177)
T ss_dssp             HHTTTCCCHH----HHHHHHHHHHH------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCT
T ss_pred             HhcCCcchHH----HHHHHHHHHHh------CCCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhhCCC
Confidence            789998  99    99999999886      2334678888999999999999999999998765443

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.61  E-value=8.1e-07  Score=62.32  Aligned_cols=98  Identities=8%  Similarity=-0.098  Sum_probs=87.6

Q ss_pred             CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-
Q 043380           50 DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-  128 (246)
Q Consensus        50 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-  128 (246)
                      +...+..+-..+.+.|++++|...|++....        -+-+...|..+-.+|...|++++|...|++..+   +.|+ 
T Consensus        35 ~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~--------~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~---l~P~~  103 (151)
T 3gyz_A           35 MMDDIYSYAYDFYNKGRIEEAEVFFRFLCIY--------DFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFA---LGKND  103 (151)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HSSSC
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--------CCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHh---hCCCC
Confidence            4567888888999999999999999999986        234678999999999999999999999999998   5566 


Q ss_pred             HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          129 RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       129 ~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ...|..+..+|...|++++    |...|+...+.
T Consensus       104 ~~~~~~lg~~~~~lg~~~e----A~~~~~~al~l  133 (151)
T 3gyz_A          104 YTPVFHTGQCQLRLKAPLK----AKECFELVIQH  133 (151)
T ss_dssp             CHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh
Confidence            7788999999999999999    99999999986

>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=98.60  E-value=1.2e-06  Score=59.35  Aligned_cols=110  Identities=15%  Similarity=0.100  Sum_probs=87.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc----
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD----   92 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~----   92 (246)
                      ...+..+-..+.+.|++++|++.|++...-.+.+...|+.+-.+|...|++++|++.+++.++..     ....++    
T Consensus         8 A~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~-----~~~~~~~~~~   82 (127)
T 4gcn_A            8 AIAEKDLGNAAYKQKDFEKAHVHYDKAIELDPSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVG-----RETRADYKLI   82 (127)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-----HHTTCCHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhC-----cccchhhHHH
Confidence            45677889999999999999999998764335678889999999999999999999999988641     001111    


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHH
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTA  134 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~  134 (246)
                      ..+|..+-.++...|++++|.+.|++...   ..||..+...
T Consensus        83 a~~~~~lg~~~~~~~~~~~A~~~~~kal~---~~~~~~~~~~  121 (127)
T 4gcn_A           83 AKAMSRAGNAFQKQNDLSLAVQWFHRSLS---EFRDPELVKK  121 (127)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HSCCHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHh---hCcCHHHHHH
Confidence            24788888899999999999999999887   4577655443

>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=98.59  E-value=9.5e-08  Score=70.01  Aligned_cols=161  Identities=8%  Similarity=-0.032  Sum_probs=105.8

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc---------
Q 043380           21 NAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP---------   91 (246)
Q Consensus        21 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p---------   91 (246)
                      +....+....|+++++.+.|+.-..........+..+...+...|++++|...|.+.....      .-.|         
T Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~------~~~~~~~~~~~~~   81 (198)
T 2fbn_A            8 HHHSSGRENLYFQGAKKSIYDYTDEEKVQSAFDIKEEGNEFFKKNEINEAIVKYKEALDFF------IHTEEWDDQILLD   81 (198)
T ss_dssp             --------------CCCSGGGCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT------TTCTTCCCHHHHH
T ss_pred             cchhhhhhhhhhccccCchhhCCHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH------hcccccchhhHHH
Confidence            3344455556677777766654322112345667788888899999999999999998751      0111         


Q ss_pred             -----cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcC
Q 043380           92 -----DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCS  165 (246)
Q Consensus        92 -----~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~  165 (246)
                           ....|..+..+|...|++++|...++....   +.|+ ...+..+..+|...|++++    |...|+...+.   
T Consensus        82 ~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~---~~p~~~~~~~~lg~~~~~~~~~~~----A~~~~~~al~~---  151 (198)
T 2fbn_A           82 KKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLK---IDKNNVKALYKLGVANMYFGFLEE----AKENLYKAASL---  151 (198)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HSTTCHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHH---
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH---hCcccHHHHHHHHHHHHHcccHHH----HHHHHHHHHHH---
Confidence                 127888899999999999999999999988   3454 7888899999999999999    99999998876   


Q ss_pred             CCCCCcchhhHHHHHHHHHhcCChhHHh-hHHHhhC
Q 043380          166 NPGLWPKPHLYVSMMHELAARVDYDIVK-SPYRRMW  200 (246)
Q Consensus       166 ~~~~~p~~~~~~~li~~~~~~g~~~~a~-~~~~~~~  200 (246)
                         -+-+...+..+..++...++.+++. ..+..+.
T Consensus       152 ---~p~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~f  184 (198)
T 2fbn_A          152 ---NPNNLDIRNSYELCVNKLKEARKKDKLTFGGMF  184 (198)
T ss_dssp             ---STTCHHHHHHHHHHHHHHHHHHC----------
T ss_pred             ---CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence               2234577788888888888777766 5555554

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=98.58  E-value=2.7e-05  Score=64.53  Aligned_cols=192  Identities=9%  Similarity=-0.022  Sum_probs=123.5

Q ss_pred             cCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhc----CCcchHHHHHHHHHhccCCCCCC
Q 043380           15 LNTIVMNAVIEASREAQ---RIDEAYQILESVEKGLEPDSLSYNILISACIKT----KKLDVTMPFNEQLKDNGQKCSSG   87 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g---~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~----~~~~~a~~~~~~m~~~~~~~~~~   87 (246)
                      .++..+..|-..|.+.|   +.++|++.|+..-..-.++...+..+-..|...    +++++|..+|++.. .       
T Consensus       174 ~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa-~-------  245 (452)
T 3e4b_A          174 TTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRGTVTAQRVDSVARVLGDATLGTPDEKTAQALLEKIA-P-------  245 (452)
T ss_dssp             TCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHG-G-------
T ss_pred             CCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHc-C-------
Confidence            33446777777777788   778888888776533356666556666666554    57788888888776 4       


Q ss_pred             CCCccHHHHHHHHHH-H--HccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcC-----ChhhhhhHHHHHHHHH
Q 043380           88 GFHPDIFTYATLLMG-F--RHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSG-----SIKVVGLYALCIFGEI  159 (246)
Q Consensus        88 ~~~p~~~~~~~ll~~-~--~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~-----~~~~~~~~a~~~~~~m  159 (246)
                      |   +...+..|-.. |  ...+++++|.+.|++..+ .|   +...+..|-..|. .|     ++++    |.+.|+..
T Consensus       246 g---~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~-~g---~~~A~~~Lg~~y~-~G~g~~~d~~~----A~~~~~~A  313 (452)
T 3e4b_A          246 G---YPASWVSLAQLLYDFPELGDVEQMMKYLDNGRA-AD---QPRAELLLGKLYY-EGKWVPADAKA----AEAHFEKA  313 (452)
T ss_dssp             G---STHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHH-TT---CHHHHHHHHHHHH-HCSSSCCCHHH----HHHHHHTT
T ss_pred             C---CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHH-CC---CHHHHHHHHHHHH-cCCCCCCCHHH----HHHHHHHH
Confidence            2   22334444444 3  457788888888888877 55   5666666666666 44     7777    88777766


Q ss_pred             HHhhcCCCCCCcchhhHHHHHHHHHh----cCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHh----cCChhH
Q 043380          160 VKRVCSNPGLWPKPHLYVSMMHELAA----RVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALN----DGQVDL  231 (246)
Q Consensus       160 ~~~~~~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~  231 (246)
                      . .     |   +...+..|-..|..    ..++++|...|+.....+  ...      +...|-..|..    ..++++
T Consensus       314 a-~-----g---~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g--~~~------A~~~Lg~~y~~G~g~~~d~~~  376 (452)
T 3e4b_A          314 V-G-----R---EVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNG--QNS------ADFAIAQLFSQGKGTKPDPLN  376 (452)
T ss_dssp             T-T-----T---CHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTT--CTT------HHHHHHHHHHSCTTBCCCHHH
T ss_pred             h-C-----C---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhC--hHH------HHHHHHHHHHhCCCCCCCHHH
Confidence            4 3     2   44556666666555    337888888888776543  111      45556666653    457788


Q ss_pred             HHHHHHHHHhhc
Q 043380          232 ALDKLSNTITRW  243 (246)
Q Consensus       232 a~~~~~~m~~~g  243 (246)
                      |..+|+.-.+.|
T Consensus       377 A~~~~~~A~~~g  388 (452)
T 3e4b_A          377 AYVFSQLAKAQD  388 (452)
T ss_dssp             HHHHHHHHHTTC
T ss_pred             HHHHHHHHHHCC
Confidence            888887766655

>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=98.57  E-value=9.9e-07  Score=61.58  Aligned_cols=98  Identities=9%  Similarity=-0.137  Sum_probs=65.7

Q ss_pred             CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-
Q 043380           50 DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-  128 (246)
Q Consensus        50 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-  128 (246)
                      +...+..+...+...|++++|...|++....        -+.+...|..+-.+|...|++++|...|++...   +.|+ 
T Consensus        20 ~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~--------~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~---l~p~~   88 (148)
T 2vgx_A           20 TLEQLYSLAFNQYQSGXYEDAHXVFQALCVL--------DHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAV---MDIXE   88 (148)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HSTTC
T ss_pred             hHHHHHHHHHHHHHcCChHHHHHHHHHHHHc--------CcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHh---cCCCC
Confidence            4445566666677777777777777777664        133556666677777777777777777777766   3344 


Q ss_pred             HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          129 RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       129 ~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ...+..+..+|...|++++    |...|+...+.
T Consensus        89 ~~~~~~lg~~~~~~g~~~~----A~~~~~~al~~  118 (148)
T 2vgx_A           89 PRFPFHAAECLLQXGELAE----AESGLFLAQEL  118 (148)
T ss_dssp             THHHHHHHHHHHHTTCHHH----HHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHcCCHHH----HHHHHHHHHHH
Confidence            5566667777777777777    77777776654

>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=98.56  E-value=1e-06  Score=61.57  Aligned_cols=99  Identities=7%  Similarity=-0.133  Sum_probs=85.8

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHH
Q 043380           15 LNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIF   94 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~   94 (246)
                      .+...+..+...+.+.|++++|...|+.....-+.+...|..+-.+|...|++++|...|++....        -+.+..
T Consensus        19 ~~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--------~p~~~~   90 (148)
T 2vgx_A           19 DTLEQLYSLAFNQYQSGXYEDAHXVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVM--------DIXEPR   90 (148)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------STTCTH
T ss_pred             hhHHHHHHHHHHHHHcCChHHHHHHHHHHHHcCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc--------CCCCch
Confidence            355667778889999999999999999876444668889999999999999999999999999986        233567


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHh
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKS  121 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~  121 (246)
                      .|..+-.+|...|++++|...|+...+
T Consensus        91 ~~~~lg~~~~~~g~~~~A~~~~~~al~  117 (148)
T 2vgx_A           91 FPFHAAECLLQXGELAEAESGLFLAQE  117 (148)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            888999999999999999999999887

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.55  E-value=2.3e-06  Score=60.46  Aligned_cols=100  Identities=7%  Similarity=-0.097  Sum_probs=87.3

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      ..+...|..+...+.+.|++++|++.|++...-.+.+...|..+..+|...|++++|...|++..+.        -+-+.
T Consensus         8 ~~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--------~p~~~   79 (164)
T 3sz7_A            8 TPESDKLKSEGNAAMARKEYSKAIDLYTQALSIAPANPIYLSNRAAAYSASGQHEKAAEDAELATVV--------DPKYS   79 (164)
T ss_dssp             CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCH
T ss_pred             hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--------CCCCH
Confidence            3456778889999999999999999999876434568889999999999999999999999999986        23357


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHh
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKS  121 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~  121 (246)
                      ..|..+-.+|...|++++|...|++..+
T Consensus        80 ~~~~~lg~~~~~~g~~~~A~~~~~~al~  107 (164)
T 3sz7_A           80 KAWSRLGLARFDMADYKGAKEAYEKGIE  107 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            7899999999999999999999999988

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.55  E-value=9.7e-07  Score=57.55  Aligned_cols=97  Identities=8%  Similarity=-0.085  Sum_probs=66.8

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc--cHH
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP--DIF   94 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p--~~~   94 (246)
                      ...|..+...+.+.|++++|...|+...+..+.+...|..+...+...|++++|...|++..+.        .+.  +..
T Consensus         6 ~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--------~~~~~~~~   77 (112)
T 2kck_A            6 PEEYYLEGVLQYDAGNYTESIDLFEKAIQLDPEESKYWLMKGKALYNLERYEEAVDCYNYVINV--------IEDEYNKD   77 (112)
T ss_dssp             TTGGGGHHHHHHSSCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--------SCCTTCHH
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--------CcccchHH
Confidence            4455666667777777777777777765333455666777777777777777777777777764        122  466


Q ss_pred             HHHHHHHHHHcc-CCHHHHHHHHHHHHh
Q 043380           95 TYATLLMGFRHA-KDLQSLLEIVFEMKS  121 (246)
Q Consensus        95 ~~~~ll~~~~~~-~~~~~a~~~~~~m~~  121 (246)
                      .+..+..++... |++++|.+.++....
T Consensus        78 ~~~~l~~~~~~~~~~~~~A~~~~~~~~~  105 (112)
T 2kck_A           78 VWAAKADALRYIEGKEVEAEIAEARAKL  105 (112)
T ss_dssp             HHHHHHHHHTTCSSCSHHHHHHHHHHGG
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHhh
Confidence            777777777777 777777777777766

>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=98.54  E-value=2.9e-06  Score=61.98  Aligned_cols=132  Identities=10%  Similarity=-0.035  Sum_probs=100.1

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCH----------------HHHHHHHHHHHhcCCcchHHHHHHHHHh
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDS----------------LSYNILISACIKTKKLDVTMPFNEQLKD   79 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~----------------~t~~~li~~~~~~~~~~~a~~~~~~m~~   79 (246)
                      ....+..+...+.+.|++++|...|++...-.+.+.                ..|..+..+|...|++++|...+++..+
T Consensus        37 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~  116 (198)
T 2fbn_A           37 SAFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLK  116 (198)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            345677788889999999999999998764223333                7888899999999999999999999998


Q ss_pred             ccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHH-HHHH
Q 043380           80 NGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYAL-CIFG  157 (246)
Q Consensus        80 ~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~-~~~~  157 (246)
                      .        -+.+...|..+..+|...|++++|...|+...+   +.|+ ...+..+...+...++..+    +. ..|.
T Consensus       117 ~--------~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~---~~p~~~~~~~~l~~~~~~~~~~~~----~~~~~~~  181 (198)
T 2fbn_A          117 I--------DKNNVKALYKLGVANMYFGFLEEAKENLYKAAS---LNPNNLDIRNSYELCVNKLKEARK----KDKLTFG  181 (198)
T ss_dssp             H--------STTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH---HSTTCHHHHHHHHHHHHHHHHHHC-----------
T ss_pred             h--------CcccHHHHHHHHHHHHHcccHHHHHHHHHHHHH---HCCCcHHHHHHHHHHHHHHHHHHH----HHHHHHH
Confidence            6        244677899999999999999999999999988   4565 6778888888888887777    65 5555


Q ss_pred             HHHHh
Q 043380          158 EIVKR  162 (246)
Q Consensus       158 ~m~~~  162 (246)
                      .+...
T Consensus       182 ~~f~~  186 (198)
T 2fbn_A          182 GMFDK  186 (198)
T ss_dssp             -----
T ss_pred             HHhcc
Confidence            55443

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.54  E-value=1e-06  Score=61.38  Aligned_cols=143  Identities=8%  Similarity=-0.082  Sum_probs=101.8

Q ss_pred             HHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhC---CCCCCC
Q 043380           52 LSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSC---CNLILD  128 (246)
Q Consensus        52 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~---~~~~p~  128 (246)
                      .++..+...+...|++++|...+.+..+...+.  .....-..++..+...+...|++++|...+++....   .+-.+.
T Consensus        10 ~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~--~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~   87 (164)
T 3ro3_A           10 RAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEF--GDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAV   87 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH--TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHh--CCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHH
Confidence            457777888888999999999998887641000  000011247888999999999999999999987651   111111


Q ss_pred             -HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhC
Q 043380          129 -RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMW  200 (246)
Q Consensus       129 -~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  200 (246)
                       ...+..+...+...|++++    |...+++..+.............++..+...+...|++++|.+.+++..
T Consensus        88 ~~~~~~~l~~~~~~~~~~~~----A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~  156 (164)
T 3ro3_A           88 EAQSCYSLGNTYTLLQDYEK----AIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHL  156 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhHHH----HHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence             4567888899999999999    9999998765421110111124678888899999999999999998764

>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=98.53  E-value=2.9e-06  Score=70.90  Aligned_cols=151  Identities=11%  Similarity=0.069  Sum_probs=108.8

Q ss_pred             HHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHH
Q 043380           58 ISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMV  136 (246)
Q Consensus        58 i~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li  136 (246)
                      ...+.+.|++++|.+.|++..+.        -+.+...|..+..+|.+.|++++|.+.+++..+   +.|+ ...|..+.
T Consensus        13 g~~~~~~g~~~~A~~~~~~Al~~--------~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~---l~p~~~~~~~~lg   81 (477)
T 1wao_1           13 ANDYFKAKDYENAIKFYSQAIEL--------NPSNAIYYGNRSLAYLRTECYGYALGDATRAIE---LDKKYIKGYYRRA   81 (477)
T ss_dssp             SSSTTTTTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---SCTTCHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHh--------CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHH---hCCCCHHHHHHHH
Confidence            34456789999999999999986        233578999999999999999999999999998   4565 78899999


Q ss_pred             HHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc-chhhHHHHHHH--HHhcCChhHHhhHHH-----------hhCCC
Q 043380          137 DALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP-KPHLYVSMMHE--LAARVDYDIVKSPYR-----------RMWPD  202 (246)
Q Consensus       137 ~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p-~~~~~~~li~~--~~~~g~~~~a~~~~~-----------~~~~~  202 (246)
                      .+|...|++++    |.+.|++..+.       .| +...+..+..+  +.+.|++++|.+.++           +....
T Consensus        82 ~~~~~~g~~~e----A~~~~~~al~~-------~p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~al~~  150 (477)
T 1wao_1           82 ASNMALGKFRA----ALRDYETVVKV-------KPHDKDAKMKYQECNKIVKQKAFERAIAGDEHKRSVVDSLDIESMTI  150 (477)
T ss_dssp             HHHHHHTCHHH----HHHHHHHHHHH-------STTCTTHHHHHHHHHHHHHHHHHCCC------CCSTTTCCTTSSCCC
T ss_pred             HHHHHcCCHHH----HHHHHHHHHHh-------CCCCHHHHHHHHHHHHHHHHHHHHHHhccccccchhHhhhhhhhccc
Confidence            99999999999    99999999886       23 33455555555  888899999999998           33322


Q ss_pred             CCCCCCch-----hhhHHHHHHHHHHHhcCChh
Q 043380          203 STGTISPE-----VQEEAGHLLMEAALNDGQVD  230 (246)
Q Consensus       203 ~~~~~~~~-----~~~~~~~~li~~~~~~g~~~  230 (246)
                      ......+.     ........++..+...+.+.
T Consensus       151 ~~~~~~~~~~~~~itl~~l~~lie~l~~~~~l~  183 (477)
T 1wao_1          151 EDEYSGPKLEDGKVTISFMKELMQWYKDQKKLH  183 (477)
T ss_dssp             CTTCCSCCCGGGSCCHHHHHHHHHHHHTCCCCC
T ss_pred             cccccccccccccccHHHHHHHHHHHHcCCCCC
Confidence            22222221     11224566777777776654

>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=98.53  E-value=1.6e-06  Score=58.19  Aligned_cols=113  Identities=11%  Similarity=0.099  Sum_probs=82.8

Q ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCC--CCC
Q 043380           51 SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNL--ILD  128 (246)
Q Consensus        51 ~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~--~p~  128 (246)
                      ...|..+...+...|++++|...|.+....        .+.+...+..+...|...|++++|...++.... ..-  .++
T Consensus         4 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~--------~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~-~~~~~~~~   74 (131)
T 1elr_A            4 ALKEKELGNDAYKKKDFDTALKHYDKAKEL--------DPTNMTYITNQAAVYFEKGDYNKCRELCEKAIE-VGRENRED   74 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH-HHHHSTTC
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhc--------CCccHHHHHHHHHHHHHhccHHHHHHHHHHHHh-hccccchh
Confidence            356777778888888899999998888875        234567788888888888999999888888776 211  112


Q ss_pred             ----HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHH
Q 043380          129 ----RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHEL  183 (246)
Q Consensus       129 ----~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~  183 (246)
                          ..++..+...|...|++++    |.+.|+...+.       .|+......+..+.
T Consensus        75 ~~~~~~~~~~la~~~~~~~~~~~----A~~~~~~~~~~-------~~~~~~~~~l~~~~  122 (131)
T 1elr_A           75 YRQIAKAYARIGNSYFKEEKYKD----AIHFYNKSLAE-------HRTPDVLKKCQQAE  122 (131)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-------CCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhccHHH----HHHHHHHHHHh-------CCCHHHHHHHHHHH
Confidence                5677788888888889888    88888888776       34555444444433

>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=9e-07  Score=61.15  Aligned_cols=98  Identities=9%  Similarity=-0.132  Sum_probs=75.8

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      +...+..+...+.+.|++++|...|+.....-+.+...|..+..+|...|++++|...|++....        -+.+...
T Consensus        17 ~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--------~p~~~~~   88 (142)
T 2xcb_A           17 TLEQLYALGFNQYQAGKWDDAQKIFQALCMLDHYDARYFLGLGACRQSLGLYEQALQSYSYGALM--------DINEPRF   88 (142)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCTHH
T ss_pred             HHHHHHHHHHHHHHHccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc--------CCCCcHH
Confidence            34455566677888888888888888875433557777888888888888888888888888875        1334567


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHh
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKS  121 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~  121 (246)
                      |..+-.+|...|++++|...|+...+
T Consensus        89 ~~~lg~~~~~~g~~~~A~~~~~~al~  114 (142)
T 2xcb_A           89 PFHAAECHLQLGDLDGAESGFYSARA  114 (142)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            77888888888888888888888777

>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=98.52  E-value=4.1e-06  Score=56.97  Aligned_cols=99  Identities=6%  Similarity=-0.121  Sum_probs=61.9

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHH
Q 043380           15 LNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIF   94 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~   94 (246)
                      .++..|..+...+.+.|++++|...|+....-.+.+...|..+..++...|++++|...+++....        .+.+..
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--------~p~~~~   78 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALEL--------DGQSVK   78 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHH
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhCcCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--------CchhHH
Confidence            455666666666667777777777766654323445566666666666667777777766666654        122455


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHh
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKS  121 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~  121 (246)
                      .|..+..+|...|++++|...|+...+
T Consensus        79 ~~~~l~~~~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           79 AHFFLGQCQLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            666666666666666666666666555

>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=98.51  E-value=4.5e-06  Score=56.08  Aligned_cols=97  Identities=5%  Similarity=-0.049  Sum_probs=86.0

Q ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-H
Q 043380           51 SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-R  129 (246)
Q Consensus        51 ~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~  129 (246)
                      ...|..+-..+.+.|++++|...|++..+.        -+.+...|..+..+|.+.|++++|...|+...+   +.|+ .
T Consensus         4 a~~~~~~g~~~~~~~~~~~A~~~~~~al~~--------~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~---~~p~~~   72 (126)
T 3upv_A            4 AEEARLEGKEYFTKSDWPNAVKAYTEMIKR--------APEDARGYSNRAAALAKLMSFPEAIADCNKAIE---KDPNFV   72 (126)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--------CCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHH---hCCCcH
Confidence            456778888899999999999999999986        244678999999999999999999999999988   4565 7


Q ss_pred             HHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          130 STFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       130 ~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ..|..+..++...|++++    |...|+...+.
T Consensus        73 ~~~~~lg~~~~~~~~~~~----A~~~~~~al~~  101 (126)
T 3upv_A           73 RAYIRKATAQIAVKEYAS----ALETLDAARTK  101 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHH----HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCHHH----HHHHHHHHHHh
Confidence            889999999999999999    99999998876

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.51  E-value=6.7e-06  Score=56.45  Aligned_cols=111  Identities=7%  Similarity=-0.090  Sum_probs=90.1

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC----HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCC
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPD----SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGF   89 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~----~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~   89 (246)
                      +.+...+..+...+.+.|++++|.+.|+...+. .|+    ...|..+..+|...+++++|...+++..+.        .
T Consensus        25 ~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~-~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~--------~   95 (148)
T 2dba_A           25 ASSVEQLRKEGNELFKCGDYGGALAAYTQALGL-DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEK--------D   95 (148)
T ss_dssp             CCCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTS-CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------T
T ss_pred             hHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH-cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhh--------C
Confidence            457788889999999999999999999987643 455    678888899999999999999999999875        2


Q ss_pred             CccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHH
Q 043380           90 HPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMV  136 (246)
Q Consensus        90 ~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li  136 (246)
                      +.+...+..+..+|...|++++|...|++...   ..|+ ...+..+.
T Consensus        96 ~~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~---~~p~~~~~~~~l~  140 (148)
T 2dba_A           96 GGDVKALYRRSQALEKLGRLDQAVLDLQRCVS---LEPKNKVFQEALR  140 (148)
T ss_dssp             SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH---HCSSCHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---cCCCcHHHHHHHH
Confidence            33577888899999999999999999999988   4465 44444333

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.50  E-value=9e-06  Score=55.79  Aligned_cols=99  Identities=9%  Similarity=-0.111  Sum_probs=87.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc----HHHHHHHHHHHHccCCHHHHHHHHHHHHhCC
Q 043380           48 EPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD----IFTYATLLMGFRHAKDLQSLLEIVFEMKSCC  123 (246)
Q Consensus        48 ~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~  123 (246)
                      +.+...+..+...+...|++++|...|++..+.         .|+    ...|..+..+|...|++++|...++....  
T Consensus        25 ~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~---------~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~--   93 (148)
T 2dba_A           25 ASSVEQLRKEGNELFKCGDYGGALAAYTQALGL---------DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIE--   93 (148)
T ss_dssp             CCCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTS---------CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--
T ss_pred             hHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH---------cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHh--
Confidence            346778888999999999999999999999975         465    67888999999999999999999999888  


Q ss_pred             CCCC-CHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          124 NLIL-DRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       124 ~~~p-~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                       ..| +...+..+...|...|++++    |...|++....
T Consensus        94 -~~~~~~~~~~~~a~~~~~~~~~~~----A~~~~~~al~~  128 (148)
T 2dba_A           94 -KDGGDVKALYRRSQALEKLGRLDQ----AVLDLQRCVSL  128 (148)
T ss_dssp             -HTSCCHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHH
T ss_pred             -hCccCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHc
Confidence             345 47788899999999999999    99999999886

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=98.49  E-value=2.7e-05  Score=64.61  Aligned_cols=189  Identities=11%  Similarity=0.028  Sum_probs=136.2

Q ss_pred             HHHHHHHHHHHHhcCCHH----HHHHHHHHHHhCCCCCHHHHHHHHHHHHhcC---CcchHHHHHHHHHhccCCCCCCCC
Q 043380           17 TIVMNAVIEASREAQRID----EAYQILESVEKGLEPDSLSYNILISACIKTK---KLDVTMPFNEQLKDNGQKCSSGGF   89 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~----~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~---~~~~a~~~~~~m~~~~~~~~~~~~   89 (246)
                      +..+..|...|...+.++    .+..+++....   .+...+..|-..|...|   +.++|.++|++..+.|        
T Consensus       141 ~~a~~~Lg~~y~~~~~~~~~~~~a~~~~~~a~~---~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g--------  209 (452)
T 3e4b_A          141 PEAGLAQVLLYRTQGTYDQHLDDVERICKAALN---TTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRG--------  209 (452)
T ss_dssp             TTHHHHHHHHHHHHTCGGGGHHHHHHHHHHHTT---TCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT--------
T ss_pred             HHHHHHHHHHHHcCCCcccCHHHHHHHHHHHHc---CCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCC--------
Confidence            334555666666666444    44444444432   33348888888999999   9999999999999873        


Q ss_pred             CccHHHHHHHHHHHHcc----CCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHH-H--HhcCChhhhhhHHHHHHHHHHHh
Q 043380           90 HPDIFTYATLLMGFRHA----KDLQSLLEIVFEMKSCCNLILDRSTFTAMVDA-L--LYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        90 ~p~~~~~~~ll~~~~~~----~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~-~--~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      .++...+..|-..|...    +++++|...|+....     -+...+..|-.. |  ...+++++    |.+.|+...+.
T Consensus       210 ~~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa~-----g~~~a~~~Lg~~~~~~~~~~d~~~----A~~~~~~Aa~~  280 (452)
T 3e4b_A          210 TVTAQRVDSVARVLGDATLGTPDEKTAQALLEKIAP-----GYPASWVSLAQLLYDFPELGDVEQ----MMKYLDNGRAA  280 (452)
T ss_dssp             CSCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHGG-----GSTHHHHHHHHHHHHSGGGCCHHH----HHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHcC-----CCHHHHHHHHHHHHhCCCCCCHHH----HHHHHHHHHHC
Confidence            55666666777777554    799999999998761     245566666665 3  56899999    99999998876


Q ss_pred             hcCCCCCCcchhhHHHHHHHHHhcC-----ChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHh----cCChhHHH
Q 043380          163 VCSNPGLWPKPHLYVSMMHELAARV-----DYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALN----DGQVDLAL  233 (246)
Q Consensus       163 ~~~~~~~~p~~~~~~~li~~~~~~g-----~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~a~  233 (246)
                           |   +...+..|-..|. .|     ++++|.+.|++.. .  +.  +.    ++..|-..|..    ..++++|.
T Consensus       281 -----g---~~~A~~~Lg~~y~-~G~g~~~d~~~A~~~~~~Aa-~--g~--~~----A~~~Lg~~y~~G~g~~~d~~~A~  342 (452)
T 3e4b_A          281 -----D---QPRAELLLGKLYY-EGKWVPADAKAAEAHFEKAV-G--RE--VA----ADYYLGQIYRRGYLGKVYPQKAL  342 (452)
T ss_dssp             -----T---CHHHHHHHHHHHH-HCSSSCCCHHHHHHHHHTTT-T--TC--HH----HHHHHHHHHHTTTTSSCCHHHHH
T ss_pred             -----C---CHHHHHHHHHHHH-cCCCCCCCHHHHHHHHHHHh-C--CC--HH----HHHHHHHHHHCCCCCCcCHHHHH
Confidence                 4   5667777777776 55     9999999999986 2  22  11    56667777766    34899999


Q ss_pred             HHHHHHHhhc
Q 043380          234 DKLSNTITRW  243 (246)
Q Consensus       234 ~~~~~m~~~g  243 (246)
                      ++|+.-.+.|
T Consensus       343 ~~~~~Aa~~g  352 (452)
T 3e4b_A          343 DHLLTAARNG  352 (452)
T ss_dssp             HHHHHHHTTT
T ss_pred             HHHHHHHhhC
Confidence            9999887765

>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=98.49  E-value=4.2e-06  Score=56.92  Aligned_cols=100  Identities=8%  Similarity=-0.070  Sum_probs=78.8

Q ss_pred             CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC
Q 043380           48 EPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL  127 (246)
Q Consensus        48 ~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p  127 (246)
                      +.+...|..+...+...|++++|...|.+....        .+.+...|..+..++...|++++|...++...+   +.|
T Consensus         6 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--------~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~---~~p   74 (137)
T 3q49_B            6 SPSAQELKEQGNRLFVGRKYPEAAACYGRAITR--------NPLVAVYYTNRALCYLKMQQPEQALADCRRALE---LDG   74 (137)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCT
T ss_pred             cccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhh--------CcCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHH---hCc
Confidence            346677888888888888888888888888875        233567888888888888888888888888877   335


Q ss_pred             C-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          128 D-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       128 ~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      + ...+..+...|...|++++    |...|+.....
T Consensus        75 ~~~~~~~~l~~~~~~~~~~~~----A~~~~~~a~~~  106 (137)
T 3q49_B           75 QSVKAHFFLGQCQLEMESYDE----AIANLQRAYSL  106 (137)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHhhHHH----HHHHHHHHHHH
Confidence            4 6778888888888888888    88888887765

>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=98.49  E-value=2.8e-06  Score=57.60  Aligned_cols=106  Identities=11%  Similarity=0.115  Sum_probs=86.2

Q ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC--
Q 043380           51 SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD--  128 (246)
Q Consensus        51 ~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~--  128 (246)
                      ...+..+...+.+.|++++|++.|.+.++.        -+-+...|+.+-.+|...|++++|.+.++...+   +.|+  
T Consensus         8 A~a~~~lG~~~~~~~~~~~A~~~y~~Al~~--------~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~---~~~~~~   76 (127)
T 4gcn_A            8 AIAEKDLGNAAYKQKDFEKAHVHYDKAIEL--------DPSNITFYNNKAAVYFEEKKFAECVQFCEKAVE---VGRETR   76 (127)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HHHHTT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--------CCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHH---hCcccc
Confidence            346778889999999999999999999986        234577899999999999999999999998876   2222  


Q ss_pred             ------HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHH
Q 043380          129 ------RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVS  178 (246)
Q Consensus       129 ------~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~  178 (246)
                            ..+|..+...+...|++++    |++.|+.....       .||..+...
T Consensus        77 ~~~~~~a~~~~~lg~~~~~~~~~~~----A~~~~~kal~~-------~~~~~~~~~  121 (127)
T 4gcn_A           77 ADYKLIAKAMSRAGNAFQKQNDLSL----AVQWFHRSLSE-------FRDPELVKK  121 (127)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-------SCCHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHHcCCHHH----HHHHHHHHHhh-------CcCHHHHHH
Confidence                  2467888889999999999    99999998775       466554443

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.48  E-value=4.5e-06  Score=58.98  Aligned_cols=99  Identities=9%  Similarity=-0.021  Sum_probs=87.0

Q ss_pred             CCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC
Q 043380           49 PDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD  128 (246)
Q Consensus        49 ~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~  128 (246)
                      .+...|..+...+...|++++|...|++..+.        .+-+...|..+..+|.+.|++++|...|++..+   +.|+
T Consensus         9 ~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~--------~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~---~~p~   77 (164)
T 3sz7_A            9 PESDKLKSEGNAAMARKEYSKAIDLYTQALSI--------APANPIYLSNRAAAYSASGQHEKAAEDAELATV---VDPK   77 (164)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTT
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--------CCcCHHHHHHHHHHHHHccCHHHHHHHHHHHHH---hCCC
Confidence            35667888889999999999999999999986        233678899999999999999999999999988   4465


Q ss_pred             -HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          129 -RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       129 -~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                       ...|..+...|...|++++    |...|++..+.
T Consensus        78 ~~~~~~~lg~~~~~~g~~~~----A~~~~~~al~~  108 (164)
T 3sz7_A           78 YSKAWSRLGLARFDMADYKG----AKEAYEKGIEA  108 (164)
T ss_dssp             CHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccCHHH----HHHHHHHHHHh
Confidence             7889999999999999999    99999998886

>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=98.48  E-value=7.7e-06  Score=53.58  Aligned_cols=98  Identities=12%  Similarity=0.057  Sum_probs=85.3

Q ss_pred             CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-
Q 043380           50 DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-  128 (246)
Q Consensus        50 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-  128 (246)
                      +...+..+...+...|++++|...|++....        .+.+...+..+..++...|++++|...+++...   ..|+ 
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--------~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~---~~~~~   71 (118)
T 1elw_A            3 QVNELKEKGNKALSVGNIDDALQCYSEAIKL--------DPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVD---LKPDW   71 (118)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH---HCTTC
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHH--------CCCcHHHHHHHHHHHHhhccHHHHHHHHHHHHH---hCccc
Confidence            4567788888999999999999999999886        234677889999999999999999999999988   3454 


Q ss_pred             HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          129 RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       129 ~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ...+..+...+...|++++    |.+.++...+.
T Consensus        72 ~~~~~~~a~~~~~~~~~~~----A~~~~~~~~~~  101 (118)
T 1elw_A           72 GKGYSRKAAALEFLNRFEE----AKRTYEEGLKH  101 (118)
T ss_dssp             HHHHHHHHHHHHHTTCHHH----HHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHhhHHH----HHHHHHHHHHc
Confidence            7888999999999999999    99999998765

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.47  E-value=1.6e-06  Score=71.07  Aligned_cols=179  Identities=9%  Similarity=-0.028  Sum_probs=121.2

Q ss_pred             HHHHhcCCcchHHHHHHHHHhccCCCCCCCCC---------ccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCH
Q 043380           59 SACIKTKKLDVTMPFNEQLKDNGQKCSSGGFH---------PDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDR  129 (246)
Q Consensus        59 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~---------p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~  129 (246)
                      +.+.+.|++++|.+.|.++.+..-...+....         .....+..+...|...|++++|.+++.......+..++.
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            45677899999999999998763111100000         011357889999999999999999999876622222332


Q ss_pred             H----HHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCC
Q 043380          130 S----TFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTG  205 (246)
Q Consensus       130 ~----~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  205 (246)
                      .    +.+.+-..+...|+++.    |..+++..............-..++..+...|...|++++|..+++++...-.+
T Consensus        92 ~~~~~~~~~l~~~~~~~~~~~~----a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~  167 (434)
T 4b4t_Q           92 KTVKVLKTLIEKFEQVPDSLDD----QIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKK  167 (434)
T ss_dssp             HHHHHHHHHHHHHCSCCSCHHH----HHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHhCCCCHHH----HHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHh
Confidence            2    23334444555788999    999998876642211112223467888999999999999999999976522111


Q ss_pred             CCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          206 TISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       206 ~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      .........+|..++..|...|++++|..+++....
T Consensus       168 ~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~  203 (434)
T 4b4t_Q          168 LDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAART  203 (434)
T ss_dssp             SSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHH
Confidence            112222234789999999999999999999987764

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.44  E-value=3e-06  Score=55.12  Aligned_cols=98  Identities=8%  Similarity=-0.061  Sum_probs=66.2

Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL-DRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP  171 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p  171 (246)
                      ...+..+...+...|++++|...|++..+   ..| +...+..+...+...|++++    |...|++..+.      ...
T Consensus         6 ~~~~~~~~~~~~~~~~~~~A~~~~~~a~~---~~~~~~~~~~~~a~~~~~~~~~~~----A~~~~~~a~~~------~~~   72 (112)
T 2kck_A            6 PEEYYLEGVLQYDAGNYTESIDLFEKAIQ---LDPEESKYWLMKGKALYNLERYEE----AVDCYNYVINV------IED   72 (112)
T ss_dssp             TTGGGGHHHHHHSSCCHHHHHHHHHHHHH---HCCCCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHT------SCC
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHH---hCcCCHHHHHHHHHHHHHccCHHH----HHHHHHHHHHh------Ccc
Confidence            34556666677777777777777777766   223 35667777777777777777    77777777664      112


Q ss_pred             --chhhHHHHHHHHHhc-CChhHHhhHHHhhCCCC
Q 043380          172 --KPHLYVSMMHELAAR-VDYDIVKSPYRRMWPDS  203 (246)
Q Consensus       172 --~~~~~~~li~~~~~~-g~~~~a~~~~~~~~~~~  203 (246)
                        +...+..+..++... |++++|.+.++......
T Consensus        73 ~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~  107 (112)
T 2kck_A           73 EYNKDVWAAKADALRYIEGKEVEAEIAEARAKLEH  107 (112)
T ss_dssp             TTCHHHHHHHHHHHTTCSSCSHHHHHHHHHHGGGC
T ss_pred             cchHHHHHHHHHHHHHHhCCHHHHHHHHHHHhhcc
Confidence              456677777777777 77777777777766443

>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=98.43  E-value=2.6e-06  Score=66.02  Aligned_cols=99  Identities=8%  Similarity=-0.071  Sum_probs=87.2

Q ss_pred             CCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC
Q 043380           49 PDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD  128 (246)
Q Consensus        49 ~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~  128 (246)
                      .+...+..+...+...|++++|...|.+....        .+.+...|..+..+|.+.|++++|...++...+   +.|+
T Consensus         2 ~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~--------~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~---~~p~   70 (281)
T 2c2l_A            2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITR--------NPLVAVYYTNRALCYLKMQQPEQALADCRRALE---LDGQ   70 (281)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTT---SCTT
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--------CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHH---hCCC
Confidence            35677888889999999999999999999986        233678899999999999999999999999988   4565


Q ss_pred             -HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          129 -RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       129 -~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                       ...+..+..+|...|++++    |...|+...+.
T Consensus        71 ~~~~~~~lg~~~~~~g~~~~----A~~~~~~al~l  101 (281)
T 2c2l_A           71 SVKAHFFLGQCQLEMESYDE----AIANLQRAYSL  101 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh
Confidence             7888999999999999999    99999998776

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.40  E-value=7.2e-06  Score=56.49  Aligned_cols=98  Identities=12%  Similarity=-0.130  Sum_probs=84.8

Q ss_pred             CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-
Q 043380           50 DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-  128 (246)
Q Consensus        50 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-  128 (246)
                      +...+..+...+.+.|++++|...|++....        -+.+...|..+-.+|.+.|++++|...|+....   +.|+ 
T Consensus        17 ~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~--------~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~---~~p~~   85 (142)
T 2xcb_A           17 TLEQLYALGFNQYQAGKWDDAQKIFQALCML--------DHYDARYFLGLGACRQSLGLYEQALQSYSYGAL---MDINE   85 (142)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTC
T ss_pred             HHHHHHHHHHHHHHHccHHHHHHHHHHHHHh--------CCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHh---cCCCC
Confidence            4455667778889999999999999999986        234677899999999999999999999999988   4455 


Q ss_pred             HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          129 RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       129 ~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ...+..+..+|...|++++    |...|+...+.
T Consensus        86 ~~~~~~lg~~~~~~g~~~~----A~~~~~~al~~  115 (142)
T 2xcb_A           86 PRFPFHAAECHLQLGDLDG----AESGFYSARAL  115 (142)
T ss_dssp             THHHHHHHHHHHHTTCHHH----HHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh
Confidence            6778889999999999999    99999998876

>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=98.38  E-value=0.00025  Score=56.44  Aligned_cols=209  Identities=11%  Similarity=-0.031  Sum_probs=147.8

Q ss_pred             CcCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhc-C-CcchHHHHHHHHHhccCCCCCCCCC
Q 043380           14 KLNTIVMNAVIEASREAQ-RIDEAYQILESVEKGLEPDSLSYNILISACIKT-K-KLDVTMPFNEQLKDNGQKCSSGGFH   90 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g-~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~-~-~~~~a~~~~~~m~~~~~~~~~~~~~   90 (246)
                      +-+..+||.--.++...| .+++++++++.+....+.+...|+.--..+.+. + ++++++++++++.+.        -+
T Consensus        85 P~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~nPKny~aW~hR~wlL~~l~~~~~~~EL~~~~k~L~~--------dp  156 (349)
T 3q7a_A           85 PAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQNLKSYQVWHHRLLLLDRISPQDPVSEIEYIHGSLLP--------DP  156 (349)
T ss_dssp             TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHCCSCCHHHHHHHHHHTSS--------CT
T ss_pred             chhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHh--------CC
Confidence            345667888777777788 599999999998765677888999887777776 6 889999999999985        34


Q ss_pred             ccHHHHHHHHHHHHccCCHH--------HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCC-------hhhhhhHHHHH
Q 043380           91 PDIFTYATLLMGFRHAKDLQ--------SLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGS-------IKVVGLYALCI  155 (246)
Q Consensus        91 p~~~~~~~ll~~~~~~~~~~--------~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~-------~~~~~~~a~~~  155 (246)
                      -|...|+----.+.+.|.++        ++++.++.+.+ .. .-|...|+.....+.+.+.       +++    +++.
T Consensus       157 kNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~-~d-p~N~SAW~~R~~lL~~l~~~~~~~~~~~e----ELe~  230 (349)
T 3q7a_A          157 KNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLR-VD-GRNNSAWGWRWYLRVSRPGAETSSRSLQD----ELIY  230 (349)
T ss_dssp             TCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHH-HC-TTCHHHHHHHHHHHTTSTTCCCCHHHHHH----HHHH
T ss_pred             CCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHH-hC-CCCHHHHHHHHHHHHhccccccchHHHHH----HHHH
Confidence            46777777666665555555        89999999988 32 2347788888887777776       577    8999


Q ss_pred             HHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCCh--------------------hHHhhHHHhhCCCCCCCCCchhhhHH
Q 043380          156 FGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDY--------------------DIVKSPYRRMWPDSTGTISPEVQEEA  215 (246)
Q Consensus       156 ~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~--------------------~~a~~~~~~~~~~~~~~~~~~~~~~~  215 (246)
                      +++....      -.-|...|+-+-..+.+.|+.                    ........++.....+........++
T Consensus       231 ~~~aI~~------~P~n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~a  304 (349)
T 3q7a_A          231 ILKSIHL------IPHNVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDIETVEAFGFPMPSDPLPEDTPLPVPLA  304 (349)
T ss_dssp             HHHHHHH------CTTCHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC--------------CCCCC-CCCSSCCSCCHHH
T ss_pred             HHHHHHh------CCCCHHHHHHHHHHHHhcCCCcccccccccccccccccccchhHHHHHHHHHhcccccccCCCcHHH
Confidence            9988886      334667787777777776654                    34444444544322110001112237


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          216 GHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       216 ~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                      ...|.+.|...|+.++|.++++.+.++
T Consensus       305 l~~l~d~~~~~~~~~~a~~~~~~l~~~  331 (349)
T 3q7a_A          305 LEYLADSFIEQNRVDDAAKVFEKLSSE  331 (349)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhh
Confidence            888999999999999999999998754

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=98.38  E-value=3.7e-05  Score=66.85  Aligned_cols=202  Identities=4%  Similarity=-0.047  Sum_probs=145.4

Q ss_pred             HHHHHHHHHHHhcC-------CHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHH-HHHHHHHhccCCCCCCCC
Q 043380           18 IVMNAVIEASREAQ-------RIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTM-PFNEQLKDNGQKCSSGGF   89 (246)
Q Consensus        18 ~~~~~li~~~~~~g-------~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~-~~~~~m~~~~~~~~~~~~   89 (246)
                      ..|...+..--..+       ..+++..+|++...-++-+...|-....-+...|+.++|. ++|++....        +
T Consensus       303 ~lW~~yi~fEk~~~~~l~~~~~~~Rv~~~Ye~aL~~~p~~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~~--------~  374 (679)
T 4e6h_A          303 LIWLEWIRWESDNKLELSDDLHKARMTYVYMQAAQHVCFAPEIWFNMANYQGEKNTDSTVITKYLKLGQQC--------I  374 (679)
T ss_dssp             HHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHH--------C
T ss_pred             HHHHHHHHHHHhCCccccchhhHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHh--------C
Confidence            45666665433332       1345667888876556778888988888888999999997 999999875        4


Q ss_pred             CccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCC---------CCCC------------HHHHHHHHHHHHhcCChhhh
Q 043380           90 HPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCN---------LILD------------RSTFTAMVDALLYSGSIKVV  148 (246)
Q Consensus        90 ~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~---------~~p~------------~~~~~~li~~~~~~~~~~~~  148 (246)
                      +.+...|-..+...-+.|+++.|.++|+.+.. ..         -.|+            ..+|...+....+.|+.+. 
T Consensus       375 P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~-~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~-  452 (679)
T 4e6h_A          375 PNSAVLAFSLSEQYELNTKIPEIETTILSCID-RIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAA-  452 (679)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHH-
T ss_pred             CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHH-HHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHH-
Confidence            55666788888888999999999999999886 21         0142            3367888888888899999 


Q ss_pred             hhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhc-CChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcC
Q 043380          149 GLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAAR-VDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDG  227 (246)
Q Consensus       149 ~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~-g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g  227 (246)
                         |..+|....+.     .-.+....|......-.+. ++.+.|.++|+...+..    +....  .|...++.....|
T Consensus       453 ---AR~vf~~A~~~-----~~~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~~----p~~~~--~w~~y~~fe~~~~  518 (679)
T 4e6h_A          453 ---SRKIFGKCRRL-----KKLVTPDIYLENAYIEYHISKDTKTACKVLELGLKYF----ATDGE--YINKYLDFLIYVN  518 (679)
T ss_dssp             ---HHHHHHHHHHT-----GGGSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHH----TTCHH--HHHHHHHHHHHHT
T ss_pred             ---HHHHHHHHHHh-----cCCCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHC----CCchH--HHHHHHHHHHhCC
Confidence               99999998774     0111233444333333344 45999999999887542    22221  4677888888899


Q ss_pred             ChhHHHHHHHHHHhhc
Q 043380          228 QVDLALDKLSNTITRW  243 (246)
Q Consensus       228 ~~~~a~~~~~~m~~~g  243 (246)
                      +.+.|..+|++.....
T Consensus       519 ~~~~AR~lferal~~~  534 (679)
T 4e6h_A          519 EESQVKSLFESSIDKI  534 (679)
T ss_dssp             CHHHHHHHHHHHTTTS
T ss_pred             CHHHHHHHHHHHHHhc
Confidence            9999999999887654

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.37  E-value=1.8e-05  Score=53.12  Aligned_cols=97  Identities=10%  Similarity=-0.016  Sum_probs=77.9

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCH---HHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc----H
Q 043380           21 NAVIEASREAQRIDEAYQILESVEKGLEPDS---LSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD----I   93 (246)
Q Consensus        21 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~---~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~----~   93 (246)
                      -.+...+.+.|++++|...|+...+..+.+.   ..+..+..++...|++++|...|++....         .|+    .
T Consensus         6 ~~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~---------~p~~~~~~   76 (129)
T 2xev_A            6 YNVAFDALKNGKYDDASQLFLSFLELYPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSR---------YPTHDKAA   76 (129)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---------CTTSTTHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHH---------CCCCcccH
Confidence            3456678889999999999998764333334   47788888999999999999999999886         233    5


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCH
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDR  129 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~  129 (246)
                      ..+..+..++...|++++|...|+....   ..|+.
T Consensus        77 ~~~~~la~~~~~~g~~~~A~~~~~~~~~---~~p~~  109 (129)
T 2xev_A           77 GGLLKLGLSQYGEGKNTEAQQTLQQVAT---QYPGS  109 (129)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH---HSTTS
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHH---HCCCC
Confidence            6788888999999999999999999988   34653

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.35  E-value=6e-06  Score=55.40  Aligned_cols=93  Identities=13%  Similarity=0.011  Sum_probs=65.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc-cHHHHHH
Q 043380           20 MNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP-DIFTYAT   98 (246)
Q Consensus        20 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p-~~~~~~~   98 (246)
                      +..+...+.+.|++++|...|+...+.-+.+...|..+-.++...|++++|...|++..+.         .| +...+..
T Consensus        20 ~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l---------~P~~~~~~~~   90 (121)
T 1hxi_A           20 PMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARML---------DPKDIAVHAA   90 (121)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---------CTTCHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---------CCCCHHHHHH
Confidence            3445566777777777777777765433556677777777777777777777777777765         33 4556777


Q ss_pred             HHHHHHccCCHHHHHHHHHHHHh
Q 043380           99 LLMGFRHAKDLQSLLEIVFEMKS  121 (246)
Q Consensus        99 ll~~~~~~~~~~~a~~~~~~m~~  121 (246)
                      +..+|...|++++|...|++..+
T Consensus        91 la~~~~~~g~~~~A~~~~~~al~  113 (121)
T 1hxi_A           91 LAVSHTNEHNANAALASLRAWLL  113 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHH
Confidence            77777777777777777777766

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=98.30  E-value=6e-06  Score=54.87  Aligned_cols=86  Identities=12%  Similarity=0.055  Sum_probs=70.6

Q ss_pred             hcCCcchHHHHHHHHHhccCCCCCCC--CCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHH
Q 043380           63 KTKKLDVTMPFNEQLKDNGQKCSSGG--FHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDAL  139 (246)
Q Consensus        63 ~~~~~~~a~~~~~~m~~~~~~~~~~~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~  139 (246)
                      ..|++++|...|++..+.       +  -+-+...|..+..+|...|++++|...|++..+   ..|+ ...+..+..++
T Consensus         2 ~~g~~~~A~~~~~~al~~-------~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~---~~p~~~~~~~~l~~~~   71 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIAS-------GLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVK---QFPNHQALRVFYAMVL   71 (117)
T ss_dssp             -----CCCHHHHHHHHSS-------CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHc-------CCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCchHHHHHHHHHH
Confidence            468899999999999975       2  133456899999999999999999999999988   4465 78888999999


Q ss_pred             HhcCChhhhhhHHHHHHHHHHHh
Q 043380          140 LYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       140 ~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ...|++++    |...|+.....
T Consensus        72 ~~~g~~~~----A~~~~~~al~~   90 (117)
T 3k9i_A           72 YNLGRYEQ----GVELLLKIIAE   90 (117)
T ss_dssp             HHHTCHHH----HHHHHHHHHHH
T ss_pred             HHcCCHHH----HHHHHHHHHHh
Confidence            99999999    99999998876

>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=98.30  E-value=1e-05  Score=67.17  Aligned_cols=147  Identities=5%  Similarity=-0.097  Sum_probs=113.5

Q ss_pred             CcchHHHHHHHHHhccCCCCCCCCCc-cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC----------------
Q 043380           66 KLDVTMPFNEQLKDNGQKCSSGGFHP-DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD----------------  128 (246)
Q Consensus        66 ~~~~a~~~~~~m~~~~~~~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~----------------  128 (246)
                      ++++|.+.|+...+.         .| ....|..+-..|.+.|++++|...|++..+   +.|+                
T Consensus       249 ~~~~A~~~~~~~~~~---------~~~~a~~~~~~G~~~~~~g~~~~A~~~y~~Al~---~~p~~~~~~~~~~~~~~~~~  316 (457)
T 1kt0_A          249 SFEKAKESWEMDTKE---------KLEQAAIVKEKGTVYFKGGKYMQAVIQYGKIVS---WLEMEYGLSEKESKASESFL  316 (457)
T ss_dssp             EEECCCCGGGSCHHH---------HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HHTTCCSCCHHHHHHHHHHH
T ss_pred             hcccCcchhhcCHHH---------HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH---HhcccccCChHHHHHHHHHH
Confidence            445565555444332         23 345788889999999999999999999887   3344                


Q ss_pred             HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCC
Q 043380          129 RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTIS  208 (246)
Q Consensus       129 ~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  208 (246)
                      ...|..+..+|.+.|++++    |+..++...+.      -..+...|..+-.+|...|++++|...|++.....+....
T Consensus       317 ~~~~~nla~~~~~~g~~~~----A~~~~~~al~~------~p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~P~~~~  386 (457)
T 1kt0_A          317 LAAFLNLAMCYLKLREYTK----AVECCDKALGL------DSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKA  386 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC----C
T ss_pred             HHHHHHHHHHHHHhcCHHH----HHHHHHHHHhc------CCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHH
Confidence            4789999999999999999    99999999886      2345788999999999999999999999998765433221


Q ss_pred             chhhhHHHHHHHHHHHhcCChhHHHH-HHHHHH
Q 043380          209 PEVQEEAGHLLMEAALNDGQVDLALD-KLSNTI  240 (246)
Q Consensus       209 ~~~~~~~~~~li~~~~~~g~~~~a~~-~~~~m~  240 (246)
                            ++..+..++.+.|+.++|.+ .++.|.
T Consensus       387 ------a~~~l~~~~~~~~~~~~a~~~~~~~~f  413 (457)
T 1kt0_A          387 ------ARLQISMCQKKAKEHNERDRRIYANMF  413 (457)
T ss_dssp             ------HHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             ------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                  68889999999999887764 455553

>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=98.29  E-value=1.8e-05  Score=65.80  Aligned_cols=131  Identities=6%  Similarity=-0.075  Sum_probs=104.5

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC---------------HHHHHHHHHHHHhcCCcchHHHHHHHHHhc
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPD---------------SLSYNILISACIKTKKLDVTMPFNEQLKDN   80 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~---------------~~t~~~li~~~~~~~~~~~a~~~~~~m~~~   80 (246)
                      ....|..+-..|.+.|++++|...|++..+-.+.+               ...|..+-.+|.+.+++++|...|++.++.
T Consensus       267 ~a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  346 (457)
T 1kt0_A          267 QAAIVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGL  346 (457)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            34578888899999999999999998875322333               588999999999999999999999999986


Q ss_pred             cCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHH-HHHHH
Q 043380           81 GQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYAL-CIFGE  158 (246)
Q Consensus        81 ~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~-~~~~~  158 (246)
                              -+.+...|..+-.+|...|++++|...|++..+   +.|+ ...+..+...+...++.++    +. ..+..
T Consensus       347 --------~p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~---l~P~~~~a~~~l~~~~~~~~~~~~----a~~~~~~~  411 (457)
T 1kt0_A          347 --------DSANEKGLYRRGEAQLLMNEFESAKGDFEKVLE---VNPQNKAARLQISMCQKKAKEHNE----RDRRIYAN  411 (457)
T ss_dssp             --------STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT---TC----CHHHHHHHHHHHHHHHHH----HHHHHHHH
T ss_pred             --------CCccHHHHHHHHHHHHHccCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHHHHHHH----HHHHHHHH
Confidence                    234678899999999999999999999999998   5565 6678888888888888887    55 34444


Q ss_pred             HHH
Q 043380          159 IVK  161 (246)
Q Consensus       159 m~~  161 (246)
                      |..
T Consensus       412 ~f~  414 (457)
T 1kt0_A          412 MFK  414 (457)
T ss_dssp             C--
T ss_pred             HHh
Confidence            443

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.28  E-value=2.8e-05  Score=59.96  Aligned_cols=130  Identities=7%  Similarity=-0.093  Sum_probs=102.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc--HHHH
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD--IFTY   96 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~--~~~~   96 (246)
                      .+-.+...+...|++++|.++|+.+..+ .|+......+-..+.+.+++++|+..|+.....        ..|.  ...+
T Consensus       104 l~LayA~~L~~~g~y~eA~~~l~~~~~~-~p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~--------~d~~~~~~a~  174 (282)
T 4f3v_A          104 ITMGFAACEAAQGNYADAMEALEAAPVA-GSEHLVAWMKAVVYGAAERWTDVIDQVKSAGKW--------PDKFLAGAAG  174 (282)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHTSSCCT-TCHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGC--------SCHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhc-CCchHHHHHHHHHHHHcCCHHHHHHHHHHhhcc--------CCcccHHHHH
Confidence            3445677888999999999999988643 354436566666889999999999999866543        1221  3478


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC--HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           97 ATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD--RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        97 ~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~--~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ..+-.++...|++++|+..|++... ....|.  .........++.+.|+.++    |..+|+++...
T Consensus       175 ~~LG~al~~LG~~~eAl~~l~~a~~-g~~~P~~~~da~~~~glaL~~lGr~de----A~~~l~~a~a~  237 (282)
T 4f3v_A          175 VAHGVAAANLALFTEAERRLTEAND-SPAGEACARAIAWYLAMARRSQGNESA----AVALLEWLQTT  237 (282)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHT-STTTTTTHHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHhc-CCCCccccHHHHHHHHHHHHHcCCHHH----HHHHHHHHHhc
Confidence            8889999999999999999999986 444354  3466778889999999999    99999999987

>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=3.5e-06  Score=70.43  Aligned_cols=120  Identities=8%  Similarity=-0.038  Sum_probs=94.4

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHH
Q 043380           23 VIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMG  102 (246)
Q Consensus        23 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~  102 (246)
                      +...+.+.|++++|.+.|++..+-.+.+...|..+..+|.+.|++++|.+.+++..+.        -+-+...|..+-.+
T Consensus        12 lg~~~~~~g~~~~A~~~~~~Al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--------~p~~~~~~~~lg~~   83 (477)
T 1wao_1           12 QANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIEL--------DKKYIKGYYRRAAS   83 (477)
T ss_dssp             SSSSTTTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--------CTTCHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--------CCCCHHHHHHHHHH
Confidence            3445677899999999999876434567899999999999999999999999999986        23457789999999


Q ss_pred             HHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHH--HHhcCChhhhhhHHHHHHH
Q 043380          103 FRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDA--LLYSGSIKVVGLYALCIFG  157 (246)
Q Consensus       103 ~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~--~~~~~~~~~~~~~a~~~~~  157 (246)
                      |...|++++|.+.|++..+   +.|+ ...+..+..+  +.+.|++++    |.+.++
T Consensus        84 ~~~~g~~~eA~~~~~~al~---~~p~~~~~~~~l~~~~~~~~~g~~~~----A~~~~~  134 (477)
T 1wao_1           84 NMALGKFRAALRDYETVVK---VKPHDKDAKMKYQECNKIVKQKAFER----AIAGDE  134 (477)
T ss_dssp             HHHHTCHHHHHHHHHHHHH---HSTTCTTHHHHHHHHHHHHHHHHHCC----C-----
T ss_pred             HHHcCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHHHHHHHHH----Hhcccc
Confidence            9999999999999999988   3344 3445555544  888899999    999988

>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=98.24  E-value=3.1e-05  Score=62.52  Aligned_cols=129  Identities=5%  Similarity=-0.030  Sum_probs=91.5

Q ss_pred             HHHHHHHHHHhcCCcchHHHHHHHHHhccCCC-------CCCCCCc-cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCC
Q 043380           53 SYNILISACIKTKKLDVTMPFNEQLKDNGQKC-------SSGGFHP-DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCN  124 (246)
Q Consensus        53 t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~-------~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~  124 (246)
                      .+..+-..+.+.|++++|.+.|++.++.--..       ......| +...|..+..+|.+.|++++|...+++..+   
T Consensus       225 ~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~---  301 (370)
T 1ihg_A          225 DLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALE---  301 (370)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT---
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHH---
Confidence            35555666667777777777777666510000       0000123 456888899999999999999999999988   


Q ss_pred             CCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhh
Q 043380          125 LILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKS  194 (246)
Q Consensus       125 ~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~  194 (246)
                      +.|+ ...|..+..+|...|++++    |...|+...+.      -.-+...+..+..++...++.+++.+
T Consensus       302 ~~p~~~~a~~~lg~~~~~~g~~~e----A~~~l~~Al~l------~P~~~~~~~~l~~~~~~~~~~~~a~k  362 (370)
T 1ihg_A          302 IDPSNTKALYRRAQGWQGLKEYDQ----ALADLKKAQEI------APEDKAIQAELLKVKQKIKAQKDKEK  362 (370)
T ss_dssp             TCTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------CTTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hCchhHHHHHHHHHHHHHccCHHH----HHHHHHHHHHh------CCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            4465 7788889999999999999    99999998886      12245677777777777777766653

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.23  E-value=4.2e-05  Score=51.22  Aligned_cols=92  Identities=10%  Similarity=0.003  Sum_probs=77.5

Q ss_pred             HHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-H---HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC--
Q 043380           55 NILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-I---FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD--  128 (246)
Q Consensus        55 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~---~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~--  128 (246)
                      ..+...+...|++++|...|++..+.         .|+ .   ..+..+..++...|++++|...|+....   ..|+  
T Consensus         6 ~~~a~~~~~~~~~~~A~~~~~~~~~~---------~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~---~~p~~~   73 (129)
T 2xev_A            6 YNVAFDALKNGKYDDASQLFLSFLEL---------YPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVS---RYPTHD   73 (129)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH---------CSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTST
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHH---------CCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHH---HCCCCc
Confidence            34566778899999999999999886         232 2   5788888999999999999999999988   3344  


Q ss_pred             --HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          129 --RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       129 --~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                        ...+..+..++...|++++    |...|+.....
T Consensus        74 ~~~~~~~~la~~~~~~g~~~~----A~~~~~~~~~~  105 (129)
T 2xev_A           74 KAAGGLLKLGLSQYGEGKNTE----AQQTLQQVATQ  105 (129)
T ss_dssp             THHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHH
Confidence              5678889999999999999    99999999886

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=98.22  E-value=1e-05  Score=64.43  Aligned_cols=132  Identities=7%  Similarity=-0.059  Sum_probs=83.1

Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHH------------------HHHHHHHHHHhcCChhhhhhHHHH
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRS------------------TFTAMVDALLYSGSIKVVGLYALC  154 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~------------------~~~~li~~~~~~~~~~~~~~~a~~  154 (246)
                      ...+..+-..+.+.|++++|...|++...   +.|+..                  .|..+..+|.+.|++++    |..
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~---~~p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~----A~~  251 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIA---YMGDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDE----AIG  251 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHH---HSCHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHH----HHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHH---HhccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHH----HHH
Confidence            34677788888999999999999999887   446643                  78899999999999999    999


Q ss_pred             HHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHH-HHhcCChhHHH
Q 043380          155 IFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEA-ALNDGQVDLAL  233 (246)
Q Consensus       155 ~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~-~~~~g~~~~a~  233 (246)
                      .++...+.      -..+...|..+..+|...|++++|...|++.....+....      ++..|... ....+..+++.
T Consensus       252 ~~~~al~~------~p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~p~~~~------a~~~L~~l~~~~~~~~~~a~  319 (338)
T 2if4_A          252 HCNIVLTE------EEKNPKALFRRGKAKAELGQMDSARDDFRKAQKYAPDDKA------IRRELRALAEQEKALYQKQK  319 (338)
T ss_dssp             HHHHHHHH------CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC---------------------------------
T ss_pred             HHHHHHHh------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHH------HHHHHHHHHHHHHHHHHHHH
Confidence            99999886      2346688999999999999999999999998765432211      45555554 34467778888


Q ss_pred             HHHHHHHhhc
Q 043380          234 DKLSNTITRW  243 (246)
Q Consensus       234 ~~~~~m~~~g  243 (246)
                      ++|+.|....
T Consensus       320 ~~~~~~l~~~  329 (338)
T 2if4_A          320 EMYKGIFKGK  329 (338)
T ss_dssp             ----------
T ss_pred             HHHHHhhCCC
Confidence            8998887654

>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=98.22  E-value=2e-05  Score=63.61  Aligned_cols=120  Identities=7%  Similarity=-0.061  Sum_probs=98.1

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHh----------------CCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhc
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEK----------------GLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDN   80 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~----------------~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~   80 (246)
                      ...+..+-..+.+.|++++|++.|++..+                ..+.+...|..+..+|.+.+++++|.+.+++..+.
T Consensus       223 a~~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  302 (370)
T 1ihg_A          223 SEDLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEI  302 (370)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHh
Confidence            34578888899999999999999987643                22235678889999999999999999999999985


Q ss_pred             cCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhh
Q 043380           81 GQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKV  147 (246)
Q Consensus        81 ~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~  147 (246)
                              -+.+...|..+-.+|...|++++|...|++..+   +.|+ ...+..+...+...++.++
T Consensus       303 --------~p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~---l~P~~~~~~~~l~~~~~~~~~~~~  359 (370)
T 1ihg_A          303 --------DPSNTKALYRRAQGWQGLKEYDQALADLKKAQE---IAPEDKAIQAELLKVKQKIKAQKD  359 (370)
T ss_dssp             --------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHHHHHH
T ss_pred             --------CchhHHHHHHHHHHHHHccCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHHHHHHH
Confidence                    233577899999999999999999999999988   4565 6667777777777777666

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=98.22  E-value=2.8e-05  Score=54.68  Aligned_cols=103  Identities=7%  Similarity=-0.118  Sum_probs=84.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhC------------------CCCCHHHHHHHHHHHHhcCCcchHHHHHHHHH
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKG------------------LEPDSLSYNILISACIKTKKLDVTMPFNEQLK   78 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~------------------~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~   78 (246)
                      +..+...-..+.+.|++++|...|.....-                  .+.+...|..+..+|.+.|++++|...+.+.+
T Consensus        11 a~~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al   90 (162)
T 3rkv_A           11 VEALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVL   90 (162)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            456778888999999999999999876431                  12234678889999999999999999999999


Q ss_pred             hccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHH
Q 043380           79 DNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRS  130 (246)
Q Consensus        79 ~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~  130 (246)
                      ..        -+.+...|..+-.+|...|++++|...|+....   +.|+..
T Consensus        91 ~~--------~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~---l~p~~~  131 (162)
T 3rkv_A           91 KR--------EETNEKALFRRAKARIAAWKLDEAEEDLKLLLR---NHPAAA  131 (162)
T ss_dssp             HH--------STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCGGGH
T ss_pred             hc--------CCcchHHHHHHHHHHHHHhcHHHHHHHHHHHHh---cCCCCH
Confidence            86        234577899999999999999999999999988   557643

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.21  E-value=1.9e-05  Score=52.88  Aligned_cols=96  Identities=3%  Similarity=-0.128  Sum_probs=75.6

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP  173 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~  173 (246)
                      .+..+...+.+.|++++|...|++..+   ..|+ ...|..+..++...|++++    |+..|++..+.      -+-+.
T Consensus        19 ~~~~~g~~~~~~g~~~~A~~~~~~al~---~~P~~~~a~~~lg~~~~~~g~~~~----A~~~~~~al~l------~P~~~   85 (121)
T 1hxi_A           19 NPMEEGLSMLKLANLAEAALAFEAVCQ---KEPEREEAWRSLGLTQAENEKDGL----AIIALNHARML------DPKDI   85 (121)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHH---HSTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------CTTCH
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHH---HCCCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh------CCCCH
Confidence            455666778888999999999998887   4564 7778888888999999999    99999988876      12245


Q ss_pred             hhHHHHHHHHHhcCChhHHhhHHHhhCCCC
Q 043380          174 HLYVSMMHELAARVDYDIVKSPYRRMWPDS  203 (246)
Q Consensus       174 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  203 (246)
                      ..+..+..++...|++++|...+++....+
T Consensus        86 ~~~~~la~~~~~~g~~~~A~~~~~~al~~~  115 (121)
T 1hxi_A           86 AVHAALAVSHTNEHNANAALASLRAWLLSQ  115 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            678888888899999999999998876543

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=98.20  E-value=1.7e-05  Score=66.30  Aligned_cols=138  Identities=7%  Similarity=-0.071  Sum_probs=101.6

Q ss_pred             HHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhC----CC-CCCC-HHHHH
Q 043380           60 ACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSC----CN-LILD-RSTFT  133 (246)
Q Consensus        60 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~----~~-~~p~-~~~~~  133 (246)
                      .+...|++++|+.++++..+...+......+-...+++.|...|...|++++|..++++....    .| -.|+ ..+++
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            355789999999999988765332222222334569999999999999999999998886551    11 2344 56799


Q ss_pred             HHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCC-CCcch-hhHHHHHHHHHhcCChhHHhhHHHhhCC
Q 043380          134 AMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPG-LWPKP-HLYVSMMHELAARVDYDIVKSPYRRMWP  201 (246)
Q Consensus       134 ~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~  201 (246)
                      .|...|...|++++    |+.++++.........| -.|+. .+...+-.++...+.+++|+.++..+.+
T Consensus       398 nLa~~~~~~G~~~e----A~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~  463 (490)
T 3n71_A          398 RAGLTNWHAGHIEV----GHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMRE  463 (490)
T ss_dssp             HHHHHHHHTTCHHH----HHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHH----HHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999    99999987654221111 12333 5566777888889999999999998863

>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=98.19  E-value=7.9e-05  Score=52.26  Aligned_cols=116  Identities=13%  Similarity=0.004  Sum_probs=90.7

Q ss_pred             HHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-------------HHHHHHHHHHHHccCCHHHHHHHHHH
Q 043380           52 LSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-------------IFTYATLLMGFRHAKDLQSLLEIVFE  118 (246)
Q Consensus        52 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-------------~~~~~~ll~~~~~~~~~~~a~~~~~~  118 (246)
                      ..+...-..+.+.|++++|...|++.++.         .|+             ...|+.+-.++.+.|++++|+..+++
T Consensus        12 ~~~~~~G~~l~~~g~~eeAi~~Y~kAL~l---------~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~k   82 (159)
T 2hr2_A           12 YLALSDAQRQLVAGEYDEAAANCRRAMEI---------SHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADK   82 (159)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHH---------HTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHhh---------CCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            34556667788899999999999999876         333             33899999999999999999999999


Q ss_pred             HHhC----CCCCCC-HHHH----HHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHH
Q 043380          119 MKSC----CNLILD-RSTF----TAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMM  180 (246)
Q Consensus       119 m~~~----~~~~p~-~~~~----~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li  180 (246)
                      ..+.    ..+.|+ ...|    .....++...|++++    |+..|+...+....+.++.+........+
T Consensus        83 AL~l~n~~~e~~pd~~~A~~~~~~~rG~aL~~lgr~eE----Al~~y~kAlel~p~d~~~~~~~~~~~~~~  149 (159)
T 2hr2_A           83 ALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAE----AMPEFKKVVEMIEERKGETPGKERMMEVA  149 (159)
T ss_dssp             HHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHHHHHCCSCCTTHHHHHHHH
T ss_pred             HHHhhhccccCCCchHHHHHHHHHhHHHHHHHCCCHHH----HHHHHHHHHhcCCCcHHHHHHHHHHHHHH
Confidence            8881    012787 6678    899999999999999    99999999887444446666555444444

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=98.16  E-value=7.5e-05  Score=52.43  Aligned_cols=105  Identities=10%  Similarity=-0.027  Sum_probs=84.0

Q ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCC---CCC-------CCccHHHHHHHHHHHHccCCHHHHHHHHHHHH
Q 043380           51 SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCS---SGG-------FHPDIFTYATLLMGFRHAKDLQSLLEIVFEMK  120 (246)
Q Consensus        51 ~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~---~~~-------~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~  120 (246)
                      ...+...-..+.+.|++++|...|.+.+..--...   ...       -+.+...|..+..+|.+.|++++|...++...
T Consensus        11 a~~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al   90 (162)
T 3rkv_A           11 VEALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVL   90 (162)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            45677788889999999999999999887400000   000       12234689999999999999999999999998


Q ss_pred             hCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          121 SCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       121 ~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      +   +.|+ ...|..+..+|...|++++    |...|+.....
T Consensus        91 ~---~~p~~~~a~~~~g~~~~~~g~~~~----A~~~~~~al~l  126 (162)
T 3rkv_A           91 K---REETNEKALFRRAKARIAAWKLDE----AEEDLKLLLRN  126 (162)
T ss_dssp             H---HSTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH
T ss_pred             h---cCCcchHHHHHHHHHHHHHhcHHH----HHHHHHHHHhc
Confidence            8   4566 7889999999999999999    99999999886

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=98.13  E-value=4.8e-06  Score=55.34  Aligned_cols=85  Identities=9%  Similarity=-0.078  Sum_probs=66.2

Q ss_pred             hcCCHHHHHHHHHHHHhC---CCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHc
Q 043380           29 EAQRIDEAYQILESVEKG---LEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRH  105 (246)
Q Consensus        29 ~~g~~~~a~~~~~~~~~~---~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~  105 (246)
                      ..|++++|+..|++...-   -+.+...+..+..+|...|++++|...|++..+.        .+-+...+..+..++..
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--------~p~~~~~~~~l~~~~~~   73 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQ--------FPNHQALRVFYAMVLYN   73 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--------CCCchHHHHHHHHHHHH
Confidence            457888999999887642   2335677888889999999999999999999886        23356788889999999


Q ss_pred             cCCHHHHHHHHHHHHh
Q 043380          106 AKDLQSLLEIVFEMKS  121 (246)
Q Consensus       106 ~~~~~~a~~~~~~m~~  121 (246)
                      .|++++|...|++...
T Consensus        74 ~g~~~~A~~~~~~al~   89 (117)
T 3k9i_A           74 LGRYEQGVELLLKIIA   89 (117)
T ss_dssp             HTCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHH
Confidence            9999999999998877

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=98.12  E-value=2e-05  Score=65.96  Aligned_cols=131  Identities=5%  Similarity=-0.057  Sum_probs=97.7

Q ss_pred             HHhcCCHHHHHHHHHHHH----hCCCC----CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-HHHHH
Q 043380           27 SREAQRIDEAYQILESVE----KGLEP----DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-IFTYA   97 (246)
Q Consensus        27 ~~~~g~~~~a~~~~~~~~----~~~~~----~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~~   97 (246)
                      +-..|++++|+.++++..    +-..|    ...+++.|..+|...|++++|+.++++..+...+... .-.|+ ..+++
T Consensus       319 ~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG-~~Hp~~a~~l~  397 (490)
T 3n71_A          319 ARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYH-HNNAQLGMAVM  397 (490)
T ss_dssp             HHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSC-TTCHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcC-CCCHHHHHHHH
Confidence            456899999999998753    22222    3467899999999999999999999988754211111 22344 56899


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHhC----CCC-CCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           98 TLLMGFRHAKDLQSLLEIVFEMKSC----CNL-ILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        98 ~ll~~~~~~~~~~~a~~~~~~m~~~----~~~-~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      .|-..|...|++++|+.++++....    .|- .|+ ..+.+.+-.++...+.++.    |+.+|..+.+.
T Consensus       398 nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~----ae~~~~~~~~~  464 (490)
T 3n71_A          398 RAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQ----NEFMYHKMREA  464 (490)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHH
Confidence            9999999999999999998876541    121 233 3456777788888999999    99999999876

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=98.10  E-value=1.2e-05  Score=64.16  Aligned_cols=129  Identities=13%  Similarity=0.014  Sum_probs=80.3

Q ss_pred             HHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHH------------------HHHHHHHHHHccCCHHHHH
Q 043380           52 LSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIF------------------TYATLLMGFRHAKDLQSLL  113 (246)
Q Consensus        52 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~------------------~~~~ll~~~~~~~~~~~a~  113 (246)
                      ..+..+-..+.+.|++++|...|.+....         .|+..                  .|..+-.+|.+.|++++|.
T Consensus       180 ~~~~~~g~~~~~~g~~~~A~~~y~~Al~~---------~p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~  250 (338)
T 2if4_A          180 DRRKMDGNSLFKEEKLEEAMQQYEMAIAY---------MGDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAI  250 (338)
T ss_dssp             HHHHHHHHHTCSSSCCHHHHHHHHHHHHH---------SCHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHH---------hccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            44666777778899999999999998875         45443                  7889999999999999999


Q ss_pred             HHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc-hhhHHHHHHH-HHhcCChh
Q 043380          114 EIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK-PHLYVSMMHE-LAARVDYD  190 (246)
Q Consensus       114 ~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~-~~~~~~li~~-~~~~g~~~  190 (246)
                      ..++...+   +.|+ ...|..+..+|...|++++    |...|+...+.       .|+ ...+..+... ....+..+
T Consensus       251 ~~~~~al~---~~p~~~~a~~~lg~a~~~~g~~~~----A~~~l~~al~l-------~p~~~~a~~~L~~l~~~~~~~~~  316 (338)
T 2if4_A          251 GHCNIVLT---EEEKNPKALFRRGKAKAELGQMDS----ARDDFRKAQKY-------APDDKAIRRELRALAEQEKALYQ  316 (338)
T ss_dssp             HHHHHHHH---HCTTCHHHHHHHHHHHHTTTCHHH----HHHHHHHTTC-------------------------------
T ss_pred             HHHHHHHH---hCCCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHH-------CCCCHHHHHHHHHHHHHHHHHHH
Confidence            99999988   4464 7889999999999999999    99999988654       343 3444444444 23455677


Q ss_pred             HHhhHHHhhCCCC
Q 043380          191 IVKSPYRRMWPDS  203 (246)
Q Consensus       191 ~a~~~~~~~~~~~  203 (246)
                      ++..+|..+....
T Consensus       317 ~a~~~~~~~l~~~  329 (338)
T 2if4_A          317 KQKEMYKGIFKGK  329 (338)
T ss_dssp             -------------
T ss_pred             HHHHHHHHhhCCC
Confidence            8888888876543

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=98.00  E-value=2.3e-05  Score=50.94  Aligned_cols=96  Identities=7%  Similarity=-0.066  Sum_probs=75.9

Q ss_pred             ccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCC
Q 043380           91 PDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGL  169 (246)
Q Consensus        91 p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~  169 (246)
                      ++...|..+-..+...|++++|...|++..+   ..|+ ...+..+..+|...|++++    |...++...+.       
T Consensus         2 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~---~~p~~~~~~~~lg~~~~~~g~~~~----A~~~~~~al~~-------   67 (111)
T 2l6j_A            2 SQFEKQKEQGNSLFKQGLYREAVHCYDQLIT---AQPQNPVGYSNKAMALIKLGEYTQ----AIQMCQQGLRY-------   67 (111)
T ss_dssp             THHHHHHHHHHHHHTTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHTS-------
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHhcCHHH----HHHHHHHHHHh-------
Confidence            4566788888899999999999999999888   3454 7788899999999999999    99999998764       


Q ss_pred             Ccc-------hhhHHHHHHHHHhcCChhHHhhHHHhhC
Q 043380          170 WPK-------PHLYVSMMHELAARVDYDIVKSPYRRMW  200 (246)
Q Consensus       170 ~p~-------~~~~~~li~~~~~~g~~~~a~~~~~~~~  200 (246)
                      .|+       ...+..+..++...|+.+.|...++++.
T Consensus        68 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~  105 (111)
T 2l6j_A           68 TSTAEHVAIRSKLQYRLELAQGAVGSVQIPVVEVDELP  105 (111)
T ss_dssp             CSSTTSHHHHHHHHHHHHHHHHHHHCCCCCSSSSSSCS
T ss_pred             CCCccHHHHHHHHHHHHHHHHHHHHhHhhhHhHHHHhH
Confidence            344       4556667777777777777777666553

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=97.95  E-value=0.0019  Score=54.11  Aligned_cols=196  Identities=12%  Similarity=0.027  Sum_probs=128.4

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCC--CCC---
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCS--SGG---   88 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~--~~~---   88 (246)
                      +.++..|-..+..+.+.|+++.|.++|++.... +.+...|.    .|+.....++.   ++.+.+.-....  ..+   
T Consensus       210 p~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~-P~~~~l~~----~y~~~~e~~~~---~~~l~~~~~~~~~~~~~~~~  281 (493)
T 2uy1_A          210 YYAEEVYFFYSEYLIGIGQKEKAKKVVERGIEM-SDGMFLSL----YYGLVMDEEAV---YGDLKRKYSMGEAESAEKVF  281 (493)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CCSSHHHH----HHHHHTTCTHH---HHHHHHHTC----------C
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC-CCcHHHHH----HHHhhcchhHH---HHHHHHHHHhhccchhhhhc
Confidence            455778888888889999999999999987744 44433332    23332222222   333333200000  000   


Q ss_pred             CCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHH--HHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCC
Q 043380           89 FHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFT--AMVDALLYSGSIKVVGLYALCIFGEIVKRVCSN  166 (246)
Q Consensus        89 ~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~--~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~  166 (246)
                      .......|...+....+.++.+.|..+|+.... .+  .+...|.  +.+.... .++.+.    |..+|+...+.    
T Consensus       282 ~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A~~-~~--~~~~v~i~~A~lE~~~-~~d~~~----ar~ife~al~~----  349 (493)
T 2uy1_A          282 SKELDLLRINHLNYVLKKRGLELFRKLFIELGN-EG--VGPHVFIYCAFIEYYA-TGSRAT----PYNIFSSGLLK----  349 (493)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTT-SC--CCHHHHHHHHHHHHHH-HCCSHH----HHHHHHHHHHH----
T ss_pred             ccccHHHHHHHHHHHHHcCCHHHHHHHHHHhhC-CC--CChHHHHHHHHHHHHH-CCChHH----HHHHHHHHHHH----
Confidence            011234677777777788899999999999933 32  2444444  3333322 336899    99999999886    


Q ss_pred             CCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          167 PGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       167 ~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                        ..-+...+...++.....|+.+.|..+|+.+.+      .    ...|...+..-...|+.+.+.+++++...
T Consensus       350 --~~~~~~~~~~yid~e~~~~~~~~aR~l~er~~k------~----~~lw~~~~~fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          350 --HPDSTLLKEEFFLFLLRIGDEENARALFKRLEK------T----SRMWDSMIEYEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             --CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHSCC------B----HHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             --CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH------H----HHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence              222234456677777889999999999999842      1    11688888887888999999999988764

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.95  E-value=2.2e-05  Score=51.08  Aligned_cols=88  Identities=9%  Similarity=-0.019  Sum_probs=71.1

Q ss_pred             CCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC
Q 043380           49 PDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD  128 (246)
Q Consensus        49 ~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~  128 (246)
                      ++...|..+...+...|++++|.+.|++..+.        .+.+...|..+-.++...|++++|...+++..+   +.|+
T Consensus         2 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--------~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~---~~p~   70 (111)
T 2l6j_A            2 SQFEKQKEQGNSLFKQGLYREAVHCYDQLITA--------QPQNPVGYSNKAMALIKLGEYTQAIQMCQQGLR---YTST   70 (111)
T ss_dssp             THHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT---SCSS
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--------CCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHH---hCCC
Confidence            35567888888999999999999999999886        234677899999999999999999999999988   4555


Q ss_pred             -------HHHHHHHHHHHHhcCChhh
Q 043380          129 -------RSTFTAMVDALLYSGSIKV  147 (246)
Q Consensus       129 -------~~~~~~li~~~~~~~~~~~  147 (246)
                             ...+..+..++...|+.+.
T Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~   96 (111)
T 2l6j_A           71 AEHVAIRSKLQYRLELAQGAVGSVQI   96 (111)
T ss_dssp             TTSHHHHHHHHHHHHHHHHHHHCCCC
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHhHhh
Confidence                   4456666667777777666

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=97.94  E-value=0.0024  Score=50.49  Aligned_cols=204  Identities=9%  Similarity=-0.087  Sum_probs=139.0

Q ss_pred             cCHHHHHHHHHHHHhcCC----------HHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCC--cchHHHHHHHHHhccC
Q 043380           15 LNTIVMNAVIEASREAQR----------IDEAYQILESVEKGLEPDSLSYNILISACIKTKK--LDVTMPFNEQLKDNGQ   82 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g~----------~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~--~~~a~~~~~~m~~~~~   82 (246)
                      -+..+||.--......+.          +++++.+++.+....+.+..+|+.-.-.+.+.++  +++++++++++.+.  
T Consensus        62 ~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~PKny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~--  139 (331)
T 3dss_A           62 DFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNWARELELCARFLEA--  139 (331)
T ss_dssp             TCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHH--
T ss_pred             hhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHhccCcccHHHHHHHHHHHHHh--
Confidence            345556655444444333          6788888888765457788999988888888774  78999999999986  


Q ss_pred             CCCCCCCCccHHHHHHHHHHHHccCC-HHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhc--------------CChhh
Q 043380           83 KCSSGGFHPDIFTYATLLMGFRHAKD-LQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYS--------------GSIKV  147 (246)
Q Consensus        83 ~~~~~~~~p~~~~~~~ll~~~~~~~~-~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~--------------~~~~~  147 (246)
                            -+-|...|+.---.+...|. ++++++.++.+.+ .. +-|...|+.....+...              +.+++
T Consensus       140 ------dprNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~-~~-p~N~SAW~~R~~ll~~l~~~~~~~~~~~~~~~~~~e  211 (331)
T 3dss_A          140 ------DERNFHCWDYRRFVAAQAAVAPAEELAFTDSLIT-RN-FSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLK  211 (331)
T ss_dssp             ------CTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH-HC-SCCHHHHHHHHHHHHHHSCCC------CCCHHHHHH
T ss_pred             ------CCCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHH-HC-CCCHHHHHHHHHHHHHhhhccccccccccchHHHHH
Confidence                  24577788888878888888 6999999999988 32 23466777666555554              34677


Q ss_pred             hhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhc-----------CChhHHhhHHHhhCCCCCCCCCchhhhHHH
Q 043380          148 VGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAAR-----------VDYDIVKSPYRRMWPDSTGTISPEVQEEAG  216 (246)
Q Consensus       148 ~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~-----------g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  216 (246)
                          +++.++.....      -+-|...|+-+-..+.+.           +.++++.+.++++....+.....-.   +.
T Consensus       212 ----Ele~~~~ai~~------~P~d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l~~el~~~~elle~~pd~~w~l~---~~  278 (331)
T 3dss_A          212 ----ELELVQNAFFT------DPNDQSAWFYHRWLLGAGSGRCELSVEKSTVLQSELESCKELQELEPENKWCLL---TI  278 (331)
T ss_dssp             ----HHHHHHHHHHH------STTCHHHHHHHHHHHHSSSCGGGCCHHHHHHHHHHHHHHHHHHHHCTTCHHHHH---HH
T ss_pred             ----HHHHHHHHHHh------CCCCHHHHHHHHHHHHhccCccccchHHHHHHHHHHHHHHHHHhhCcccchHHH---HH
Confidence                99999998886      234567776555555554           4567888888888765443221111   11


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          217 HLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       217 ~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      ..++.+.-..|..+++..++.++++
T Consensus       279 ~~~~~~~~~~~~~~~~~~~l~~l~~  303 (331)
T 3dss_A          279 ILLMRALDPLLYEKETLQYFSTLKA  303 (331)
T ss_dssp             HHHHHHHCTTTTHHHHHHHHHHHHH
T ss_pred             HHHHHhhcccccHHHHHHHHHHHHH
Confidence            2222233346778888889888865

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=97.91  E-value=0.0034  Score=49.12  Aligned_cols=184  Identities=8%  Similarity=-0.064  Sum_probs=135.8

Q ss_pred             cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcC--CcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHH----
Q 043380           30 AQRIDEAYQILESVEKGLEPDSLSYNILISACIKTK--KLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGF----  103 (246)
Q Consensus        30 ~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~--~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~----  103 (246)
                      ....++|+++++.+..--+-+...|+.--..+...+  ++++++++++.+...        .+-+..+|+.--..+    
T Consensus        46 ~e~s~~aL~~t~~~L~~nP~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~--------nPk~y~aW~~R~~iL~~~~  117 (306)
T 3dra_A           46 EEYSERALHITELGINELASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALD--------NEKNYQIWNYRQLIIGQIM  117 (306)
T ss_dssp             TCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHH--------CTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHCcHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHH--------CcccHHHHHHHHHHHHHHH
Confidence            344578999999876433456677898888888888  999999999999986        233445566544444    


Q ss_pred             Hcc---CCHHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHhcCChh--hhhhHHHHHHHHHHHhhcCCCCCCcchhhHH
Q 043380          104 RHA---KDLQSLLEIVFEMKSCCNLIL-DRSTFTAMVDALLYSGSIK--VVGLYALCIFGEIVKRVCSNPGLWPKPHLYV  177 (246)
Q Consensus       104 ~~~---~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~~~~~--~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~  177 (246)
                      ...   +++++++.+++.+.+   ..| +-.+|+.-.-.+...|.++  +    +++.++.+.+.      -.-|...|+
T Consensus       118 ~~l~~~~~~~~EL~~~~~~l~---~~pkny~aW~~R~~vl~~l~~~~~~~----EL~~~~~~i~~------d~~N~sAW~  184 (306)
T 3dra_A          118 ELNNNDFDPYREFDILEAMLS---SDPKNHHVWSYRKWLVDTFDLHNDAK----ELSFVDKVIDT------DLKNNSAWS  184 (306)
T ss_dssp             HHTTTCCCTHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCTTCHH----HHHHHHHHHHH------CTTCHHHHH
T ss_pred             HhccccCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHhcccChHH----HHHHHHHHHHh------CCCCHHHHH
Confidence            444   789999999999998   334 4778887777888888888  8    99999999987      234668888


Q ss_pred             HHHHHHHhcCC------hhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhH-HHHHHHHHH
Q 043380          178 SMMHELAARVD------YDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDL-ALDKLSNTI  240 (246)
Q Consensus       178 ~li~~~~~~g~------~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~-a~~~~~~m~  240 (246)
                      .-...+...++      ++++.+.++.....++..      .++|+.+-..+.+.|+... +..+...+.
T Consensus       185 ~R~~ll~~l~~~~~~~~~~eEl~~~~~aI~~~p~n------~SaW~y~~~ll~~~~~~~~~~~~~~~~~~  248 (306)
T 3dra_A          185 HRFFLLFSKKHLATDNTIDEELNYVKDKIVKCPQN------PSTWNYLLGIHERFDRSITQLEEFSLQFV  248 (306)
T ss_dssp             HHHHHHHSSGGGCCHHHHHHHHHHHHHHHHHCSSC------HHHHHHHHHHHHHTTCCGGGGHHHHHTTE
T ss_pred             HHHHHHHhccccchhhhHHHHHHHHHHHHHhCCCC------ccHHHHHHHHHHhcCCChHHHHHHHHHHH
Confidence            87777777777      888999988877554322      2278888888888887544 444555443

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.81  E-value=0.00026  Score=46.42  Aligned_cols=80  Identities=9%  Similarity=-0.036  Sum_probs=66.6

Q ss_pred             chHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChh
Q 043380           68 DVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIK  146 (246)
Q Consensus        68 ~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~  146 (246)
                      ++|.+.|++..+.        -+.+...+..+...|...|++++|...|++...   ..|+ ...|..+...|...|+++
T Consensus         2 ~~a~~~~~~al~~--------~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~~la~~~~~~g~~~   70 (115)
T 2kat_A            2 QAITERLEAMLAQ--------GTDNMLLRFTLGKTYAEHEQFDAALPHLRAALD---FDPTYSVAWKWLGKTLQGQGDRA   70 (115)
T ss_dssp             CCHHHHHHHHHTT--------TCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHTCHH
T ss_pred             hHHHHHHHHHHHh--------CCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHH---HCCCcHHHHHHHHHHHHHcCCHH
Confidence            4677888888875        234677888999999999999999999999888   3455 778888999999999999


Q ss_pred             hhhhHHHHHHHHHHHh
Q 043380          147 VVGLYALCIFGEIVKR  162 (246)
Q Consensus       147 ~~~~~a~~~~~~m~~~  162 (246)
                      +    |...|+...+.
T Consensus        71 ~----A~~~~~~al~~   82 (115)
T 2kat_A           71 G----ARQAWESGLAA   82 (115)
T ss_dssp             H----HHHHHHHHHHH
T ss_pred             H----HHHHHHHHHHh
Confidence            9    99999988765

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.78  E-value=0.00013  Score=48.00  Aligned_cols=79  Identities=11%  Similarity=-0.046  Sum_probs=59.0

Q ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHH
Q 043380           35 EAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLE  114 (246)
Q Consensus        35 ~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~  114 (246)
                      .|++.|+...+..+.+...+..+...|...|++++|...|++..+.        -+.+...|..+..+|...|++++|..
T Consensus         3 ~a~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--------~p~~~~~~~~la~~~~~~g~~~~A~~   74 (115)
T 2kat_A            3 AITERLEAMLAQGTDNMLLRFTLGKTYAEHEQFDAALPHLRAALDF--------DPTYSVAWKWLGKTLQGQGDRAGARQ   74 (115)
T ss_dssp             CHHHHHHHHHTTTCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHHhCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH--------CCCcHHHHHHHHHHHHHcCCHHHHHH
Confidence            4566676665434556777888888888888888888888888875        13346677888888888888888888


Q ss_pred             HHHHHHh
Q 043380          115 IVFEMKS  121 (246)
Q Consensus       115 ~~~~m~~  121 (246)
                      .|+....
T Consensus        75 ~~~~al~   81 (115)
T 2kat_A           75 AWESGLA   81 (115)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8887766

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.77  E-value=0.00034  Score=43.40  Aligned_cols=82  Identities=11%  Similarity=-0.020  Sum_probs=65.9

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      +...+..+...+.+.|++++|...|++.....+.+...+..+..++...|++++|...|++..+.        .+.+...
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~--------~p~~~~~   79 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALEL--------DPNNAEA   79 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc--------CCCCHHH
Confidence            45678888899999999999999999876434567788999999999999999999999999886        1234556


Q ss_pred             HHHHHHHHHc
Q 043380           96 YATLLMGFRH  105 (246)
Q Consensus        96 ~~~ll~~~~~  105 (246)
                      +..+-.++.+
T Consensus        80 ~~~l~~~~~~   89 (91)
T 1na3_A           80 KQNLGNAKQK   89 (91)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            6666666544

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=97.75  E-value=0.0008  Score=47.12  Aligned_cols=97  Identities=10%  Similarity=0.014  Sum_probs=78.1

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC--------CH-----HHHHHHHHHHHhcCCcchHHHHHHHHHhc----
Q 043380           18 IVMNAVIEASREAQRIDEAYQILESVEKGLEP--------DS-----LSYNILISACIKTKKLDVTMPFNEQLKDN----   80 (246)
Q Consensus        18 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~--------~~-----~t~~~li~~~~~~~~~~~a~~~~~~m~~~----   80 (246)
                      ..+...-..+.+.|++++|++.|+.... +.|        +.     ..|+.+-.++.+.|++++|+..+++.++.    
T Consensus        12 ~~~~~~G~~l~~~g~~eeAi~~Y~kAL~-l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~   90 (159)
T 2hr2_A           12 YLALSDAQRQLVAGEYDEAAANCRRAME-ISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRR   90 (159)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHH-HHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHh-hCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhcc
Confidence            4456677788899999999999987642 122        23     38999999999999999999999999873    


Q ss_pred             cCCCCCCCCCcc-HHHH----HHHHHHHHccCCHHHHHHHHHHHHh
Q 043380           81 GQKCSSGGFHPD-IFTY----ATLLMGFRHAKDLQSLLEIVFEMKS  121 (246)
Q Consensus        81 ~~~~~~~~~~p~-~~~~----~~ll~~~~~~~~~~~a~~~~~~m~~  121 (246)
                      +      .+.|+ ...|    ...-.++...|++++|+..|+...+
T Consensus        91 ~------e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAle  130 (159)
T 2hr2_A           91 G------ELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  130 (159)
T ss_dssp             C------CTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             c------cCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHh
Confidence            1      12565 4578    8999999999999999999998866

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=97.68  E-value=0.0097  Score=47.00  Aligned_cols=202  Identities=6%  Similarity=-0.090  Sum_probs=140.5

Q ss_pred             CHHHHHHHHHHHH---hcCCH-HHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCC----------cchHHHHHHHHHhcc
Q 043380           16 NTIVMNAVIEASR---EAQRI-DEAYQILESVEKGLEPDSLSYNILISACIKTKK----------LDVTMPFNEQLKDNG   81 (246)
Q Consensus        16 ~~~~~~~li~~~~---~~g~~-~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~----------~~~a~~~~~~m~~~~   81 (246)
                      -+..|..++..+.   +.|.. ++|+++++.+..--+-+...|+.--..+...+.          +++++.+++.+... 
T Consensus        25 ki~~y~~~~~~~~~~~~~~e~s~eaL~~t~~~L~~nP~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~-  103 (331)
T 3dss_A           25 KLKLYQSATQAVFQKRQAGELDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRV-  103 (331)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCSHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCchhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHh-
Confidence            3456666655443   45665 479999998875334456667754444433332          67899999999885 


Q ss_pred             CCCCCCCCCccHHHHHHHHHHHHccC--CHHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHhcCC-hhhhhhHHHHHHH
Q 043380           82 QKCSSGGFHPDIFTYATLLMGFRHAK--DLQSLLEIVFEMKSCCNLIL-DRSTFTAMVDALLYSGS-IKVVGLYALCIFG  157 (246)
Q Consensus        82 ~~~~~~~~~p~~~~~~~ll~~~~~~~--~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~~~-~~~~~~~a~~~~~  157 (246)
                             -+-+..+|+.--..+.+.+  ++++++.+++.+.+   ..| |-.+|+.-.-.+...|. +++    +++.++
T Consensus       104 -------~PKny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~---~dprNy~AW~~R~~vl~~l~~~~~e----el~~~~  169 (331)
T 3dss_A          104 -------NPKSYGTWHHRCWLLSRLPEPNWARELELCARFLE---ADERNFHCWDYRRFVAAQAAVAPAE----ELAFTD  169 (331)
T ss_dssp             -------CTTCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCCHHH----HHHHHH
T ss_pred             -------CCCCHHHHHHHHHHHhccCcccHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHhCcCHHH----HHHHHH
Confidence                   2446778888777777777  48999999999998   334 47778777777777888 588    999999


Q ss_pred             HHHHhhcCCCCCCcchhhHHHHHHHHHhc--------------CChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHH
Q 043380          158 EIVKRVCSNPGLWPKPHLYVSMMHELAAR--------------VDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAA  223 (246)
Q Consensus       158 ~m~~~~~~~~~~~p~~~~~~~li~~~~~~--------------g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~  223 (246)
                      .+.+.      -.-|..+|+.....+...              +.++++.+.+.......+..      .++|+.+-..+
T Consensus       170 ~~I~~------~p~N~SAW~~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~P~d------~SaW~Y~r~ll  237 (331)
T 3dss_A          170 SLITR------NFSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPND------QSAWFYHRWLL  237 (331)
T ss_dssp             HHHHH------CSCCHHHHHHHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHHSTTC------HHHHHHHHHHH
T ss_pred             HHHHH------CCCCHHHHHHHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHhCCCC------HHHHHHHHHHH
Confidence            99987      234667787777766665              45778888888876543322      22676665555


Q ss_pred             Hhc-----------CChhHHHHHHHHHHhhcc
Q 043380          224 LND-----------GQVDLALDKLSNTITRWK  244 (246)
Q Consensus       224 ~~~-----------g~~~~a~~~~~~m~~~g~  244 (246)
                      .+.           +.++++++.++++.+..+
T Consensus       238 ~~~~~~~~~~~~~~~~l~~el~~~~elle~~p  269 (331)
T 3dss_A          238 GAGSGRCELSVEKSTVLQSELESCKELQELEP  269 (331)
T ss_dssp             HSSSCGGGCCHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HhccCccccchHHHHHHHHHHHHHHHHHhhCc
Confidence            554           457899999988876544

>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=0.00031  Score=44.99  Aligned_cols=67  Identities=10%  Similarity=0.003  Sum_probs=57.9

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhc
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDN   80 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~   80 (246)
                      +-++..+..+..+|.+.|++++|+..|+...+-.+.+...|..+-.+|...|++++|.+.|++..+.
T Consensus         4 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l   70 (100)
T 3ma5_A            4 PEDPFTRYALAQEHLKHDNASRALALFEELVETDPDYVGTYYHLGKLYERLDRTDDAIDTYAQGIEV   70 (100)
T ss_dssp             -CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            3467788999999999999999999999876434557788999999999999999999999998864

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.62  E-value=0.0013  Score=40.60  Aligned_cols=82  Identities=9%  Similarity=0.032  Sum_probs=65.6

Q ss_pred             cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCC
Q 043380           92 DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL-DRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLW  170 (246)
Q Consensus        92 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~  170 (246)
                      +...+..+-..+...|++++|...|++..+   ..| +...+..+...+...|++++    |...|++..+.      -+
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~---~~~~~~~~~~~l~~~~~~~~~~~~----A~~~~~~a~~~------~p   74 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALE---LDPNNAEAWYNLGNAYYKQGDYDE----AIEYYQKALEL------DP   74 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------CT
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHhhHHH----HHHHHHHHHhc------CC
Confidence            456788888999999999999999999988   334 47788899999999999999    99999999886      12


Q ss_pred             cchhhHHHHHHHHHhc
Q 043380          171 PKPHLYVSMMHELAAR  186 (246)
Q Consensus       171 p~~~~~~~li~~~~~~  186 (246)
                      .+...+..+-.++...
T Consensus        75 ~~~~~~~~l~~~~~~~   90 (91)
T 1na3_A           75 NNAEAKQNLGNAKQKQ   90 (91)
T ss_dssp             TCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhc
Confidence            3455666666655543

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=97.62  E-value=0.013  Score=46.64  Aligned_cols=177  Identities=8%  Similarity=-0.084  Sum_probs=129.6

Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcC-CcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHH
Q 043380           26 ASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTK-KLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFR  104 (246)
Q Consensus        26 ~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~-~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~  104 (246)
                      ...+.+..++|+++++.+..-.+-+...|+.--..+...+ .+++++++++.+...        .+-+..+|+.--..+.
T Consensus        63 ~~~~~e~se~AL~lt~~~L~~nP~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~--------nPKny~aW~hR~wlL~  134 (349)
T 3q7a_A           63 IAAKEEKSERALELTEIIVRMNPAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQ--------NLKSYQVWHHRLLLLD  134 (349)
T ss_dssp             HHHTTCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHT--------TCCCHHHHHHHHHHHH
T ss_pred             HHHhCCCCHHHHHHHHHHHHhCchhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHh--------CCCcHHHHHHHHHHHH
Confidence            3344455678999999886433567777888888888888 599999999999986        3446678888777776


Q ss_pred             cc-C-CHHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHhcCChh--------hhhhHHHHHHHHHHHhhcCCCCCCcch
Q 043380          105 HA-K-DLQSLLEIVFEMKSCCNLIL-DRSTFTAMVDALLYSGSIK--------VVGLYALCIFGEIVKRVCSNPGLWPKP  173 (246)
Q Consensus       105 ~~-~-~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~~~~~--------~~~~~a~~~~~~m~~~~~~~~~~~p~~  173 (246)
                      +. + ++++++++++.+.+   ..| +-.+|+.-.-.+...+.++        +    +++.++.+.+.      -.-|.
T Consensus       135 ~l~~~~~~~EL~~~~k~L~---~dpkNy~AW~~R~wvl~~l~~~~~~~~~~~~e----ELe~~~k~I~~------dp~N~  201 (349)
T 3q7a_A          135 RISPQDPVSEIEYIHGSLL---PDPKNYHTWAYLHWLYSHFSTLGRISEAQWGS----ELDWCNEMLRV------DGRNN  201 (349)
T ss_dssp             HHCCSCCHHHHHHHHHHTS---SCTTCHHHHHHHHHHHHHHHHTTCCCHHHHHH----HHHHHHHHHHH------CTTCH
T ss_pred             HhcCCChHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHhccccccchhhHHH----HHHHHHHHHHh------CCCCH
Confidence            66 6 88999999999988   334 4667776665666666666        7    99999999987      23467


Q ss_pred             hhHHHHHHHHHhcCC-------hhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCCh
Q 043380          174 HLYVSMMHELAARVD-------YDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQV  229 (246)
Q Consensus       174 ~~~~~li~~~~~~g~-------~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~  229 (246)
                      ..|+.--..+.+.++       ++++.+.+++....++..      .++|+.+-..+.+.|+.
T Consensus       202 SAW~~R~~lL~~l~~~~~~~~~~~eELe~~~~aI~~~P~n------~SaW~Ylr~Ll~~~~~~  258 (349)
T 3q7a_A          202 SAWGWRWYLRVSRPGAETSSRSLQDELIYILKSIHLIPHN------VSAWNYLRGFLKHFSLP  258 (349)
T ss_dssp             HHHHHHHHHHTTSTTCCCCHHHHHHHHHHHHHHHHHCTTC------HHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHhCCCC------HHHHHHHHHHHHhcCCC
Confidence            889888888888876       678888887766543322      22677776666666654

>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=97.55  E-value=0.0012  Score=54.24  Aligned_cols=102  Identities=7%  Similarity=-0.132  Sum_probs=78.7

Q ss_pred             HHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhC----C-CCCCC-HH
Q 043380           57 LISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSC----C-NLILD-RS  130 (246)
Q Consensus        57 li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~----~-~~~p~-~~  130 (246)
                      .+..+.+.|++++|++++++..+...+...........+++.|..+|...|++++|+.++++....    . .-.|+ ..
T Consensus       293 ~ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~  372 (429)
T 3qwp_A          293 KIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGV  372 (429)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHH
T ss_pred             HHHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHH
Confidence            345566789999999999999875333323333334569999999999999999999999977651    1 23344 56


Q ss_pred             HHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          131 TFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       131 ~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      +++.|...|...|++++    |+.++++..+.
T Consensus       373 ~l~nLa~~~~~~g~~~e----A~~~~~~Al~i  400 (429)
T 3qwp_A          373 QVMKVGKLQLHQGMFPQ----AMKNLRLAFDI  400 (429)
T ss_dssp             HHHHHHHHHHHTTCHHH----HHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHH----HHHHHHHHHHH
Confidence            79999999999999999    99999987664

>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=97.54  E-value=0.00022  Score=58.67  Aligned_cols=91  Identities=8%  Similarity=0.038  Sum_probs=68.9

Q ss_pred             cCCHHHHHHHHHHHH----hCCCCC----HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-HHHHHHHH
Q 043380           30 AQRIDEAYQILESVE----KGLEPD----SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-IFTYATLL  100 (246)
Q Consensus        30 ~g~~~~a~~~~~~~~----~~~~~~----~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~~~ll  100 (246)
                      .|++++|+.++++..    +-..|+    ..+++.|..+|...|++++|+.++++..+...+... .-.|+ ..+|+.|-
T Consensus       311 ~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG-~~Hp~~a~~l~nLa  389 (433)
T 3qww_A          311 YKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYP-VYSLNVASMWLKLG  389 (433)
T ss_dssp             TSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSC-SSCHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcC-CCChHHHHHHHHHH
Confidence            578999999998753    222232    467899999999999999999999998753111111 22444 45899999


Q ss_pred             HHHHccCCHHHHHHHHHHHHh
Q 043380          101 MGFRHAKDLQSLLEIVFEMKS  121 (246)
Q Consensus       101 ~~~~~~~~~~~a~~~~~~m~~  121 (246)
                      ..|...|++++|+.++++..+
T Consensus       390 ~~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          390 RLYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhccCHHHHHHHHHHHHH
Confidence            999999999999999987665

>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=97.53  E-value=0.00043  Score=56.97  Aligned_cols=96  Identities=6%  Similarity=-0.091  Sum_probs=73.6

Q ss_pred             hcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhC----CC-CCCC-HHHHHHHH
Q 043380           63 KTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSC----CN-LILD-RSTFTAMV  136 (246)
Q Consensus        63 ~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~----~~-~~p~-~~~~~~li  136 (246)
                      ..|++++|+.++++..+...+......+-...+++.|..+|...|++++|+.++++....    .| -.|+ ..+|+.|.
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            357889999999988764322222222233568999999999999999999999987651    12 2355 56799999


Q ss_pred             HHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          137 DALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       137 ~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ..|...|++++    |+.++++..+.
T Consensus       390 ~~~~~qg~~~e----A~~~~~~Al~i  411 (433)
T 3qww_A          390 RLYMGLENKAA----GEKALKKAIAI  411 (433)
T ss_dssp             HHHHHTTCHHH----HHHHHHHHHHH
T ss_pred             HHHHhccCHHH----HHHHHHHHHHH
Confidence            99999999999    99999987664

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.53  E-value=0.00038  Score=44.57  Aligned_cols=66  Identities=12%  Similarity=0.081  Sum_probs=55.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHh
Q 043380           48 EPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKS  121 (246)
Q Consensus        48 ~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~  121 (246)
                      +-+...+..+...|...|++++|...|++..+.        -+.+...|..+-.+|...|++++|.+.|++..+
T Consensus         4 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--------~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~   69 (100)
T 3ma5_A            4 PEDPFTRYALAQEHLKHDNASRALALFEELVET--------DPDYVGTYYHLGKLYERLDRTDDAIDTYAQGIE   69 (100)
T ss_dssp             -CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------STTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--------CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            346778888999999999999999999999886        123466889999999999999999999998776

>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=97.50  E-value=0.00055  Score=56.30  Aligned_cols=99  Identities=11%  Similarity=0.071  Sum_probs=74.7

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHh----CCCC----CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-
Q 043380           22 AVIEASREAQRIDEAYQILESVEK----GLEP----DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-   92 (246)
Q Consensus        22 ~li~~~~~~g~~~~a~~~~~~~~~----~~~~----~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-   92 (246)
                      ..+..+.+.|++++|++++++...    -..|    -..+++.+..+|...|++++|+.++++..+...+... .-.|+ 
T Consensus       292 ~~ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg-~~Hp~~  370 (429)
T 3qwp_A          292 KKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFP-GSHPVR  370 (429)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSC-SSCHHH
T ss_pred             HHHHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcC-CCChHH
Confidence            345566778999999999988642    1223    2467899999999999999999999988753111111 23344 


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHh
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKS  121 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~  121 (246)
                      ..+++.|-..|...|++++|+.++++..+
T Consensus       371 a~~l~nLa~~~~~~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          371 GVQVMKVGKLQLHQGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            46899999999999999999999887655

>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=97.45  E-value=0.00044  Score=48.36  Aligned_cols=99  Identities=7%  Similarity=-0.038  Sum_probs=79.5

Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCc----------chHHHHHHHHHhccCCCCCCCCCc-cHHHH
Q 043380           28 REAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKL----------DVTMPFNEQLKDNGQKCSSGGFHP-DIFTY   96 (246)
Q Consensus        28 ~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~----------~~a~~~~~~m~~~~~~~~~~~~~p-~~~~~   96 (246)
                      .+.+.+++|.+.++....--+.+...|+.+-.++...+++          ++|+..|++.++.         .| +...|
T Consensus        13 ~r~~~feeA~~~~~~Ai~l~P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~l---------dP~~~~A~   83 (158)
T 1zu2_A           13 DRILLFEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLI---------DPKKDEAV   83 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHH---------CTTCHHHH
T ss_pred             HHHhHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHh---------CcCcHHHH
Confidence            4567789999999887543466888899888888888765          5999999999986         55 46789


Q ss_pred             HHHHHHHHccC-----------CHHHHHHHHHHHHhCCCCCCCHHHHHHHHHH
Q 043380           97 ATLLMGFRHAK-----------DLQSLLEIVFEMKSCCNLILDRSTFTAMVDA  138 (246)
Q Consensus        97 ~~ll~~~~~~~-----------~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~  138 (246)
                      ..+-.+|...|           ++++|.+.|++..+   +.|+...|..-+..
T Consensus        84 ~~LG~ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl~---l~P~~~~y~~al~~  133 (158)
T 1zu2_A           84 WCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVD---EQPDNTHYLKSLEM  133 (158)
T ss_dssp             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH---HCTTCHHHHHHHHH
T ss_pred             HHHHHHHHHhcccCcchhhhhccHHHHHHHHHHHHH---hCCCCHHHHHHHHH
Confidence            99999998764           89999999999999   77887766555543

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=97.45  E-value=0.006  Score=52.01  Aligned_cols=186  Identities=7%  Similarity=-0.091  Sum_probs=133.7

Q ss_pred             HHHHHHHHHHH---hcCC-HHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCC----------cchHHHHHHHHHhccCC
Q 043380           18 IVMNAVIEASR---EAQR-IDEAYQILESVEKGLEPDSLSYNILISACIKTKK----------LDVTMPFNEQLKDNGQK   83 (246)
Q Consensus        18 ~~~~~li~~~~---~~g~-~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~----------~~~a~~~~~~m~~~~~~   83 (246)
                      ..|..++..+.   +.|. -++|++.++.+..--+-+...|+.--.++...++          ++++.++++++.+.   
T Consensus        26 ~~y~~~~~~~~~~~~~~~~~eeal~~~~~~l~~nP~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~---  102 (567)
T 1dce_A           26 KLYQSATQAVFQKRQAGELDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRV---  102 (567)
T ss_dssp             HHHHHHHHHHHHHHHTTCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHH---
T ss_pred             HHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCchhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHh---
Confidence            34444444332   3344 5678999988764335566778877666666666          89999999999986   


Q ss_pred             CCCCCCCccHHHHHHHHHHHHccC--CHHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHhcC-ChhhhhhHHHHHHHHH
Q 043380           84 CSSGGFHPDIFTYATLLMGFRHAK--DLQSLLEIVFEMKSCCNLIL-DRSTFTAMVDALLYSG-SIKVVGLYALCIFGEI  159 (246)
Q Consensus        84 ~~~~~~~p~~~~~~~ll~~~~~~~--~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~~-~~~~~~~~a~~~~~~m  159 (246)
                           -+-+..+|+.--..+.+.+  +++++++.++.+.+   ..| +-.+|+.-...+...| .+++    +++.++.+
T Consensus       103 -----~pK~y~aW~hR~w~l~~l~~~~~~~el~~~~k~l~---~d~~N~~aW~~R~~~l~~l~~~~~~----el~~~~~~  170 (567)
T 1dce_A          103 -----NPKSYGTWHHRCWLLSRLPEPNWARELELCARFLE---ADERNFHCWDYRRFVAAQAAVAPAE----ELAFTDSL  170 (567)
T ss_dssp             -----CTTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTCCCHHH----HHHHHHTT
T ss_pred             -----CCCCHHHHHHHHHHHHHcccccHHHHHHHHHHHHh---hccccccHHHHHHHHHHHcCCChHH----HHHHHHHH
Confidence                 2446778988888888889  77999999999999   334 4778888888888888 8888    99999998


Q ss_pred             HHhhcCCCCCCcchhhHHHHHHHHHhc--------------CChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHh
Q 043380          160 VKRVCSNPGLWPKPHLYVSMMHELAAR--------------VDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALN  225 (246)
Q Consensus       160 ~~~~~~~~~~~p~~~~~~~li~~~~~~--------------g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~  225 (246)
                      .+.      -.-|..+|+.....+.+.              +.++++.+.++.....++..      ..+|..+-..+.+
T Consensus       171 I~~------~p~n~saW~~r~~ll~~l~~~~~~~~~~~~~~~~~~eel~~~~~ai~~~P~~------~saW~y~~~ll~~  238 (567)
T 1dce_A          171 ITR------NFSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPND------QSAWFYHRWLLGR  238 (567)
T ss_dssp             TTT------TCCCHHHHHHHHHHHHHHSCCCCSSSCCSSCHHHHHHHHHHHHHHHHHCSSC------SHHHHHHHHHHSC
T ss_pred             HHH------CCCCccHHHHHHHHHHhhcccccccccccccHHHHHHHHHHHHHHHhhCCCC------ccHHHHHHHHHhc
Confidence            875      234667888877777663              45688888888766443222      2268777777766


Q ss_pred             cCChh
Q 043380          226 DGQVD  230 (246)
Q Consensus       226 ~g~~~  230 (246)
                      .+..+
T Consensus       239 ~~~~~  243 (567)
T 1dce_A          239 AEPHD  243 (567)
T ss_dssp             CCCCS
T ss_pred             CCCcc
Confidence            66533

>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=97.41  E-value=0.0071  Score=41.14  Aligned_cols=110  Identities=12%  Similarity=-0.040  Sum_probs=88.2

Q ss_pred             cCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHc---
Q 043380           30 AQRIDEAYQILESVE-KGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRH---  105 (246)
Q Consensus        30 ~g~~~~a~~~~~~~~-~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~---  105 (246)
                      .++.++|.+.|+..- .+ .|+..    |-..|...+..++|.++|++..+.          -+...+..|-..|..   
T Consensus         8 ~~d~~~A~~~~~~aa~~g-~~~a~----lg~~y~~g~~~~~A~~~~~~Aa~~----------g~~~a~~~Lg~~y~~G~g   72 (138)
T 1klx_A            8 KKDLKKAIQYYVKACELN-EMFGC----LSLVSNSQINKQKLFQYLSKACEL----------NSGNGCRFLGDFYENGKY   72 (138)
T ss_dssp             HHHHHHHHHHHHHHHHTT-CTTHH----HHHHTCTTSCHHHHHHHHHHHHHT----------TCHHHHHHHHHHHHHCSS
T ss_pred             ccCHHHHHHHHHHHHcCC-CHhhh----HHHHHHcCCCHHHHHHHHHHHHcC----------CCHHHHHHHHHHHHcCCC
Confidence            356889999998875 44 44443    666677777888899999999886          355677788888877   


Q ss_pred             -cCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHh----cCChhhhhhHHHHHHHHHHHh
Q 043380          106 -AKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLY----SGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       106 -~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~----~~~~~~~~~~a~~~~~~m~~~  162 (246)
                       .+++++|.+.|+...+ .|   +...+..|-..|..    .+++++    |...|+...+.
T Consensus        73 ~~~d~~~A~~~~~~Aa~-~g---~~~a~~~Lg~~y~~G~g~~~d~~~----A~~~~~~Aa~~  126 (138)
T 1klx_A           73 VKKDLRKAAQYYSKACG-LN---DQDGCLILGYKQYAGKGVVKNEKQ----AVKTFEKACRL  126 (138)
T ss_dssp             SCCCHHHHHHHHHHHHH-TT---CHHHHHHHHHHHHHTSSSCCCHHH----HHHHHHHHHHT
T ss_pred             CCccHHHHHHHHHHHHc-CC---CHHHHHHHHHHHHCCCCCCcCHHH----HHHHHHHHHHC
Confidence             8899999999999988 54   57778888888888    889999    99999998886

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=97.34  E-value=0.023  Score=48.47  Aligned_cols=151  Identities=9%  Similarity=-0.064  Sum_probs=115.4

Q ss_pred             CCcchHHHHHHHHHhccCCCCCCCCCcc-HHHHHHHHHHHHccCC----------HHHHHHHHHHHHhCCCCCCC-HHHH
Q 043380           65 KKLDVTMPFNEQLKDNGQKCSSGGFHPD-IFTYATLLMGFRHAKD----------LQSLLEIVFEMKSCCNLILD-RSTF  132 (246)
Q Consensus        65 ~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~~~ll~~~~~~~~----------~~~a~~~~~~m~~~~~~~p~-~~~~  132 (246)
                      ...++|.+.++++...         .|+ ...|+.--.++...|+          ++++++.++.+.+   ..|. ..+|
T Consensus        43 ~~~eeal~~~~~~l~~---------nP~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~---~~pK~y~aW  110 (567)
T 1dce_A           43 ELDESVLELTSQILGA---------NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLR---VNPKSYGTW  110 (567)
T ss_dssp             CCSHHHHHHHHHHHHH---------CTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHH---HCTTCHHHH
T ss_pred             CCCHHHHHHHHHHHHH---------CchhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHH---hCCCCHHHH
Confidence            3456789999999986         454 5567766666666666          8999999999998   4455 7788


Q ss_pred             HHHHHHHHhcC--ChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcC-ChhHHhhHHHhhCCCCCCCCCc
Q 043380          133 TAMVDALLYSG--SIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARV-DYDIVKSPYRRMWPDSTGTISP  209 (246)
Q Consensus       133 ~~li~~~~~~~--~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g-~~~~a~~~~~~~~~~~~~~~~~  209 (246)
                      +.---.+.+.+  ++++    +++.++.+.+.      -.-|.++|+.--.++...| .++++.+.++++...++...  
T Consensus       111 ~hR~w~l~~l~~~~~~~----el~~~~k~l~~------d~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~n~--  178 (567)
T 1dce_A          111 HHRCWLLSRLPEPNWAR----ELELCARFLEA------DERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNY--  178 (567)
T ss_dssp             HHHHHHHHTCSSCCHHH----HHHHHHHHHHH------CTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCH--
T ss_pred             HHHHHHHHHcccccHHH----HHHHHHHHHhh------ccccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCCCc--
Confidence            88888888888  6799    99999999997      2346788999888888999 89999999999887654322  


Q ss_pred             hhhhHHHHHHHHHHHhc--------------CChhHHHHHHHHHHhhc
Q 043380          210 EVQEEAGHLLMEAALND--------------GQVDLALDKLSNTITRW  243 (246)
Q Consensus       210 ~~~~~~~~~li~~~~~~--------------g~~~~a~~~~~~m~~~g  243 (246)
                          ++|+.....+.+.              +.++++.+++++.....
T Consensus       179 ----saW~~r~~ll~~l~~~~~~~~~~~~~~~~~~eel~~~~~ai~~~  222 (567)
T 1dce_A          179 ----SSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTD  222 (567)
T ss_dssp             ----HHHHHHHHHHHHHSCCCCSSSCCSSCHHHHHHHHHHHHHHHHHC
T ss_pred             ----cHHHHHHHHHHhhcccccccccccccHHHHHHHHHHHHHHHhhC
Confidence                2677766666552              55788988888776544

>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=97.28  E-value=0.0056  Score=41.66  Aligned_cols=111  Identities=7%  Similarity=-0.063  Sum_probs=87.5

Q ss_pred             CCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHh-
Q 043380          107 KDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAA-  185 (246)
Q Consensus       107 ~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~-  185 (246)
                      .++++|.+.|++..+ .| .|+..    |-..|...+.++.    |.+.|+...+.     |   +...+..|-..|.. 
T Consensus         9 ~d~~~A~~~~~~aa~-~g-~~~a~----lg~~y~~g~~~~~----A~~~~~~Aa~~-----g---~~~a~~~Lg~~y~~G   70 (138)
T 1klx_A            9 KDLKKAIQYYVKACE-LN-EMFGC----LSLVSNSQINKQK----LFQYLSKACEL-----N---SGNGCRFLGDFYENG   70 (138)
T ss_dssp             HHHHHHHHHHHHHHH-TT-CTTHH----HHHHTCTTSCHHH----HHHHHHHHHHT-----T---CHHHHHHHHHHHHHC
T ss_pred             cCHHHHHHHHHHHHc-CC-CHhhh----HHHHHHcCCCHHH----HHHHHHHHHcC-----C---CHHHHHHHHHHHHcC
Confidence            468899999999988 66 34433    6677777788888    99999998876     3   56777788888887 


Q ss_pred             ---cCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHh----cCChhHHHHHHHHHHhhc
Q 043380          186 ---RVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALN----DGQVDLALDKLSNTITRW  243 (246)
Q Consensus       186 ---~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g  243 (246)
                         .+++++|.+.|++....+  .  +.    ++..|-..|..    .+++++|.++|+.-.+.|
T Consensus        71 ~g~~~d~~~A~~~~~~Aa~~g--~--~~----a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g  127 (138)
T 1klx_A           71 KYVKKDLRKAAQYYSKACGLN--D--QD----GCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  127 (138)
T ss_dssp             SSSCCCHHHHHHHHHHHHHTT--C--HH----HHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             CCCCccHHHHHHHHHHHHcCC--C--HH----HHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCC
Confidence               789999999999986542  1  11    57778888888    899999999999887766

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=97.23  E-value=0.0013  Score=58.20  Aligned_cols=84  Identities=6%  Similarity=-0.056  Sum_probs=40.4

Q ss_pred             cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc
Q 043380           92 DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP  171 (246)
Q Consensus        92 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p  171 (246)
                      +...|..|-..+.+.++++.|.+.|..+..          |..+...|...|+.+.    ..++-+.....     |   
T Consensus       680 ~~~~W~~la~~al~~~~~~~A~~~y~~~~d----------~~~l~~l~~~~~~~~~----~~~~~~~a~~~-----~---  737 (814)
T 3mkq_A          680 AEMKWRALGDASLQRFNFKLAIEAFTNAHD----------LESLFLLHSSFNNKEG----LVTLAKDAETT-----G---  737 (814)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHTC----------HHHHHHHHHHTTCHHH----HHHHHHHHHHT-----T---
T ss_pred             cHhHHHHHHHHHHHcCCHHHHHHHHHHccC----------hhhhHHHHHHcCCHHH----HHHHHHHHHHc-----C---
Confidence            334555555555555555555555555544          3344444444555444    33333333332     1   


Q ss_pred             chhhHHHHHHHHHhcCChhHHhhHHHhhC
Q 043380          172 KPHLYVSMMHELAARVDYDIVKSPYRRMW  200 (246)
Q Consensus       172 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~  200 (246)
                         -++.-..+|...|++++|.+++.++.
T Consensus       738 ---~~~~A~~~~~~~g~~~~a~~~~~~~~  763 (814)
T 3mkq_A          738 ---KFNLAFNAYWIAGDIQGAKDLLIKSQ  763 (814)
T ss_dssp             ---CHHHHHHHHHHHTCHHHHHHHHHHTT
T ss_pred             ---chHHHHHHHHHcCCHHHHHHHHHHcC
Confidence               12333344455566666666655553

>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=97.16  E-value=0.0012  Score=46.10  Aligned_cols=99  Identities=10%  Similarity=-0.020  Sum_probs=78.9

Q ss_pred             HhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCH----------HHHHHHHHHHHhCCCCCCC-HH
Q 043380           62 IKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDL----------QSLLEIVFEMKSCCNLILD-RS  130 (246)
Q Consensus        62 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~----------~~a~~~~~~m~~~~~~~p~-~~  130 (246)
                      .+.+.+++|.+.+++..+.        -+-+...|+.+-.++...+++          ++|...|++..+   +.|+ ..
T Consensus        13 ~r~~~feeA~~~~~~Ai~l--------~P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~---ldP~~~~   81 (158)
T 1zu2_A           13 DRILLFEQIRQDAENTYKS--------NPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALL---IDPKKDE   81 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHH---HCTTCHH
T ss_pred             HHHhHHHHHHHHHHHHHHH--------CCCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHH---hCcCcHH
Confidence            3455688999999999986        234677888888888887764          599999999998   7787 78


Q ss_pred             HHHHHHHHHHhcC-----------ChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHH
Q 043380          131 TFTAMVDALLYSG-----------SIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHE  182 (246)
Q Consensus       131 ~~~~li~~~~~~~-----------~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~  182 (246)
                      +|..+-.+|...|           ++++    |.+.|++..+.       .|+...|..-+..
T Consensus        82 A~~~LG~ay~~lg~l~P~~~~a~g~~~e----A~~~~~kAl~l-------~P~~~~y~~al~~  133 (158)
T 1zu2_A           82 AVWCIGNAYTSFAFLTPDETEAKHNFDL----ATQFFQQAVDE-------QPDNTHYLKSLEM  133 (158)
T ss_dssp             HHHHHHHHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHH-------CTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcccCcchhhhhccHHH----HHHHHHHHHHh-------CCCCHHHHHHHHH
Confidence            8999999998874           8999    99999999885       6777666555543

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=97.09  E-value=0.063  Score=47.31  Aligned_cols=155  Identities=14%  Similarity=0.057  Sum_probs=95.9

Q ss_pred             HHHHhcCCHHHHHH-HHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHH
Q 043380           25 EASREAQRIDEAYQ-ILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGF  103 (246)
Q Consensus        25 ~~~~~~g~~~~a~~-~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~  103 (246)
                      ......+++++|.+ ++..+     |+......++..+.+.|.+++|.++.+.              |...     ....
T Consensus       607 ~~~~~~~~~~~a~~~~l~~i-----~~~~~~~~~~~~l~~~~~~~~a~~~~~~--------------~~~~-----f~~~  662 (814)
T 3mkq_A          607 QTLTLRGEIEEAIENVLPNV-----EGKDSLTKIARFLEGQEYYEEALNISPD--------------QDQK-----FELA  662 (814)
T ss_dssp             HHHHHTTCHHHHHHHTGGGC-----CCHHHHHHHHHHHHHTTCHHHHHHHCCC--------------HHHH-----HHHH
T ss_pred             hHHHHhCCHHHHHHHHHhcC-----CchHHHHHHHHHHHhCCChHHheecCCC--------------cchh-----eehh
Confidence            34456789999877 55222     2122337778888888988888765532              2111     2334


Q ss_pred             HccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHH
Q 043380          104 RHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHEL  183 (246)
Q Consensus       104 ~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~  183 (246)
                      ...|+++.|.++.+.+       .+...|..+...+.+.++++.    |.++|..+..-              ..+...|
T Consensus       663 l~~~~~~~A~~~~~~~-------~~~~~W~~la~~al~~~~~~~----A~~~y~~~~d~--------------~~l~~l~  717 (814)
T 3mkq_A          663 LKVGQLTLARDLLTDE-------SAEMKWRALGDASLQRFNFKL----AIEAFTNAHDL--------------ESLFLLH  717 (814)
T ss_dssp             HHHTCHHHHHHHHTTC-------CCHHHHHHHHHHHHHTTCHHH----HHHHHHHHTCH--------------HHHHHHH
T ss_pred             hhcCCHHHHHHHHHhh-------CcHhHHHHHHHHHHHcCCHHH----HHHHHHHccCh--------------hhhHHHH
Confidence            5679999999985443       357889999999999999999    99999987542              3344444


Q ss_pred             HhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHH
Q 043380          184 AARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNT  239 (246)
Q Consensus       184 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  239 (246)
                      ...|+.+...++.+.....+           -++....+|.+.|++++|++++.++
T Consensus       718 ~~~~~~~~~~~~~~~a~~~~-----------~~~~A~~~~~~~g~~~~a~~~~~~~  762 (814)
T 3mkq_A          718 SSFNNKEGLVTLAKDAETTG-----------KFNLAFNAYWIAGDIQGAKDLLIKS  762 (814)
T ss_dssp             HHTTCHHHHHHHHHHHHHTT-----------CHHHHHHHHHHHTCHHHHHHHHHHT
T ss_pred             HHcCCHHHHHHHHHHHHHcC-----------chHHHHHHHHHcCCHHHHHHHHHHc
Confidence            55555555544444433221           1333334444455555555555443

>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=97.09  E-value=0.016  Score=46.34  Aligned_cols=147  Identities=6%  Similarity=-0.041  Sum_probs=98.4

Q ss_pred             cccCcCHHHHHHHHHHHHh--cCC---HHHHHHHHHHHHhCCCCCHHHHHHHHHHHHh---cCCc--chHHH---HHHHH
Q 043380           11 EHWKLNTIVMNAVIEASRE--AQR---IDEAYQILESVEKGLEPDSLSYNILISACIK---TKKL--DVTMP---FNEQL   77 (246)
Q Consensus        11 ~~~~~~~~~~~~li~~~~~--~g~---~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~---~~~~--~~a~~---~~~~m   77 (246)
                      ...+.+...|...+.+...  .++   ..+|..+|++..+--+-....|..+.-+|.-   .+..  .....   -+...
T Consensus       188 ~~~p~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~lDP~~a~A~A~la~a~~~~~~~~~~~~~~~~~l~~a~~a~  267 (372)
T 3ly7_A          188 KILPHRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQSSPEFTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNI  267 (372)
T ss_dssp             HHSCSSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHH
T ss_pred             ccCCCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHH
Confidence            3466778888888876553  333   5789999998764223344555544444431   1111  11111   11111


Q ss_pred             HhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHH
Q 043380           78 KDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFG  157 (246)
Q Consensus        78 ~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~  157 (246)
                      ...      ..-+.+..+|..+...+...|++++|...+++... .  .|+...|..+-..+...|++++    |.+.|+
T Consensus       268 ~a~------~~~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~-L--n~s~~a~~llG~~~~~~G~~~e----A~e~~~  334 (372)
T 3ly7_A          268 VTL------PELNNLSIIYQIKAVSALVKGKTDESYQAINTGID-L--EMSWLNYVLLGKVYEMKGMNRE----AADAYL  334 (372)
T ss_dssp             HTC------GGGTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH-H--CCCHHHHHHHHHHHHHTTCHHH----HHHHHH
T ss_pred             Hhc------ccCCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHh-c--CCCHHHHHHHHHHHHHCCCHHH----HHHHHH
Confidence            111      12356778888887777778999999999999999 3  4888888888899999999999    999999


Q ss_pred             HHHHhhcCCCCCCcchhhHH
Q 043380          158 EIVKRVCSNPGLWPKPHLYV  177 (246)
Q Consensus       158 ~m~~~~~~~~~~~p~~~~~~  177 (246)
                      +....       .|...||.
T Consensus       335 ~AlrL-------~P~~~t~~  347 (372)
T 3ly7_A          335 TAFNL-------RPGANTLY  347 (372)
T ss_dssp             HHHHH-------SCSHHHHH
T ss_pred             HHHhc-------CCCcChHH
Confidence            98875       56666544

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=96.79  E-value=0.0056  Score=38.50  Aligned_cols=58  Identities=16%  Similarity=0.081  Sum_probs=43.6

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCHH-HHHHHHHHHHhcCCcchHHHHHHHHHhc
Q 043380           23 VIEASREAQRIDEAYQILESVEKGLEPDSL-SYNILISACIKTKKLDVTMPFNEQLKDN   80 (246)
Q Consensus        23 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~-t~~~li~~~~~~~~~~~a~~~~~~m~~~   80 (246)
                      ....+.+.|++++|.+.|+...+..+.+.. .|..+-.+|...|++++|.+.|++..+.
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~   64 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTEPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIEL   64 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHCSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            345667788888888888876543344566 7778888888888888888888888875

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=96.73  E-value=0.0048  Score=38.81  Aligned_cols=57  Identities=14%  Similarity=0.131  Sum_probs=45.6

Q ss_pred             HHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HH-HHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           99 LLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RS-TFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        99 ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~-~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ....+.+.|++++|...|+...+   ..|+ .. .+..+..+|...|++++    |...|+...+.
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~---~~p~~~~~~~~~lg~~~~~~~~~~~----A~~~~~~al~~   64 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQ---TEPVGKDEAYYLMGNAYRKLGDWQK----ALNNYQSAIEL   64 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHH---HCSSTHHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHH---HCCCcHHHHHHHHHHHHHHcCCHHH----HHHHHHHHHhc
Confidence            34556778899999999998887   3454 56 78888888888999999    99999988876

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=96.68  E-value=0.066  Score=44.77  Aligned_cols=126  Identities=5%  Similarity=0.020  Sum_probs=92.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHH--HHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHH
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYN--ILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIF   94 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~--~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~   94 (246)
                      ..+|-..+....+.+.++.|..+|+..+ .-..+...|-  +.+.... .++.+.|.++|+...+.        .+-+..
T Consensus       286 ~~lw~~y~~~~~r~~~~~~AR~i~~~A~-~~~~~~~v~i~~A~lE~~~-~~d~~~ar~ife~al~~--------~~~~~~  355 (493)
T 2uy1_A          286 DLLRINHLNYVLKKRGLELFRKLFIELG-NEGVGPHVFIYCAFIEYYA-TGSRATPYNIFSSGLLK--------HPDSTL  355 (493)
T ss_dssp             HHHHHHHHHHHHHHHCHHHHHHHHHHHT-TSCCCHHHHHHHHHHHHHH-HCCSHHHHHHHHHHHHH--------CTTCHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHhh-CCCCChHHHHHHHHHHHHH-CCChHHHHHHHHHHHHH--------CCCCHH
Confidence            3567777777778899999999999883 1112333443  3333322 33699999999999886        222344


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      .+...+....+.|+.+.|..+|++...      ....|...+..-...|+.+.    +..++++....
T Consensus       356 ~~~~yid~e~~~~~~~~aR~l~er~~k------~~~lw~~~~~fE~~~G~~~~----~r~v~~~~~~~  413 (493)
T 2uy1_A          356 LKEEFFLFLLRIGDEENARALFKRLEK------TSRMWDSMIEYEFMVGSMEL----FRELVDQKMDA  413 (493)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHSCC------BHHHHHHHHHHHHHHSCHHH----HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHH------HHHHHHHHHHHHHHCCCHHH----HHHHHHHHHHH
Confidence            566677777889999999999999733      57788888888888899999    99989888764

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=96.64  E-value=0.051  Score=43.39  Aligned_cols=138  Identities=10%  Similarity=-0.035  Sum_probs=95.4

Q ss_pred             CCCCCHHHHHHHHHHHHhc--C---CcchHHHHHHHHHhccCCCCCCCCCcc-HHHHHHHHHHHHc----cC-C---HHH
Q 043380           46 GLEPDSLSYNILISACIKT--K---KLDVTMPFNEQLKDNGQKCSSGGFHPD-IFTYATLLMGFRH----AK-D---LQS  111 (246)
Q Consensus        46 ~~~~~~~t~~~li~~~~~~--~---~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~~~ll~~~~~----~~-~---~~~  111 (246)
                      +.+.+...|...+++....  +   ...+|..+|++.++.         .|+ ...|..+.-+|..    .+ .   ...
T Consensus       189 ~~p~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~l---------DP~~a~A~A~la~a~~~~~~~~~~~~~~~~~  259 (372)
T 3ly7_A          189 ILPHRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQS---------SPEFTYARAEKALVDIVRHSQHPLDEKQLAA  259 (372)
T ss_dssp             HSCSSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHH---------CTTCHHHHHHHHHHHHHHHHHSCCCHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHh---------CCCCHHHHHHHHHHHHHHhccCCCchhhHHH
Confidence            3467788898888776542  2   357899999999986         676 3445544444421    11 1   111


Q ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhH
Q 043380          112 LLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDI  191 (246)
Q Consensus       112 a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~  191 (246)
                      ....+........-..+..+|..+...+...|++++    |...+++....     +  |+...|..+-..+.-.|++++
T Consensus       260 l~~a~~a~~a~~~~~~~a~~~~alal~~l~~gd~d~----A~~~l~rAl~L-----n--~s~~a~~llG~~~~~~G~~~e  328 (372)
T 3ly7_A          260 LNTEIDNIVTLPELNNLSIIYQIKAVSALVKGKTDE----SYQAINTGIDL-----E--MSWLNYVLLGKVYEMKGMNRE  328 (372)
T ss_dssp             HHHHHHHHHTCGGGTTCHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHH-----C--CCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHhcccCCcCHHHHHHHHHHHHhCCCHHH----HHHHHHHHHhc-----C--CCHHHHHHHHHHHHHCCCHHH
Confidence            112222222211124458888888888888899999    99999999997     4  788888888899999999999


Q ss_pred             HhhHHHhhCCCC
Q 043380          192 VKSPYRRMWPDS  203 (246)
Q Consensus       192 a~~~~~~~~~~~  203 (246)
                      |.+.+++....+
T Consensus       329 A~e~~~~AlrL~  340 (372)
T 3ly7_A          329 AADAYLTAFNLR  340 (372)
T ss_dssp             HHHHHHHHHHHS
T ss_pred             HHHHHHHHHhcC
Confidence            999999876543

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=96.51  E-value=0.043  Score=38.92  Aligned_cols=47  Identities=17%  Similarity=0.248  Sum_probs=31.1

Q ss_pred             HccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHH
Q 043380          104 RHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVK  161 (246)
Q Consensus       104 ~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~  161 (246)
                      ...|+++.|.++.+.+.       +...|..|.......|+++-    |.++|.....
T Consensus        16 L~lg~l~~A~e~a~~l~-------~~~~Wk~Lg~~AL~~gn~~l----Ae~cy~~~~D   62 (177)
T 3mkq_B           16 LEYGNLDAALDEAKKLN-------DSITWERLIQEALAQGNASL----AEMIYQTQHS   62 (177)
T ss_dssp             HHTTCHHHHHHHHHHHC-------CHHHHHHHHHHHHHTTCHHH----HHHHHHHTTC
T ss_pred             HhcCCHHHHHHHHHHhC-------CHHHHHHHHHHHHHcCChHH----HHHHHHHhCC
Confidence            44577777777765541       46667777777777777777    7777766543

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=96.38  E-value=0.038  Score=35.35  Aligned_cols=76  Identities=12%  Similarity=-0.060  Sum_probs=58.0

Q ss_pred             CCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC
Q 043380           49 PDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD  128 (246)
Q Consensus        49 ~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~  128 (246)
                      .+..-+-.|...+.+.++++.|..+|+...+.-... ...-.+....+..|..+|.+.|+++.|..++++..+   +.|+
T Consensus         3 Lsa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~-~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~---l~P~   78 (104)
T 2v5f_A            3 LTAEDCFELGKVAYTEADYYHTELWMEQALRQLDEG-EISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLE---LDPE   78 (104)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT-CCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTT
T ss_pred             CCHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhcc-CCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHh---cCCC
Confidence            355566778888889999999999999887641000 001134567899999999999999999999999988   6676

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=96.32  E-value=0.026  Score=35.48  Aligned_cols=67  Identities=10%  Similarity=0.057  Sum_probs=56.5

Q ss_pred             CcCHHHHHHHHHHHHhcCC---HHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhc
Q 043380           14 KLNTIVMNAVIEASREAQR---IDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDN   80 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~---~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~   80 (246)
                      +.|+..+..+..++...++   .++|..+|++..+--+-++.....+-..+...|++++|...|+++.+.
T Consensus         3 p~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~   72 (93)
T 3bee_A            3 AVTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLDS   72 (93)
T ss_dssp             CCCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            5677888888888876555   799999999876444667888889999999999999999999999987

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=96.25  E-value=0.049  Score=37.65  Aligned_cols=85  Identities=12%  Similarity=0.013  Sum_probs=57.1

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcC---CcchHHHHHHHHHhccCCCCCCCCCc--cHHHHHHHHHHHHccC
Q 043380           33 IDEAYQILESVEKGLEPDSLSYNILISACIKTK---KLDVTMPFNEQLKDNGQKCSSGGFHP--DIFTYATLLMGFRHAK  107 (246)
Q Consensus        33 ~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~---~~~~a~~~~~~m~~~~~~~~~~~~~p--~~~~~~~ll~~~~~~~  107 (246)
                      +..+++-|.+....-.++..+.-.+--++++++   +.+++..++++..+.       . .|  +...+-.|--+|.+.|
T Consensus        14 l~~~~~~y~~e~~~~~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~-------~-~p~~~rd~lY~LAv~~~kl~   85 (152)
T 1pc2_A           14 LLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPK-------G-SKEEQRDYVFYLAVGNYRLK   85 (152)
T ss_dssp             HHHHHHHHHHHHHTTCCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHH-------S-CHHHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHHccCCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhc-------C-CccchHHHHHHHHHHHHHcc
Confidence            455566665543222466666666667777777   556888888888876       2 24  2445555666678888


Q ss_pred             CHHHHHHHHHHHHhCCCCCCC
Q 043380          108 DLQSLLEIVFEMKSCCNLILD  128 (246)
Q Consensus       108 ~~~~a~~~~~~m~~~~~~~p~  128 (246)
                      ++++|.+.++.+.+   +.|+
T Consensus        86 ~Y~~A~~y~~~lL~---ieP~  103 (152)
T 1pc2_A           86 EYEKALKYVRGLLQ---TEPQ  103 (152)
T ss_dssp             CHHHHHHHHHHHHH---HCTT
T ss_pred             CHHHHHHHHHHHHh---cCCC
Confidence            88888888888888   6675

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=96.15  E-value=0.049  Score=37.63  Aligned_cols=84  Identities=13%  Similarity=-0.022  Sum_probs=63.5

Q ss_pred             HHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcC---ChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCC
Q 043380          152 ALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARV---DYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQ  228 (246)
Q Consensus       152 a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g---~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~  228 (246)
                      +.+-|.+..+.     + .++..+...+-.++++++   +++++..+|+.+.+..    .|...+..+-.|.-+|.+.|+
T Consensus        17 ~~~~y~~e~~~-----~-~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~----~p~~~rd~lY~LAv~~~kl~~   86 (152)
T 1pc2_A           17 FEKKFQSEKAA-----G-SVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG----SKEEQRDYVFYLAVGNYRLKE   86 (152)
T ss_dssp             HHHHHHHHHHT-----T-CCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS----CHHHHHHHHHHHHHHHHHTSC
T ss_pred             HHHHHHHHHcc-----C-CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC----CccchHHHHHHHHHHHHHccC
Confidence            66666666554     3 378888888888999988   6779999999987643    232223366677788899999


Q ss_pred             hhHHHHHHHHHHhhccC
Q 043380          229 VDLALDKLSNTITRWKG  245 (246)
Q Consensus       229 ~~~a~~~~~~m~~~g~~  245 (246)
                      +++|.++++.+.+..|+
T Consensus        87 Y~~A~~y~~~lL~ieP~  103 (152)
T 1pc2_A           87 YEKALKYVRGLLQTEPQ  103 (152)
T ss_dssp             HHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHhcCCC
Confidence            99999999999876553

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=96.10  E-value=0.095  Score=32.84  Aligned_cols=66  Identities=6%  Similarity=-0.035  Sum_probs=54.4

Q ss_pred             CccHHHHHHHHHHHHccCC---HHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           90 HPDIFTYATLLMGFRHAKD---LQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        90 ~p~~~~~~~ll~~~~~~~~---~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      +.|...+..+-.++...++   .++|..++++...   ..|+ ......+...+...|++++    |...|+.+.+.
T Consensus         3 p~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~---~dp~~~rA~~~lg~~~~~~g~y~~----Ai~~w~~~l~~   72 (93)
T 3bee_A            3 AVTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQ---LEPYNEAALSLIANDHFISFRFQE----AIDTWVLLLDS   72 (93)
T ss_dssp             CCCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHH---HCcCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHhh
Confidence            3456677777777754444   7999999999998   6677 7788888999999999999    99999999886

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=95.66  E-value=0.11  Score=33.05  Aligned_cols=67  Identities=10%  Similarity=-0.003  Sum_probs=55.6

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-------CCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhc
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEK-------GLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDN   80 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~-------~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~   80 (246)
                      ..++.-+-.|-..+.+.|+++.|...|+...+       .-.+....+..+..++.+.|+++.|...+++..+.
T Consensus         2 ~Lsa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l   75 (104)
T 2v5f_A            2 FLTAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (104)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhc
Confidence            35666777899999999999999999987532       11345677899999999999999999999999875

>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=95.60  E-value=0.18  Score=38.84  Aligned_cols=79  Identities=10%  Similarity=-0.007  Sum_probs=66.9

Q ss_pred             chHHHHHHHHHhccCCCCCCCCCcc---HHHHHHHHHHHHcc-----CCHHHHHHHHHHHHhCCCCCCC--HHHHHHHHH
Q 043380           68 DVTMPFNEQLKDNGQKCSSGGFHPD---IFTYATLLMGFRHA-----KDLQSLLEIVFEMKSCCNLILD--RSTFTAMVD  137 (246)
Q Consensus        68 ~~a~~~~~~m~~~~~~~~~~~~~p~---~~~~~~ll~~~~~~-----~~~~~a~~~~~~m~~~~~~~p~--~~~~~~li~  137 (246)
                      ..|...+++.++.         .|+   ...|..|...|.+.     |+.++|.+.|++..+   +.|+  ..++.....
T Consensus       180 ~~A~a~lerAleL---------DP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~---LnP~~~id~~v~YA~  247 (301)
T 3u64_A          180 HAAVMMLERACDL---------WPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTR---YCSAHDPDHHITYAD  247 (301)
T ss_dssp             HHHHHHHHHHHHH---------CTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHH---HCCTTCSHHHHHHHH
T ss_pred             HHHHHHHHHHHHh---------CCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHH---hCCCCCchHHHHHHH
Confidence            5677777777765         676   56899999999985     999999999999999   6673  677888889


Q ss_pred             HHHhc-CChhhhhhHHHHHHHHHHHh
Q 043380          138 ALLYS-GSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       138 ~~~~~-~~~~~~~~~a~~~~~~m~~~  162 (246)
                      .++.. |+.+.    +.+.+++..+.
T Consensus       248 ~l~~~~gd~~~----a~~~L~kAL~a  269 (301)
T 3u64_A          248 ALCIPLNNRAG----FDEALDRALAI  269 (301)
T ss_dssp             HTTTTTTCHHH----HHHHHHHHHHC
T ss_pred             HHHHhcCCHHH----HHHHHHHHHcC
Confidence            99885 99999    99999999886

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=95.55  E-value=0.39  Score=33.99  Aligned_cols=131  Identities=17%  Similarity=0.156  Sum_probs=95.7

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHH
Q 043380           24 IEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGF  103 (246)
Q Consensus        24 i~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~  103 (246)
                      .......|+++.|.++.+.+     .+...|..|-......|+++-|++.|.+...-                ..|.-.|
T Consensus        12 F~LAL~lg~l~~A~e~a~~l-----~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D~----------------~~L~~Ly   70 (177)
T 3mkq_B           12 FDLALEYGNLDAALDEAKKL-----NDSITWERLIQEALAQGNASLAEMIYQTQHSF----------------DKLSFLY   70 (177)
T ss_dssp             HHHHHHTTCHHHHHHHHHHH-----CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTCH----------------HHHHHHH
T ss_pred             HHHHHhcCCHHHHHHHHHHh-----CCHHHHHHHHHHHHHcCChHHHHHHHHHhCCH----------------HHHHHHH
Confidence            34556789999999998876     35678999999999999999999999997653                4666777


Q ss_pred             HccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHH
Q 043380          104 RHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHEL  183 (246)
Q Consensus       104 ~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~  183 (246)
                      ...|+.++...+-+.... .|-      ++.-...+...|++++    +.++|.+.        |..|....+      .
T Consensus        71 ~~tg~~e~L~kla~iA~~-~g~------~n~af~~~l~lGdv~~----~i~lL~~~--------~r~~eA~~~------A  125 (177)
T 3mkq_B           71 LVTGDVNKLSKMQNIAQT-RED------FGSMLLNTFYNNSTKE----RSSIFAEG--------GSLPLAYAV------A  125 (177)
T ss_dssp             HHHTCHHHHHHHHHHHHH-TTC------HHHHHHHHHHHTCHHH----HHHHHHHT--------TCHHHHHHH------H
T ss_pred             HHhCCHHHHHHHHHHHHH-Ccc------HHHHHHHHHHcCCHHH----HHHHHHHC--------CChHHHHHH------H
Confidence            778988887766655555 331      5666666777899999    99888554        333432211      1


Q ss_pred             HhcCChhHHhhHHHhhC
Q 043380          184 AARVDYDIVKSPYRRMW  200 (246)
Q Consensus       184 ~~~g~~~~a~~~~~~~~  200 (246)
                      ...|..+.|.++.+++.
T Consensus       126 ~t~g~~~~a~~~~~~~~  142 (177)
T 3mkq_B          126 KANGDEAAASAFLEQAE  142 (177)
T ss_dssp             HHTTCHHHHHHHHHHTT
T ss_pred             HHcCcHHHHHHHHHHhC
Confidence            23667788888888764

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=95.14  E-value=0.41  Score=31.79  Aligned_cols=84  Identities=13%  Similarity=-0.038  Sum_probs=62.3

Q ss_pred             HHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhH---HhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCC
Q 043380          152 ALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDI---VKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQ  228 (246)
Q Consensus       152 a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~---a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~  228 (246)
                      +.+-|......     |. |+..+-..+..++.++.+...   +..+++.+...+    .|...+...-.|.-++.+.|+
T Consensus        20 ~~~~y~~e~~~-----~~-~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~----~p~~~Rd~lY~LAvg~yklg~   89 (126)
T 1nzn_A           20 FEKKFQSEKAA-----GS-VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKG----SKEEQRDYVFYLAVGNYRLKE   89 (126)
T ss_dssp             HHHHHHHHHHH-----SC-CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTS----CHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhcc-----CC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC----CcchHHHHHHHHHHHHHHhhh
Confidence            66666666554     33 777777788888888887665   999999987652    232333356667788999999


Q ss_pred             hhHHHHHHHHHHhhccC
Q 043380          229 VDLALDKLSNTITRWKG  245 (246)
Q Consensus       229 ~~~a~~~~~~m~~~g~~  245 (246)
                      +++|.++++.+.+..++
T Consensus        90 Y~~A~~~~~~lL~~eP~  106 (126)
T 1nzn_A           90 YEKALKYVRGLLQTEPQ  106 (126)
T ss_dssp             HHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHHhCCC
Confidence            99999999999876653

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=95.00  E-value=0.5  Score=31.99  Aligned_cols=62  Identities=23%  Similarity=0.083  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHH
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVK  161 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~  161 (246)
                      ..+...+..+...|.-++-.+++..+..  +-.|++...-.+..+|.+.|+..+    |.+++.+.-+
T Consensus        92 e~vd~ALd~lv~~~KkDqLdki~~~~l~--n~~~~~~~l~kia~Ay~Klg~~r~----a~eLl~~AC~  153 (172)
T 1wy6_A           92 EHVNKALDILVIQGKRDKLEEIGREILK--NNEVSASILVAIANALRRVGDERD----ATTLLIEACK  153 (172)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHC----CCSCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHhHHHHHHHHHhc--cCCCChHHHHHHHHHHHHhcchhh----HHHHHHHHHH
Confidence            3445555666666666666666666432  134555555566666666666666    6666655544

>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=94.87  E-value=0.14  Score=32.44  Aligned_cols=51  Identities=22%  Similarity=0.270  Sum_probs=38.6

Q ss_pred             HhcccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 043380            9 NREHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILIS   59 (246)
Q Consensus         9 ~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~   59 (246)
                      ....+-|++.+..+.+.+|-|.+++..|.++|+-++..+.+....|..++.
T Consensus        37 ~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~~~~~~iY~~~lq   87 (109)
T 1v54_E           37 VGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVIQ   87 (109)
T ss_dssp             TTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHHH
T ss_pred             hccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCchhhHHHHHH
Confidence            334478888888999999999999999999998887445555556776654

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=94.58  E-value=0.66  Score=31.40  Aligned_cols=147  Identities=11%  Similarity=0.036  Sum_probs=96.3

Q ss_pred             HHHHHHH--HHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHH
Q 043380           54 YNILISA--CIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRST  131 (246)
Q Consensus        54 ~~~li~~--~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~  131 (246)
                      ...||.+  ..-.|..++..++..+....          .+..-||.+|--....-+=+-..++++.+-+...+.     
T Consensus         8 ~kkLmeAK~~ildG~v~qGveii~k~~~s----------sni~E~NW~ICNiiD~a~C~y~v~vLd~IGkiFDis-----   72 (172)
T 1wy6_A            8 IRKLMDAKKFLLDGYIDEGVKIVLEITKS----------STKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLD-----   72 (172)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH----------SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGG-----
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHcCC----------CCccccceeeeecchhhchhHHHHHHHHHhhhcCcH-----
Confidence            3444444  23467888888888888775          456677777777777777777777777776633222     


Q ss_pred             HHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchh
Q 043380          132 FTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEV  211 (246)
Q Consensus       132 ~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~  211 (246)
                               .+|++..    ....+-.+.          .+..-+..-++.+..+|+-|+..++...+.....  +.|. 
T Consensus        73 ---------~C~NlKr----Vi~C~~~~n----------~~se~vd~ALd~lv~~~KkDqLdki~~~~l~n~~--~~~~-  126 (172)
T 1wy6_A           73 ---------KCQNLKS----VVECGVINN----------TLNEHVNKALDILVIQGKRDKLEEIGREILKNNE--VSAS-  126 (172)
T ss_dssp             ---------GCSCTHH----HHHHHHHTT----------CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC--CC--SCHH-
T ss_pred             ---------hhhcHHH----HHHHHHHhc----------chHHHHHHHHHHHHHhccHhHHHHHHHHHhccCC--CChH-
Confidence                     2455555    444443331          1334455566777788888888888888654321  3333 


Q ss_pred             hhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          212 QEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       212 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                         ..-.+..+|.+.|+..+|.+++.+..++|.
T Consensus       127 ---~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~  156 (172)
T 1wy6_A          127 ---ILVAIANALRRVGDERDATTLLIEACKKGE  156 (172)
T ss_dssp             ---HHHHHHHHHHHTTCHHHHHHHHHHHHHTTC
T ss_pred             ---HHHHHHHHHHHhcchhhHHHHHHHHHHhhh
Confidence               356678888899999999999888888773

>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=94.54  E-value=0.51  Score=29.95  Aligned_cols=72  Identities=15%  Similarity=0.192  Sum_probs=57.3

Q ss_pred             HHHHHccC-CHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHH
Q 043380          100 LMGFRHAK-DLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVS  178 (246)
Q Consensus       100 l~~~~~~~-~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~  178 (246)
                      ..-+.+.. |.-++.+-++.+.. ..+.|++....+.+++|.+.+++..    |.++|+.++.+      ..+...+|..
T Consensus        16 ~~~F~~~~iD~~e~rrglN~l~~-~DlVP~P~ii~aaLrAcRRvND~al----AVR~lE~iK~K------~~~~~~iY~~   84 (109)
T 1v54_E           16 VTYFNKPDIDAWELRKGMNTLVG-YDLVPEPKIIDAALRACRRLNDFAS----AVRILEVVKDK------AGPHKEIYPY   84 (109)
T ss_dssp             HHHHTCTTCCHHHHHHHHHHHTT-SSBCCCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------TTTCTTHHHH
T ss_pred             HHHcCCcCccHHHHHHHHHHHhc-cccCCCcHHHHHHHHHHHHhhhHHH----HHHHHHHHHHH------hcCchhhHHH
Confidence            33344555 66778888888888 8899999999999999999999999    99999999987      4444556777


Q ss_pred             HHHH
Q 043380          179 MMHE  182 (246)
Q Consensus       179 li~~  182 (246)
                      ++.-
T Consensus        85 ~lqE   88 (109)
T 1v54_E           85 VIQE   88 (109)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6643

>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=94.02  E-value=1.8  Score=34.89  Aligned_cols=101  Identities=7%  Similarity=0.004  Sum_probs=51.6

Q ss_pred             HHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCC-CCCchhh
Q 043380          134 AMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTG-TISPEVQ  212 (246)
Q Consensus       134 ~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~~  212 (246)
                      -+...|...|++.+    |..++..+.+....-..-.--...+..-+..|...+++.++...+......... ..+|.+.
T Consensus       104 kL~~l~~~~~~y~~----a~~~i~~l~~~~~~~dd~~~llev~lle~~~~~~~~n~~k~k~~l~~a~~~~~ai~~~p~i~  179 (394)
T 3txn_A          104 RLIALYFDTALYTE----ALALGAQLLRELKKLDDKNLLVEVQLLESKTYHALSNLPKARAALTSARTTANAIYCPPKVQ  179 (394)
T ss_dssp             HHHHHHHHTTCHHH----HHHHHHHHHHHHTTSSCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHH
T ss_pred             HHHHHHHHhhhHHH----HHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHhccHHHHHHHHHHHHhhhccCCCCHHHH
Confidence            46667777777777    777777776641100000011134555666677777777777777655421111 1333332


Q ss_pred             hHHHHHHHHHHH-hcCChhHHHHHHHH
Q 043380          213 EEAGHLLMEAAL-NDGQVDLALDKLSN  238 (246)
Q Consensus       213 ~~~~~~li~~~~-~~g~~~~a~~~~~~  238 (246)
                      ......--..+. ..+++..|...|-+
T Consensus       180 a~i~~~~Gi~~l~~~rdyk~A~~~F~e  206 (394)
T 3txn_A          180 GALDLQSGILHAADERDFKTAFSYFYE  206 (394)
T ss_dssp             HHHHHHHHHHHHHTTSCHHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHhccCHHHHHHHHHH
Confidence            222222222344 56777777666544

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=93.83  E-value=1  Score=34.76  Aligned_cols=121  Identities=12%  Similarity=0.003  Sum_probs=83.4

Q ss_pred             hHHHHhccc--CcCHHHHHHHHH-HHHhc--CC------HHHHHHHHHHHHhCCCCC---HHHHHHHHHHHHhc-----C
Q 043380            5 NEIVNREHW--KLNTIVMNAVIE-ASREA--QR------IDEAYQILESVEKGLEPD---SLSYNILISACIKT-----K   65 (246)
Q Consensus         5 ~~~~~~~~~--~~~~~~~~~li~-~~~~~--g~------~~~a~~~~~~~~~~~~~~---~~t~~~li~~~~~~-----~   65 (246)
                      ++.+....-  .+....|..++. .++..  |.      ...|..++++... +.|+   ...|..+...|.+.     |
T Consensus       140 ~~~~l~~~~~~dve~L~W~ai~~ss~a~~~~gg~~Al~~l~~A~a~lerAle-LDP~~~~GsA~~~LG~lY~~vPp~~gG  218 (301)
T 3u64_A          140 LHKVLSRCTRVDVGTLYWVGTGYVAAFALTPLGSALPDTVHAAVMMLERACD-LWPSYQEGAVWNVLTKFYAAAPESFGG  218 (301)
T ss_dssp             HHHHHTTCCGGGHHHHHHHHHHHHHHHTTSCTTSCCHHHHHHHHHHHHHHHH-HCTTHHHHHHHHHHHHHHHHSCTTTTC
T ss_pred             HHHHHHHcCccccHHHHHHHHHHHHHHhcCCCChHHHHhHHHHHHHHHHHHH-hCCCcccCHHHHHHHHHHHhCCCccCC
Confidence            344444442  233445665554 33432  32      4556666666542 3555   56899999999995     9


Q ss_pred             CcchHHHHHHHHHhccCCCCCCCCCc--cHHHHHHHHHHHHcc-CCHHHHHHHHHHHHhCCCCC--CCHHHHHHHH
Q 043380           66 KLDVTMPFNEQLKDNGQKCSSGGFHP--DIFTYATLLMGFRHA-KDLQSLLEIVFEMKSCCNLI--LDRSTFTAMV  136 (246)
Q Consensus        66 ~~~~a~~~~~~m~~~~~~~~~~~~~p--~~~~~~~ll~~~~~~-~~~~~a~~~~~~m~~~~~~~--p~~~~~~~li  136 (246)
                      +.++|.+.|++.++.         .|  +..++...-..+++. |+.+++.+.+++... ....  |+....+.+-
T Consensus       219 d~ekA~~~ferAL~L---------nP~~~id~~v~YA~~l~~~~gd~~~a~~~L~kAL~-a~p~~~P~~~lan~~~  284 (301)
T 3u64_A          219 GMEKAHTAFEHLTRY---------CSAHDPDHHITYADALCIPLNNRAGFDEALDRALA-IDPESVPHNKLLVILS  284 (301)
T ss_dssp             CHHHHHHHHHHHHHH---------CCTTCSHHHHHHHHHTTTTTTCHHHHHHHHHHHHH-CCGGGCSSCHHHHHHH
T ss_pred             CHHHHHHHHHHHHHh---------CCCCCchHHHHHHHHHHHhcCCHHHHHHHHHHHHc-CCCCCCCChhHHHHHH
Confidence            999999999999986         56  367888888888884 999999999999999 6665  6655555443

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=93.82  E-value=0.36  Score=38.92  Aligned_cols=112  Identities=13%  Similarity=-0.005  Sum_probs=80.8

Q ss_pred             cCcCHHHHHHHHHHHH---hcCCHHHHHHHHHHHH---hCC-CCCH------H------------HHHHHHHHHHhcCCc
Q 043380           13 WKLNTIVMNAVIEASR---EAQRIDEAYQILESVE---KGL-EPDS------L------------SYNILISACIKTKKL   67 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~---~~g~~~~a~~~~~~~~---~~~-~~~~------~------------t~~~li~~~~~~~~~   67 (246)
                      ...|...|..++....   ..|+.+.|.+.+++..   +|- -++.      .            ....++.++...|++
T Consensus       108 ~~~D~~~f~~l~~~~~~~~~~~~~~~a~~~l~~Al~L~rG~~L~~~~~~~w~~~~r~~l~~~~~~a~~~~~~~~l~~g~~  187 (388)
T 2ff4_A          108 NTCDLGRFVAEKTAGVHAAAAGRFEQASRHLSAALREWRGPVLDDLRDFQFVEPFATALVEDKVLAHTAKAEAEIACGRA  187 (388)
T ss_dssp             GGBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTTCH
T ss_pred             ccchHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH
Confidence            3456777777776543   3578888888887753   221 1111      1            123455667788999


Q ss_pred             chHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHh----CCCCCCCHHHH
Q 043380           68 DVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKS----CCNLILDRSTF  132 (246)
Q Consensus        68 ~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~----~~~~~p~~~~~  132 (246)
                      ++|......+...        -+-+...|..+|.++.+.|+..+|++.|+...+    ..|+.|+..+-
T Consensus       188 ~~a~~~l~~~~~~--------~P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~  248 (388)
T 2ff4_A          188 SAVIAELEALTFE--------HPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLR  248 (388)
T ss_dssp             HHHHHHHHHHHHH--------STTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHH
T ss_pred             HHHHHHHHHHHHh--------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Confidence            9999999998875        355788999999999999999999999998654    25899987653

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=93.46  E-value=0.85  Score=30.27  Aligned_cols=93  Identities=13%  Similarity=0.040  Sum_probs=53.3

Q ss_pred             HHHHHhcCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHHHHhcCCcch---HHHHHHHHHhccCCCCCCCCCc--cHHHHH
Q 043380           24 IEASREAQRIDEAYQILESVE-KGLEPDSLSYNILISACIKTKKLDV---TMPFNEQLKDNGQKCSSGGFHP--DIFTYA   97 (246)
Q Consensus        24 i~~~~~~g~~~~a~~~~~~~~-~~~~~~~~t~~~li~~~~~~~~~~~---a~~~~~~m~~~~~~~~~~~~~p--~~~~~~   97 (246)
                      +..-.....+..+.+-|.... .+ .|+..+--.+--++.++...+.   +..+++++...       + .|  .....-
T Consensus         8 l~~~~~~~~l~~~~~~y~~e~~~~-~~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~-------~-~p~~~Rd~lY   78 (126)
T 1nzn_A            8 LNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPK-------G-SKEEQRDYVF   78 (126)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTT-------S-CHHHHHHHHH
T ss_pred             HhccCCHHHHHHHHHHHHHHhccC-CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhc-------C-CcchHHHHHH
Confidence            333333444555555565443 33 3555554444555566665544   77777777764       2 23  233444


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHhCCCCCCC
Q 043380           98 TLLMGFRHAKDLQSLLEIVFEMKSCCNLILD  128 (246)
Q Consensus        98 ~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~  128 (246)
                      .|--++.+.|++++|.+.++.+.+   +.|+
T Consensus        79 ~LAvg~yklg~Y~~A~~~~~~lL~---~eP~  106 (126)
T 1nzn_A           79 YLAVGNYRLKEYEKALKYVRGLLQ---TEPQ  106 (126)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHH---HCTT
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHH---hCCC
Confidence            455566778888888888888877   5564

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=93.43  E-value=0.48  Score=38.20  Aligned_cols=75  Identities=16%  Similarity=0.089  Sum_probs=58.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      ....++..+...|+.++|...+..+....+-+...|..+|.++.+.|+..+|++.|++....=  ..+.|+.|+..+
T Consensus       173 a~~~~~~~~l~~g~~~~a~~~l~~~~~~~P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L--~~eLG~~P~~~l  247 (388)
T 2ff4_A          173 AHTAKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTL--ADDLGIDPGPTL  247 (388)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHH--HHHHSCCCCHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH--HHHhCCCCCHHH
Confidence            344567778889999999999988764457788999999999999999999999999876420  001277887765

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.41  E-value=2.8  Score=34.44  Aligned_cols=198  Identities=14%  Similarity=0.103  Sum_probs=126.7

Q ss_pred             CCHHHHHHHHHHHHh------CCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHH--HHHHHHHH
Q 043380           31 QRIDEAYQILESVEK------GLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIF--TYATLLMG  102 (246)
Q Consensus        31 g~~~~a~~~~~~~~~------~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~--~~~~ll~~  102 (246)
                      |+++.|++.+-.+.+      ...........++..|...++++...+.+.-+...      +|-.+...  ..+.++..
T Consensus        30 ~~~~~a~e~ll~lEK~~r~~~d~~s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lskk------r~qlk~ai~~~V~~~~~~  103 (445)
T 4b4t_P           30 NDCNSALDQLLVLEKKTRQASDLASSKEVLAKIVDLLASRNKWDDLNEQLTLLSKK------HGQLKLSIQYMIQKVMEY  103 (445)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSCSTTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHTT------TTTSHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHH------hhhhHHHHHHHHHHHHHH
Confidence            678888887766542      23344566788999999999999998888776654      24333332  23333443


Q ss_pred             HHccCCHHH--HHHHHHHHHhC--CCCCC---CHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc---
Q 043380          103 FRHAKDLQS--LLEIVFEMKSC--CNLIL---DRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK---  172 (246)
Q Consensus       103 ~~~~~~~~~--a~~~~~~m~~~--~~~~p---~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~---  172 (246)
                      .......+.  -..+.+.....  ..+..   .......|...|-..|++.+    |.+++..+.....   +..+.   
T Consensus       104 l~~~~~~d~~~~~~~i~~l~~vte~kiflE~erarl~~~La~i~e~~g~~~e----A~~iL~~l~~Et~---~~~~~~~k  176 (445)
T 4b4t_P          104 LKSSKSLDLNTRISVIETIRVVTENKIFVEVERARVTKDLVEIKKEEGKIDE----AADILCELQVETY---GSMEMSEK  176 (445)
T ss_dssp             HHHHCTTHHHHHHHHHHCCSSSSSCCCCCCHHHHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHHHC---SSSCHHHH
T ss_pred             HhcCCchhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHHccCHHH----HHHHHHHHHHHHH---hcccHHHH
Confidence            333333332  22233222210  11212   22345678889999999999    9999999875411   11111   


Q ss_pred             hhhHHHHHHHHHhcCChhHHhhHHHhhCC-CCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          173 PHLYVSMMHELAARVDYDIVKSPYRRMWP-DSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       173 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~-~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      ...+..-++.|...+++.+|..++.++.. ......+|.....-|...+..+...+++.+|.+.|.+..+
T Consensus       177 ve~~l~q~rl~l~~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~~~~~~~~~~~~e~~y~~a~~~y~e~~~  246 (445)
T 4b4t_P          177 IQFILEQMELSILKGDYSQATVLSRKILKKTFKNPKYESLKLEYYNLLVKISLHKREYLEVAQYLQEIYQ  246 (445)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhcccCCcHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Confidence            25677788999999999999999998742 1112244555445678888888899999999988887643

>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=93.25  E-value=0.4  Score=32.19  Aligned_cols=50  Identities=22%  Similarity=0.290  Sum_probs=36.2

Q ss_pred             hcccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 043380           10 REHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILIS   59 (246)
Q Consensus        10 ~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~   59 (246)
                      ...+-|++.+..+.+.+|-|.+++..|.++|+-++..+.+....|..++.
T Consensus        81 ~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K~~~~~~iY~y~lq  130 (152)
T 2y69_E           81 GYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVIQ  130 (152)
T ss_dssp             TSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHHH
T ss_pred             ccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhcCCchhhHHHHHH
Confidence            33477888888888888888888888888888887445555556666554

>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=93.25  E-value=1.2  Score=29.87  Aligned_cols=68  Identities=15%  Similarity=0.183  Sum_probs=54.0

Q ss_pred             HccC-CHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHH
Q 043380          104 RHAK-DLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHE  182 (246)
Q Consensus       104 ~~~~-~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~  182 (246)
                      .+.. |.-+..+-++.+.. ..+.|++....+-+++|.+.+++..    |.++|+.++.+      ..+...+|..+++-
T Consensus        63 ~~~~iD~wElrrglN~l~~-~DlVPeP~Ii~AALrAcRRvNDfal----AVR~lE~vK~K------~~~~~~iY~y~lqE  131 (152)
T 2y69_E           63 NKPDIDAWELRKGMNTLVG-YDLVPEPKIIDAALRACRRLNDFAS----AVRILEVVKDK------AGPHKEIYPYVIQE  131 (152)
T ss_dssp             TCTTCCHHHHHHHHHHHTT-SSBCCCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------TTTCTTHHHHHHHH
T ss_pred             CCcCccHHHHHHHHHHHhc-cccCCCcHHHHHHHHHHHHhhhHHH----HHHHHHHHHHh------cCCchhhHHHHHHH
Confidence            3444 55567777888888 8899999999999999999999999    99999999887      45555667776643

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=92.75  E-value=1.6  Score=29.98  Aligned_cols=116  Identities=12%  Similarity=0.160  Sum_probs=79.9

Q ss_pred             CCCHHHHHHHHHHHHhcCCc------chHHHHHHHHHhccCCCCCCCCCccHH----HHHHHHHH---HHccCCHHHHHH
Q 043380           48 EPDSLSYNILISACIKTKKL------DVTMPFNEQLKDNGQKCSSGGFHPDIF----TYATLLMG---FRHAKDLQSLLE  114 (246)
Q Consensus        48 ~~~~~t~~~li~~~~~~~~~------~~a~~~~~~m~~~~~~~~~~~~~p~~~----~~~~ll~~---~~~~~~~~~a~~  114 (246)
                      +-|..+|=..+...-+.|++      +...++|++....        ++|+..    .|--|.--   +...+|+++|.+
T Consensus        10 p~~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~--------~Pp~k~~~wrrYI~LWIrYA~~~ei~D~d~aR~   81 (161)
T 4h7y_A           10 ANNPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEA--------LPPDKYGQNESFARIQVRFAELKAIQEPDDARD   81 (161)
T ss_dssp             CCSHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHH--------SCGGGGTTCHHHHHHHHHHHHHHHHHCGGGCHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHc--------CCccccccHHHHHHHHHHHHHHHHhcCHHHHHH
Confidence            44667777777777777888      8888999988885        666531    11111111   123489999999


Q ss_pred             HHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHH
Q 043380          115 IVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHEL  183 (246)
Q Consensus       115 ~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~  183 (246)
                      +|+.+.+ .+-.. ...|-....--.+.|++..    |.+++......     +-+|. ..+.+.|..+
T Consensus        82 vy~~a~~-~hKkF-AKiwi~~AqFEiRqgnl~k----ARkILg~AiG~-----~~k~~-~~le~a~~nl  138 (161)
T 4h7y_A           82 YFQMARA-NCKKF-AFVHISFAQFELSQGNVKK----SKQLLQKAVER-----GAVPL-EMLEIALRNL  138 (161)
T ss_dssp             HHHHHHH-HCTTB-HHHHHHHHHHHHHTTCHHH----HHHHHHHHHHT-----TCBCH-HHHHHHHHHH
T ss_pred             HHHHHHH-HhHHH-HHHHHHHHHHHHHcccHHH----HHHHHHHHhcc-----CCCcH-HHHHHHHHhh
Confidence            9999977 33333 7778788888888999999    99999999886     44443 4445555443

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=92.62  E-value=1.1  Score=39.44  Aligned_cols=126  Identities=14%  Similarity=0.105  Sum_probs=80.4

Q ss_pred             HHHHHHHHhcCC-cchHHHHHHHHHhccCCCCCCCCCccHHH--HHHHHHHHHccCC-HHHHHHHHHHHHhC-----CCC
Q 043380           55 NILISACIKTKK-LDVTMPFNEQLKDNGQKCSSGGFHPDIFT--YATLLMGFRHAKD-LQSLLEIVFEMKSC-----CNL  125 (246)
Q Consensus        55 ~~li~~~~~~~~-~~~a~~~~~~m~~~~~~~~~~~~~p~~~~--~~~ll~~~~~~~~-~~~a~~~~~~m~~~-----~~~  125 (246)
                      ..+++.+...++ .+.|..+|+++...         .|...+  ...++..+...++ --+|.+++.+..+.     ...
T Consensus       252 ~~Ll~~~~~t~~~~~~a~~~le~L~~~---------~p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l  322 (754)
T 4gns_B          252 YSLKSFIAITPSLVDFTIDYLKGLTKK---------DPIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDL  322 (754)
T ss_dssp             HHHHHHHHTCGGGHHHHHHHHHHHHHH---------CGGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHcccccHHHHHHHHHHHHHhh---------CCchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhh
Confidence            445555555666 58899999999886         453332  2334444333332 23344444443220     011


Q ss_pred             CCC-H----------HHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch-hhHHHHHHHHHhcCChhHHh
Q 043380          126 ILD-R----------STFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP-HLYVSMMHELAARVDYDIVK  193 (246)
Q Consensus       126 ~p~-~----------~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~-~~~~~li~~~~~~g~~~~a~  193 (246)
                      .+. .          ...+.-..-|...|+++.    |+.+-++....       .|+. .+|..|..+|...|+++.|.
T Consensus       323 ~~~~~~~~~~~~~~~~LL~~Qa~FLl~K~~~el----AL~~Ak~AV~~-------aPseF~tW~~La~vYi~l~d~e~AL  391 (754)
T 4gns_B          323 PPRDADSARLMNCMSDLLNIQTNFLLNRGDYEL----ALGVSNTSTEL-------ALDSFESWYNLARCHIKKEEYEKAL  391 (754)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH-------CSSCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             cccccccccccCcchHHHHHHHHHHhccCcHHH----HHHHHHHHHhc-------CchhhHHHHHHHHHHHHhccHHHHH
Confidence            111 1          122223445667899999    99999998775       5664 89999999999999999999


Q ss_pred             hHHHhhC
Q 043380          194 SPYRRMW  200 (246)
Q Consensus       194 ~~~~~~~  200 (246)
                      -.++.+-
T Consensus       392 LtLNScP  398 (754)
T 4gns_B          392 FAINSMP  398 (754)
T ss_dssp             HHHHHSC
T ss_pred             HHHhcCC
Confidence            9999884

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=92.61  E-value=1.9  Score=38.00  Aligned_cols=129  Identities=13%  Similarity=0.088  Sum_probs=75.9

Q ss_pred             HHHHHHHhcCC-HHHHHHHHHHHHhCCCCCH-HHHHH-HHHHHHhcC-CcchHHHHHHHHHhccCCCCCCCCCc-cH---
Q 043380           22 AVIEASREAQR-IDEAYQILESVEKGLEPDS-LSYNI-LISACIKTK-KLDVTMPFNEQLKDNGQKCSSGGFHP-DI---   93 (246)
Q Consensus        22 ~li~~~~~~g~-~~~a~~~~~~~~~~~~~~~-~t~~~-li~~~~~~~-~~~~a~~~~~~m~~~~~~~~~~~~~p-~~---   93 (246)
                      .++..+...++ ++.|..+|+.+... .|.. ..+.. ++..+...+ +--+|..++.+..+.-.... ....+ +.   
T Consensus       253 ~Ll~~~~~t~~~~~~a~~~le~L~~~-~p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~-~~l~~~~~~~~  330 (754)
T 4gns_B          253 SLKSFIAITPSLVDFTIDYLKGLTKK-DPIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLL-NDLPPRDADSA  330 (754)
T ss_dssp             HHHHHHHTCGGGHHHHHHHHHHHHHH-CGGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHH-HTCSSCCHHHH
T ss_pred             HHHHHHcccccHHHHHHHHHHHHHhh-CCchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhh-hhhcccccccc
Confidence            34444444556 68899999998743 3433 33332 333222222 12234444444432100000 00111 11   


Q ss_pred             -------HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHH
Q 043380           94 -------FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEI  159 (246)
Q Consensus        94 -------~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m  159 (246)
                             ...+.-..-+...|+++-|+.+-++...   +.|+ -.+|..|..+|...|+++.    |+-.++.+
T Consensus       331 ~~~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~---~aPseF~tW~~La~vYi~l~d~e~----ALLtLNSc  397 (754)
T 4gns_B          331 RLMNCMSDLLNIQTNFLLNRGDYELALGVSNTSTE---LALDSFESWYNLARCHIKKEEYEK----ALFAINSM  397 (754)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCSSCHHHHHHHHHHHHHTTCHHH----HHHHHHHS
T ss_pred             cccCcchHHHHHHHHHHhccCcHHHHHHHHHHHHh---cCchhhHHHHHHHHHHHHhccHHH----HHHHHhcC
Confidence                   1111222335678999999999999888   6788 6789999999999999999    99999887

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=91.18  E-value=1.6  Score=35.61  Aligned_cols=101  Identities=12%  Similarity=-0.135  Sum_probs=72.0

Q ss_pred             HHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhC--CCCCCCHH
Q 043380           53 SYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSC--CNLILDRS  130 (246)
Q Consensus        53 t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~--~~~~p~~~  130 (246)
                      +...+...|.+.|++++|.+.|.++....     .+...-...+-.+++.+...+|+..+...++.....  .+-.|+..
T Consensus       133 ~~~~la~~~~~~Gd~~~A~~~~~~~~~~~-----~~~~~kid~~l~~irl~l~~~d~~~~~~~~~ka~~~~~~~~d~~~~  207 (429)
T 4b4t_R          133 AWINLGEYYAQIGDKDNAEKTLGKSLSKA-----ISTGAKIDVMLTIARLGFFYNDQLYVKEKLEAVNSMIEKGGDWERR  207 (429)
T ss_dssp             CCHHHHHHHHHHCCCTTHHHHHHHHHHHH-----TCCCSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTCCCTHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhc-----CChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhhhcCCCHHHH
Confidence            56678888999999999999999998752     122334568889999999999999999999887552  22223321


Q ss_pred             H--HHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          131 T--FTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       131 ~--~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      .  ...-...+...+++..    |-..|-+....
T Consensus       208 ~~lk~~~gl~~l~~r~f~~----Aa~~f~e~~~t  237 (429)
T 4b4t_R          208 NRYKTYYGIHCLAVRNFKE----AAKLLVDSLAT  237 (429)
T ss_dssp             HHHHHHHHHGGGGTSCHHH----HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhChHHH----HHHHHHHHhcc
Confidence            1  1122223456788999    88888887665

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=90.22  E-value=9  Score=35.60  Aligned_cols=198  Identities=10%  Similarity=-0.004  Sum_probs=116.1

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCC--------------
Q 043380           22 AVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSG--------------   87 (246)
Q Consensus        22 ~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~--------------   87 (246)
                      .++..+.+.+..+.|.++....    +.+...--.+-.+|...|++++|..+|.+.-.. +.....              
T Consensus       817 ~l~~~l~~~~~~~~~~~l~~~~----~~~~~~~yl~g~~~L~~ge~~~A~~~F~kaa~~-~~~~~~l~~~~~~~~~~~~~  891 (1139)
T 4fhn_B          817 ELVEKLFLFKQYNACMQLIGWL----NSDPIAVYLKALIYLKSKEAVKAVRCFKTTSLV-LYSHTSQFAVLREFQEIAEK  891 (1139)
T ss_dssp             HHHHHHHHHSCTTHHHHHHHHS----CCCHHHHHHHHHHHHHTTCHHHHHHHHHTCCCS-CTTCCCSCSSHHHHHHHHHT
T ss_pred             HHHHHHHHhhhHHHHHHHhhhc----cCCcHHHHHHHHHHHhcCCHHHHHHHHHHHhhh-hcccchhhhhhccccccccc
Confidence            4555666677777666654443    334444445566788899999999999875321 100000              


Q ss_pred             --CCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC-C--HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           88 --GFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL-D--RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        88 --~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p-~--~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                        ....-..-|..++..+-+.+.++.+.++-....+..+-.+ +  ...|+.+..++...|++++    |...+-.+...
T Consensus       892 ~~~~~~l~~YY~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~~~~~~~l~~~iFk~~L~l~~ye~----Ay~aL~~~pd~  967 (1139)
T 4fhn_B          892 YHHQNLLSCYYLHLSKKLFEESAYIDALEFSLLADASKETDDEDLSIAITHETLKTACAAGKFDA----AHVALMVLSTT  967 (1139)
T ss_dssp             TTSCCSSHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHCCSGG----GGHHHHHHHHS
T ss_pred             ccccccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccCCChhhHHHHHHHHHHHHHhhCCHHH----HHHHHHhCCCH
Confidence              0011123477888889999999988887766554122211 1  1258899999999999999    99888877664


Q ss_pred             hcCCCCCCcchhhHHHHHHHHHhcCCh------------hHHhhHHHhhCCC--CCCCCCchhhhHHHHHHHHHHHhcCC
Q 043380          163 VCSNPGLWPKPHLYVSMMHELAARVDY------------DIVKSPYRRMWPD--STGTISPEVQEEAGHLLMEAALNDGQ  228 (246)
Q Consensus       163 ~~~~~~~~p~~~~~~~li~~~~~~g~~------------~~a~~~~~~~~~~--~~~~~~~~~~~~~~~~li~~~~~~g~  228 (246)
                           ..+  ......||...|..|..            +++.+++..--..  ... -.|.    -|..|-..+...|+
T Consensus       968 -----~~r--~~cLr~LV~~lce~~~~~~L~~lpf~gl~~~Vd~IL~~kAr~~~~~~-~~p~----Yy~iLYs~ri~r~d 1035 (1139)
T 4fhn_B          968 -----PLK--KSCLLDFVNQLTKQGKINQLLNYSMPTLRQDVDNLLERKAFQMINVE-SQPC----WYNILFSWRYKHQN 1035 (1139)
T ss_dssp             -----SSC--HHHHHHHHHHHHHHCCHHHHHHHTTTSCHHHHHHHHHHHHHHHHHHC-CSTH----HHHHHHHHHHHHHT
T ss_pred             -----HHH--HHHHHHHHHHHHhCCChhhhhCCCCccHHHHHHHHHHHHHHhCCccc-cCCC----HHHHhHhhhhccCC
Confidence                 332  34455666666666544            3444444332110  001 1111    24555555677788


Q ss_pred             hhHHHHH-HHHHH
Q 043380          229 VDLALDK-LSNTI  240 (246)
Q Consensus       229 ~~~a~~~-~~~m~  240 (246)
                      +.+|-.+ |+...
T Consensus      1036 yR~AA~vmYe~~~ 1048 (1139)
T 4fhn_B         1036 YRDAAAIIYEKLS 1048 (1139)
T ss_dssp             TSCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHH
Confidence            8766555 45443

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=89.02  E-value=1.8  Score=35.31  Aligned_cols=104  Identities=11%  Similarity=-0.044  Sum_probs=70.6

Q ss_pred             HHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCc
Q 043380          130 STFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISP  209 (246)
Q Consensus       130 ~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  209 (246)
                      .+...+...|.+.|+++.    |.+++.++.... .  +..--...+-.+|..+...+++..+...+.+..........+
T Consensus       132 ~~~~~la~~~~~~Gd~~~----A~~~~~~~~~~~-~--~~~~kid~~l~~irl~l~~~d~~~~~~~~~ka~~~~~~~~d~  204 (429)
T 4b4t_R          132 QAWINLGEYYAQIGDKDN----AEKTLGKSLSKA-I--STGAKIDVMLTIARLGFFYNDQLYVKEKLEAVNSMIEKGGDW  204 (429)
T ss_dssp             SCCHHHHHHHHHHCCCTT----HHHHHHHHHHHH-T--CCCSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTCCCT
T ss_pred             HHHHHHHHHHHHcCCHHH----HHHHHHHHHHhc-C--ChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhhhcCCCH
Confidence            357778999999999999    999999998862 1  222334678889999999999999999999875211111122


Q ss_pred             hhhhHHHHHHHHHHHhcCChhHHHHHHHHHH
Q 043380          210 EVQEEAGHLLMEAALNDGQVDLALDKLSNTI  240 (246)
Q Consensus       210 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  240 (246)
                      .........-...+...+++..|.+.|-+..
T Consensus       205 ~~~~~lk~~~gl~~l~~r~f~~Aa~~f~e~~  235 (429)
T 4b4t_R          205 ERRNRYKTYYGIHCLAVRNFKEAAKLLVDSL  235 (429)
T ss_dssp             HHHHHHHHHHHHGGGGTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhChHHHHHHHHHHHh
Confidence            2211111122223456788999988887653

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=88.37  E-value=16  Score=33.96  Aligned_cols=150  Identities=9%  Similarity=-0.014  Sum_probs=95.9

Q ss_pred             HHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC--------
Q 043380           56 ILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL--------  127 (246)
Q Consensus        56 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p--------  127 (246)
                      .++..+...+.++.+.++....            +-+...--.+-.+|...|++++|.+.|.+...  |+..        
T Consensus       817 ~l~~~l~~~~~~~~~~~l~~~~------------~~~~~~~yl~g~~~L~~ge~~~A~~~F~kaa~--~~~~~~~l~~~~  882 (1139)
T 4fhn_B          817 ELVEKLFLFKQYNACMQLIGWL------------NSDPIAVYLKALIYLKSKEAVKAVRCFKTTSL--VLYSHTSQFAVL  882 (1139)
T ss_dssp             HHHHHHHHHSCTTHHHHHHHHS------------CCCHHHHHHHHHHHHHTTCHHHHHHHHHTCCC--SCTTCCCSCSSH
T ss_pred             HHHHHHHHhhhHHHHHHHhhhc------------cCCcHHHHHHHHHHHhcCCHHHHHHHHHHHhh--hhcccchhhhhh
Confidence            3445555666666665544322            22333334566778899999999999987532  2211        


Q ss_pred             ---------------CHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc--hhhHHHHHHHHHhcCChh
Q 043380          128 ---------------DRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK--PHLYVSMMHELAARVDYD  190 (246)
Q Consensus       128 ---------------~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~--~~~~~~li~~~~~~g~~~  190 (246)
                                     -..=|..++..+-+.+.++.    +.++-+...+...   .-.++  ...|..+.+++...|+++
T Consensus       883 ~~~~~~~~~~~~~~~l~~YY~hv~~LFe~~~~~~~----vi~fa~lAi~~~~---~~~~~~~~~l~~~iFk~~L~l~~ye  955 (1139)
T 4fhn_B          883 REFQEIAEKYHHQNLLSCYYLHLSKKLFEESAYID----ALEFSLLADASKE---TDDEDLSIAITHETLKTACAAGKFD  955 (1139)
T ss_dssp             HHHHHHHHTTTSCCSSHHHHHHHHHHHHHTSCCHH----HHHHHHHHHHHCC---SCCHHHHHHHHHHHHHHHHHHCCSG
T ss_pred             cccccccccccccccHHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHhcc---CCChhhHHHHHHHHHHHHHhhCCHH
Confidence                           11236678888888999998    7777776665410   11122  236889999999999999


Q ss_pred             HHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHH
Q 043380          191 IVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLAL  233 (246)
Q Consensus       191 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~  233 (246)
                      +|...+-.+....   ...    .....|+..++..|..+.-.
T Consensus       956 ~Ay~aL~~~pd~~---~r~----~cLr~LV~~lce~~~~~~L~  991 (1139)
T 4fhn_B          956 AAHVALMVLSTTP---LKK----SCLLDFVNQLTKQGKINQLL  991 (1139)
T ss_dssp             GGGHHHHHHHHSS---SCH----HHHHHHHHHHHHHCCHHHHH
T ss_pred             HHHHHHHhCCCHH---HHH----HHHHHHHHHHHhCCChhhhh
Confidence            9999998875322   121    25677777777777665543

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=88.14  E-value=9.7  Score=31.20  Aligned_cols=172  Identities=15%  Similarity=0.141  Sum_probs=109.3

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHH-h--CCCCC---HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVE-K--GLEPD---SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~-~--~~~~~---~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      ....|...|-..|++.+|.+++..+. .  +..+.   ...+..-++.|...+++..|..++.+.......   ....|+
T Consensus       139 l~~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~rl~l~~~d~~~a~~~~~ki~~~~~~---~~~~~~  215 (445)
T 4b4t_P          139 VTKDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMELSILKGDYSQATVLSRKILKKTFK---NPKYES  215 (445)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHH---SSCCHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhcc---cCCcHH
Confidence            34567888999999999999999885 2  22121   345777888999999999999999987532100   022333


Q ss_pred             --HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHH----HHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCC
Q 043380           93 --IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTF----TAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSN  166 (246)
Q Consensus        93 --~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~----~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~  166 (246)
                        ...|...+..+...+++.+|-..|.+........-|...+    ..++....-.+....    -.++.......    
T Consensus       216 lk~~~~~~~~~~~~~e~~y~~a~~~y~e~~~~~~~~~d~~~~~~~L~~~v~~~iLa~~~~~----~~~ll~~~~~~----  287 (445)
T 4b4t_P          216 LKLEYYNLLVKISLHKREYLEVAQYLQEIYQTDAIKSDEAKWKPVLSHIVYFLVLSPYGNL----QNDLIHKIQND----  287 (445)
T ss_dssp             HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHSSCSST----THHHHHSHHHH----
T ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHhCCCCch----HHHHHHHHhhc----
Confidence              2467777788888999999988888776522222233222    222222222333333    34445555444    


Q ss_pred             CCCCcchhhHHHHHHHHHhc--CChhHHhhHHHhhCCC
Q 043380          167 PGLWPKPHLYVSMMHELAAR--VDYDIVKSPYRRMWPD  202 (246)
Q Consensus       167 ~~~~p~~~~~~~li~~~~~~--g~~~~a~~~~~~~~~~  202 (246)
                       ...++...|..++.+|...  .+++.+.+.|......
T Consensus       288 -~~~~~l~~~~~L~k~f~~~~L~~~~~~~~~~~~~L~~  324 (445)
T 4b4t_P          288 -NNLKKLESQESLVKLFTTNELMRWPIVQKTYEPVLNE  324 (445)
T ss_dssp             -SSCHHHHHHHHHHHHHHHCCSSSHHHHHHHTCSSTTT
T ss_pred             -ccccccHHHHHHHHHHHhchHhhhHHHHHHHHHHhcc
Confidence             3346778899999998764  4567777777665433

>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=87.03  E-value=5.7  Score=27.33  Aligned_cols=114  Identities=7%  Similarity=0.002  Sum_probs=79.7

Q ss_pred             CcCHHHHHHHHHHHHhcCCH------HHHHHHHHHHHhCCCCCHHH-HHHHHHH---H---HhcCCcchHHHHHHHHHhc
Q 043380           14 KLNTIVMNAVIEASREAQRI------DEAYQILESVEKGLEPDSLS-YNILISA---C---IKTKKLDVTMPFNEQLKDN   80 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~------~~a~~~~~~~~~~~~~~~~t-~~~li~~---~---~~~~~~~~a~~~~~~m~~~   80 (246)
                      +-|..+|=..+...-+.|++      ++.+++|++.-..++|+... |..-+..   |   ...+++++|.++|+.++..
T Consensus        10 p~~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~~Pp~k~~~wrrYI~LWIrYA~~~ei~D~d~aR~vy~~a~~~   89 (161)
T 4h7y_A           10 ANNPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEALPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARAN   89 (161)
T ss_dssp             CCSHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHHSCGGGGTTCHHHHHHHHHHHHHHHHHCGGGCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHcCCccccccHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence            45778888888888888999      89999999887667776421 1111111   1   2347999999999999875


Q ss_pred             cCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHH
Q 043380           81 GQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVD  137 (246)
Q Consensus        81 ~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~  137 (246)
                      +     ..+   ...|.....--.+.|+.+.|.+++..... .+-.| .......|+
T Consensus        90 h-----KkF---AKiwi~~AqFEiRqgnl~kARkILg~AiG-~~~k~-~~~le~a~~  136 (161)
T 4h7y_A           90 C-----KKF---AFVHISFAQFELSQGNVKKSKQLLQKAVE-RGAVP-LEMLEIALR  136 (161)
T ss_dssp             C-----TTB---HHHHHHHHHHHHHTTCHHHHHHHHHHHHH-TTCBC-HHHHHHHHH
T ss_pred             h-----HHH---HHHHHHHHHHHHHcccHHHHHHHHHHHhc-cCCCc-HHHHHHHHH
Confidence            1     123   66666666667899999999999999988 55444 333444443

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=85.93  E-value=6.1  Score=27.53  Aligned_cols=69  Identities=7%  Similarity=-0.067  Sum_probs=45.6

Q ss_pred             ccCcCHHHHHH--HHHHHHhcCCHHHHHHHHHHHH--hCCCCCH-------HHHHHHHHHHHhcCCcchHHHHHHHHHhc
Q 043380           12 HWKLNTIVMNA--VIEASREAQRIDEAYQILESVE--KGLEPDS-------LSYNILISACIKTKKLDVTMPFNEQLKDN   80 (246)
Q Consensus        12 ~~~~~~~~~~~--li~~~~~~g~~~~a~~~~~~~~--~~~~~~~-------~t~~~li~~~~~~~~~~~a~~~~~~m~~~   80 (246)
                      |..|....|+.  -+..+...|.++.|+-+.+.+.  .+..|+.       .++..+.+++...+++..|...|++.++.
T Consensus        13 ~~~~~~~~~~l~dqik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qALq~   92 (167)
T 3ffl_A           13 GLVPRGSHMNVIDHVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMALQQ   92 (167)
T ss_dssp             --------CCHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCCCCccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHH
Confidence            34444444433  3777888999999998887753  2234442       35677888899999999999999997654

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=84.01  E-value=4.9  Score=30.48  Aligned_cols=118  Identities=10%  Similarity=-0.016  Sum_probs=79.3

Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHH
Q 043380           25 EASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFR  104 (246)
Q Consensus        25 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~  104 (246)
                      ....+.|++++|++....-.+..+-|...-..++..+|-.|+++.|.+-++...+..     ....|...+|-.+|.+- 
T Consensus         5 ~~ll~~g~L~~al~~~~~~VR~~P~da~~R~~LfqLLcv~G~w~RA~~QL~~~a~l~-----p~~~~~a~~yr~lI~aE-   78 (273)
T 1zbp_A            5 KNALSEGQLQQALELLIEAIKASPKDASLRSSFIELLCIDGDFERADEQLMQSIKLF-----PEYLPGASQLRHLVKAA-   78 (273)
T ss_dssp             HHHTTTTCHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-----GGGHHHHHHHHHHHHHH-
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC-----chhhHHHHHHHHHHHHH-
Confidence            456788999999998866544457788889999999999999999999888887751     12233444566666552 


Q ss_pred             ccCCHHHHHHHHHHHHhCCCCCC-----CHHHHHHHHHHHHh--cCChhhhhhHHHHHHHHHHHh
Q 043380          105 HAKDLQSLLEIVFEMKSCCNLIL-----DRSTFTAMVDALLY--SGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       105 ~~~~~~~a~~~~~~m~~~~~~~p-----~~~~~~~li~~~~~--~~~~~~~~~~a~~~~~~m~~~  162 (246)
                               ..=.+... .+-.|     ...-...++.+...  .|+.+.    |.++-.+..+.
T Consensus        79 ---------~~R~~vfa-G~~~P~~~g~~~~w~~~ll~Al~~~~~G~~~~----A~~lr~~A~e~  129 (273)
T 1zbp_A           79 ---------QARKDFAQ-GAATAKVLGENEELTKSLVSFNLSMVSQDYEQ----VSELALQIEEL  129 (273)
T ss_dssp             ---------HHHHHHTT-SCCCEECCCSCHHHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHH
T ss_pred             ---------HHHHHHHc-CCCCCCCCCCCHHHHHHHHHHHHHhhcCCHHH----HHHHHHHHHhc
Confidence                     22222222 22222     23334556665554  589999    99888888776

>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=83.33  E-value=6.5  Score=26.29  Aligned_cols=71  Identities=8%  Similarity=0.033  Sum_probs=51.4

Q ss_pred             CcchhhHHHHHHHHHhcCCh---hHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhccC
Q 043380          170 WPKPHLYVSMMHELAARVDY---DIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWKG  245 (246)
Q Consensus       170 ~p~~~~~~~li~~~~~~g~~---~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~  245 (246)
                      .|+..|--....++.++.+.   .++..+++++...+     |...+...-.|.-++.+.|++++|.++.+.+.+..++
T Consensus        37 ~vs~qt~F~yAw~Lv~S~~~~d~~~GI~LLe~l~~~~-----~~~~Rd~LYyLAvg~yklgdY~~Ar~y~d~lL~~eP~  110 (134)
T 3o48_A           37 TATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEA-----ESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHERN  110 (134)
T ss_dssp             GSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHC-----GGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTCTT
T ss_pred             CCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-----cchhHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhCCC
Confidence            45666666666677777654   57888888887543     3223336677888999999999999999999876553

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=82.60  E-value=6.2  Score=27.50  Aligned_cols=77  Identities=16%  Similarity=0.136  Sum_probs=53.1

Q ss_pred             CCCcch--hhHHHHHHHHHhcCChhHHhhHHHhhC---CCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          168 GLWPKP--HLYVSMMHELAARVDYDIVKSPYRRMW---PDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       168 ~~~p~~--~~~~~li~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                      |+.|-.  .++-.=+..+...|.++.|+-+.+.+.   ..+....+|.....+...+.+++...|++.+|...|++..+.
T Consensus        13 ~~~~~~~~~~l~dqik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qALq~   92 (167)
T 3ffl_A           13 GLVPRGSHMNVIDHVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMALQQ   92 (167)
T ss_dssp             --------CCHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCCCCccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHH
Confidence            555554  344555677788889998887777644   333344567766667888999999999999999999997665


Q ss_pred             cc
Q 043380          243 WK  244 (246)
Q Consensus       243 g~  244 (246)
                      .+
T Consensus        93 ~k   94 (167)
T 3ffl_A           93 KK   94 (167)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} PDB: 4b4t_N

Probab=82.51  E-value=29  Score=31.58  Aligned_cols=196  Identities=10%  Similarity=-0.023  Sum_probs=87.6

Q ss_pred             HHhcCCHHHHHHHHHHHH-hCCCCCHHHHH--HHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCC--CccHHHHHHHHH
Q 043380           27 SREAQRIDEAYQILESVE-KGLEPDSLSYN--ILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGF--HPDIFTYATLLM  101 (246)
Q Consensus        27 ~~~~g~~~~a~~~~~~~~-~~~~~~~~t~~--~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~--~p~~~~~~~ll~  101 (246)
                      ....|++++++.++.... .+...+..+-.  .+--+....|..+++.+++..........  .|-  .+....-.++--
T Consensus       384 lIh~g~~~~gl~~L~~yL~~~~s~~~~ik~GAllaLGli~ag~~~~~~~lL~~~L~~~~~~--~~~~~~~~ir~gAaLGL  461 (963)
T 4ady_A          384 VIHKGNLLEGKKVMAPYLPGSRASSRFIKGGSLYGLGLIYAGFGRDTTDYLKNIIVENSGT--SGDEDVDVLLHGASLGI  461 (963)
T ss_dssp             HHTSSCTTTHHHHHTTTSTTSCCSCHHHHHHHHHHHHHHTTTTTHHHHHHHHHHHHHHSSC--CSCHHHHHHHHHHHHHH
T ss_pred             hhccCchHHHHHHHHHhccccCCCcHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHcCcccc--ccccccHHHHHHHHHHH
Confidence            334555555555554432 11012223222  22233445565566777777666531000  000  122223333333


Q ss_pred             HHHccCC-HHHHHHHHHHHHhCCCCCCCHHHHHH--HHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHH
Q 043380          102 GFRHAKD-LQSLLEIVFEMKSCCNLILDRSTFTA--MVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVS  178 (246)
Q Consensus       102 ~~~~~~~-~~~a~~~~~~m~~~~~~~p~~~~~~~--li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~  178 (246)
                      +++-.|. -+++.+.+..+.....  +......+  |...++..|+-+.    ...+++.+.+.      ..-+..-...
T Consensus       462 Gla~~GS~~eev~e~L~~~L~dd~--~~~~~~AalALGli~vGTgn~~a----i~~LL~~~~e~------~~e~vrR~aa  529 (963)
T 4ady_A          462 GLAAMGSANIEVYEALKEVLYNDS--ATSGEAAALGMGLCMLGTGKPEA----IHDMFTYSQET------QHGNITRGLA  529 (963)
T ss_dssp             HHHSTTCCCHHHHHHHHHHHHTCC--HHHHHHHHHHHHHHHTTCCCHHH----HHHHHHHHHHC------SCHHHHHHHH
T ss_pred             HHHhcCCCCHHHHHHHHHHHhcCC--HHHHHHHHHHHhhhhcccCCHHH----HHHHHHHHhcc------CcHHHHHHHH
Confidence            3333332 2344555555444121  11111222  2333445666666    66666665553      1111122222


Q ss_pred             HHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHH
Q 043380          179 MMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTI  240 (246)
Q Consensus       179 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  240 (246)
                      +--++...|+.+.+..+.+.+...    ..|.+...+-.++.-+|+..|+.....++++.+.
T Consensus       530 lgLGll~~g~~e~~~~li~~L~~~----~dp~vRygaa~alglAyaGTGn~~aIq~LL~~~~  587 (963)
T 4ady_A          530 VGLALINYGRQELADDLITKMLAS----DESLLRYGGAFTIALAYAGTGNNSAVKRLLHVAV  587 (963)
T ss_dssp             HHHHHHTTTCGGGGHHHHHHHHHC----SCHHHHHHHHHHHHHHTTTSCCHHHHHHHHHHHH
T ss_pred             HHHHhhhCCChHHHHHHHHHHHhC----CCHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhc
Confidence            333334667777777777776543    2233321123344556677777766666666554

>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=82.47  E-value=18  Score=29.18  Aligned_cols=143  Identities=8%  Similarity=0.012  Sum_probs=89.6

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC---HHHHHHHHHHHHhcCC-hhhhhhHHHHHHHHHHHhhcCCCCC
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD---RSTFTAMVDALLYSGS-IKVVGLYALCIFGEIVKRVCSNPGL  169 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~---~~~~~~li~~~~~~~~-~~~~~~~a~~~~~~m~~~~~~~~~~  169 (246)
                      .....|...|.+.|+.++..+++...+.-.+..|-   ......++..+....+ .+.    -.++..+..+-...+..+
T Consensus        20 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~kak~~k~v~~l~~~~~~~~~~~~~----~~~~~~~~~~~a~~~~r~   95 (394)
T 3txn_A           20 QGILQQGELYKQEGKAKELADLIKVTRPFLSSISKAKAAKLVRSLVDMFLDMDAGTGI----EVQLCKDCIEWAKQEKRT   95 (394)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHTTTGGGGSCHHHHHHHHHHHHHHHTTSCCCHHH----HHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHhcCCCcHHH----HHHHHHHHHHHHHHHHHH
Confidence            36678889999999999999999987762222232   2346678888877543 333    344444433320000000


Q ss_pred             CcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHH
Q 043380          170 WPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTI  240 (246)
Q Consensus       170 ~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  240 (246)
                      -.....=..+...|...|++.+|.+++..+...-...-.+......|-.-+..|...+++.++...+..-.
T Consensus        96 flr~~l~~kL~~l~~~~~~y~~a~~~i~~l~~~~~~~dd~~~llev~lle~~~~~~~~n~~k~k~~l~~a~  166 (394)
T 3txn_A           96 FLRQSLEARLIALYFDTALYTEALALGAQLLRELKKLDDKNLLVEVQLLESKTYHALSNLPKARAALTSAR  166 (394)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSSCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            01111223689999999999999888887663211111123333467778888999999999998887654

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	246
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.63
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.52
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.48
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.35
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.29
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	99.15
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	99.1
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.06
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.98
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.94
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	98.88
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.72
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.68
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.61
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.61
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.6
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.55
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	98.55
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.53
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.49
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.49
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	98.48
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.48
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.41
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.3
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.24
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.24
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.18
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.17
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	98.05
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.04
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.03
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.99
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.98
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.96
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.93
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.92
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.9
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	97.88
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	97.73
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.68
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.6
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.55
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	97.54
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.53
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.44
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.39
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.3
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	97.29
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	97.14
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	96.89
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	96.53
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	95.0
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	94.45
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	94.02
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	93.53
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	92.48
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	91.82
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	90.78
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	90.46
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	87.15
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	82.66

>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=99.63  E-value=1.9e-13  Score=107.96  Aligned_cols=204  Identities=10%  Similarity=-0.031  Sum_probs=174.1

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      +-+...+..+...+...|+.++|...++......+-+...|..+...+...|++++|...+.+....        .+.+.
T Consensus       166 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--------~~~~~  237 (388)
T d1w3ba_         166 PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSL--------SPNHA  237 (388)
T ss_dssp             TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHH--------CTTCH
T ss_pred             cchhHHHHhhcccccccCcHHHHHHHHHHHHHhCcccHHHHHHHhhhhhccccHHHHHHHHHHhHHH--------hhhHH
Confidence            3456778888899999999999999998875433556788999999999999999999999999886        24566


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK  172 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~  172 (246)
                      ..+..+...+.+.|++++|...|++..+   +.|+ ..++..+...+...|++++    |.+.++.....      .+.+
T Consensus       238 ~~~~~l~~~~~~~~~~~~A~~~~~~al~---~~p~~~~~~~~l~~~~~~~~~~~~----A~~~~~~~~~~------~~~~  304 (388)
T d1w3ba_         238 VVHGNLACVYYEQGLIDLAIDTYRRAIE---LQPHFPDAYCNLANALKEKGSVAE----AEDCYNTALRL------CPTH  304 (388)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH---TCSSCHHHHHHHHHHHHHHSCHHH----HHHHHHHHHHH------CTTC
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcCCHHH----HHHHHHhhhcc------CCcc
Confidence            7888899999999999999999999988   4566 7889999999999999999    99999998886      4567


Q ss_pred             hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          173 PHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       173 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      ...+..+...+...|++++|.+.|++..+..+.    ..  .++..+..+|...|++++|.+.|++..+..+
T Consensus       305 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~----~~--~~~~~la~~~~~~g~~~~A~~~~~~al~l~P  370 (388)
T d1w3ba_         305 ADSLNNLANIKREQGNIEEAVRLYRKALEVFPE----FA--AAHSNLASVLQQQGKLQEALMHYKEAIRISP  370 (388)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTT----CH--HHHHHHHHHHHTTTCCHHHHHHHHHHHTTCT
T ss_pred             chhhhHHHHHHHHCCCHHHHHHHHHHHHHhCCC----CH--HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC
Confidence            788999999999999999999999998765432    12  2788899999999999999999998876543

>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=99.52  E-value=3.3e-12  Score=99.24  Aligned_cols=194  Identities=12%  Similarity=0.041  Sum_probs=133.2

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHH
Q 043380           24 IEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGF  103 (246)
Q Consensus        24 i~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~  103 (246)
                      ...+.+.|++++|.+.|+...+.-+-+..+|..+..++...|++++|...|.+..+.        -+-+...|..+..+|
T Consensus        26 g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~--------~p~~~~~~~~la~~~   97 (323)
T d1fcha_          26 GLRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLEL--------KPDNQTALMALAVSF   97 (323)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHhhhcc--------ccccccccccccccc
Confidence            334556666666666666654333444556666666666666666666666666553        122344555566666


Q ss_pred             HccCCHHHHHHHHHHHHh-------------------------------------------------CCCCCCCHHHHHH
Q 043380          104 RHAKDLQSLLEIVFEMKS-------------------------------------------------CCNLILDRSTFTA  134 (246)
Q Consensus       104 ~~~~~~~~a~~~~~~m~~-------------------------------------------------~~~~~p~~~~~~~  134 (246)
                      ...|++++|.+.++....                                                 ...-.++..++..
T Consensus        98 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~  177 (323)
T d1fcha_          98 TNESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCG  177 (323)
T ss_dssp             HHTTCHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHH
T ss_pred             cccccccccccchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchh
Confidence            666666666665555433                                                 0111234566778


Q ss_pred             HHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhH
Q 043380          135 MVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEE  214 (246)
Q Consensus       135 li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~  214 (246)
                      +...+...|++++    |...|+.....      .+-+..+|..+..+|...|++++|.+.|++..+.++..    .  .
T Consensus       178 l~~~~~~~~~~~~----A~~~~~~al~~------~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~----~--~  241 (323)
T d1fcha_         178 LGVLFNLSGEYDK----AVDCFTAALSV------RPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGY----I--R  241 (323)
T ss_dssp             HHHHHHHTTCHHH----HHHHHHHHHHH------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTC----H--H
T ss_pred             hHHHHHHHHHHhh----hhccccccccc------ccccccchhhhhhcccccccchhHHHHHHHHHHHhhcc----H--H
Confidence            8888999999999    99999998876      22346788899999999999999999999877544321    1  2


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          215 AGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       215 ~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      +|..+..+|.+.|++++|++.|++.++
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            688899999999999999999988765

>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=99.48  E-value=3.8e-12  Score=100.38  Aligned_cols=188  Identities=9%  Similarity=-0.018  Sum_probs=157.9

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccH
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDI   93 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~   93 (246)
                      +-++..|..+...+...|++++|...|+....-.+.+...+..+...+.+.|++++|...|++..+.        .+-+.
T Consensus       200 p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--------~p~~~  271 (388)
T d1w3ba_         200 PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIEL--------QPHFP  271 (388)
T ss_dssp             TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--------CSSCH
T ss_pred             cccHHHHHHHhhhhhccccHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--------CCCCH
Confidence            3467788999999999999999999999886444677788899999999999999999999999885        23356


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc-c
Q 043380           94 FTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP-K  172 (246)
Q Consensus        94 ~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p-~  172 (246)
                      .+|..+...+...|++++|.+.++.... . .+.+...+..+...+...|++++    |...|++..+.       .| +
T Consensus       272 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~-~-~~~~~~~~~~l~~~~~~~~~~~~----A~~~~~~al~~-------~p~~  338 (388)
T d1w3ba_         272 DAYCNLANALKEKGSVAEAEDCYNTALR-L-CPTHADSLNNLANIKREQGNIEE----AVRLYRKALEV-------FPEF  338 (388)
T ss_dssp             HHHHHHHHHHHHHSCHHHHHHHHHHHHH-H-CTTCHHHHHHHHHHHHTTTCHHH----HHHHHHHHTTS-------CTTC
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHhhhc-c-CCccchhhhHHHHHHHHCCCHHH----HHHHHHHHHHh-------CCCC
Confidence            7899999999999999999999999887 2 33457888999999999999999    99999998764       34 4


Q ss_pred             hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCC
Q 043380          173 PHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQ  228 (246)
Q Consensus       173 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~  228 (246)
                      ..++..+..+|...|++++|...|++..+.++..    .  .+|..|..+|.+.|+
T Consensus       339 ~~~~~~la~~~~~~g~~~~A~~~~~~al~l~P~~----~--~a~~~lg~~~~~~~D  388 (388)
T d1w3ba_         339 AAAHSNLASVLQQQGKLQEALMHYKEAIRISPTF----A--DAYSNMGNTLKEMQD  388 (388)
T ss_dssp             HHHHHHHHHHHHTTTCCHHHHHHHHHHHTTCTTC----H--HHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC----H--HHHHHHHHHHHHcCC
Confidence            5788999999999999999999999987654321    1  278888888887765

>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=99.35  E-value=5.9e-10  Score=86.16  Aligned_cols=209  Identities=8%  Similarity=-0.113  Sum_probs=157.3

Q ss_pred             CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCC--------
Q 043380           14 KLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCS--------   85 (246)
Q Consensus        14 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~--------   85 (246)
                      +-++..|..+..+|...|++++|...|++..+-.+-+...|..+...|...|++++|.+.+.+.....-...        
T Consensus        50 P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~  129 (323)
T d1fcha_          50 PKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEE  129 (323)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC----
T ss_pred             CCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccccccccccccccccccccccccccccchhhHHHhccchHHHHHhhhh
Confidence            346888999999999999999999999887643355678889999999999999999999998765421000        


Q ss_pred             -----------------------------------CCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-H
Q 043380           86 -----------------------------------SGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-R  129 (246)
Q Consensus        86 -----------------------------------~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~  129 (246)
                                                         ...-.++..++..+...+...|++++|...|+....   ..|+ .
T Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~---~~p~~~  206 (323)
T d1fcha_         130 GAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALS---VRPNDY  206 (323)
T ss_dssp             -----------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCH
T ss_pred             hhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHHHHHhhhhcccccccc---cccccc
Confidence                                               000123456777888889999999999999999887   4455 7


Q ss_pred             HHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCC-
Q 043380          130 STFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTIS-  208 (246)
Q Consensus       130 ~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~-  208 (246)
                      .+|..+...|...|++++    |.+.|+...+.      -+-+..++..+..+|...|++++|...|++.....+.... 
T Consensus       207 ~~~~~lg~~~~~~g~~~~----A~~~~~~al~~------~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~  276 (323)
T d1fcha_         207 LLWNKLGATLANGNQSEE----AVAAYRRALEL------QPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGP  276 (323)
T ss_dssp             HHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC---
T ss_pred             cchhhhhhcccccccchh----HHHHHHHHHHH------hhccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcChhh
Confidence            889999999999999999    99999998886      1224578999999999999999999999986531111111 


Q ss_pred             ----chhhhHHHHHHHHHHHhcCChhHHHHH
Q 043380          209 ----PEVQEEAGHLLMEAALNDGQVDLALDK  235 (246)
Q Consensus       209 ----~~~~~~~~~~li~~~~~~g~~~~a~~~  235 (246)
                          .......|..+-.++...|+.+.+...
T Consensus       277 ~~~~~~~~~~~~~~l~~al~~~~~~d~~~~~  307 (323)
T d1fcha_         277 RGEGGAMSENIWSTLRLALSMLGQSDAYGAA  307 (323)
T ss_dssp             ---CCCCCHHHHHHHHHHHHHHTCGGGHHHH
T ss_pred             hhhhHHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence                111122566677777777777665544

>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=1.6e-09  Score=83.53  Aligned_cols=190  Identities=16%  Similarity=0.107  Sum_probs=146.0

Q ss_pred             CHHHHHHHHHHHHhC-CCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHH
Q 043380           32 RIDEAYQILESVEKG-LEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQ  110 (246)
Q Consensus        32 ~~~~a~~~~~~~~~~-~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~  110 (246)
                      ..++|..+|++.... .+.+...|...+....+.|+.+.|..+|+++.+.       ........|...+..+.+.|+.+
T Consensus        79 ~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~-------~~~~~~~~w~~~~~~~~~~~~~~  151 (308)
T d2onda1          79 FSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI-------EDIDPTLVYIQYMKFARRAEGIK  151 (308)
T ss_dssp             HHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS-------SSSCTHHHHHHHHHHHHHHHCHH
T ss_pred             chHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHH-------hcCChHHHHHHHHHHHHHcCChH
Confidence            457888999887643 3445667888888899999999999999999875       22233557999999999999999


Q ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHH-HHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCCh
Q 043380          111 SLLEIVFEMKSCCNLILDRSTFTAMVD-ALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDY  189 (246)
Q Consensus       111 ~a~~~~~~m~~~~~~~p~~~~~~~li~-~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~  189 (246)
                      .|.++|+.... .+. .+...|..... -+...|+.+.    |..+|+.....      ...+...|...+..+...|++
T Consensus       152 ~ar~i~~~al~-~~~-~~~~~~~~~a~~e~~~~~~~~~----a~~i~e~~l~~------~p~~~~~w~~y~~~~~~~g~~  219 (308)
T d2onda1         152 SGRMIFKKARE-DAR-TRHHVYVTAALMEYYCSKDKSV----AFKIFELGLKK------YGDIPEYVLAYIDYLSHLNED  219 (308)
T ss_dssp             HHHHHHHHHHT-STT-CCTHHHHHHHHHHHHTSCCHHH----HHHHHHHHHHH------HTTCHHHHHHHHHHHHTTCCH
T ss_pred             HHHHHHHHHHH-hCC-CcHHHHHHHHHHHHHhccCHHH----HHHHHHHHHHh------hhhhHHHHHHHHHHHHHcCCh
Confidence            99999999988 321 22334433333 2344688999    99999999886      344568899999999999999


Q ss_pred             hHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          190 DIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       190 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                      +.|..+|++.....+  .+|......|...+..-...|+.+.+..+++++.+.
T Consensus       220 ~~aR~~fe~ai~~~~--~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~~  270 (308)
T d2onda1         220 NNTRVLFERVLTSGS--LPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             HHHHHHHHHHHHSSS--SCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCC--CChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            999999999765432  333322337888888888999999999999987653

>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=99.15  E-value=5.2e-09  Score=78.07  Aligned_cols=202  Identities=7%  Similarity=-0.089  Sum_probs=135.4

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc-cHHH
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP-DIFT   95 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p-~~~~   95 (246)
                      ..+|..+-.+|.+.|++++|.+.|++...--+-+..+|+.+-.+|.+.|++++|.+.|++..+.         .| +..+
T Consensus        37 a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~---------~p~~~~a  107 (259)
T d1xnfa_          37 AQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLEL---------DPTYNYA  107 (259)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---------CTTCTHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHhhccCCCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHH---------Hhhhhhh
Confidence            3467777889999999999999998876434667889999999999999999999999999986         34 4568


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchh
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPH  174 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~  174 (246)
                      +..+..+|...|++++|...|+...+   ..|+ ......+..++.+.+....    +..+.......       .++..
T Consensus       108 ~~~lg~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~-------~~~~~  173 (259)
T d1xnfa_         108 HLNRGIALYYGGRDKLAQDDLLAFYQ---DDPNDPFRSLWLYLAEQKLDEKQA----KEVLKQHFEKS-------DKEQW  173 (259)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHCHHHH----HHHHHHHHHHS-------CCCST
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHh---hccccHHHHHHHHHHHHHhhhHHH----HHHHHHHhhcc-------chhhh
Confidence            88899999999999999999999888   3344 4444445555666666555    55555555443       22222


Q ss_pred             hHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhcc
Q 043380          175 LYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       175 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      .+. ++..+...........-.......... ..+. ...+|..+...|...|++++|.+.|+......+
T Consensus       174 ~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p  240 (259)
T d1xnfa_         174 GWN-IVEFYLGNISEQTLMERLKADATDNTS-LAEH-LSETNFYLGKYYLSLGDLDSATALFKLAVANNV  240 (259)
T ss_dssp             HHH-HHHHHTTSSCHHHHHHHHHHHCCSHHH-HHHH-HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCC
T ss_pred             hhh-HHHHHHHHHHHHHHHHHHHHHHHHhhh-cCcc-cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCC
Confidence            222 222222222222111111111111100 1111 122677788999999999999999998876543

>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=99.10  E-value=8e-09  Score=79.87  Aligned_cols=197  Identities=7%  Similarity=-0.019  Sum_probs=138.7

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcC-CcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTK-KLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~-~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      ...|+.+-..+.+.+..++|+++++.+..--+-+...|+....++...+ ++++|+..++...+.        -+-+..+
T Consensus        43 ~~a~~~~~~~~~~~e~~~~Al~~~~~ai~lnP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~--------~p~~~~a  114 (315)
T d2h6fa1          43 RDVYDYFRAVLQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEE--------QPKNYQV  114 (315)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH--------CTTCHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHHCCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHH--------HHhhhhH
Confidence            4456666667778888899999998876433556677888888877766 478899998888875        2335678


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchh
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPH  174 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~  174 (246)
                      |+.+-..+.+.|++++|++.++.+.+   +.|+ ...|+.+...+...|++++    |+..++...+.      -.-+..
T Consensus       115 ~~~~~~~~~~l~~~~eAl~~~~kal~---~dp~n~~a~~~~~~~~~~~~~~~~----Al~~~~~al~~------~p~n~~  181 (315)
T d2h6fa1         115 WHHRRVLVEWLRDPSQELEFIADILN---QDAKNYHAWQHRQWVIQEFKLWDN----ELQYVDQLLKE------DVRNNS  181 (315)
T ss_dssp             HHHHHHHHHHHTCCTTHHHHHHHHHH---HCTTCHHHHHHHHHHHHHHTCCTT----HHHHHHHHHHH------CTTCHH
T ss_pred             HHHHhHHHHhhccHHHHHHHHhhhhh---hhhcchHHHHHHHHHHHHHHhhHH----HHHHHHHHHHH------CCccHH
Confidence            88888888888999999999998888   5555 7788888888888999999    99999988886      123456


Q ss_pred             hHHHHHHHHHhcCC------hhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          175 LYVSMMHELAARVD------YDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       175 ~~~~li~~~~~~g~------~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      .|+.+...+.+.+.      +++|.+.+.......+..    .  ..|..+...+.. ...+++.+.++...+
T Consensus       182 a~~~r~~~l~~~~~~~~~~~~~~ai~~~~~al~~~P~~----~--~~~~~l~~ll~~-~~~~~~~~~~~~~~~  247 (315)
T d2h6fa1         182 VWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKLVPHN----E--SAWNYLKGILQD-RGLSKYPNLLNQLLD  247 (315)
T ss_dssp             HHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHHSTTC----H--HHHHHHHHHHTT-TCGGGCHHHHHHHHH
T ss_pred             HHHHHHHHHHHccccchhhhhHHhHHHHHHHHHhCCCc----h--HHHHHHHHHHHh-cChHHHHHHHHHHHH
Confidence            67766666666554      456777777655433221    1  145555555443 335666666665544

>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=99.06  E-value=3.8e-08  Score=75.59  Aligned_cols=180  Identities=12%  Similarity=0.051  Sum_probs=140.8

Q ss_pred             hhHHHHhcccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHHhcCCcchHHHHHHHHHhccC
Q 043380            4 ENEIVNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPD-SLSYNILISACIKTKKLDVTMPFNEQLKDNGQ   82 (246)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~-~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~   82 (246)
                      .++.+.+.+.+.+...|...+....+.|+++.|..+|+.+....+.+ ...|...+..+.+.++.+.|.++|.++.+.  
T Consensus        86 i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al~~--  163 (308)
T d2onda1          86 IYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKARED--  163 (308)
T ss_dssp             HHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTS--
T ss_pred             HHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHHHHh--
Confidence            44555556667788889999999999999999999999986433334 447899999999999999999999999886  


Q ss_pred             CCCCCCCCccHHHHHHHHHH-HHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHH
Q 043380           83 KCSSGGFHPDIFTYATLLMG-FRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVK  161 (246)
Q Consensus        83 ~~~~~~~~p~~~~~~~ll~~-~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~  161 (246)
                            .+.+...|...... +...|+.+.|..+|+.+.. . .+.+...|...+..+...|+++.    |..+|++...
T Consensus       164 ------~~~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~-~-~p~~~~~w~~y~~~~~~~g~~~~----aR~~fe~ai~  231 (308)
T d2onda1         164 ------ARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLK-K-YGDIPEYVLAYIDYLSHLNEDNN----TRVLFERVLT  231 (308)
T ss_dssp             ------TTCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHH-H-HTTCHHHHHHHHHHHHTTCCHHH----HHHHHHHHHH
T ss_pred             ------CCCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHH-h-hhhhHHHHHHHHHHHHHcCChHH----HHHHHHHHHH
Confidence                  23333444443333 4456899999999999998 3 33347889999999999999999    9999999887


Q ss_pred             hhcCCCCCCcc--hhhHHHHHHHHHhcCChhHHhhHHHhhCC
Q 043380          162 RVCSNPGLWPK--PHLYVSMMHELAARVDYDIVKSPYRRMWP  201 (246)
Q Consensus       162 ~~~~~~~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~~~~  201 (246)
                      ..    +..|+  ...|...+.--...|+.+.+.++++++.+
T Consensus       232 ~~----~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~  269 (308)
T d2onda1         232 SG----SLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFT  269 (308)
T ss_dssp             SS----SSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             hC----CCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            61    23443  35788888888899999999999997753

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.98  E-value=9.2e-08  Score=73.74  Aligned_cols=187  Identities=9%  Similarity=-0.010  Sum_probs=140.4

Q ss_pred             cCcCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc
Q 043380           13 WKLNTIVMNAVIEASREAQ-RIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP   91 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g-~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p   91 (246)
                      -+-+...|+....++...| ++++|+..++.....-+-+..+|+.+...+.+.|++++|++.+.++.+.        -+-
T Consensus        73 nP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p~~~~a~~~~~~~~~~l~~~~eAl~~~~kal~~--------dp~  144 (315)
T d2h6fa1          73 NAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLVEWLRDPSQELEFIADILNQ--------DAK  144 (315)
T ss_dssp             CTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHH--------CTT
T ss_pred             CCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHhhhhHHHHHhHHHHhhccHHHHHHHHhhhhhh--------hhc
Confidence            3456678888888888876 5999999999876444678899999999999999999999999999986        244


Q ss_pred             cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCC------hhhhhhHHHHHHHHHHHhhc
Q 043380           92 DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGS------IKVVGLYALCIFGEIVKRVC  164 (246)
Q Consensus        92 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~------~~~~~~~a~~~~~~m~~~~~  164 (246)
                      +...|..+...+.+.|++++|.+.++...+   +.|+ ...|+.+...+.+.+.      +++    |.+.+....+.  
T Consensus       145 n~~a~~~~~~~~~~~~~~~~Al~~~~~al~---~~p~n~~a~~~r~~~l~~~~~~~~~~~~~~----ai~~~~~al~~--  215 (315)
T d2h6fa1         145 NYHAWQHRQWVIQEFKLWDNELQYVDQLLK---EDVRNNSVWNQRYFVISNTTGYNDRAVLER----EVQYTLEMIKL--  215 (315)
T ss_dssp             CHHHHHHHHHHHHHHTCCTTHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTTCSCSHHHHHH----HHHHHHHHHHH--
T ss_pred             chHHHHHHHHHHHHHHhhHHHHHHHHHHHH---HCCccHHHHHHHHHHHHHccccchhhhhHH----hHHHHHHHHHh--
Confidence            688999999999999999999999999999   5565 7778877777766665      466    88888887775  


Q ss_pred             CCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHh
Q 043380          165 SNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALN  225 (246)
Q Consensus       165 ~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~  225 (246)
                          -+-+...|..+...+... ..+++...++......+....+.    .+..+...|..
T Consensus       216 ----~P~~~~~~~~l~~ll~~~-~~~~~~~~~~~~~~l~~~~~~~~----~~~~l~~~y~~  267 (315)
T d2h6fa1         216 ----VPHNESAWNYLKGILQDR-GLSKYPNLLNQLLDLQPSHSSPY----LIAFLVDIYED  267 (315)
T ss_dssp             ----STTCHHHHHHHHHHHTTT-CGGGCHHHHHHHHHHTTTCCCHH----HHHHHHHHHHH
T ss_pred             ----CCCchHHHHHHHHHHHhc-ChHHHHHHHHHHHHhCCCcCCHH----HHHHHHHHHHH
Confidence                223566777766665544 45777777776654332222222    45666666644

>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=98.94  E-value=7.8e-08  Score=73.17  Aligned_cols=215  Identities=11%  Similarity=-0.033  Sum_probs=144.0

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHh-----CCCC-CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc
Q 043380           18 IVMNAVIEASREAQRIDEAYQILESVEK-----GLEP-DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP   91 (246)
Q Consensus        18 ~~~~~li~~~~~~g~~~~a~~~~~~~~~-----~~~~-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p   91 (246)
                      ..|......|-..|++++|.+.|.+...     +-++ -..+|+.+..+|.+.|++++|.+.+++..+....  ......
T Consensus        38 ~~y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~--~~~~~~  115 (290)
T d1qqea_          38 DLCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTH--RGQFRR  115 (290)
T ss_dssp             HHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH--TTCHHH
T ss_pred             HHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhh--cccchh
Confidence            3588888888899999999999987531     1122 2467899999999999999999999987653100  001222


Q ss_pred             cHHHHHHHHHHHH-ccCCHHHHHHHHHHHHhC---CCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCC
Q 043380           92 DIFTYATLLMGFR-HAKDLQSLLEIVFEMKSC---CNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSN  166 (246)
Q Consensus        92 ~~~~~~~ll~~~~-~~~~~~~a~~~~~~m~~~---~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~  166 (246)
                      ...++..+...|- ..|++++|.+.|++....   .+-.+. ..+|..+...|...|++++    |...|++........
T Consensus       116 ~~~~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~----A~~~~~~~~~~~~~~  191 (290)
T d1qqea_         116 GANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIE----ASDIYSKLIKSSMGN  191 (290)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHTTSSC
T ss_pred             HHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHH----HHHHHHHHHHhCccc
Confidence            3456777777774 569999999999876541   222222 4568889999999999999    999999988863222


Q ss_pred             CCCCcch-hhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHh--cCChhHHHHHHHHH
Q 043380          167 PGLWPKP-HLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALN--DGQVDLALDKLSNT  239 (246)
Q Consensus       167 ~~~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~--~g~~~~a~~~~~~m  239 (246)
                      +...... ..+...+..+...|+++.|...+++..+..+..... ........++.++-.  .+.+++|+..|+.+
T Consensus       192 ~~~~~~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~s-re~~~l~~l~~a~~~~d~e~~~eai~~y~~~  266 (290)
T d1qqea_         192 RLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADS-RESNFLKSLIDAVNEGDSEQLSEHCKEFDNF  266 (290)
T ss_dssp             TTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC----------HHHHHHHHHHHHTTCTTTHHHHHHHHTTS
T ss_pred             hhhhhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccch-HHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence            2222222 234455667778999999999999988665432221 111134567777655  34577888777544

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=98.88  E-value=1.2e-06  Score=67.18  Aligned_cols=218  Identities=7%  Similarity=-0.093  Sum_probs=142.8

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHh--CCCCC----HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc
Q 043380           18 IVMNAVIEASREAQRIDEAYQILESVEK--GLEPD----SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP   91 (246)
Q Consensus        18 ~~~~~li~~~~~~g~~~~a~~~~~~~~~--~~~~~----~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p   91 (246)
                      ..++.+..+|...|++++|...|++...  ...++    ..++..+...+...+++..+...+.+...............
T Consensus        52 ~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~  131 (366)
T d1hz4a_          52 VATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPM  131 (366)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhH
Confidence            4666777888888999999988877531  11121    34456666777788888888888877654311110111112


Q ss_pred             cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCC---CCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCC
Q 043380           92 DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCC---NLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPG  168 (246)
Q Consensus        92 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~---~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~  168 (246)
                      ....+..+-..+...|+++.+...+.......   +.......+..+...+...++...    +...+............
T Consensus       132 ~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----a~~~~~~a~~~~~~~~~  207 (366)
T d1hz4a_         132 HEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDN----ARSQLNRLENLLGNGKY  207 (366)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHHHTTSCC
T ss_pred             HHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHhhhhHHH----HHHHHHHHHHHHHHhcc
Confidence            23466677788899999999999998876621   222335567777788888999999    88888876664221111


Q ss_pred             CCcc-hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          169 LWPK-PHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       169 ~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      ..|. ...+..+...+...|++++|...+...........+  .....+..+..++...|++++|.+.++....
T Consensus       208 ~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  279 (366)
T d1hz4a_         208 HSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNH--FLQGQWRNIARAQILLGEFEPAEIVLEELNE  279 (366)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCG--GGHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccch--HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            1111 244566677788888999999888887654432222  2222566678888888899988888887653

>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=98.72  E-value=1.6e-06  Score=61.68  Aligned_cols=128  Identities=9%  Similarity=-0.066  Sum_probs=103.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHH
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYAT   98 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~   98 (246)
                      .|+- -..+...|+++.|++.|..+.   +|+..+|..+-.+|...|++++|++.|++.++.        -+-+...|..
T Consensus         8 l~~~-g~~~~~~~d~~~Al~~~~~i~---~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~l--------dp~~~~a~~~   75 (192)
T d1hh8a_           8 LWNE-GVLAADKKDWKGALDAFSAVQ---DPHSRICFNIGCMYTILKNMTEAEKAFTRSINR--------DKHLAVAYFQ   75 (192)
T ss_dssp             HHHH-HHHHHHTTCHHHHHHHHHTSS---SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHHHH
T ss_pred             HHHH-HHHHHHCCCHHHHHHHHHhcC---CCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHH--------hhhhhhhHHH
Confidence            4543 556788999999999998764   678889999999999999999999999999986        1345779999


Q ss_pred             HHHHHHccCCHHHHHHHHHHHHhCC-----------C--CCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           99 LLMGFRHAKDLQSLLEIVFEMKSCC-----------N--LILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        99 ll~~~~~~~~~~~a~~~~~~m~~~~-----------~--~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      +-.+|.+.|++++|...|+......           |  ..++ ..++..+..++...|++++    |.+.+....+.
T Consensus        76 ~g~~~~~~g~~~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~----A~~~l~~A~~~  149 (192)
T d1hh8a_          76 RGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKK----AEEQLALATSM  149 (192)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHTT
T ss_pred             HHHHHHhhccHHHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHH----HHHHHHHHHhc
Confidence            9999999999999999999876510           0  1112 3566778889999999999    99999887664

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=98.68  E-value=1.9e-07  Score=69.26  Aligned_cols=173  Identities=11%  Similarity=-0.069  Sum_probs=113.7

Q ss_pred             cCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc
Q 043380           13 WKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD   92 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~   92 (246)
                      -+-++.+|+.+-.+|.+.|++++|++.|++...-.+-+..++..+..+|...|++++|.+.|+...+.        .+.+
T Consensus        67 ~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~--------~p~~  138 (259)
T d1xnfa_          67 RPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD--------DPND  138 (259)
T ss_dssp             CCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTC
T ss_pred             CCCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHHHhhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhh--------cccc
Confidence            45678899999999999999999999999886433556778999999999999999999999999886        1334


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK  172 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~  172 (246)
                      ......+..++.+.+..+.+..+...... .  .++...++ ++..+............+...+.....       ..|+
T Consensus       139 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~--~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~  207 (259)
T d1xnfa_         139 PFRSLWLYLAEQKLDEKQAKEVLKQHFEK-S--DKEQWGWN-IVEFYLGNISEQTLMERLKADATDNTS-------LAEH  207 (259)
T ss_dssp             HHHHHHHHHHHHHHCHHHHHHHHHHHHHH-S--CCCSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHH-------HHHH
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHhhc-c--chhhhhhh-HHHHHHHHHHHHHHHHHHHHHHHHhhh-------cCcc
Confidence            44444455555666666666666666665 2  22222222 222222221111100002222222111       1232


Q ss_pred             -hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCC
Q 043380          173 -PHLYVSMMHELAARVDYDIVKSPYRRMWPDST  204 (246)
Q Consensus       173 -~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  204 (246)
                       ..+|..+-..|...|++++|.+.|+.....++
T Consensus       208 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p  240 (259)
T d1xnfa_         208 LSETNFYLGKYYLSLGDLDSATALFKLAVANNV  240 (259)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCC
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCC
Confidence             25677788999999999999999999876543

>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=98.61  E-value=1.1e-06  Score=57.25  Aligned_cols=97  Identities=11%  Similarity=-0.074  Sum_probs=83.6

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHH
Q 043380           22 AVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLM  101 (246)
Q Consensus        22 ~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~  101 (246)
                      .--+.+.+.|++++|+..|++..+-.+.+...|..+-.+|...|++++|+..+.+....        -+.+...|..+..
T Consensus         8 ~~g~~~~~~g~~~eAi~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~--------~p~~~~~~~~~g~   79 (117)
T d1elwa_           8 EKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDL--------KPDWGKGYSRKAA   79 (117)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCcchhhhhcccccccccccccccchhhhhHHHh--------ccchhhHHHHHHH
Confidence            34567889999999999999876444678888999999999999999999999999986        2457789999999


Q ss_pred             HHHccCCHHHHHHHHHHHHhCCCCCCCH
Q 043380          102 GFRHAKDLQSLLEIVFEMKSCCNLILDR  129 (246)
Q Consensus       102 ~~~~~~~~~~a~~~~~~m~~~~~~~p~~  129 (246)
                      ++...|++++|...|+...+   ..|+.
T Consensus        80 ~~~~~~~~~~A~~~~~~a~~---~~p~~  104 (117)
T d1elwa_          80 ALEFLNRFEEAKRTYEEGLK---HEANN  104 (117)
T ss_dssp             HHHHTTCHHHHHHHHHHHHT---TCTTC
T ss_pred             HHHHccCHHHHHHHHHHHHH---hCCCC
Confidence            99999999999999999998   56763

>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=98.61  E-value=1.6e-06  Score=65.75  Aligned_cols=180  Identities=10%  Similarity=-0.034  Sum_probs=122.8

Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc-cHHHHHHHHHHHHccCCHHHHHHHHHHHHhC---CCCC-CC
Q 043380           54 YNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP-DIFTYATLLMGFRHAKDLQSLLEIVFEMKSC---CNLI-LD  128 (246)
Q Consensus        54 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~---~~~~-p~  128 (246)
                      |.-..+.|...+++++|.+.|.+..+...+.   +-++ -..+|+.+..+|.+.|++++|...++...+.   .|-. ..
T Consensus        40 y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~---~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~  116 (290)
T d1qqea_          40 CVQAATIYRLRKELNLAGDSFLKAADYQKKA---GNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRG  116 (290)
T ss_dssp             HHHHHHHHHHTTCTHHHHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHCcCHHHHHHHHHHHHHHHHHc---CCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhH
Confidence            4445667888999999999999887631100   1122 3468999999999999999999999876541   1111 11


Q ss_pred             HHHHHHHHHHHHh-cCChhhhhhHHHHHHHHHHHhhcCCCCCCcc-hhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCC
Q 043380          129 RSTFTAMVDALLY-SGSIKVVGLYALCIFGEIVKRVCSNPGLWPK-PHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGT  206 (246)
Q Consensus       129 ~~~~~~li~~~~~-~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  206 (246)
                      ..++..+...|-. .|++++    |.+.+++..+..... +..+. ..++..+...+...|++++|...|+++.......
T Consensus       117 ~~~~~~l~~~~~~~~~~~~~----A~~~~~~A~~l~~~~-~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~  191 (290)
T d1qqea_         117 ANFKFELGEILENDLHDYAK----AIDCYELAGEWYAQD-QSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGN  191 (290)
T ss_dssp             HHHHHHHHHHHHHTTCCHHH----HHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSC
T ss_pred             HHHHHHHHHhHhhHHHHHHH----HHHHHHHHHHHHHhc-CchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccc
Confidence            4456666767744 699999    999999876531110 22222 3568889999999999999999999876433221


Q ss_pred             --CCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhh
Q 043380          207 --ISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITR  242 (246)
Q Consensus       207 --~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  242 (246)
                        ..... ...+...+..+...|+++.|.+.+++..+.
T Consensus       192 ~~~~~~~-~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~  228 (290)
T d1qqea_         192 RLSQWSL-KDYFLKKGLCQLAATDAVAAARTLQEGQSE  228 (290)
T ss_dssp             TTTGGGH-HHHHHHHHHHHHHTTCHHHHHHHHHGGGCC
T ss_pred             hhhhhhH-HHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence              11111 113445666778899999999999887543

>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=98.60  E-value=6e-07  Score=63.87  Aligned_cols=97  Identities=7%  Similarity=-0.065  Sum_probs=53.7

Q ss_pred             cCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc-c
Q 043380           15 LNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPD-SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP-D   92 (246)
Q Consensus        15 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~-~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p-~   92 (246)
                      |+...+...-+.|.+.|++++|+..|+.... ..|+ ...|+.+..+|.+.|++++|...|.+.++.         .| +
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~-~~p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l---------~p~~   71 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAIT-RNPLVAVYYTNRALCYLKMQQPEQALADCRRALEL---------DGQS   71 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS---------CTTC
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-hCCCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHh---------CCCc
Confidence            4455555555566666666666666655431 2553 334555555566666666666666665543         33 3


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHh
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKS  121 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~  121 (246)
                      ..+|..+-.+|.+.|++++|...|+....
T Consensus        72 ~~a~~~lg~~~~~l~~~~~A~~~~~~al~  100 (201)
T d2c2la1          72 VKAHFFLGQCQLEMESYDEAIANLQRAYS  100 (201)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            44555566666666666666666655544

>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=98.55  E-value=2.8e-06  Score=58.28  Aligned_cols=105  Identities=8%  Similarity=-0.032  Sum_probs=87.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHH
Q 043380           20 MNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATL   99 (246)
Q Consensus        20 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~l   99 (246)
                      +...-+.|.+.|++++|+..|++..+--+.+...|..+..+|...|++++|...|++.++.        -+-+...|..+
T Consensus        13 l~~~gn~~~~~~~y~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~--------~p~~~~a~~~~   84 (159)
T d1a17a_          13 LKTQANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIEL--------DKKYIKGYYRR   84 (159)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHhhhccccchhhhhhhhhhHHHHHhccccchHHHHHHHHHHH--------cccchHHHHHH
Confidence            3445667889999999999999876434678888999999999999999999999999986        23456799999


Q ss_pred             HHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHH
Q 043380          100 LMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAM  135 (246)
Q Consensus       100 l~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~l  135 (246)
                      ..+|...|++++|...+++...   +.|+ ...+..+
T Consensus        85 g~~~~~~g~~~eA~~~~~~a~~---~~p~~~~~~~~l  118 (159)
T d1a17a_          85 AASNMALGKFRAALRDYETVVK---VKPHDKDAKMKY  118 (159)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH---HSTTCHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHH---cCCCCHHHHHHH
Confidence            9999999999999999999998   5566 4444443

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=98.55  E-value=1.6e-06  Score=66.86  Aligned_cols=194  Identities=8%  Similarity=-0.132  Sum_probs=135.5

Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCC--cchHHHHHHHHHhccCCCCCCCCCccHHHHH-HHHHHHHc
Q 043380           29 EAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKK--LDVTMPFNEQLKDNGQKCSSGGFHPDIFTYA-TLLMGFRH  105 (246)
Q Consensus        29 ~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~--~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~-~ll~~~~~  105 (246)
                      ..|++++|+.+++...+..+.+...|..+..++...+.  +++|...+.++.+.        -+++...+. .....+..
T Consensus        85 ~~~~~~~al~~~~~~l~~~pk~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~--------~~~~~~~~~~~~~~~~~~  156 (334)
T d1dcea1          85 SAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNWARELELCARFLEA--------DERNFHCWDYRRFVAAQA  156 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHhCCCcHHHHHHhhHHHHHhccccHHHHHHHHHHHHhh--------CchhhhhhhhHHHHHHHh
Confidence            34557889999988765446677888888888877664  67899999999885        233455544 44467778


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHH--------------HHHHHhhcCCC---
Q 043380          106 AKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIF--------------GEIVKRVCSNP---  167 (246)
Q Consensus       106 ~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~--------------~~m~~~~~~~~---  167 (246)
                      .+.+++|+..++....   ..|+ ...|+.+...+...|++++    |...+              ...........   
T Consensus       157 ~~~~~~Al~~~~~~i~---~~p~~~~a~~~l~~~~~~~~~~~~----A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~a~~  229 (334)
T d1dcea1         157 AVAPAEELAFTDSLIT---RNFSNYSSWHYRSCLLPQLHPQPD----SGPQGRLPENVLLKELELVQNAFFTDPNDQSAW  229 (334)
T ss_dssp             CCCHHHHHHHHHTTTT---TTCCCHHHHHHHHHHHHHHSCCCC----SSSCCSSCHHHHHHHHHHHHHHHHHCSSCSHHH
T ss_pred             ccccHHHHHHHHHHHH---cCCCCHHHHHHHHHHHHHhcCHHH----HHHHHHHhHHhHHHHHHHHHHHHHhcchhHHHH
Confidence            8999999999998887   4455 7788888888888887765    32111              11111100000   


Q ss_pred             -------CCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHH
Q 043380          168 -------GLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTI  240 (246)
Q Consensus       168 -------~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  240 (246)
                             .-.++...+..+...+...++.++|...+.+..+.++    ..  ..+|..+..+|...|++++|.++++...
T Consensus       230 ~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~p----~~--~~~~~~l~~~~~~~~~~~eA~~~~~~ai  303 (334)
T d1dcea1         230 FYHRWLLGRAEPLFRCELSVEKSTVLQSELESCKELQELEPENK----WC--LLTIILLMRALDPLLYEKETLQYFSTLK  303 (334)
T ss_dssp             HHHHHHHSCCCCSSSCCCCHHHHHHHHHHHHHHHHHHHHCTTCH----HH--HHHHHHHHHHHCTGGGHHHHHHHHHHHH
T ss_pred             HHHHHHHhCcchhhHHHHHHHHHHHHhhHHHHHHHHHHHHhhCc----hH--HHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence                   1123334555667777888999999999998876542    12  2278889999999999999999999887


Q ss_pred             hhc
Q 043380          241 TRW  243 (246)
Q Consensus       241 ~~g  243 (246)
                      +-.
T Consensus       304 ~ld  306 (334)
T d1dcea1         304 AVD  306 (334)
T ss_dssp             HHC
T ss_pred             HHC
Confidence            643

>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=1.2e-06  Score=62.34  Aligned_cols=100  Identities=7%  Similarity=-0.086  Sum_probs=89.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCC
Q 043380           48 EPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLIL  127 (246)
Q Consensus        48 ~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p  127 (246)
                      .|+...+....+.+.+.|++++|+..|.+.++.        -+-+...|+.+..+|.+.|++++|...|+...+..   |
T Consensus         1 ~~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~--------~p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~---p   69 (201)
T d2c2la1           1 SPSAQELKEQGNRLFVGRKYPEAAACYGRAITR--------NPLVAVYYTNRALCYLKMQQPEQALADCRRALELD---G   69 (201)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC---T
T ss_pred             ChhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--------CCCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhC---C
Confidence            377788888899999999999999999999986        24567889999999999999999999999998775   4


Q ss_pred             C-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          128 D-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       128 ~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      + ..+|..+..+|...|++++    |...|+...+.
T Consensus        70 ~~~~a~~~lg~~~~~l~~~~~----A~~~~~~al~l  101 (201)
T d2c2la1          70 QSVKAHFFLGQCQLEMESYDE----AIANLQRAYSL  101 (201)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHCCCHHH----HHHHHHHHHHh
Confidence            4 7789999999999999999    99999988765

>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=98.49  E-value=4.1e-06  Score=59.41  Aligned_cols=127  Identities=10%  Similarity=-0.049  Sum_probs=98.7

Q ss_pred             HHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHH
Q 043380          100 LMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSM  179 (246)
Q Consensus       100 l~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~l  179 (246)
                      -..+...|++++|.+.|.++..     |+..+|..+...|...|++++    |++.|++..+.      -+-+...|..+
T Consensus        12 g~~~~~~~d~~~Al~~~~~i~~-----~~~~~~~nlG~~~~~~g~~~~----A~~~~~kAl~l------dp~~~~a~~~~   76 (192)
T d1hh8a_          12 GVLAADKKDWKGALDAFSAVQD-----PHSRICFNIGCMYTILKNMTE----AEKAFTRSINR------DKHLAVAYFQR   76 (192)
T ss_dssp             HHHHHHTTCHHHHHHHHHTSSS-----CCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------CTTCHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHhcCC-----CCHHHHHHHHHHHHHcCCchh----HHHHHHHHHHH------hhhhhhhHHHH
Confidence            4556789999999999986543     678889999999999999999    99999999887      23456889999


Q ss_pred             HHHHHhcCChhHHhhHHHhhCCCCCCCC----------CchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          180 MHELAARVDYDIVKSPYRRMWPDSTGTI----------SPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       180 i~~~~~~g~~~~a~~~~~~~~~~~~~~~----------~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                      -.+|.+.|++++|.+.|++......+..          .......++..+..++.+.|++++|.+.+....+
T Consensus        77 g~~~~~~g~~~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~  148 (192)
T d1hh8a_          77 GMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATS  148 (192)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHhhccHHHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            9999999999999999988643211110          0000112566778889999999999999987764

>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=98.49  E-value=3.8e-06  Score=57.59  Aligned_cols=92  Identities=13%  Similarity=0.098  Sum_probs=81.0

Q ss_pred             HHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHH
Q 043380           56 ILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTA  134 (246)
Q Consensus        56 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~  134 (246)
                      ..-+.|.+.|++++|...|.+.++.        -+-+...|..+-.+|...|++++|...|+...+   +.|+ ..+|..
T Consensus        15 ~~gn~~~~~~~y~~A~~~~~~al~~--------~p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~---~~p~~~~a~~~   83 (159)
T d1a17a_          15 TQANDYFKAKDYENAIKFYSQAIEL--------NPSNAIYYGNRSLAYLRTECYGYALGDATRAIE---LDKKYIKGYYR   83 (159)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH--------STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHhhhcccc--------chhhhhhhhhhHHHHHhccccchHHHHHHHHHH---HcccchHHHHH
Confidence            3456788999999999999999986        244677899999999999999999999999988   4566 688999


Q ss_pred             HHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          135 MVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       135 li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      +..+|...|++++    |...++.....
T Consensus        84 ~g~~~~~~g~~~e----A~~~~~~a~~~  107 (159)
T d1a17a_          84 RAASNMALGKFRA----ALRDYETVVKV  107 (159)
T ss_dssp             HHHHHHHTTCHHH----HHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHH----HHHHHHHHHHc
Confidence            9999999999999    99999999886

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=98.48  E-value=1.5e-05  Score=60.77  Aligned_cols=214  Identities=11%  Similarity=-0.007  Sum_probs=146.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHH----h-CCC--C-CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCC
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVE----K-GLE--P-DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGG   88 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~----~-~~~--~-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~   88 (246)
                      ...+..+...+...|++..+...+....    . ...  + ....+..+-..+...|+++.+...+........   ..+
T Consensus        91 ~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~---~~~  167 (366)
T d1hz4a_          91 LWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLS---SYQ  167 (366)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTT---TSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhh---hhh
Confidence            3456667778889999999999987642    1 111  1 123455667788899999999999998876521   112


Q ss_pred             CCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhC---CCCCCC--HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhh
Q 043380           89 FHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSC---CNLILD--RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRV  163 (246)
Q Consensus        89 ~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~---~~~~p~--~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~  163 (246)
                      ......++..+...+...++...+...+......   .+..+.  ...+..+...+...|+++.    |...++......
T Consensus       168 ~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----a~~~~~~~~~~~  243 (366)
T d1hz4a_         168 PQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAA----AANWLRHTAKPE  243 (366)
T ss_dssp             GGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHH----HHHHHHHSCCCC
T ss_pred             hhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHH----HHHHHHHHHHhc
Confidence            3334556777778888899999988887765441   111111  3346667778889999999    999888765431


Q ss_pred             cCCCCC-CcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCC-CCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          164 CSNPGL-WPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTG-TISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       164 ~~~~~~-~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                         ++. ......+..+..++...|++++|...++........ ...+. ...++..+...|...|++++|.+.+++..+
T Consensus       244 ---~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~-~~~~~~~la~~~~~~g~~~~A~~~l~~Al~  319 (366)
T d1hz4a_         244 ---FANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSD-LNRNLLLLNQLYWQAGRKSDAQRVLLDALK  319 (366)
T ss_dssp             ---CTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH-HHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             ---cccchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChH-HHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence               111 122355667888999999999999999987521110 01121 223688888999999999999999987654

>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=98.48  E-value=2.3e-06  Score=55.57  Aligned_cols=91  Identities=13%  Similarity=0.079  Sum_probs=80.9

Q ss_pred             HHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHH
Q 043380           57 LISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAM  135 (246)
Q Consensus        57 li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~l  135 (246)
                      --+.+.+.|++++|..+|.+.++.        -+-+...|..+-.+|...|++++|...++...+   +.|+ ...|..+
T Consensus         9 ~g~~~~~~g~~~eAi~~~~~al~~--------~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~---~~p~~~~~~~~~   77 (117)
T d1elwa_           9 KGNKALSVGNIDDALQCYSEAIKL--------DPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVD---LKPDWGKGYSRK   77 (117)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH---HCTTCHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhc--------CCcchhhhhcccccccccccccccchhhhhHHH---hccchhhHHHHH
Confidence            456678899999999999999986        344677899999999999999999999999998   4455 8889999


Q ss_pred             HHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          136 VDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       136 i~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ..++...|++++    |+..|+...+.
T Consensus        78 g~~~~~~~~~~~----A~~~~~~a~~~  100 (117)
T d1elwa_          78 AAALEFLNRFEE----AKRTYEEGLKH  100 (117)
T ss_dssp             HHHHHHTTCHHH----HHHHHHHHHTT
T ss_pred             HHHHHHccCHHH----HHHHHHHHHHh
Confidence            999999999999    99999999875

>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=98.41  E-value=1.8e-06  Score=56.59  Aligned_cols=99  Identities=12%  Similarity=0.013  Sum_probs=79.2

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCc---chHHHHHHHHHhccCCCCCCCCCcc-HHHH
Q 043380           21 NAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKL---DVTMPFNEQLKDNGQKCSSGGFHPD-IFTY   96 (246)
Q Consensus        21 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~---~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~   96 (246)
                      ..+++.+...+++++|++.|+....--+.+..++..+-.++.+.++.   ++|..+|+++...       ...|+ ..+|
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~-------~~~~~~~~~~   75 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPK-------GSKEEQRDYV   75 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTT-------SCHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhc-------cCCchHHHHH
Confidence            56888899999999999999887644467888888888888875544   5699999998875       33343 2477


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCH
Q 043380           97 ATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDR  129 (246)
Q Consensus        97 ~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~  129 (246)
                      ..|-.+|.+.|++++|.+.|++..+   +.|+-
T Consensus        76 ~~Lg~~y~~~g~~~~A~~~~~~aL~---~~P~~  105 (122)
T d1nzna_          76 FYLAVGNYRLKEYEKALKYVRGLLQ---TEPQN  105 (122)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH---HCTTC
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHH---hCcCC
Confidence            8889999999999999999999998   66773

>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=98.30  E-value=3.8e-06  Score=54.01  Aligned_cols=90  Identities=12%  Similarity=-0.008  Sum_probs=73.9

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHH
Q 043380           22 AVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLM  101 (246)
Q Consensus        22 ~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~  101 (246)
                      .+...+.+.|++++|...|++...-.+-+...|..+..++.+.+++++|...|++..+.        -+-+...|..+..
T Consensus        21 ~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~--------~p~~~~a~~~la~   92 (112)
T d1hxia_          21 EEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARML--------DPKDIAVHAALAV   92 (112)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHH
T ss_pred             HHHHHHHHHhhhHHHHHHHhhhcccccccchhhhhhhhhhhhhhhHHHhhccccccccc--------ccccccchHHHHH
Confidence            34567788899999999998876433557888999999999999999999999998875        2335778888999


Q ss_pred             HHHccCCHHHHHHHHHHH
Q 043380          102 GFRHAKDLQSLLEIVFEM  119 (246)
Q Consensus       102 ~~~~~~~~~~a~~~~~~m  119 (246)
                      +|...|++++|.+.+++.
T Consensus        93 ~y~~~g~~~~A~~~l~~~  110 (112)
T d1hxia_          93 SHTNEHNANAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHH
Confidence            999999999999988875

>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=98.24  E-value=8.2e-06  Score=53.27  Aligned_cols=95  Identities=7%  Similarity=-0.092  Sum_probs=78.5

Q ss_pred             HHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCH---HHHHHHHHHHHhCCCCCCC-HH
Q 043380           55 NILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDL---QSLLEIVFEMKSCCNLILD-RS  130 (246)
Q Consensus        55 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~---~~a~~~~~~m~~~~~~~p~-~~  130 (246)
                      ..+++.+...+++++|++.|++....        -+.+..++..+-.++.+.++.   ++|..+|+.... .+..|+ ..
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~--------~p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~-~~~~~~~~~   73 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAA--------GSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLP-KGSKEEQRD   73 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH--------SCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTT-TSCHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhh--------CCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHh-ccCCchHHH
Confidence            46788889999999999999999986        255678899999999876654   569999999887 433333 34


Q ss_pred             HHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          131 TFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       131 ~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ++..+..+|.+.|++++    |.+.|+...+.
T Consensus        74 ~~~~Lg~~y~~~g~~~~----A~~~~~~aL~~  101 (122)
T d1nzna_          74 YVFYLAVGNYRLKEYEK----ALKYVRGLLQT  101 (122)
T ss_dssp             HHHHHHHHHHHTTCHHH----HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhHH----HHHHHHHHHHh
Confidence            67889999999999999    99999999986

>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=98.24  E-value=6.2e-06  Score=52.97  Aligned_cols=88  Identities=10%  Similarity=-0.038  Sum_probs=78.5

Q ss_pred             HHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc-cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHH
Q 043380           56 ILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP-DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFT  133 (246)
Q Consensus        56 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~  133 (246)
                      .+...+.+.|++++|...|++....         .| +...|..+-.++.+.|++++|...|+...+   +.|+ ...+.
T Consensus        21 ~~g~~~~~~g~~~~A~~~~~~al~~---------~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~---~~p~~~~a~~   88 (112)
T d1hxia_          21 EEGLSMLKLANLAEAALAFEAVCQK---------EPEREEAWRSLGLTQAENEKDGLAIIALNHARM---LDPKDIAVHA   88 (112)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH---------STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHH
T ss_pred             HHHHHHHHHhhhHHHHHHHhhhccc---------ccccchhhhhhhhhhhhhhhHHHhhcccccccc---cccccccchH
Confidence            3456678899999999999999986         45 578999999999999999999999999988   5676 88899


Q ss_pred             HHHHHHHhcCChhhhhhHHHHHHHHH
Q 043380          134 AMVDALLYSGSIKVVGLYALCIFGEI  159 (246)
Q Consensus       134 ~li~~~~~~~~~~~~~~~a~~~~~~m  159 (246)
                      .+...|...|++++    |.+.+++.
T Consensus        89 ~la~~y~~~g~~~~----A~~~l~~~  110 (112)
T d1hxia_          89 ALAVSHTNEHNANA----ALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHHHHHH----HHHHHHHH
T ss_pred             HHHHHHHHCCCHHH----HHHHHHHH
Confidence            99999999999999    99999875

>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=98.18  E-value=7e-05  Score=51.67  Aligned_cols=112  Identities=8%  Similarity=-0.039  Sum_probs=85.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCC--C-------------CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccC
Q 043380           18 IVMNAVIEASREAQRIDEAYQILESVEKGLE--P-------------DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQ   82 (246)
Q Consensus        18 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~--~-------------~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~   82 (246)
                      ..+...-+.+.+.|++++|+..|.....-++  +             -..+|+.+..+|.+.|++++|+..++..+..  
T Consensus        14 ~~l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~--   91 (170)
T d1p5qa1          14 TIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALEL--   91 (170)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhc--
Confidence            3455667789999999999999987532111  1             1345677888899999999999999999986  


Q ss_pred             CCCCCCCCc-cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHh
Q 043380           83 KCSSGGFHP-DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLY  141 (246)
Q Consensus        83 ~~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~  141 (246)
                             .| +...|..+..+|...|++++|...|+...+   +.|+ ......+-...-.
T Consensus        92 -------~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~---l~P~n~~~~~~l~~~~~~  142 (170)
T d1p5qa1          92 -------DSNNEKGLSRRGEAHLAVNDFELARADFQKVLQ---LYPNNKAAKTQLAVCQQR  142 (170)
T ss_dssp             -------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCSSCHHHHHHHHHHHHH
T ss_pred             -------cccchhhhHHHHHHHHHhhhHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHH
Confidence                   44 778999999999999999999999999988   5675 5444444444333

>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=98.17  E-value=3.8e-05  Score=50.39  Aligned_cols=110  Identities=5%  Similarity=-0.017  Sum_probs=83.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-HHHHH
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-IFTYA   97 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~~   97 (246)
                      -+..+-+.|.+.|++++|+..|.+...-.+.+...|..+-.+|.+.|++++|...+.++++..  +......+. ..+|.
T Consensus         6 ~~k~~G~~~~~~~~y~~Ai~~y~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~--~~~~~~~~~~a~~~~   83 (128)
T d1elra_           6 KEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVG--RENREDYRQIAKAYA   83 (128)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH--HHSTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhC--cccHHHHHHHHHHHH
Confidence            455677889999999999999988764446678999999999999999999999999988641  000011111 24777


Q ss_pred             HHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHH
Q 043380           98 TLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFT  133 (246)
Q Consensus        98 ~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~  133 (246)
                      .+-..+...+++++|.+.|+....   ..|+.....
T Consensus        84 ~lg~~~~~~~~~~~A~~~~~kal~---~~~~~~~~~  116 (128)
T d1elra_          84 RIGNSYFKEEKYKDAIHFYNKSLA---EHRTPDVLK  116 (128)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHH---HCCCHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHh---cCCCHHHHH
Confidence            888888999999999999998776   335554433

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.05  E-value=0.00012  Score=50.39  Aligned_cols=64  Identities=8%  Similarity=-0.065  Sum_probs=55.8

Q ss_pred             cHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           92 DIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        92 ~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      +...|..+-.+|.+.|++++|+..++...+   +.|+ ..+|..+..+|...|+++.    |...|+...+.
T Consensus        76 ~~~~~~nla~~~~~~~~~~~Ai~~~~~al~---~~p~~~~a~~~~g~~~~~l~~~~~----A~~~~~~al~l  140 (169)
T d1ihga1          76 ALSCVLNIGACKLKMSDWQGAVDSCLEALE---IDPSNTKALYRRAQGWQGLKEYDQ----ALADLKKAQEI  140 (169)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHT---TCTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhhcccchhhhhhhhhhh---hhhhhhhHHHhHHHHHHHccCHHH----HHHHHHHHHHh
Confidence            455778888889999999999999999988   5566 7889999999999999999    99999998886

>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=98.04  E-value=9.8e-05  Score=50.88  Aligned_cols=102  Identities=11%  Similarity=0.044  Sum_probs=71.0

Q ss_pred             HHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc---------cHHHHHHHHHHHHccCCHHHHHHHHHHHHhC
Q 043380           52 LSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP---------DIFTYATLLMGFRHAKDLQSLLEIVFEMKSC  122 (246)
Q Consensus        52 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p---------~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~  122 (246)
                      ..+....+.+.+.|++++|...|.+.+..--  ...+...         -..+|+.+..+|.+.|++++|...++.... 
T Consensus        14 ~~l~~~G~~~~~~~~~~~Ai~~y~~al~~~~--~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~-   90 (170)
T d1p5qa1          14 TIVKERGTVYFKEGKYKQALLQYKKIVSWLE--YESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALE-   90 (170)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHTT--TCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHhh--hccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhh-
Confidence            3455666788999999999999998876410  0001111         123566677777778888888888877777 


Q ss_pred             CCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          123 CNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       123 ~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                        +.|+ ..+|..+..+|...|++++    |...|+...+.
T Consensus        91 --~~p~~~~a~~~~g~~~~~~g~~~~----A~~~~~~al~l  125 (170)
T d1p5qa1          91 --LDSNNEKGLSRRGEAHLAVNDFEL----ARADFQKVLQL  125 (170)
T ss_dssp             --HCTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH
T ss_pred             --ccccchhhhHHHHHHHHHhhhHHH----HHHHHHHHHHh
Confidence              4454 6677777778888888888    88888877765

>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=98.03  E-value=7.7e-05  Score=48.84  Aligned_cols=95  Identities=9%  Similarity=0.089  Sum_probs=79.2

Q ss_pred             HHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC----
Q 043380           53 SYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD----  128 (246)
Q Consensus        53 t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~----  128 (246)
                      .+-.+-+.+.+.|++++|...|.+.++.        -+.+...|..+-.+|.+.|++++|...+++..+   +.|+    
T Consensus         6 ~~k~~G~~~~~~~~y~~Ai~~y~~al~~--------~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~---l~~~~~~~   74 (128)
T d1elra_           6 KEKELGNDAYKKKDFDTALKHYDKAKEL--------DPTNMTYITNQAAVYFEKGDYNKCRELCEKAIE---VGRENRED   74 (128)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH---HHHHSTTC
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHh--------CcccHHHHHhHHHHHHHcCchHHHHHHHHHHHH---hCcccHHH
Confidence            3456677899999999999999999986        244688999999999999999999999999776   2221    


Q ss_pred             ----HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          129 ----RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       129 ----~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                          ..+|..+...+...+++++    |.+.|+.....
T Consensus        75 ~~~~a~~~~~lg~~~~~~~~~~~----A~~~~~kal~~  108 (128)
T d1elra_          75 YRQIAKAYARIGNSYFKEEKYKD----AIHFYNKSLAE  108 (128)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHH----HHHHHHHHHhc
Confidence                2467788888999999999    99999987765

>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=97.99  E-value=5.7e-05  Score=52.66  Aligned_cols=76  Identities=12%  Similarity=0.121  Sum_probs=63.2

Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCc
Q 043380           93 IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWP  171 (246)
Q Consensus        93 ~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p  171 (246)
                      ...+..+..++.+.|++++|...++....   +.|. ...|..++.+|...|+..+    |++.|++.........|+.|
T Consensus        67 ~~a~~~la~~~~~~g~~~~Al~~~~~al~---~~P~~e~~~~~l~~al~~~Gr~~e----Al~~y~~~~~~L~~eLG~~P  139 (179)
T d2ff4a2          67 VLAHTAKAEAEIACGRASAVIAELEALTF---EHPYREPLWTQLITAYYLSDRQSD----ALGAYRRVKTTLADDLGIDP  139 (179)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HSTTCHHHHHHHHHHHHTTTCHHH----HHHHHHHHHHHHHHHHSCCC
T ss_pred             HHHHHHHHHHHHHCCCchHHHHHHHHHHH---hCCccHHHHHHHHHHHHHhcCHHH----HHHHHHHHHHHHHHHhCCCc
Confidence            35788899999999999999999999998   5565 8899999999999999999    99999998553211228888


Q ss_pred             chhh
Q 043380          172 KPHL  175 (246)
Q Consensus       172 ~~~~  175 (246)
                      ...+
T Consensus       140 ~~~l  143 (179)
T d2ff4a2         140 GPTL  143 (179)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            8754

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=97.98  E-value=0.00021  Score=48.23  Aligned_cols=99  Identities=12%  Similarity=-0.039  Sum_probs=74.3

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCC-----CCC-----------HHHHHHHHHHHHhcCCcchHHHHHHHHHhccC
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVEKGL-----EPD-----------SLSYNILISACIKTKKLDVTMPFNEQLKDNGQ   82 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~-----~~~-----------~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~   82 (246)
                      .+..--+.+.+.|++++|+..|.+...-.     .++           ..+|+.+..+|.+.|++++|++.+.+.++.  
T Consensus        19 ~~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~--   96 (153)
T d2fbna1          19 DIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKI--   96 (153)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhccccc--
Confidence            44556678889999999999998754211     111           245667778888888888888888888875  


Q ss_pred             CCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC
Q 043380           83 KCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD  128 (246)
Q Consensus        83 ~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~  128 (246)
                            -+.+..+|..+..++...|++++|...|+...+   +.|+
T Consensus        97 ------~p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~---l~P~  133 (153)
T d2fbna1          97 ------DKNNVKALYKLGVANMYFGFLEEAKENLYKAAS---LNPN  133 (153)
T ss_dssp             ------STTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH---HSTT
T ss_pred             ------cchhhhhhHHhHHHHHHcCCHHHHHHHHHHHHH---hCCC
Confidence                  234667888888888888888888888888887   5566

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=97.96  E-value=0.00029  Score=47.46  Aligned_cols=101  Identities=10%  Similarity=0.016  Sum_probs=80.5

Q ss_pred             HHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCC----------ccHHHHHHHHHHHHccCCHHHHHHHHHHHHhC
Q 043380           53 SYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFH----------PDIFTYATLLMGFRHAKDLQSLLEIVFEMKSC  122 (246)
Q Consensus        53 t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~----------p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~  122 (246)
                      .+....+.+.+.|++.+|...|.+....-...  ....          ....+|+.+..+|.+.|++++|++.++...+ 
T Consensus        19 ~~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~--~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~-   95 (153)
T d2fbna1          19 DIKEEGNEFFKKNEINEAIVKYKEALDFFIHT--EEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLK-   95 (153)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTC--TTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCcch--hhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhcccc-
Confidence            44555667889999999999999987641000  0011          1234788899999999999999999999988 


Q ss_pred             CCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          123 CNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       123 ~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                        +.|+ ..+|..+..+|...|++++    |...|+...+.
T Consensus        96 --~~p~~~ka~~~~g~~~~~lg~~~~----A~~~~~~al~l  130 (153)
T d2fbna1          96 --IDKNNVKALYKLGVANMYFGFLEE----AKENLYKAASL  130 (153)
T ss_dssp             --HSTTCHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHH
T ss_pred             --ccchhhhhhHHhHHHHHHcCCHHH----HHHHHHHHHHh
Confidence              4565 8899999999999999999    99999999886

>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=97.93  E-value=0.00024  Score=48.69  Aligned_cols=131  Identities=4%  Similarity=-0.115  Sum_probs=93.0

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHh----CCCC-----------CHHHHHHHHHHHHhcCCcchHHHHHHHHHhcc
Q 043380           17 TIVMNAVIEASREAQRIDEAYQILESVEK----GLEP-----------DSLSYNILISACIKTKKLDVTMPFNEQLKDNG   81 (246)
Q Consensus        17 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~----~~~~-----------~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~   81 (246)
                      ...+.-....+.+.|++++|...|.....    ...+           ....|+.+-.+|.+.+++++|+..+++.+.. 
T Consensus        15 a~~~~e~G~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l-   93 (168)
T d1kt1a1          15 AAIVKEKGTVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGL-   93 (168)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhc-
Confidence            34566778889999999999999977431    1111           1234566777889999999999999999986 


Q ss_pred             CCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHH
Q 043380           82 QKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIV  160 (246)
Q Consensus        82 ~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~  160 (246)
                             -+.+...|..+..+|...|++++|...|+....   +.|+ ......+-......+...+.   ..++|..|.
T Consensus        94 -------~p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~---l~P~n~~~~~~l~~~~~~~~~~~e~---~kk~~~~~f  160 (168)
T d1kt1a1          94 -------DSANEKGLYRRGEAQLLMNEFESAKGDFEKVLE---VNPQNKAARLQIFMCQKKAKEHNER---DRRTYANMF  160 (168)
T ss_dssp             -------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---SCTTCHHHHHHHHHHHHHHHHHHHH---HHHHHHHHH
T ss_pred             -------ccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHHHhHHHH---HHHHHHHHH
Confidence                   245678999999999999999999999999998   6676 44444444444444333221   444444444


Q ss_pred             H
Q 043380          161 K  161 (246)
Q Consensus       161 ~  161 (246)
                      +
T Consensus       161 ~  161 (168)
T d1kt1a1         161 K  161 (168)
T ss_dssp             H
T ss_pred             h
Confidence            4

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.92  E-value=0.00014  Score=50.00  Aligned_cols=110  Identities=7%  Similarity=-0.008  Sum_probs=85.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHh---------------CCC-CCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccC
Q 043380           19 VMNAVIEASREAQRIDEAYQILESVEK---------------GLE-PDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQ   82 (246)
Q Consensus        19 ~~~~li~~~~~~g~~~~a~~~~~~~~~---------------~~~-~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~   82 (246)
                      .+......+.+.|++++|++.|.+..+               .+. .+...|..+-.++.+.|++++|+..+.+.++.  
T Consensus        29 ~~~~~~~~~~~~~~y~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~--  106 (169)
T d1ihga1          29 DLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEI--  106 (169)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhhhhhhhhhhhHHHHHhChhhHHHHHHHHHHHHhhcccchhhhhhhhhhhh--
Confidence            345667778899999999998876421               112 24456777888999999999999999999986  


Q ss_pred             CCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHH
Q 043380           83 KCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDAL  139 (246)
Q Consensus        83 ~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~  139 (246)
                            -+.+...|..+-.+|...|++++|.+.|+...+   +.|+ ......+....
T Consensus       107 ------~p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~---l~p~n~~~~~~l~~~~  155 (169)
T d1ihga1         107 ------DPSNTKALYRRAQGWQGLKEYDQALADLKKAQE---IAPEDKAIQAELLKVK  155 (169)
T ss_dssp             ------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHH
T ss_pred             ------hhhhhhHHHhHHHHHHHccCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHH
Confidence                  234677999999999999999999999999998   5565 45555554443

>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=97.90  E-value=0.00029  Score=48.92  Aligned_cols=109  Identities=14%  Similarity=0.033  Sum_probs=84.8

Q ss_pred             cCHHHHHHHH---HHHHhcCCHHHHHHHHHHHHh---CCC-CC------------------HHHHHHHHHHHHhcCCcch
Q 043380           15 LNTIVMNAVI---EASREAQRIDEAYQILESVEK---GLE-PD------------------SLSYNILISACIKTKKLDV   69 (246)
Q Consensus        15 ~~~~~~~~li---~~~~~~g~~~~a~~~~~~~~~---~~~-~~------------------~~t~~~li~~~~~~~~~~~   69 (246)
                      .|+..|..+.   ......|++++|.+.|.....   |-. ++                  ...+..+..++...|++++
T Consensus         6 ~D~~~f~~~~~~g~~~~~~g~~e~A~~~~~~AL~l~rG~~l~~~~~~~w~~~~r~~l~~~~~~a~~~la~~~~~~g~~~~   85 (179)
T d2ff4a2           6 CDLGRFVAEKTAGVHAAAAGRFEQASRHLSAALREWRGPVLDDLRDFQFVEPFATALVEDKVLAHTAKAEAEIACGRASA   85 (179)
T ss_dssp             BHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             ccHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCchH
Confidence            3455555555   467788999999999988542   211 11                  1346788889999999999


Q ss_pred             HHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHh----CCCCCCCHHH
Q 043380           70 TMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKS----CCNLILDRST  131 (246)
Q Consensus        70 a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~----~~~~~p~~~~  131 (246)
                      |...++++...        -+-+...|..++.+|.+.|+.++|++.|+++..    ..|+.|+..+
T Consensus        86 Al~~~~~al~~--------~P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          86 VIAELEALTFE--------HPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HHHHHHHHHHH--------STTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHHHh--------CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            99999999986        345788999999999999999999999998743    1689998755

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.88  E-value=0.00014  Score=55.58  Aligned_cols=157  Identities=10%  Similarity=-0.019  Sum_probs=106.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHH----------hcCCcchHHHHHHHHHhccCCCCCCC
Q 043380           20 MNAVIEASREAQRIDEAYQILESVEKGLEPD-SLSYNILISACI----------KTKKLDVTMPFNEQLKDNGQKCSSGG   88 (246)
Q Consensus        20 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~-~~t~~~li~~~~----------~~~~~~~a~~~~~~m~~~~~~~~~~~   88 (246)
                      +..++...-+....++|+++++....- .|+ ...|+..-..+.          ..+.+++|+.+++...+.        
T Consensus        32 ~~~~~~~~~~~~~~~~al~~~~~~l~~-~P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~--------  102 (334)
T d1dcea1          32 TQAVFQKRQAGELDESVLELTSQILGA-NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRV--------  102 (334)
T ss_dssp             HHHHHHHHHTTCCSHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHH--------
T ss_pred             HHHHHHHHhcccccHHHHHHHHHHHHH-CCCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHh--------
Confidence            344444333344458999999987532 454 445554333322          234478899999999875        


Q ss_pred             CCccHHHHHHHHHHHHccC--CHHHHHHHHHHHHhCCCCCCC-HHHHH-HHHHHHHhcCChhhhhhHHHHHHHHHHHhhc
Q 043380           89 FHPDIFTYATLLMGFRHAK--DLQSLLEIVFEMKSCCNLILD-RSTFT-AMVDALLYSGSIKVVGLYALCIFGEIVKRVC  164 (246)
Q Consensus        89 ~~p~~~~~~~ll~~~~~~~--~~~~a~~~~~~m~~~~~~~p~-~~~~~-~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~  164 (246)
                      -+-+...|..+..++...+  ++++|...++....   ..|+ ...+. .....+...+.++.    |+..++.....  
T Consensus       103 ~pk~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~---~~~~~~~~~~~~~~~~~~~~~~~~~----Al~~~~~~i~~--  173 (334)
T d1dcea1         103 NPKSYGTWHHRCWLLSRLPEPNWARELELCARFLE---ADERNFHCWDYRRFVAAQAAVAPAE----ELAFTDSLITR--  173 (334)
T ss_dssp             CTTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHHTCCCHHH----HHHHHHTTTTT--
T ss_pred             CCCcHHHHHHhhHHHHHhccccHHHHHHHHHHHHh---hCchhhhhhhhHHHHHHHhccccHH----HHHHHHHHHHc--
Confidence            2335667777777776655  58999999999988   3343 55554 44567777899999    99999988775  


Q ss_pred             CCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHh
Q 043380          165 SNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRR  198 (246)
Q Consensus       165 ~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  198 (246)
                          -+-+..+|..+..++...|++++|...+..
T Consensus       174 ----~p~~~~a~~~l~~~~~~~~~~~~A~~~~~~  203 (334)
T d1dcea1         174 ----NFSNYSSWHYRSCLLPQLHPQPDSGPQGRL  203 (334)
T ss_dssp             ----TCCCHHHHHHHHHHHHHHSCCCCSSSCCSS
T ss_pred             ----CCCCHHHHHHHHHHHHHhcCHHHHHHHHHH
Confidence                223567888888889999888776554443

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.73  E-value=0.0023  Score=48.82  Aligned_cols=127  Identities=6%  Similarity=-0.084  Sum_probs=67.0

Q ss_pred             ccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCC
Q 043380           91 PDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLW  170 (246)
Q Consensus        91 p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~  170 (246)
                      .+......++..|-..|.+++...+++.... . -.++...++-++..|++.+.        .++.+.++..     +  
T Consensus        97 ~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~-~-~~~~~~~~~~L~~lyak~~~--------~kl~e~l~~~-----s--  159 (336)
T d1b89a_          97 VHADELEELINYYQDRGYFEELITMLEAALG-L-ERAHMGMFTELAILYSKFKP--------QKMREHLELF-----W--  159 (336)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHTT-S-TTCCHHHHHHHHHHHHTTCH--------HHHHHHHHHH-----S--
T ss_pred             cCHHHHHHHHHHHHHcCChHHHHHHHHHHHc-C-CccchHHHHHHHHHHHHhCh--------HHHHHHHHhc-----c--
Confidence            3444456777888888888888877776644 1 23456667777777777532        2233333332     1  


Q ss_pred             cchhhHHHHHHHHHhcCChhHHhhHHHhhCCCC---------CCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 043380          171 PKPHLYVSMMHELAARVDYDIVKSPYRRMWPDS---------TGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTIT  241 (246)
Q Consensus       171 p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~---------~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  241 (246)
                       +..-...++..|-..+.+.++.-++..+..-.         ....+      -...+++.+.+..+++...+++.-..+
T Consensus       160 -~~y~~~k~~~~c~~~~l~~elv~Ly~~~~~~~~A~~~~i~~~~~~~------~~~~f~e~~~k~~N~e~~~~~i~~yL~  232 (336)
T d1b89a_         160 -SRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAW------KEGQFKDIITKVANVELYYRAIQFYLE  232 (336)
T ss_dssp             -TTSCHHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHHHHSTTTTC------CHHHHHHHHHHCSSTHHHHHHHHHHHH
T ss_pred             -ccCCHHHHHHHHHHcCChHHHHHHHHhcCCHHHHHHHHHHcchhhh------hHHHHHHHHHccCChHHHHHHHHHHHH
Confidence             11122333444444444444444444332100         00011      123466777888888777777665554

>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=97.68  E-value=0.00056  Score=46.78  Aligned_cols=102  Identities=11%  Similarity=-0.009  Sum_probs=70.2

Q ss_pred             HHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc---------cHHHHHHHHHHHHccCCHHHHHHHHHHHHhC
Q 043380           52 LSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP---------DIFTYATLLMGFRHAKDLQSLLEIVFEMKSC  122 (246)
Q Consensus        52 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p---------~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~  122 (246)
                      ..+.-....+.+.|++++|...|.+.+..-  .......+         ....|+.+-.+|.+.|++++|...++.... 
T Consensus        16 ~~~~e~G~~~~~~~~~~~A~~~Y~~al~~~--~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~-   92 (168)
T d1kt1a1          16 AIVKEKGTVYFKGGKYVQAVIQYGKIVSWL--EMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALG-   92 (168)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHH--TTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHH--HHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhh-
Confidence            345566778899999999999998877530  00001111         123456666777788888888888888777 


Q ss_pred             CCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          123 CNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       123 ~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                        +.|+ ..+|..+..+|...|++++    |...|+...+.
T Consensus        93 --l~p~~~~a~~~~~~~~~~l~~~~~----A~~~~~~al~l  127 (168)
T d1kt1a1          93 --LDSANEKGLYRRGEAQLLMNEFES----AKGDFEKVLEV  127 (168)
T ss_dssp             --HCTTCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHS
T ss_pred             --cccchHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHh
Confidence              3444 6777777888888888888    88888887764

>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=0.0001  Score=54.69  Aligned_cols=121  Identities=10%  Similarity=-0.041  Sum_probs=85.6

Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-HHHHHHHHHHHHc
Q 043380           27 SREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-IFTYATLLMGFRH  105 (246)
Q Consensus        27 ~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~~~ll~~~~~  105 (246)
                      ..+.|++++|+..+++..+..+.|...+..+...++..|++++|.+.|+...+.         .|+ ...+..+...+..
T Consensus         6 aL~~G~l~eAl~~l~~al~~~P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l---------~P~~~~~~~~l~~ll~a   76 (264)
T d1zbpa1           6 ALSEGQLQQALELLIEAIKASPKDASLRSSFIELLCIDGDFERADEQLMQSIKL---------FPEYLPGASQLRHLVKA   76 (264)
T ss_dssp             HTTTTCHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---------CGGGHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh---------CCCcHHHHHHHHHHHHh
Confidence            456799999999999876555778999999999999999999999999999986         565 4455545444443


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380          106 AKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       106 ~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      .+..+++..-...-.. . ..|+ ...+......+...|+.++    |.+.+++..+.
T Consensus        77 ~~~~~~a~~~~~~~~~-~-~~p~~~~~~l~~a~~~~~~gd~~~----A~~~~~~a~e~  128 (264)
T d1zbpa1          77 AQARKDFAQGAATAKV-L-GENEELTKSLVSFNLSMVSQDYEQ----VSELALQIEEL  128 (264)
T ss_dssp             HHHHHHHTTSCCCEEC-C-CSCHHHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHH
T ss_pred             ccccHHHHHHhhhhhc-c-cCchHHHHHHHHHHHHHhCCCHHH----HHHHHHHHHhc
Confidence            3333333222111111 1 1233 3444555677888999999    99999998887

>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=97.55  E-value=0.0008  Score=45.30  Aligned_cols=122  Identities=16%  Similarity=0.079  Sum_probs=81.4

Q ss_pred             HHHHHH--HHHHHhcCCcchHHHHHHHHHhccCCCCCC-CC--Cc-cHHHHHHHHHHHHccCCHHHHHHHHHHHHhC---
Q 043380           52 LSYNIL--ISACIKTKKLDVTMPFNEQLKDNGQKCSSG-GF--HP-DIFTYATLLMGFRHAKDLQSLLEIVFEMKSC---  122 (246)
Q Consensus        52 ~t~~~l--i~~~~~~~~~~~a~~~~~~m~~~~~~~~~~-~~--~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~---  122 (246)
                      .+|..+  ...+...|++++|+..|.+.++..-...+. ..  .+ ....|+.+-.+|...|++++|...+++..+.   
T Consensus         8 ~a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~   87 (156)
T d2hr2a1           8 GAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNR   87 (156)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhcccc
Confidence            455555  445667899999999999998742110000 00  01 2468999999999999999999998887641   


Q ss_pred             -CCCCCC-----HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHH
Q 043380          123 -CNLILD-----RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYV  177 (246)
Q Consensus       123 -~~~~p~-----~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~  177 (246)
                       ....++     ...|+.+..+|...|++++    |...|++..+......+..+....+.
T Consensus        88 ~~~~~~~~~~~~~~a~~~~g~~~~~lg~~ee----A~~~~~~Al~l~~~~~~~~~~~~~~~  144 (156)
T d2hr2a1          88 RGELNQDEGKLWISAVYSRALALDGLGRGAE----AMPEFKKVVEMIEERKGETPGKERMM  144 (156)
T ss_dssp             HCCTTSTHHHHHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHHHHHCCSCCTTHHHHH
T ss_pred             cccccccccchhHHHHhhhHHHHHHHHHHHH----HHHHHHHHHHhhHHhhchHHHHHHHH
Confidence             112222     2357778899999999999    99999997765332334444443333

>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=97.54  E-value=0.0017  Score=52.46  Aligned_cols=116  Identities=9%  Similarity=-0.008  Sum_probs=71.0

Q ss_pred             CCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC
Q 043380           49 PDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD  128 (246)
Q Consensus        49 ~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~  128 (246)
                      ++...+..+-..+.+.++.++|...+......         .| ..++..+-..+...|++++|...|++..+   +.|+
T Consensus       118 ~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~---------~~-~~~~~~LG~l~~~~~~~~~A~~~y~~A~~---l~P~  184 (497)
T d1ya0a1         118 PCRVKSSQLGIISNKQTHTSAIVKPQSSSCSY---------IC-QHCLVHLGDIARYRNQTSQAESYYRHAAQ---LVPS  184 (497)
T ss_dssp             -------------------------CCHHHHH---------HH-HHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTT
T ss_pred             hhHHHHHHhHHHHHhCCCHHHHHHHHHHHhCC---------CH-HHHHHHHHHHHHHcccHHHHHHHHHHHHH---HCCC
Confidence            34555666777777778888877777665542         12 34677788888899999999999999888   6677


Q ss_pred             -HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcC
Q 043380          129 -RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARV  187 (246)
Q Consensus       129 -~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g  187 (246)
                       ...|+.|...+...|+..+    |...|.+....      -.|-..++..|...+.+..
T Consensus       185 ~~~~~~~Lg~~~~~~~~~~~----A~~~y~ral~~------~~~~~~a~~nL~~~~~~~~  234 (497)
T d1ya0a1         185 NGQPYNQLAILASSKGDHLT----TIFYYCRSIAV------KFPFPAASTNLQKALSKAL  234 (497)
T ss_dssp             BSHHHHHHHHHHHHTTCHHH----HHHHHHHHHSS------SBCCHHHHHHHHHHHHHHT
T ss_pred             chHHHHHHHHHHHHcCCHHH----HHHHHHHHHhC------CCCCHHHHHHHHHHHHHhh
Confidence             6789999999999999999    99988888765      3567788888887776544

>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=97.53  E-value=0.00073  Score=49.92  Aligned_cols=122  Identities=12%  Similarity=0.024  Sum_probs=84.4

Q ss_pred             HHccCCHHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcch-hhHHHHH
Q 043380          103 FRHAKDLQSLLEIVFEMKSCCNLILD-RSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKP-HLYVSMM  180 (246)
Q Consensus       103 ~~~~~~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~-~~~~~li  180 (246)
                      ..+.|++++|...+++..+   ..|+ ...+..+...|+..|++++    |...++...+.       .|+. ..+..+.
T Consensus         6 aL~~G~l~eAl~~l~~al~---~~P~d~~ar~~La~lL~~~G~~e~----A~~~l~~a~~l-------~P~~~~~~~~l~   71 (264)
T d1zbpa1           6 ALSEGQLQQALELLIEAIK---ASPKDASLRSSFIELLCIDGDFER----ADEQLMQSIKL-------FPEYLPGASQLR   71 (264)
T ss_dssp             HTTTTCHHHHHHHHHHHHH---TCTTCHHHHHHHHHHHHHHTCHHH----HHHHHHHHHHH-------CGGGHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHH---HCCCCHHHHHHHHHHHHHCCCHHH----HHHHHHHHHHh-------CCCcHHHHHHHH
Confidence            4567999999999999998   5566 8889999999999999999    99999999886       4554 4444444


Q ss_pred             HHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhc
Q 043380          181 HELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRW  243 (246)
Q Consensus       181 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  243 (246)
                      ..+...+..+++..-...-...  + -++..  ..+......+...|+.++|.+.+++..+.-
T Consensus        72 ~ll~a~~~~~~a~~~~~~~~~~--~-~p~~~--~~~l~~a~~~~~~gd~~~A~~~~~~a~e~~  129 (264)
T d1zbpa1          72 HLVKAAQARKDFAQGAATAKVL--G-ENEEL--TKSLVSFNLSMVSQDYEQVSELALQIEELR  129 (264)
T ss_dssp             HHHHHHHHHHHHTTSCCCEECC--C-SCHHH--HHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHhccccHHHHHHhhhhhcc--c-CchHH--HHHHHHHHHHHhCCCHHHHHHHHHHHHhcC
Confidence            4444444444433322211111  1 12221  134445667888999999999999887654

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.44  E-value=0.00048  Score=45.95  Aligned_cols=115  Identities=8%  Similarity=-0.072  Sum_probs=84.3

Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhc----------CCcchHHHHHHHHHhccCCCCCCCCCccHHHH
Q 043380           27 SREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKT----------KKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTY   96 (246)
Q Consensus        27 ~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~----------~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~   96 (246)
                      |-+.+.+++|.+.|+...+--+.+...+..+-.++...          +.+++|...|++.++.        -+-+..+|
T Consensus         7 ~~r~~~fe~A~~~~e~al~~~P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l--------~P~~~~a~   78 (145)
T d1zu2a1           7 FDRILLFEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLI--------DPKKDEAV   78 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHH--------CTTCHHHH
T ss_pred             HHHHccHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHh--------cchhhHHH
Confidence            45667799999999987644467788888888887754          4457899999999875        13356788


Q ss_pred             HHHHHHHHccC-----------CHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHh
Q 043380           97 ATLLMGFRHAK-----------DLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus        97 ~~ll~~~~~~~-----------~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ..+-.+|...|           ++++|.+.|+...+   +.|+...|..-+..+      ..    |.+++.+..++
T Consensus        79 ~~lG~~y~~~g~~~~~~~~~~~~~~~A~~~~~kal~---l~P~~~~~~~~L~~~------~k----a~~~~~e~~k~  142 (145)
T d1zu2a1          79 WCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVD---EQPDNTHYLKSLEMT------AK----APQLHAEAYKQ  142 (145)
T ss_dssp             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH---HCTTCHHHHHHHHHH------HT----HHHHHHHHHHS
T ss_pred             hhHHHHHHHcccchhhHHHHHHhHHHhhhhhhcccc---cCCCHHHHHHHHHHH------HH----HHHHHHHHHHH
Confidence            88888887654           36889999999988   778876666555443      35    66677666655

>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=97.39  E-value=0.0015  Score=43.90  Aligned_cols=104  Identities=11%  Similarity=-0.042  Sum_probs=74.9

Q ss_pred             HHHHHHH--HHHHHccCCHHHHHHHHHHHHhCCCCCCC----------HHHHHHHHHHHHhcCChhhhhhHHHHHHHHHH
Q 043380           93 IFTYATL--LMGFRHAKDLQSLLEIVFEMKSCCNLILD----------RSTFTAMVDALLYSGSIKVVGLYALCIFGEIV  160 (246)
Q Consensus        93 ~~~~~~l--l~~~~~~~~~~~a~~~~~~m~~~~~~~p~----------~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~  160 (246)
                      ..+|..+  ...+...|++++|...|++..+...-.|+          ...|+.+..+|...|++++    |...+++..
T Consensus         7 a~a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~----A~~~~~~al   82 (156)
T d2hr2a1           7 VGAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDE----ALHSADKAL   82 (156)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHH----HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccch----hhHhhhhhh
Confidence            3466666  44566789999999999998762111122          4678899999999999999    999999877


Q ss_pred             HhhcCCCCCCcc-----hhhHHHHHHHHHhcCChhHHhhHHHhhC
Q 043380          161 KRVCSNPGLWPK-----PHLYVSMMHELAARVDYDIVKSPYRRMW  200 (246)
Q Consensus       161 ~~~~~~~~~~p~-----~~~~~~li~~~~~~g~~~~a~~~~~~~~  200 (246)
                      ..........++     ..++..+-.+|...|++++|...|++..
T Consensus        83 ~~~~~~~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al  127 (156)
T d2hr2a1          83 HYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVV  127 (156)
T ss_dssp             HHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             hcccccccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHH
Confidence            642111112222     2356778899999999999999999754

>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=97.30  E-value=0.00064  Score=45.31  Aligned_cols=101  Identities=10%  Similarity=-0.044  Sum_probs=73.1

Q ss_pred             HHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHcc----------CCHHHHHHHHHHHHhCCCCCCC-H
Q 043380           61 CIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHA----------KDLQSLLEIVFEMKSCCNLILD-R  129 (246)
Q Consensus        61 ~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~----------~~~~~a~~~~~~m~~~~~~~p~-~  129 (246)
                      |-+.+.+++|...|+...+.        -+.+...+..+-.+|...          +.+++|...|+...+   +.|+ .
T Consensus         7 ~~r~~~fe~A~~~~e~al~~--------~P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~---l~P~~~   75 (145)
T d1zu2a1           7 FDRILLFEQIRQDAENTYKS--------NPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALL---IDPKKD   75 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHH---HCTTCH
T ss_pred             HHHHccHHHHHHHHHHHHhh--------CCcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHH---hcchhh
Confidence            34556789999999999986        244566777777777643          445789999999988   6677 7


Q ss_pred             HHHHHHHHHHHhcCC-----------hhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHH
Q 043380          130 STFTAMVDALLYSGS-----------IKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHEL  183 (246)
Q Consensus       130 ~~~~~li~~~~~~~~-----------~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~  183 (246)
                      .+|..+..+|...|+           ++.    |.+.|+...+.       .|+...|..-+..+
T Consensus        76 ~a~~~lG~~y~~~g~~~~~~~~~~~~~~~----A~~~~~kal~l-------~P~~~~~~~~L~~~  129 (145)
T d1zu2a1          76 EAVWCIGNAYTSFAFLTPDETEAKHNFDL----ATQFFQQAVDE-------QPDNTHYLKSLEMT  129 (145)
T ss_dssp             HHHHHHHHHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHH-------CTTCHHHHHHHHHH
T ss_pred             HHHhhHHHHHHHcccchhhHHHHHHhHHH----hhhhhhccccc-------CCCHHHHHHHHHHH
Confidence            788888888877653           466    78888877764       56666555544443

>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=97.29  E-value=0.0014  Score=40.09  Aligned_cols=80  Identities=13%  Similarity=-0.034  Sum_probs=59.6

Q ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCcc-HHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCC-
Q 043380           51 SLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPD-IFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILD-  128 (246)
Q Consensus        51 ~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~-  128 (246)
                      ...+-.+...+.+.|++++|..+|++..+....  .....++ ..+++.|-.+|.+.|++++|...+++..+   +.|+ 
T Consensus         5 addc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~--~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~---l~P~~   79 (95)
T d1tjca_           5 AEDSFELGKVAYTEADYYHTELWMEQALRQLDE--GEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLE---LDPEH   79 (95)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHT--TCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCTTC
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhh--hhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHH---hCcCC
Confidence            344556778888999999999999988764110  0111222 56899999999999999999999999999   6677 


Q ss_pred             HHHHHHH
Q 043380          129 RSTFTAM  135 (246)
Q Consensus       129 ~~~~~~l  135 (246)
                      ..+++.+
T Consensus        80 ~~a~~Nl   86 (95)
T d1tjca_          80 QRANGNL   86 (95)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            5566554

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=97.14  E-value=0.023  Score=41.06  Aligned_cols=195  Identities=10%  Similarity=-0.001  Sum_probs=106.4

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHh----cCCcchHHHHHHHHHhccCCCCCCCCCc
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIK----TKKLDVTMPFNEQLKDNGQKCSSGGFHP   91 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~~~~~~~~p   91 (246)
                      |+..+..|-..+.+.++.++|++.|++..+  .-+...+..|-..|..    ..++..|..++......+        .|
T Consensus         1 ~p~~~~~lG~~~~~~~d~~~A~~~~~kAa~--~g~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~--------~~   70 (265)
T d1ouva_           1 DPKELVGLGAKSYKEKDFTQAKKYFEKACD--LKENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN--------YS   70 (265)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--TTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT--------CH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHH--CCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccc--------cc
Confidence            455666777777778888888888887652  1244444445555554    345666666666665541        11


Q ss_pred             cHHHHHHHHHHHH----ccCCHHHHHHHHHHHHhCCCCC---------------------------------CCHHHHHH
Q 043380           92 DIFTYATLLMGFR----HAKDLQSLLEIVFEMKSCCNLI---------------------------------LDRSTFTA  134 (246)
Q Consensus        92 ~~~~~~~ll~~~~----~~~~~~~a~~~~~~m~~~~~~~---------------------------------p~~~~~~~  134 (246)
                      .  ....|...+.    ...+.+.|...++...+ .|..                                 .+...+..
T Consensus        71 ~--a~~~l~~~~~~~~~~~~~~~~a~~~~~~a~~-~g~~~a~~~l~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  147 (265)
T d1ouva_          71 N--GCHLLGNLYYSGQGVSQNTNKALQYYSKACD-LKYAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLNDGDGCTI  147 (265)
T ss_dssp             H--HHHHHHHHHHHTSSSCCCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             c--hhhccccccccccccchhhHHHHHHHhhhhh-hhhhhHHHhhcccccCCCcccchhHHHHHHhhhhhcccccchhhh
Confidence            1  1122222221    13344555555544443 2211                                 23344444


Q ss_pred             HHHHHHh----cCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHh----cCChhHHhhHHHhhCCCCCCC
Q 043380          135 MVDALLY----SGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAA----RVDYDIVKSPYRRMWPDSTGT  206 (246)
Q Consensus       135 li~~~~~----~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~  206 (246)
                      |...|..    ..+...    +...++...+.     |   +..+...+-..|..    ..++++|...|....+.+   
T Consensus       148 L~~~~~~~~~~~~~~~~----~~~~~~~a~~~-----g---~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~~g---  212 (265)
T d1ouva_         148 LGSLYDAGRGTPKDLKK----ALASYDKACDL-----K---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---  212 (265)
T ss_dssp             HHHHHHHTSSSCCCHHH----HHHHHHHHHHT-----T---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---
T ss_pred             hhhhhccCCCccccccc----chhhhhccccc-----c---ccccccchhhhcccCcccccchhhhhhhHhhhhccc---
Confidence            5555544    222333    44444444443     2   34444444444444    567888999998876543   


Q ss_pred             CCchhhhHHHHHHHHHHHh----cCChhHHHHHHHHHHhhc
Q 043380          207 ISPEVQEEAGHLLMEAALN----DGQVDLALDKLSNTITRW  243 (246)
Q Consensus       207 ~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g  243 (246)
                       .+.    ++..|...|.+    ..+.++|.++|+.-.+.|
T Consensus       213 -~~~----a~~~LG~~y~~G~g~~~n~~~A~~~~~kAa~~g  248 (265)
T d1ouva_         213 -NGG----GCFNLGAMQYNGEGVTRNEKQAIENFKKGCKLG  248 (265)
T ss_dssp             -CHH----HHHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHT
T ss_pred             -CHH----HHHHHHHHHHcCCCCccCHHHHHHHHHHHHHCc
Confidence             121    45566666664    447889999999887766

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.89  E-value=0.0012  Score=53.26  Aligned_cols=118  Identities=8%  Similarity=-0.117  Sum_probs=71.9

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHH
Q 043380           16 NTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFT   95 (246)
Q Consensus        16 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~   95 (246)
                      +...+..+-..+.+.|+.++|...+.....  .....++..+...+...+++++|...|.+..+.        .+-+...
T Consensus       119 ~~~~~~~lg~~~~~~~~~~~A~~~~~~al~--~~~~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l--------~P~~~~~  188 (497)
T d1ya0a1         119 CRVKSSQLGIISNKQTHTSAIVKPQSSSCS--YICQHCLVHLGDIARYRNQTSQAESYYRHAAQL--------VPSNGQP  188 (497)
T ss_dssp             ------------------------CCHHHH--HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTBSHH
T ss_pred             hHHHHHHhHHHHHhCCCHHHHHHHHHHHhC--CCHHHHHHHHHHHHHHcccHHHHHHHHHHHHHH--------CCCchHH
Confidence            344455555556666666666665544321  112356777888899999999999999999986        2334679


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCCh
Q 043380           96 YATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSI  145 (246)
Q Consensus        96 ~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~  145 (246)
                      |+.|-..+...|+..+|...|.+... . -.|-..++..|...+.+....
T Consensus       189 ~~~Lg~~~~~~~~~~~A~~~y~ral~-~-~~~~~~a~~nL~~~~~~~~~~  236 (497)
T d1ya0a1         189 YNQLAILASSKGDHLTTIFYYCRSIA-V-KFPFPAASTNLQKALSKALES  236 (497)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHS-S-SBCCHHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHh-C-CCCCHHHHHHHHHHHHHhhhh
Confidence            99999999999999999999999888 3 234588888888888765543

>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=96.53  E-value=0.012  Score=35.68  Aligned_cols=72  Identities=3%  Similarity=-0.131  Sum_probs=56.9

Q ss_pred             CHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcc-hhhHHHHHHHHHhcCChhHHhhHHHhhCCCC
Q 043380          128 DRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPK-PHLYVSMMHELAARVDYDIVKSPYRRMWPDS  203 (246)
Q Consensus       128 ~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  203 (246)
                      +...+-.+...+.+.|+++.    |...|++..+.....+...++ ..++..+-.+|.+.|++++|...+++..+.+
T Consensus         4 saddc~~lG~~~~~~g~y~~----A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~   76 (95)
T d1tjca_           4 TAEDSFELGKVAYTEADYYH----TELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELD   76 (95)
T ss_dssp             CHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHCCCHHH----HHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhC
Confidence            44455678889999999999    999999987764333333344 4678999999999999999999999987654

>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=95.00  E-value=0.48  Score=35.54  Aligned_cols=190  Identities=11%  Similarity=0.048  Sum_probs=111.6

Q ss_pred             ccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCc
Q 043380           12 HWKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHP   91 (246)
Q Consensus        12 ~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p   91 (246)
                      ....++..-..++..|-..|.++....+++.....-.++...++.++..|++.+ .++..+.+.....        .+.+
T Consensus        94 ~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~~~~~~~~~~~L~~lyak~~-~~kl~e~l~~~s~--------~y~~  164 (336)
T d1b89a_          94 HIVVHADELEELINYYQDRGYFEELITMLEAALGLERAHMGMFTELAILYSKFK-PQKMREHLELFWS--------RVNI  164 (336)
T ss_dssp             TTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSTTCCHHHHHHHHHHHHTTC-HHHHHHHHHHHST--------TSCH
T ss_pred             HhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcCCccchHHHHHHHHHHHHhC-hHHHHHHHHhccc--------cCCH
Confidence            345566666789999999999999999998765333667778899999999865 3444444433221        1222


Q ss_pred             cHH--------HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhh
Q 043380           92 DIF--------TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRV  163 (246)
Q Consensus        92 ~~~--------~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~  163 (246)
                      ...        .|.-++-.|.+.|+++.|..+.-.      -.++.+-...++..+.+..+.+.    ..++.....+. 
T Consensus       165 ~k~~~~c~~~~l~~elv~Ly~~~~~~~~A~~~~i~------~~~~~~~~~~f~e~~~k~~N~e~----~~~~i~~yL~~-  233 (336)
T d1b89a_         165 PKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMN------HPTDAWKEGQFKDIITKVANVEL----YYRAIQFYLEF-  233 (336)
T ss_dssp             HHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHHHH------STTTTCCHHHHHHHHHHCSSTHH----HHHHHHHHHHH-
T ss_pred             HHHHHHHHHcCChHHHHHHHHhcCCHHHHHHHHHH------cchhhhhHHHHHHHHHccCChHH----HHHHHHHHHHc-
Confidence            211        134455555555555555443221      11233334456666777777777    66666666554 


Q ss_pred             cCCCCCCcchhhHHHHHHHHH-------------hcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChh
Q 043380          164 CSNPGLWPKPHLYVSMMHELA-------------ARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVD  230 (246)
Q Consensus       164 ~~~~~~~p~~~~~~~li~~~~-------------~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~  230 (246)
                            .|  ...+.++....             +.+++......++.....+   . .    ...++|.+.|+..++++
T Consensus       234 ------~p--~~i~~lL~~v~~~~d~~r~V~~~~k~~~l~li~p~Le~v~~~n---~-~----~vn~al~~lyie~~d~~  297 (336)
T d1b89a_         234 ------KP--LLLNDLLMVLSPRLDHTRAVNYFSKVKQLPLVKPYLRSVQNHN---N-K----SVNESLNNLFITEEDYQ  297 (336)
T ss_dssp             ------CG--GGHHHHHHHHGGGCCHHHHHHHHHHTTCTTTTHHHHHHHHTTC---C-H----HHHHHHHHHHHHTTCHH
T ss_pred             ------CH--HHHHHHHHHhccCCCHHHHHHHHHhcCCcHHHHHHHHHHHHcC---h-H----HHHHHHHHHHhCcchhH
Confidence                  23  23344444444             4444444455554443322   1 1    26889999999999876


Q ss_pred             HHHHHHH
Q 043380          231 LALDKLS  237 (246)
Q Consensus       231 ~a~~~~~  237 (246)
                      .-.+.++
T Consensus       298 ~l~~~i~  304 (336)
T d1b89a_         298 ALRTSID  304 (336)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            6554443

>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=94.45  E-value=0.1  Score=31.37  Aligned_cols=52  Identities=21%  Similarity=0.276  Sum_probs=37.6

Q ss_pred             HHhcccCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q 043380            8 VNREHWKLNTIVMNAVIEASREAQRIDEAYQILESVEKGLEPDSLSYNILIS   59 (246)
Q Consensus         8 ~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~t~~~li~   59 (246)
                      +.....-|++.+..+.+.+|-|.+++..|.++|+.++..+.++...|..++.
T Consensus        32 l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~~~~k~~y~yilq   83 (105)
T d1v54e_          32 LVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVIQ   83 (105)
T ss_dssp             HTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHHH
T ss_pred             HhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCcHHHHHHHHH
Confidence            3334477888888888888888888888888888887444455556666544

>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=94.02  E-value=0.31  Score=29.19  Aligned_cols=68  Identities=15%  Similarity=0.199  Sum_probs=54.0

Q ss_pred             HHccC-CHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHH
Q 043380          103 FRHAK-DLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMH  181 (246)
Q Consensus       103 ~~~~~-~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~  181 (246)
                      +.+.. |.-++.+-++.+.. ..+.|++....+-+++|.+.+++..    |.++|+..+.+      ..++...|..++.
T Consensus        15 F~~~~iD~we~rrgmN~l~~-~DlVPeP~Ii~aALrAcRRvND~al----AVR~lE~vK~K------~~~~k~~y~yilq   83 (105)
T d1v54e_          15 FNKPDIDAWELRKGMNTLVG-YDLVPEPKIIDAALRACRRLNDFAS----AVRILEVVKDK------AGPHKEIYPYVIQ   83 (105)
T ss_dssp             HTCTTCCHHHHHHHHHHHTT-SSBCCCHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHH------TTTCTTHHHHHHH
T ss_pred             hcCcCccHHHHHHHHHHHhc-cccCCCcHHHHHHHHHHHHhhhHHH----HHHHHHHHHHH------hcCcHHHHHHHHH
Confidence            34444 66677888888888 8899999999999999999999999    99999999886      4445556666654

>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=93.53  E-value=0.49  Score=29.93  Aligned_cols=139  Identities=10%  Similarity=0.023  Sum_probs=94.1

Q ss_pred             HhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHh
Q 043380           62 IKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLY  141 (246)
Q Consensus        62 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~  141 (246)
                      ...|..++..+++.+...+          .+..-||.++--....-+-+...++++.+-+...+.|              
T Consensus        13 ildG~ve~Gveii~k~~~s----------s~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~FDls~--------------   68 (161)
T d1wy6a1          13 LLDGYIDEGVKIVLEITKS----------STKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDK--------------   68 (161)
T ss_dssp             HHTTCHHHHHHHHHHHHHH----------SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGG--------------
T ss_pred             HHhhhHHhHHHHHHHHccc----------CCccccceeeeecccccchHHHHHHHHHHhhhcCchh--------------
Confidence            3457778888888887764          4566777777777777777777778777766333322              


Q ss_pred             cCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHhcCChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHH
Q 043380          142 SGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAARVDYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLME  221 (246)
Q Consensus       142 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~  221 (246)
                      ++++..    ....+-.+.          .+..-+..-++.+..+|+-++..++.+.+.+.+  .++|.    ..-.+..
T Consensus        69 C~Nlk~----vv~C~~~~n----------~~se~vdlALd~lv~~~kkd~Ld~i~~~l~kn~--~i~~~----~llkia~  128 (161)
T d1wy6a1          69 CQNLKS----VVECGVINN----------TLNEHVNKALDILVIQGKRDKLEEIGREILKNN--EVSAS----ILVAIAN  128 (161)
T ss_dssp             CSCTHH----HHHHHHHTT----------CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC--C--CSCHH----HHHHHHH
T ss_pred             hhcHHH----HHHHHHHhc----------chHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC--CCCHH----HHHHHHH
Confidence            344444    443333221          123345556777788889899999988876643  35555    3566888


Q ss_pred             HHHhcCChhHHHHHHHHHHhhcc
Q 043380          222 AALNDGQVDLALDKLSNTITRWK  244 (246)
Q Consensus       222 ~~~~~g~~~~a~~~~~~m~~~g~  244 (246)
                      +|-+-|...++-+++.+..++|.
T Consensus       129 A~kkig~~re~nell~~ACe~G~  151 (161)
T d1wy6a1         129 ALRRVGDERDATTLLIEACKKGE  151 (161)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHhcchhhHHHHHHHHHHHhH
Confidence            99999999999999999888873

>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=92.48  E-value=0.24  Score=31.24  Aligned_cols=70  Identities=9%  Similarity=0.042  Sum_probs=49.8

Q ss_pred             cchhhHHHHHHHHHhcC---ChhHHhhHHHhhCCCCCCCCCchhhhHHHHHHHHHHHhcCChhHHHHHHHHHHhhccC
Q 043380          171 PKPHLYVSMMHELAARV---DYDIVKSPYRRMWPDSTGTISPEVQEEAGHLLMEAALNDGQVDLALDKLSNTITRWKG  245 (246)
Q Consensus       171 p~~~~~~~li~~~~~~g---~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~  245 (246)
                      |+..|--....++.++.   +++++..+|+++...+     |...+..+..|.-+|.+.|++++|.++++.+.+..++
T Consensus        33 ~s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~~~~~-----p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~ieP~  105 (124)
T d2pqrb1          33 ATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEA-----ESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHERN  105 (124)
T ss_dssp             SCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHC-----GGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT
T ss_pred             CCcchHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcC-----chhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHccCCC
Confidence            44455555666666554   5678999999987532     2222236677888899999999999999999876653

>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=91.82  E-value=0.9  Score=28.70  Aligned_cols=60  Identities=20%  Similarity=0.059  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHhcCChhhhhhHHHHHHHHHH
Q 043380           95 TYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLYSGSIKVVGLYALCIFGEIV  160 (246)
Q Consensus        95 ~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~~~~~~~~~~a~~~~~~m~  160 (246)
                      .++..++...+.|+-++-.++++.+.+ . -.|++...-.+..+|.+.|+..+    +.+++.+.-
T Consensus        88 ~vdlALd~lv~~~kkd~Ld~i~~~l~k-n-~~i~~~~llkia~A~kkig~~re----~nell~~AC  147 (161)
T d1wy6a1          88 HVNKALDILVIQGKRDKLEEIGREILK-N-NEVSASILVAIANALRRVGDERD----ATTLLIEAC  147 (161)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHC----CCSCHHHHHHHHHHHHHTTCHHH----HHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHh-c-CCCCHHHHHHHHHHHHHhcchhh----HHHHHHHHH
Confidence            444555555555555555555555444 2 23444445555555555555555    555555443

>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=90.78  E-value=0.81  Score=28.69  Aligned_cols=68  Identities=12%  Similarity=0.036  Sum_probs=48.8

Q ss_pred             cCcCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhCCCCCH-HHHHHHHHHHHhcCCcchHHHHHHHHHhc
Q 043380           13 WKLNTIVMNAVIEASREAQ---RIDEAYQILESVEKGLEPDS-LSYNILISACIKTKKLDVTMPFNEQLKDN   80 (246)
Q Consensus        13 ~~~~~~~~~~li~~~~~~g---~~~~a~~~~~~~~~~~~~~~-~t~~~li~~~~~~~~~~~a~~~~~~m~~~   80 (246)
                      ..|++.+-=...-+++++.   ++++++.+|+.+.++.+.+. ..+-.|--+|.+.|++++|.+.++.+.+.
T Consensus        31 ~~~s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~~~~~p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~i  102 (124)
T d2pqrb1          31 PTATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEH  102 (124)
T ss_dssp             GGSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             CCCCcchHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHcc
Confidence            3455555445555666554   46789999988764333343 46667778899999999999999999986

>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=90.46  E-value=2  Score=30.15  Aligned_cols=95  Identities=14%  Similarity=0.033  Sum_probs=61.8

Q ss_pred             CHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHc----cCCHHHHHHHHHHHHhCCCC
Q 043380           50 DSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRH----AKDLQSLLEIVFEMKSCCNL  125 (246)
Q Consensus        50 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~----~~~~~~a~~~~~~m~~~~~~  125 (246)
                      |+..+..|-..+.+.+++++|.++|++..+.       |   +...+..|-..|..    ..+...|...+..... .+ 
T Consensus         1 ~p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~-------g---~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~-~~-   68 (265)
T d1ouva_           1 DPKELVGLGAKSYKEKDFTQAKKYFEKACDL-------K---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACD-LN-   68 (265)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT-------T---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHH-TT-
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHC-------C---CHHHHHHHHHHHHcCCCcchhHHHHHHhhccccc-cc-
Confidence            4556667777788899999999999999886       3   33444455555654    5688888888888777 43 


Q ss_pred             CCCHHHHHHHHHHHHh----cCChhhhhhHHHHHHHHHHHh
Q 043380          126 ILDRSTFTAMVDALLY----SGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       126 ~p~~~~~~~li~~~~~----~~~~~~~~~~a~~~~~~m~~~  162 (246)
                        +......+...+..    ..+.+.    |...++.....
T Consensus        69 --~~~a~~~l~~~~~~~~~~~~~~~~----a~~~~~~a~~~  103 (265)
T d1ouva_          69 --YSNGCHLLGNLYYSGQGVSQNTNK----ALQYYSKACDL  103 (265)
T ss_dssp             --CHHHHHHHHHHHHHTSSSCCCHHH----HHHHHHHHHHT
T ss_pred             --ccchhhccccccccccccchhhHH----HHHHHhhhhhh
Confidence              23333344333333    344555    77766665543

>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=87.15  E-value=2.2  Score=26.54  Aligned_cols=108  Identities=7%  Similarity=-0.035  Sum_probs=64.7

Q ss_pred             CcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHccCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHh----
Q 043380           66 KLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRHAKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLY----  141 (246)
Q Consensus        66 ~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~----  141 (246)
                      ++++|.++|.+..+.       |. |.  ....|  +.....+.++|...+++..+ .|   ++..+..|-..|..    
T Consensus         8 d~~~A~~~~~kaa~~-------g~-~~--a~~~l--~~~~~~~~~~a~~~~~~aa~-~g---~~~a~~~Lg~~y~~g~~~   71 (133)
T d1klxa_           8 DLKKAIQYYVKACEL-------NE-MF--GCLSL--VSNSQINKQKLFQYLSKACE-LN---SGNGCRFLGDFYENGKYV   71 (133)
T ss_dssp             HHHHHHHHHHHHHHT-------TC-TT--HHHHH--HTCTTSCHHHHHHHHHHHHH-TT---CHHHHHHHHHHHHHCSSS
T ss_pred             CHHHHHHHHHHHHHC-------CC-hh--hhhhh--ccccccCHHHHHHHHhhhhc-cc---chhhhhhHHHhhhhcccc
Confidence            567888888888776       32 22  12222  22345678888888888877 54   34455555555554    


Q ss_pred             cCChhhhhhHHHHHHHHHHHhhcCCCCCCcchhhHHHHHHHHHh----cCChhHHhhHHHhhCC
Q 043380          142 SGSIKVVGLYALCIFGEIVKRVCSNPGLWPKPHLYVSMMHELAA----RVDYDIVKSPYRRMWP  201 (246)
Q Consensus       142 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~  201 (246)
                      ..+.+.    |.++|+...+.     |   ++.....|-..|..    ..+.++|.++|+..-+
T Consensus        72 ~~d~~~----A~~~~~~aa~~-----g---~~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~  123 (133)
T d1klxa_          72 KKDLRK----AAQYYSKACGL-----N---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACR  123 (133)
T ss_dssp             CCCHHH----HHHHHHHHHHT-----T---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHH
T ss_pred             chhhHH----HHHHHhhhhcc-----C---cchHHHHHHHHHHcCCccCCCHHHHHHHHHHHHH
Confidence            445677    88888888775     3   23334444444443    3467777777776543

>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=82.66  E-value=3.8  Score=25.37  Aligned_cols=109  Identities=11%  Similarity=-0.005  Sum_probs=71.0

Q ss_pred             CCHHHHHHHHHHHH-hCCCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHhccCCCCCCCCCccHHHHHHHHHHHHc----
Q 043380           31 QRIDEAYQILESVE-KGLEPDSLSYNILISACIKTKKLDVTMPFNEQLKDNGQKCSSGGFHPDIFTYATLLMGFRH----  105 (246)
Q Consensus        31 g~~~~a~~~~~~~~-~~~~~~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~p~~~~~~~ll~~~~~----  105 (246)
                      .++++|.++|++.- .|   +......|.  .....+.++|.+++++..+.       |   +......|-..|..    
T Consensus         7 kd~~~A~~~~~kaa~~g---~~~a~~~l~--~~~~~~~~~a~~~~~~aa~~-------g---~~~a~~~Lg~~y~~g~~~   71 (133)
T d1klxa_           7 KDLKKAIQYYVKACELN---EMFGCLSLV--SNSQINKQKLFQYLSKACEL-------N---SGNGCRFLGDFYENGKYV   71 (133)
T ss_dssp             HHHHHHHHHHHHHHHTT---CTTHHHHHH--TCTTSCHHHHHHHHHHHHHT-------T---CHHHHHHHHHHHHHCSSS
T ss_pred             cCHHHHHHHHHHHHHCC---Chhhhhhhc--cccccCHHHHHHHHhhhhcc-------c---chhhhhhHHHhhhhcccc
Confidence            36788999998764 43   222233332  23345778999999998886       3   23334444444432    


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHh----cCChhhhhhHHHHHHHHHHHh
Q 043380          106 AKDLQSLLEIVFEMKSCCNLILDRSTFTAMVDALLY----SGSIKVVGLYALCIFGEIVKR  162 (246)
Q Consensus       106 ~~~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~----~~~~~~~~~~a~~~~~~m~~~  162 (246)
                      ..|.++|.+.|++..+ .|   ++.....|-..|..    ..+.+.    |.++|+...+.
T Consensus        72 ~~d~~~A~~~~~~aa~-~g---~~~a~~~Lg~~y~~G~gv~~d~~~----A~~~~~~Aa~~  124 (133)
T d1klxa_          72 KKDLRKAAQYYSKACG-LN---DQDGCLILGYKQYAGKGVVKNEKQ----AVKTFEKACRL  124 (133)
T ss_dssp             CCCHHHHHHHHHHHHH-TT---CHHHHHHHHHHHHHTSSSCCCHHH----HHHHHHHHHHT
T ss_pred             chhhHHHHHHHhhhhc-cC---cchHHHHHHHHHHcCCccCCCHHH----HHHHHHHHHHC
Confidence            4578999999999988 55   34455556555555    457788    99999887776