Citrus Sinensis ID: 039275

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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---
Protein Sequence
MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKSNIFLTTAIIEMYAKM
Secondary Structure (PSIPRED)
ccHHHHccccccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHccccccccccccHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHcccccHHHHHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHccccHHHHHHHHHHHHHccccccccHHHHHHHHHHHHcHHHHHHHHHHccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccccHHHHHHHHHHHHccHHcccccEHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
misgysqagrfnealepfgkleslgvhtdeVTMVVVLTASSGPGAWILAKELQIELDlssyslssktsryahsgrirlardpvsCKAMISGYSqagrfnealepfgkleslgvhtdeVTMVVVLAAssgpgaldfgksnIFLTTAIIEMYAKM
Flexible Loop (DISEMBL)
MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIELDLSSyslssktsryahsgrirlardpvSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASsgpgaldfgksnIFLTTAIIEMYAKM
Low Complexity Region (SEG)
MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIEldlssyslssktsRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKSNIFLTTAIIEMYAKM
Disordered region (IsUnstruct)
***************EPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIELDLSSYSL*****RYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKSNIFLTTAIIEMY***
Disordered Region (DISOPRED)
MISGYS*AGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKSNIFLTTAIIEMYAKM
Disordered Region (DISEMBL)
MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKSNIFLTTAIIEMYAKM
Disordered Region (DISPRO)
MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKSNIFLTTAIIEMYAKM
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKSNIFLTTAIIEMYAKM
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	153	2.2.26 [Sep-21-2011]
O64705	621	Pentatricopeptide repeat-	yes	no	0.993	0.244	0.353	8e-16
Q9SR82	685	Putative pentatricopeptid	no	no	0.993	0.221	0.286	3e-14
Q9LN01	741	Pentatricopeptide repeat-	no	no	0.993	0.205	0.288	2e-13
Q9LIC3	628	Putative pentatricopeptid	no	no	0.993	0.242	0.337	8e-13
Q9LSB8	687	Putative pentatricopeptid	no	no	0.993	0.221	0.282	4e-12
Q3ECB8	467	Pentatricopeptide repeat-	no	no	0.973	0.319	0.321	8e-12
Q9FMA1	530	Pentatricopeptide repeat-	no	no	0.895	0.258	0.324	1e-11
Q9LW63	715	Putative pentatricopeptid	no	no	0.993	0.212	0.303	4e-11
Q9MA95	565	Putative pentatricopeptid	no	no	0.993	0.269	0.290	1e-10
Q9FIF7	544	Putative pentatricopeptid	no	no	0.888	0.25	0.313	2e-10

>sp|O64705|PP184_ARATH Pentatricopeptide repeat-containing protein At2g34400 OS=Arabidopsis thaliana GN=PCMP-E23 PE=3 SV=2

 Score = 82.8 bits (203), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 63/178 (35%), Positives = 92/178 (51%), Gaps = 26/178 (14%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWI---LAKELQI--E 55
           MISGYS+AG   +A++ F K+E  G   DE T+V +L A S  G      L +E+ I  +
Sbjct: 204 MISGYSEAGYAKDAMDLFRKMEEEGFEPDERTLVSMLGACSHLGDLRTGRLLEEMAITKK 263

Query: 56  LDLSSYSLSSKTSRYAHSGRIRLAR---------DPVSCKAMISGYSQAGRFNEALEPFG 106
           + LS++  S   S Y   G +  AR         D V+  AMI+ YSQ G+ +EA + F 
Sbjct: 264 IGLSTFLGSKLISMYGKCGDLDSARRVFNQMIKKDRVAWTAMITVYSQNGKSSEAFKLFF 323

Query: 107 KLESLGVHTDEVTMVVVLAASSGPGALDFGKS------------NIFLTTAIIEMYAK 152
           ++E  GV  D  T+  VL+A    GAL+ GK             NI++ T +++MY K
Sbjct: 324 EMEKTGVSPDAGTLSTVLSACGSVGALELGKQIETHASELSLQHNIYVATGLVDMYGK 381

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SR82|PP219_ARATH Putative pentatricopeptide repeat-containing protein At3g08820 OS=Arabidopsis thaliana GN=PCMP-H84 PE=3 SV=1

 Score = 77.4 bits (189), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 51/178 (28%), Positives = 89/178 (50%), Gaps = 26/178 (14%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASS-----GPGAWILAKELQIE 55
           + SGY+ +GR  EA++ F K+  +GV  D   +V VL+A         G WI+    ++E
Sbjct: 183 LFSGYTTSGRHREAIDLFKKMVEMGVKPDSYFIVQVLSACVHVGDLDSGEWIVKYMEEME 242

Query: 56  LDLSSYSLSSKTSRYAHSGRIRLAR---------DPVSCKAMISGYSQAGRFNEALEPFG 106
           +  +S+  ++  + YA  G++  AR         D V+   MI GY+      E +E F 
Sbjct: 243 MQKNSFVRTTLVNLYAKCGKMEKARSVFDSMVEKDIVTWSTMIQGYASNSFPKEGIELFL 302

Query: 107 KLESLGVHTDEVTMVVVLAASSGPGALDFGK------------SNIFLTTAIIEMYAK 152
           ++    +  D+ ++V  L++ +  GALD G+            +N+F+  A+I+MYAK
Sbjct: 303 QMLQENLKPDQFSIVGFLSSCASLGALDLGEWGISLIDRHEFLTNLFMANALIDMYAK 360

Arabidopsis thaliana (taxid: 3702)

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

 Score = 74.7 bits (182), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 52/180 (28%), Positives = 89/180 (49%), Gaps = 28/180 (15%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIELDLSS 60
           MISGY++ G + EALE F  +    V  DE TMV V++A +  G+  L +++ + +D   
Sbjct: 237 MISGYAETGNYKEALELFKDMMKTNVRPDESTMVTVVSACAQSGSIELGRQVHLWIDDHG 296

Query: 61  YSLSSKTSR-----YAHSGRIRLA---------RDPVSCKAMISGYSQAGRFNEALEPFG 106
           +  + K        Y+  G +  A         +D +S   +I GY+    + EAL  F 
Sbjct: 297 FGSNLKIVNALIDLYSKCGELETACGLFERLPYKDVISWNTLIGGYTHMNLYKEALLLFQ 356

Query: 107 KLESLGVHTDEVTMVVVLAASSGPGALDFGKS-NIF-------------LTTAIIEMYAK 152
           ++   G   ++VTM+ +L A +  GA+D G+  +++             L T++I+MYAK
Sbjct: 357 EMLRSGETPNDVTMLSILPACAHLGAIDIGRWIHVYIDKRLKGVTNASSLRTSLIDMYAK 416

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LIC3|PP227_ARATH Putative pentatricopeptide repeat-containing protein At3g13770, mitochondrial OS=Arabidopsis thaliana GN=PCMP-H85 PE=3 SV=1

 Score = 72.8 bits (177), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 60/178 (33%), Positives = 85/178 (47%), Gaps = 26/178 (14%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQ---IELD 57
           MIS YSQ G  +EAL  F ++       +E T   VLT+        L K++    ++ +
Sbjct: 124 MISRYSQTGHSSEALTVFAEMMRSDGKPNEFTFATVLTSCIRASGLGLGKQIHGLIVKWN 183

Query: 58  LSSYSL--SSKTSRYAHSGRIRLAR---------DPVSCKAMISGYSQAGRFNEALEPFG 106
             S+    SS    YA +G+I+ AR         D VSC A+I+GY+Q G   EALE F 
Sbjct: 184 YDSHIFVGSSLLDMYAKAGQIKEAREIFECLPERDVVSCTAIIAGYAQLGLDEEALEMFH 243

Query: 107 KLESLGVHTDEVTMVVVLAASSGPGALDFGKSN------------IFLTTAIIEMYAK 152
           +L S G+  + VT   +L A SG   LD GK                L  ++I+MY+K
Sbjct: 244 RLHSEGMSPNYVTYASLLTALSGLALLDHGKQAHCHVLRRELPFYAVLQNSLIDMYSK 301

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LSB8|PP235_ARATH Putative pentatricopeptide repeat-containing protein At3g15930 OS=Arabidopsis thaliana GN=PCMP-E51 PE=3 SV=2

 Score = 70.5 bits (171), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 59/209 (28%), Positives = 93/209 (44%), Gaps = 57/209 (27%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQI------ 54
           MISGY++   + E++E   ++E   V    VT+++VL+A S      L K +        
Sbjct: 207 MISGYNRMKEYEESIELLVEMERNLVSPTSVTLLLVLSACSKVKDKDLCKRVHEYVSECK 266

Query: 55  -------------------ELDLSSYSLSSKTSR-----------YAHSGRIRLAR---- 80
                              E+D++     S  +R           Y   G ++LAR    
Sbjct: 267 TEPSLRLENALVNAYAACGEMDIAVRIFRSMKARDVISWTSIVKGYVERGNLKLARTYFD 326

Query: 81  -----DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDF 135
                D +S   MI GY +AG FNE+LE F +++S G+  DE TMV VL A +  G+L+ 
Sbjct: 327 QMPVRDRISWTIMIDGYLRAGCFNESLEIFREMQSAGMIPDEFTMVSVLTACAHLGSLEI 386

Query: 136 G------------KSNIFLTTAIIEMYAK 152
           G            K+++ +  A+I+MY K
Sbjct: 387 GEWIKTYIDKNKIKNDVVVGNALIDMYFK 415

Arabidopsis thaliana (taxid: 3702)

>sp|Q3ECB8|PP128_ARATH Pentatricopeptide repeat-containing protein At1g77170 OS=Arabidopsis thaliana GN=PCMP-E21 PE=2 SV=1

 Score = 69.3 bits (168), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 53/165 (32%), Positives = 80/165 (48%), Gaps = 16/165 (9%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-------Q 53
           +I G + AGR NEA+E F  ++  G+  D+ TMV V  +  G G   LA +L       +
Sbjct: 189 IIGGLNHAGRANEAVEMFVDMKRSGLEPDDFTMVSVTASCGGLGDLSLAFQLHKCVLQAK 248

Query: 54  IELDLSSYSLSSKTSRYAHSGRIRLA---------RDPVSCKAMISGYSQAGRFNEALEP 104
            E       L+S    Y   GR+ LA         R+ VS  +MI GY+  G   EALE 
Sbjct: 249 TEEKSDIMMLNSLIDMYGKCGRMDLASHIFEEMRQRNVVSWSSMIVGYAANGNTLEALEC 308

Query: 105 FGKLESLGVHTDEVTMVVVLAASSGPGALDFGKSNIFLTTAIIEM 149
           F ++   GV  +++T V VL+A    G ++ GK+   +  +  E+
Sbjct: 309 FRQMREFGVRPNKITFVGVLSACVHGGLVEEGKTYFAMMKSEFEL 353

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FMA1|PP433_ARATH Pentatricopeptide repeat-containing protein At5g56310 OS=Arabidopsis thaliana GN=PCMP-E13 PE=2 SV=1

 Score = 68.9 bits (167), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 49/151 (32%), Positives = 79/151 (52%), Gaps = 14/151 (9%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIELDL-- 58
           +ISGY+++GR +EA+E F ++    V  DEVT++ VL+A +  G+  L + +   +D   
Sbjct: 221 VISGYAKSGRASEAIEVFQRMLMENVEPDEVTLLAVLSACADLGSLELGERICSYVDHRG 280

Query: 59  --SSYSLSSKT-SRYAHSGRIRLARDPVSC---------KAMISGYSQAGRFNEALEPFG 106
              + SL++     YA SG I  A D   C           +I+G +  G   EAL  F 
Sbjct: 281 MNRAVSLNNAVIDMYAKSGNITKALDVFECVNERNVVTWTTIIAGLATHGHGAEALAMFN 340

Query: 107 KLESLGVHTDEVTMVVVLAASSGPGALDFGK 137
           ++   GV  ++VT + +L+A S  G +D GK
Sbjct: 341 RMVKAGVRPNDVTFIAILSACSHVGWVDLGK 371

Arabidopsis thaliana (taxid: 3702)

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

 Score = 67.0 bits (162), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 54/178 (30%), Positives = 85/178 (47%), Gaps = 26/178 (14%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-----QIE 55
           +I+GY+Q+G + +AL    ++ +  +  D  T+  VL   S     I  KE+     +  
Sbjct: 213 IIAGYAQSGMYEDALRMVREMGTTDLKPDSFTLSSVLPIFSEYVDVIKGKEIHGYVIRKG 272

Query: 56  LDLSSYSLSSKTSRYAHSGRI--------RL-ARDPVSCKAMISGYSQAGRFNEALEPFG 106
           +D   Y  SS    YA S RI        RL  RD +S  ++++GY Q GR+NEAL  F 
Sbjct: 273 IDSDVYIGSSLVDMYAKSARIEDSERVFSRLYCRDGISWNSLVAGYVQNGRYNEALRLFR 332

Query: 107 KLESLGVHTDEVTMVVVLAASSGPGALDFGK------------SNIFLTTAIIEMYAK 152
           ++ +  V    V    V+ A +    L  GK            SNIF+ +A+++MY+K
Sbjct: 333 QMVTAKVKPGAVAFSSVIPACAHLATLHLGKQLHGYVLRGGFGSNIFIASALVDMYSK 390

Arabidopsis thaliana (taxid: 3702)

>sp|Q9MA95|PP214_ARATH Putative pentatricopeptide repeat-containing protein At3g05240 OS=Arabidopsis thaliana GN=PCMP-E82 PE=3 SV=2

 Score = 65.1 bits (157), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 54/186 (29%), Positives = 82/186 (44%), Gaps = 34/186 (18%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSG-----PGAWI-------- 47
           +ISG+    RF++A+E F +++S GV  +E  MV +L A         G W         
Sbjct: 179 LISGFVNNNRFSDAIEAFREMQSNGVKANETIMVDLLVACGRCKDIVTGKWFHGFLQGLG 238

Query: 48  LAKELQIELDLSSYSLSSKTSRYAHSGRIRLAR---------DPVSCKAMISGYSQAGRF 98
                Q ++  +    +S    YA  G +R AR           VS  ++I+GYSQ G  
Sbjct: 239 FDPYFQSKVGFNVILATSLIDMYAKCGDLRTARYLFDGMPERTLVSWNSIITGYSQNGDA 298

Query: 99  NEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS------------NIFLTTAI 146
            EAL  F  +  LG+  D+VT + V+ AS   G    G+S            +  +  A+
Sbjct: 299 EEALCMFLDMLDLGIAPDKVTFLSVIRASMIQGCSQLGQSIHAYVSKTGFVKDAAIVCAL 358

Query: 147 IEMYAK 152
           + MYAK
Sbjct: 359 VNMYAK 364

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FIF7|PP435_ARATH Putative pentatricopeptide repeat-containing protein At5g59200, chloroplastic OS=Arabidopsis thaliana GN=PCMP-E41 PE=3 SV=1

 Score = 64.3 bits (155), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 47/150 (31%), Positives = 73/150 (48%), Gaps = 14/150 (9%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGA-----WILAKELQIE 55
           MI G  +    N+ALE F +++   V  +E T V VL+A S  GA     W+ +      
Sbjct: 226 MIDGLVRNKEMNKALELFREMQMENVSANEFTAVCVLSACSDLGALELGRWVHSFVENQR 285

Query: 56  LDLSSYSLSSKTSRYAHSGRIRLAR---------DPVSCKAMISGYSQAGRFNEALEPFG 106
           ++LS++  ++  + Y+  G I  AR         D +S   MISG +  G   EA+  F 
Sbjct: 286 MELSNFVGNALINMYSRCGDINEARRVFRVMRDKDVISYNTMISGLAMHGASVEAINEFR 345

Query: 107 KLESLGVHTDEVTMVVVLAASSGPGALDFG 136
            + + G   ++VT+V +L A S  G LD G
Sbjct: 346 DMVNRGFRPNQVTLVALLNACSHGGLLDIG 375

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	153
225446273	618	PREDICTED: pentatricopeptide repeat-cont	0.993	0.245	0.365	2e-19
224119830	617	predicted protein [Populus trichocarpa]	0.993	0.246	0.353	3e-17
356498444	634	PREDICTED: putative pentatricopeptide re	0.993	0.239	0.365	4e-16
297606175	590	Os06g0613100 [Oryza sativa Japonica Grou	0.993	0.257	0.365	5e-16
125597850	583	hypothetical protein OsJ_21964 [Oryza sa	0.993	0.260	0.365	6e-16
51090919	615	selenium-binding protein-like [Oryza sat	0.993	0.247	0.365	6e-16
125556054	252	hypothetical protein OsI_23695 [Oryza sa	0.954	0.579	0.393	6e-16
255582620	446	pentatricopeptide repeat-containing prot	0.993	0.340	0.325	1e-15
225441187	722	PREDICTED: pentatricopeptide repeat-cont	0.993	0.210	0.309	2e-15
356553819	608	PREDICTED: pentatricopeptide repeat-cont	0.993	0.25	0.346	1e-14

>gi|225446273|ref|XP_002266689.1| PREDICTED: pentatricopeptide repeat-containing protein At2g34400 [Vitis vinifera] gi|296090299|emb|CBI40118.3| unnamed protein product [Vitis vinifera]

 Score =  100 bits (249), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 65/178 (36%), Positives = 100/178 (56%), Gaps = 26/178 (14%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASS-----GPGAWILAKELQIE 55
           MISGYS+ G   +A+  FG++   G   DE+T+V +L A       G G+WI    ++ E
Sbjct: 198 MISGYSRMGYAGDAVGLFGEMRDAGFEPDEMTLVSILGACGDLGDLGLGSWIEGFVVENE 257

Query: 56  LDLSSYSLSSKTSRYAHSGRIRLAR---------DPVSCKAMISGYSQAGRFNEALEPFG 106
           +DL+S+  S+    Y   G +  AR         D V+  AMI+GY+Q G  +EA+  F 
Sbjct: 258 MDLNSFVGSALIGMYGKCGDLSSARRVFDRMVKKDVVTWNAMITGYAQNGVSDEAIILFS 317

Query: 107 KLESLGVHTDEVTMVVVLAASSGPGALDFGK------------SNIFLTTAIIEMYAK 152
            +   GV+ D++T+V VL+A +  GALDFGK            ++I+++TA+I+MYAK
Sbjct: 318 GMRESGVNPDKITLVGVLSACASIGALDFGKWLDTYASERGLQNDIYVSTALIDMYAK 375

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224119830|ref|XP_002318172.1| predicted protein [Populus trichocarpa] gi|222858845|gb|EEE96392.1| predicted protein [Populus trichocarpa]

 Score = 93.2 bits (230), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 63/178 (35%), Positives = 93/178 (52%), Gaps = 26/178 (14%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASS-----GPGAWILAKELQIE 55
           MISGYS+ G   EA+  F ++   G   DE+T+V VL A       G G W+    L+ +
Sbjct: 200 MISGYSKMGFTKEAIGLFMEMREEGFEPDEMTLVSVLGACGDLGDLGLGRWVEGFVLEKK 259

Query: 56  LDLSSYSLSSKTSRYAHSGRIRLAR---------DPVSCKAMISGYSQAGRFNEALEPFG 106
           ++++SY  S+    Y   G +  AR         D V+  A+I+GY+Q G  NEA+  F 
Sbjct: 260 MEVNSYMGSALIDMYGKCGDLISARRVFDSMPNKDVVTWNAIITGYAQNGASNEAIVLFN 319

Query: 107 KLESLGVHTDEVTMVVVLAASSGPGALDFGK------------SNIFLTTAIIEMYAK 152
            +   G H D VTM+ VL+A S  GALD GK             ++++ +A+I+MYAK
Sbjct: 320 GMREAGPHPDRVTMIEVLSACSTIGALDLGKWVETHASEKGLQHDVYVASALIDMYAK 377

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356498444|ref|XP_003518062.1| PREDICTED: putative pentatricopeptide repeat-containing protein At3g13770, mitochondrial-like [Glycine max]

 Score = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 65/178 (36%), Positives = 92/178 (51%), Gaps = 26/178 (14%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQ---IELD 57
           MIS YSQ G  ++AL  F ++   G   +E T   VLT+  G   ++L +++    I+L+
Sbjct: 130 MISAYSQRGYASQALSLFVQMLRSGTEPNEFTFATVLTSCIGSSGFVLGRQIHSHIIKLN 189

Query: 58  LSS--YSLSSKTSRYAHSGRIRLAR---------DPVSCKAMISGYSQAGRFNEALEPFG 106
             +  Y  SS    YA  G+I  AR         D VSC A+ISGY+Q G   EALE F 
Sbjct: 190 YEAHVYVGSSLLDMYAKDGKIHEARGIFQCLPERDVVSCTAIISGYAQLGLDEEALELFR 249

Query: 107 KLESLGVHTDEVTMVVVLAASSGPGALDFGK------------SNIFLTTAIIEMYAK 152
           +L+  G+ ++ VT   VL A SG  ALD GK            S + L  ++I+MY+K
Sbjct: 250 RLQREGMQSNYVTYTSVLTALSGLAALDHGKQVHNHLLRSEVPSYVVLQNSLIDMYSK 307

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297606175|ref|NP_001058069.2| Os06g0613100 [Oryza sativa Japonica Group] gi|255677226|dbj|BAF19983.2| Os06g0613100 [Oryza sativa Japonica Group]

 Score = 89.0 bits (219), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 65/178 (36%), Positives = 92/178 (51%), Gaps = 26/178 (14%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKE---LQIELD 57
           MISGYSQ  R  EAL+ F K+   G   +E T+  VLT+ SGP +    K+   L ++ +
Sbjct: 82  MISGYSQTERHVEALDLFIKMLRAGCIPNEYTLATVLTSCSGPQSIYQGKQVHSLLVKTN 141

Query: 58  LSSYSL--SSKTSRYAHSGRIRLAR---------DPVSCKAMISGYSQAGRFNEALEPFG 106
             S+    SS    YA S  I+ AR         D VSC A+ISGY+Q G   EAL+ F 
Sbjct: 142 FESHMFVGSSLLDMYAKSENIQEARRVFDTLPERDVVSCTAIISGYAQKGLDEEALDLFR 201

Query: 107 KLESLGVHTDEVTMVVVLAASSGPGALDFGKSN------------IFLTTAIIEMYAK 152
           +L S G+  + VT   ++ A SG  +LD+GK              + L  ++I+MY+K
Sbjct: 202 QLYSEGMQCNHVTFTTLVTALSGLASLDYGKQVHALILRKELPFFVALQNSLIDMYSK 259

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125597850|gb|EAZ37630.1| hypothetical protein OsJ_21964 [Oryza sativa Japonica Group]

 Score = 89.0 bits (219), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 65/178 (36%), Positives = 92/178 (51%), Gaps = 26/178 (14%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKE---LQIELD 57
           MISGYSQ  R  EAL+ F K+   G   +E T+  VLT+ SGP +    K+   L ++ +
Sbjct: 82  MISGYSQTERHVEALDLFIKMLRAGCIPNEYTLATVLTSCSGPQSIYQGKQVHSLLVKTN 141

Query: 58  LSSYSL--SSKTSRYAHSGRIRLAR---------DPVSCKAMISGYSQAGRFNEALEPFG 106
             S+    SS    YA S  I+ AR         D VSC A+ISGY+Q G   EAL+ F 
Sbjct: 142 FESHMFVGSSLLDMYAKSENIQEARRVFDTLPERDVVSCTAIISGYAQKGLDEEALDLFR 201

Query: 107 KLESLGVHTDEVTMVVVLAASSGPGALDFGKS------------NIFLTTAIIEMYAK 152
           +L S G+  + VT   ++ A SG  +LD+GK              + L  ++I+MY+K
Sbjct: 202 QLYSEGMQCNHVTFTTLVTALSGLASLDYGKQVHALILRKELPFFVALQNSLIDMYSK 259

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|51090919|dbj|BAD35524.1| selenium-binding protein-like [Oryza sativa Japonica Group] gi|51090953|dbj|BAD35556.1| selenium-binding protein-like [Oryza sativa Japonica Group]

 Score = 89.0 bits (219), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 65/178 (36%), Positives = 92/178 (51%), Gaps = 26/178 (14%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKE---LQIELD 57
           MISGYSQ  R  EAL+ F K+   G   +E T+  VLT+ SGP +    K+   L ++ +
Sbjct: 114 MISGYSQTERHVEALDLFIKMLRAGCIPNEYTLATVLTSCSGPQSIYQGKQVHSLLVKTN 173

Query: 58  LSSYSL--SSKTSRYAHSGRIRLAR---------DPVSCKAMISGYSQAGRFNEALEPFG 106
             S+    SS    YA S  I+ AR         D VSC A+ISGY+Q G   EAL+ F 
Sbjct: 174 FESHMFVGSSLLDMYAKSENIQEARRVFDTLPERDVVSCTAIISGYAQKGLDEEALDLFR 233

Query: 107 KLESLGVHTDEVTMVVVLAASSGPGALDFGKS------------NIFLTTAIIEMYAK 152
           +L S G+  + VT   ++ A SG  +LD+GK              + L  ++I+MY+K
Sbjct: 234 QLYSEGMQCNHVTFTTLVTALSGLASLDYGKQVHALILRKELPFFVALQNSLIDMYSK 291

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125556054|gb|EAZ01660.1| hypothetical protein OsI_23695 [Oryza sativa Indica Group]

 Score = 89.0 bits (219), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 65/165 (39%), Positives = 87/165 (52%), Gaps = 19/165 (11%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKE---LQIELD 57
           MISGYSQ  R  EAL+ F K+   G   +E T+  VLT+ SGP +    K+   L ++ +
Sbjct: 82  MISGYSQTERHVEALDLFIKMLRAGCIPNEYTLATVLTSCSGPQSIYQGKQVHSLLVKTN 141

Query: 58  LSSYSL--SSKTSRYAHSGRIRLAR---------DPVSCKAMISGYSQAGRFNEALEPFG 106
             S+    SS    YA S  I+ AR         D VSC A+ISGY+Q G   EAL+ F 
Sbjct: 142 FESHMFVGSSLLDMYAKSENIQEARRVFDTLPERDVVSCTAIISGYAQKGLDEEALDLFR 201

Query: 107 KLESLGVHTDEVTMVVVLAASSGPGALDFGK-----SNIFLTTAI 146
           +L S G+  + VT   ++ A SG  +LD+GK     S IFL   I
Sbjct: 202 QLYSEGMQCNHVTFTTLVTALSGLASLDYGKQTEDWSMIFLIQVI 246

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255582620|ref|XP_002532091.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis] gi|223528238|gb|EEF30293.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis]

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 58/178 (32%), Positives = 93/178 (52%), Gaps = 26/178 (14%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASS-----GPGAWILAKELQIE 55
           MISGY++ G   EA+  F ++   G    E+T+V +L A         G W+ A     +
Sbjct: 199 MISGYTKMGFAREAVRLFMEMREQGFEPVEMTLVSILGACGDLGDLALGKWVEALIGDKK 258

Query: 56  LDLSSYSLSSKTSRYAHSGRIRLAR---------DPVSCKAMISGYSQAGRFNEALEPFG 106
           ++L+SY+ S+    Y   G +  AR         D V+  AMI+GY+Q G  +EA+  F 
Sbjct: 259 MELNSYTASALIDMYGKCGDLMSARRVFDNMAEKDIVTWNAMITGYAQNGASDEAMTLFN 318

Query: 107 KLESLGVHTDEVTMVVVLAASSGPGALDFGK------------SNIFLTTAIIEMYAK 152
            +   G+  +E+TMVVVL+A +  GALD GK             ++++ +A+++MYAK
Sbjct: 319 VMREAGITPNEITMVVVLSACASIGALDLGKWVEMYASQRGLQHDVYVASALVDMYAK 376

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225441187|ref|XP_002266244.1| PREDICTED: pentatricopeptide repeat-containing protein At2g29760, chloroplastic-like [Vitis vinifera]

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 66/213 (30%), Positives = 98/213 (46%), Gaps = 61/213 (28%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIEL---- 56
           MI GY++  +   AL  FG++++ G+  DE T V + +  S      + K++  ++    
Sbjct: 183 MIKGYAEVNQPESALCLFGEMQNSGILPDEFTFVALFSVCSVLNEPNVGKQIHAQVYKNL 242

Query: 57  --------------DL---------------------SSYSLSSKTSRYAHSGRIRLAR- 80
                         D+                     S+ + SS    YA  G I +AR 
Sbjct: 243 RSIDSNILLKSAIVDMYAKCGLINIAERVFSTMGTSKSAAAWSSMVCGYARCGEINVARK 302

Query: 81  --------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGA 132
                   D +S  AMISGYSQAG+ +EALE F ++E+LG+  DEVT+V VL+A +  GA
Sbjct: 303 LFNHMHERDVISWTAMISGYSQAGQCSEALELFKEMEALGIKPDEVTLVAVLSACARLGA 362

Query: 133 LDFGK-------------SNIFLTTAIIEMYAK 152
            D GK              N  LT A+++MYAK
Sbjct: 363 FDLGKRLYHQYIENGVFNQNTILTAAVMDMYAK 395

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356553819|ref|XP_003545249.1| PREDICTED: pentatricopeptide repeat-containing protein At2g34400-like [Glycine max]

 Score = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 62/179 (34%), Positives = 97/179 (54%), Gaps = 27/179 (15%)

Query: 1   MISGYSQAGRFNEALEPFGKL-ESLGVHTDEVTMVVVLTASSGPG-----AWILAKELQI 54
           MI+GY++AG   EA+E FG++    G   DE+++V VL A    G      W+    ++ 
Sbjct: 188 MIAGYAKAGCAREAVEVFGEMGRRDGFEPDEMSLVSVLGACGELGDLELGRWVEGFVVER 247

Query: 55  ELDLSSYSLSSKTSRYAHSGRI----RL-----ARDPVSCKAMISGYSQAGRFNEALEPF 105
            + L+SY  S+  S YA  G +    R+     ARD ++  A+ISGY+Q G  +EA+  F
Sbjct: 248 GMTLNSYIGSALISMYAKCGDLGSARRIFDGMAARDVITWNAVISGYAQNGMADEAISLF 307

Query: 106 GKLESLGVHTDEVTMVVVLAASSGPGALDFGKS------------NIFLTTAIIEMYAK 152
             ++   V  +++T+  VL+A +  GALD GK             +IF+ TA+I+MYAK
Sbjct: 308 HAMKEDCVTENKITLTAVLSACATIGALDLGKQIDEYASQRGFQHDIFVATALIDMYAK 366

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	153
TAIR|locus:2093920	687	AT3G15930 "AT3G15930" [Arabido	0.477	0.106	0.4	1.5e-07
TAIR|locus:2091546	628	AT3G13770 [Arabidopsis thalian	0.895	0.218	0.364	7.9e-11
TAIR|locus:2206164	570	AT1G31430 [Arabidopsis thalian	0.915	0.245	0.303	2.6e-10
TAIR|locus:2161018	530	AT5G56310 "AT5G56310" [Arabido	0.895	0.258	0.304	2.7e-10
TAIR|locus:2195980	467	AT1G77170 "AT1G77170" [Arabido	0.973	0.319	0.309	3.5e-10
TAIR|locus:2041198	681	SLO1 "SLOW GROWTH 1" [Arabidop	0.895	0.201	0.264	3.3e-05
TAIR|locus:2077878	685	AT3G08820 "AT3G08820" [Arabido	0.993	0.221	0.280	1.1e-09
TAIR|locus:2060640	738	OTP81 "ORGANELLE TRANSCRIPT PR	0.477	0.098	0.376	2.9e-05
TAIR|locus:2205200	741	OTP82 "AT1G08070" [Arabidopsis	0.895	0.184	0.284	3.2e-09
TAIR|locus:2195296	484	AT1G09190 "AT1G09190" [Arabido	0.379	0.119	0.465	7.2e-09

TAIR|locus:2093920 AT3G15930 "AT3G15930" [Arabidopsis thaliana (taxid:3702)]

 Score = 131 (51.2 bits), Expect = 1.5e-07, P = 1.5e-07
 Identities = 34/85 (40%), Positives = 50/85 (58%)

Query:    80 RDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFG--- 136
             RD +S   MI GY +AG FNE+LE F +++S G+  DE TMV VL A +  G+L+ G   
Sbjct:   331 RDRISWTIMIDGYLRAGCFNESLEIFREMQSAGMIPDEFTMVSVLTACAHLGSLEIGEWI 390

Query:   137 ---------KSNIFLTTAIIEMYAK 152
                      K+++ +  A+I+MY K
Sbjct:   391 KTYIDKNKIKNDVVVGNALIDMYFK 415

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2091546 AT3G13770 [Arabidopsis thaliana (taxid:3702)]

 Score = 161 (61.7 bits), Expect = 7.9e-11, P = 7.9e-11
 Identities = 55/151 (36%), Positives = 71/151 (47%)

Query:     1 MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLT----ASS-GPGAWILAKELQIE 55
             MIS YSQ G  +EAL  F ++       +E T   VLT    AS  G G  I    ++  
Sbjct:   124 MISRYSQTGHSSEALTVFAEMMRSDGKPNEFTFATVLTSCIRASGLGLGKQIHGLIVKWN 183

Query:    56 XXXXXXXXXXXXXRYAHSGRIRLAR---------DPVSCKAMISGYSQAGRFNEALEPFG 106
                           YA +G+I+ AR         D VSC A+I+GY+Q G   EALE F 
Sbjct:   184 YDSHIFVGSSLLDMYAKAGQIKEAREIFECLPERDVVSCTAIIAGYAQLGLDEEALEMFH 243

Query:   107 KLESLGVHTDEVTMVVVLAASSGPGALDFGK 137
             +L S G+  + VT   +L A SG   LD GK
Sbjct:   244 RLHSEGMSPNYVTYASLLTALSGLALLDHGK 274

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2206164 AT1G31430 [Arabidopsis thaliana (taxid:3702)]

 Score = 140 (54.3 bits), Expect = 2.6e-10, Sum P(2) = 2.6e-10
 Identities = 47/155 (30%), Positives = 71/155 (45%)

Query:     1 MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLT--ASSGP---GAWILAKELQIE 55
             M++GY Q  RF+EALE F  +++ G+  D   +V +LT  A +G    G WI     +  
Sbjct:   250 MMNGYVQFNRFDEALELFRCMQTAGIRPDNFVLVSLLTGCAQTGALEQGKWIHGYINENR 309

Query:    56 XXXXXXXXXXXXXRYAHSGRIRLA---------RDPVSCKAMISGYSQAGRFNEALEPFG 106
                           YA  G I  A         RD  S  ++I G +  G    AL+ + 
Sbjct:   310 VTVDKVVGTALVDMYAKCGCIETALEVFYEIKERDTASWTSLIYGLAMNGMSGRALDLYY 369

Query:   107 KLESLGVHTDEVTMVVVLAASSGPGALDFGKSNIF 141
             ++E++GV  D +T V VL A +  G +  G+  IF
Sbjct:   370 EMENVGVRLDAITFVAVLTACNHGGFVAEGRK-IF 403

GO:0005739 "mitochondrion" evidence=ISM

TAIR|locus:2161018 AT5G56310 "AT5G56310" [Arabidopsis thaliana (taxid:3702)]

 Score = 155 (59.6 bits), Expect = 2.7e-10, P = 2.7e-10
 Identities = 46/151 (30%), Positives = 74/151 (49%)

Query:     1 MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL--QIEXXX 58
             +ISGY+++GR +EA+E F ++    V  DEVT++ VL+A +  G+  L + +   ++   
Sbjct:   221 VISGYAKSGRASEAIEVFQRMLMENVEPDEVTLLAVLSACADLGSLELGERICSYVDHRG 280

Query:    59 XXXXXXXXXX---RYAHSGRIRLARDPVSC---------KAMISGYSQAGRFNEALEPFG 106
                           YA SG I  A D   C           +I+G +  G   EAL  F 
Sbjct:   281 MNRAVSLNNAVIDMYAKSGNITKALDVFECVNERNVVTWTTIIAGLATHGHGAEALAMFN 340

Query:   107 KLESLGVHTDEVTMVVVLAASSGPGALDFGK 137
             ++   GV  ++VT + +L+A S  G +D GK
Sbjct:   341 RMVKAGVRPNDVTFIAILSACSHVGWVDLGK 371

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2195980 AT1G77170 "AT1G77170" [Arabidopsis thaliana (taxid:3702)]

 Score = 153 (58.9 bits), Expect = 3.5e-10, P = 3.5e-10
 Identities = 51/165 (30%), Positives = 77/165 (46%)

Query:     1 MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-------Q 53
             +I G + AGR NEA+E F  ++  G+  D+ TMV V  +  G G   LA +L       +
Sbjct:   189 IIGGLNHAGRANEAVEMFVDMKRSGLEPDDFTMVSVTASCGGLGDLSLAFQLHKCVLQAK 248

Query:    54 IEXXXXXXXXXXXXXRYAHSGRIRLA---------RDPVSCKAMISGYSQAGRFNEALEP 104
              E              Y   GR+ LA         R+ VS  +MI GY+  G   EALE 
Sbjct:   249 TEEKSDIMMLNSLIDMYGKCGRMDLASHIFEEMRQRNVVSWSSMIVGYAANGNTLEALEC 308

Query:   105 FGKLESLGVHTDEVTMVVVLAASSGPGALDFGKSNIFLTTAIIEM 149
             F ++   GV  +++T V VL+A    G ++ GK+   +  +  E+
Sbjct:   309 FRQMREFGVRPNKITFVGVLSACVHGGLVEEGKTYFAMMKSEFEL 353

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2041198 SLO1 "SLOW GROWTH 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 109 (43.4 bits), Expect = 3.3e-05, P = 3.3e-05
 Identities = 40/151 (26%), Positives = 65/151 (43%)

Query:     1 MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGA-----WILAKELQIE 55
             MI G  QA R  +AL  F ++++     DE+TM+  L+A S  GA     WI     +  
Sbjct:   360 MIGGSVQAKRGQDALALFQEMQTSNTKPDEITMIHCLSACSQLGALDVGIWIHRYIEKYS 419

Query:    56 XXXXXXXXXXXXXRYAHSGRIRLA---------RDPVSCKAMISGYSQAGRFNEALEPFG 106
                           YA  G I  A         R+ ++  A+I G +  G  + A+  F 
Sbjct:   420 LSLNVALGTSLVDMYAKCGNISEALSVFHGIQTRNSLTYTAIIGGLALHGDASTAISYFN 479

Query:   107 KLESLGVHTDEVTMVVVLAASSGPGALDFGK 137
             ++   G+  DE+T + +L+A    G +  G+
Sbjct:   480 EMIDAGIAPDEITFIGLLSACCHGGMIQTGR 510

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2077878 AT3G08820 "AT3G08820" [Arabidopsis thaliana (taxid:3702)]

 Score = 151 (58.2 bits), Expect = 1.1e-09, P = 1.1e-09
 Identities = 50/178 (28%), Positives = 82/178 (46%)

Query:     1 MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTA-----SSGPGAWILAKELQIE 55
             + SGY+ +GR  EA++ F K+  +GV  D   +V VL+A         G WI+    ++E
Sbjct:   183 LFSGYTTSGRHREAIDLFKKMVEMGVKPDSYFIVQVLSACVHVGDLDSGEWIVKYMEEME 242

Query:    56 XXXXXXXXXXXXXRYAHSGRIRLAR---------DPVSCKAMISGYSQAGRFNEALEPFG 106
                           YA  G++  AR         D V+   MI GY+      E +E F 
Sbjct:   243 MQKNSFVRTTLVNLYAKCGKMEKARSVFDSMVEKDIVTWSTMIQGYASNSFPKEGIELFL 302

Query:   107 KLESLGVHTDEVTMVVVLAASSGPGALDFGK------------SNIFLTTAIIEMYAK 152
             ++    +  D+ ++V  L++ +  GALD G+            +N+F+  A+I+MYAK
Sbjct:   303 QMLQENLKPDQFSIVGFLSSCASLGALDLGEWGISLIDRHEFLTNLFMANALIDMYAK 360

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2060640 OTP81 "ORGANELLE TRANSCRIPT PROCESSING 81" [Arabidopsis thaliana (taxid:3702)]

 Score = 110 (43.8 bits), Expect = 2.9e-05, P = 2.9e-05
 Identities = 32/85 (37%), Positives = 47/85 (55%)

Query:    80 RDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS- 138
             +D VS  +MI+G+ Q G  ++ALE F K+ES  V    VTMV VL+A +    L+FG+  
Sbjct:   195 KDVVSWNSMINGFVQKGSPDKALELFKKMESEDVKASHVTMVGVLSACAKIRNLEFGRQV 254

Query:   139 -----------NIFLTTAIIEMYAK 152
                        N+ L  A+++MY K
Sbjct:   255 CSYIEENRVNVNLTLANAMLDMYTK 279

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0031425 "chloroplast RNA processing" evidence=IMP

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

 Score = 147 (56.8 bits), Expect = 3.2e-09, P = 3.2e-09
 Identities = 43/151 (28%), Positives = 71/151 (47%)

Query:     1 MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIEXXXXX 60
             MISGY++ G + EALE F  +    V  DE TMV V++A +  G+  L +++ +      
Sbjct:   237 MISGYAETGNYKEALELFKDMMKTNVRPDESTMVTVVSACAQSGSIELGRQVHLWIDDHG 296

Query:    61 XXXXXXXXR-----YAHSGRIRLA---------RDPVSCKAMISGYSQAGRFNEALEPFG 106
                           Y+  G +  A         +D +S   +I GY+    + EAL  F 
Sbjct:   297 FGSNLKIVNALIDLYSKCGELETACGLFERLPYKDVISWNTLIGGYTHMNLYKEALLLFQ 356

Query:   107 KLESLGVHTDEVTMVVVLAASSGPGALDFGK 137
             ++   G   ++VTM+ +L A +  GA+D G+
Sbjct:   357 EMLRSGETPNDVTMLSILPACAHLGAIDIGR 387

GO:0003674 "molecular_function" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0031425 "chloroplast RNA processing" evidence=IMP

TAIR|locus:2195296 AT1G09190 "AT1G09190" [Arabidopsis thaliana (taxid:3702)]

 Score = 107 (42.7 bits), Expect = 7.2e-09, Sum P(2) = 7.2e-09
 Identities = 27/58 (46%), Positives = 33/58 (56%)

Query:    80 RDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGK 137
             R  VS  +MIS  S+ GR  EALE F ++   G   DE T+V VL  S+  G LD GK
Sbjct:   197 RSIVSWNSMISSLSKCGRDREALELFCEMIDQGFDPDEATVVTVLPISASLGVLDTGK 254

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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00001532001 SubName- Full=Chromosome chr11 scaffold_118, whole genome shotgun sequence; (618 aa) (Vitis vinifera)

Predicted Functional Partners:

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

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	153
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	4e-17
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	2e-11
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	6e-11
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	1e-09
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	9e-09
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	4e-07
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	3e-05
pfam13041	50	pfam13041, PPR_2, PPR repeat family	4e-04
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	0.003
pfam13041	50	pfam13041, PPR_2, PPR repeat family	0.004
pfam01535	31	pfam01535, PPR, PPR repeat	0.004

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

 Score = 76.8 bits (189), Expect = 4e-17
 Identities = 57/180 (31%), Positives = 82/180 (45%), Gaps = 30/180 (16%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQ------- 53
           MISGY + G   E LE F  +  L V  D +T+  V++A    G   L +E+        
Sbjct: 259 MISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTG 318

Query: 54  IELDLSSYSLSSKTSRYAHSGRIRLA---------RDPVSCKAMISGYSQAGRFNEALEP 104
             +D+S  +  S    Y   G    A         +D VS  AMISGY + G  ++ALE 
Sbjct: 319 FAVDVSVCN--SLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALET 376

Query: 105 FGKLESLGVHTDEVTMVVVLAASSGPGALDFG------------KSNIFLTTAIIEMYAK 152
           +  +E   V  DE+T+  VL+A +  G LD G             S + +  A+IEMY+K
Sbjct: 377 YALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSK 436

Length = 857

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

 Score = 60.6 bits (147), Expect = 2e-11
 Identities = 45/177 (25%), Positives = 76/177 (42%), Gaps = 26/177 (14%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIEL---- 56
           ++ GY++AG F+EAL  + ++   GV  D  T   VL    G       +E+   +    
Sbjct: 158 LVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFG 217

Query: 57  -DLSSYSLSSKTSRYAHSGRIRLAR---------DPVSCKAMISGYSQAGRFNEALEPFG 106
            +L    +++  + Y   G +  AR         D +S  AMISGY + G   E LE F 
Sbjct: 218 FELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFF 277

Query: 107 KLESLGVHTDEVTMVVVLAASSGPGALDFGKS------------NIFLTTAIIEMYA 151
            +  L V  D +T+  V++A    G    G+             ++ +  ++I+MY 
Sbjct: 278 TMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYL 334

Length = 857

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

 Score = 59.1 bits (143), Expect = 6e-11
 Identities = 49/178 (27%), Positives = 82/178 (46%), Gaps = 27/178 (15%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAW---ILAKELQIELD 57
           MISGY + G  ++ALE +  +E   V  DE+T+  VL+A +  G     +   EL     
Sbjct: 360 MISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKG 419

Query: 58  LSSYSL--SSKTSRYAHSGRIRLA---------RDPVSCKAMISGYSQAGRFNEALEPFG 106
           L SY +  ++    Y+    I  A         +D +S  ++I+G     R  EAL  F 
Sbjct: 420 LISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFR 479

Query: 107 KLESLGVHTDEVTMVVVLAASSGPGALDFGK------------SNIFLTTAIIEMYAK 152
           ++  L +  + VT++  L+A +  GAL  GK             + FL  A++++Y +
Sbjct: 480 QML-LTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVR 536

Length = 857

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

 Score = 54.9 bits (132), Expect = 1e-09
 Identities = 42/156 (26%), Positives = 72/156 (46%), Gaps = 15/156 (9%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIELDLSS 60
           M++GY+  G   EAL  + ++   GV  D+ T  +++   S       AK+    L  + 
Sbjct: 296 MLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTG 355

Query: 61  YSL-----SSKTSRYAHSGRIRLAR---------DPVSCKAMISGYSQAGRFNEALEPFG 106
           + L     ++    Y+  GR+  AR         + +S  A+I+GY   GR  +A+E F 
Sbjct: 356 FPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFE 415

Query: 107 KLESLGVHTDEVTMVVVLAASSGPGALDFGKSNIFL 142
           ++ + GV  + VT + VL+A    G  + G   IF 
Sbjct: 416 RMIAEGVAPNHVTFLAVLSACRYSGLSEQGW-EIFQ 450

Length = 697

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

 Score = 52.5 bits (126), Expect = 9e-09
 Identities = 40/144 (27%), Positives = 69/144 (47%), Gaps = 14/144 (9%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKE-----LQIE 55
           +I+G     R  EAL  F ++  L +  + VT++  L+A +  GA +  KE     L+  
Sbjct: 461 IIAGLRLNNRCFEALIFFRQML-LTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTG 519

Query: 56  LDLSSYSLSSKTSRYAHSGRIRLA--------RDPVSCKAMISGYSQAGRFNEALEPFGK 107
           +    +  ++    Y   GR+  A        +D VS   +++GY   G+ + A+E F +
Sbjct: 520 IGFDGFLPNALLDLYVRCGRMNYAWNQFNSHEKDVVSWNILLTGYVAHGKGSMAVELFNR 579

Query: 108 LESLGVHTDEVTMVVVLAASSGPG 131
           +   GV+ DEVT + +L A S  G
Sbjct: 580 MVESGVNPDEVTFISLLCACSRSG 603

Length = 857

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

 Score = 47.9 bits (114), Expect = 4e-07
 Identities = 43/178 (24%), Positives = 76/178 (42%), Gaps = 26/178 (14%)

Query: 1   MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQI-ELDL- 58
           +I G   AG + EA   F ++   G   +  T VV+L AS+G G+    ++L    L   
Sbjct: 195 IIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTG 254

Query: 59  ---SSYSLSSKTSRYAHSGRIRLAR---------DPVSCKAMISGYSQAGRFNEALEPFG 106
               ++   +    Y+  G I  AR           V+  +M++GY+  G   EAL  + 
Sbjct: 255 VVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYY 314

Query: 107 KLESLGVHTDEVTMVVVLAASSGPGALDFGK------------SNIFLTTAIIEMYAK 152
           ++   GV  D+ T  +++   S    L+  K             +I   TA++++Y+K
Sbjct: 315 EMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSK 372

Length = 697

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

 Score = 42.6 bits (100), Expect = 3e-05
 Identities = 42/172 (24%), Positives = 67/172 (38%), Gaps = 27/172 (15%)

Query: 8   AGRFNEALEPFGKLE-----SLGVHT-DEVTMVVVLTASSGPGAWILAKELQIELDLSSY 61
            GR  EALE F  LE     +L   T D +    +   S      +         +   Y
Sbjct: 100 CGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQY 159

Query: 62  SLSSKTSRYAHSGRI----RL-----ARDPVSCKAMISGYSQAGRFNEALEPFGKLESLG 112
            ++     +   G +    RL      R+  S   +I G   AG + EA   F ++   G
Sbjct: 160 MMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDG 219

Query: 113 VHTDEVTMVVVLAASSGPGALDFGKS------------NIFLTTAIIEMYAK 152
              +  T VV+L AS+G G+   G+             + F++ A+I+MY+K
Sbjct: 220 SDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSK 271

Length = 697

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

 Score = 35.8 bits (84), Expect = 4e-04
 Identities = 12/39 (30%), Positives = 22/39 (56%)

Query: 81  DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVT 119
           D V+   +I GY + G+  EAL+ F +++  G+  +  T
Sbjct: 2   DVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYT 40

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

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

 Score = 36.4 bits (84), Expect = 0.003
 Identities = 25/85 (29%), Positives = 38/85 (44%), Gaps = 12/85 (14%)

Query: 80  RDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGK-- 137
           RD  S   ++ GY++AG F+EAL  + ++   GV  D  T   VL    G   L  G+  
Sbjct: 150 RDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREV 209

Query: 138 ----------SNIFLTTAIIEMYAK 152
                      ++ +  A+I MY K
Sbjct: 210 HAHVVRFGFELDVDVVNALITMYVK 234

Length = 857

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

 Score = 33.1 bits (77), Expect = 0.004
 Identities = 10/39 (25%), Positives = 22/39 (56%)

Query: 1  MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTA 39
          +I GY + G+  EAL+ F +++  G+  +  T  +++  
Sbjct: 9  LIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDG 47

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

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

 Score = 32.8 bits (76), Expect = 0.004
 Identities = 14/31 (45%), Positives = 22/31 (70%)

Query: 83  VSCKAMISGYSQAGRFNEALEPFGKLESLGV 113
           V+  ++ISGY +AG+  EALE F +++  GV
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	153
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	99.97
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	99.97
PLN03077	857	Protein ECB2; Provisional	99.97
PLN03218	1060	maturation of RBCL 1; Provisional	99.97
PLN03077	857	Protein ECB2; Provisional	99.97
PF13041	50	PPR_2: PPR repeat family	99.71
PF13041	50	PPR_2: PPR repeat family	99.45
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.12
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.09
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	99.08
PF12854	34	PPR_1: PPR repeat	98.97
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.97
KOG4422	625	consensus Uncharacterized conserved protein [Funct	98.93
KOG4422	625	consensus Uncharacterized conserved protein [Funct	98.88
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	98.86
PF12854	34	PPR_1: PPR repeat	98.83
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	98.82
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.8
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	98.73
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.48
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.46
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.42
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.4
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.4
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.34
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.25
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	98.18
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	98.17
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	98.09
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	98.07
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	98.06
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.04
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	98.02
PRK12370	553	invasion protein regulator; Provisional	97.99
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	97.94
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	97.91
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	97.88
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.85
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.82
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.81
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	97.8
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	97.74
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	97.67
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.6
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	97.59
PRK12370	553	invasion protein regulator; Provisional	97.53
PRK14574	822	hmsH outer membrane protein; Provisional	97.5
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	97.47
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	97.41
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	97.38
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	97.38
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	97.38
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	97.36
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.32
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	97.3
PRK14574	822	hmsH outer membrane protein; Provisional	97.23
KOG2003	840	consensus TPR repeat-containing protein [General f	97.2
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	97.17
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	97.17
PRK15359	144	type III secretion system chaperone protein SscB;	97.08
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.07
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	97.05
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	96.98
KOG1129	478	consensus TPR repeat-containing protein [General f	96.96
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	96.95
PRK10370	198	formate-dependent nitrite reductase complex subuni	96.94
KOG2003	840	consensus TPR repeat-containing protein [General f	96.83
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.79
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	96.77
KOG1126	638	consensus DNA-binding cell division cycle control	96.76
COG4783	484	Putative Zn-dependent protease, contains TPR repea	96.74
PRK11189	296	lipoprotein NlpI; Provisional	96.69
PF03704	146	BTAD: Bacterial transcriptional activator domain;	96.65
COG4783	484	Putative Zn-dependent protease, contains TPR repea	96.63
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	96.61
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	96.57
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	96.55
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	96.53
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	96.52
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	96.51
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	96.46
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	96.43
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	96.42
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	96.42
KOG2076	895	consensus RNA polymerase III transcription factor	96.41
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	96.39
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	96.39
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	96.37
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	96.33
smart00299	140	CLH Clathrin heavy chain repeat homology.	96.33
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	96.32
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	96.29
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	96.27
KOG0547	606	consensus Translocase of outer mitochondrial membr	96.26
PRK15359	144	type III secretion system chaperone protein SscB;	96.24
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	96.19
PRK11189	296	lipoprotein NlpI; Provisional	96.1
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	96.07
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	95.97
KOG3616	1636	consensus Selective LIM binding factor [Transcript	95.97
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	95.94
KOG3941	406	consensus Intermediate in Toll signal transduction	95.94
KOG1128	777	consensus Uncharacterized conserved protein, conta	95.93
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	95.92
KOG0553	304	consensus TPR repeat-containing protein [General f	95.92
KOG2376	652	consensus Signal recognition particle, subunit Srp	95.9
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	95.87
KOG1126	638	consensus DNA-binding cell division cycle control	95.86
TIGR02552	135	LcrH_SycD type III secretion low calcium response	95.79
PRK10370	198	formate-dependent nitrite reductase complex subuni	95.77
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	95.62
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	95.56
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	95.56
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	95.56
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	95.54
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	95.51
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	95.4
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	95.4
KOG1915	677	consensus Cell cycle control protein (crooked neck	95.37
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	95.25
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	95.24
PF03704	146	BTAD: Bacterial transcriptional activator domain;	95.19
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	95.19
PF12688	120	TPR_5: Tetratrico peptide repeat	95.18
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	94.75
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	94.69
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	94.65
KOG4340	459	consensus Uncharacterized conserved protein [Funct	94.49
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	94.42
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	94.36
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	94.2
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	94.16
KOG3616	1636	consensus Selective LIM binding factor [Transcript	94.06
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	93.85
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	93.84
smart00299	140	CLH Clathrin heavy chain repeat homology.	93.72
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	93.69
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	93.55
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	93.5
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	93.23
KOG2076	895	consensus RNA polymerase III transcription factor	92.99
COG3629	280	DnrI DNA-binding transcriptional activator of the	92.94
KOG2047	835	consensus mRNA splicing factor [RNA processing and	92.94
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	92.79
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	92.79
PF13371	73	TPR_9: Tetratricopeptide repeat	92.78
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	92.76
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	92.49
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	92.4
PRK10803	263	tol-pal system protein YbgF; Provisional	92.34
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	92.17
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	92.16
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	92.06
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	92.05
PF11848	48	DUF3368: Domain of unknown function (DUF3368); Int	92.03
PRK14720	906	transcript cleavage factor/unknown domain fusion p	92.03
PF13428	44	TPR_14: Tetratricopeptide repeat	91.65
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	91.64
KOG3785	557	consensus Uncharacterized conserved protein [Funct	91.6
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	91.42
KOG1129	478	consensus TPR repeat-containing protein [General f	90.99
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	90.98
PF10366	108	Vps39_1: Vacuolar sorting protein 39 domain 1; Int	90.96
PRK14720	906	transcript cleavage factor/unknown domain fusion p	90.7
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	90.67
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	90.58
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	90.45
PF13371	73	TPR_9: Tetratricopeptide repeat	90.42
KOG0547	606	consensus Translocase of outer mitochondrial membr	90.19
KOG2376	652	consensus Signal recognition particle, subunit Srp	90.06
PF12688	120	TPR_5: Tetratrico peptide repeat	90.0
PRK04841	903	transcriptional regulator MalT; Provisional	89.89
KOG1125	579	consensus TPR repeat-containing protein [General f	89.82
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	89.73
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	89.52
KOG0495	913	consensus HAT repeat protein [RNA processing and m	89.45
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	89.07
KOG4570	418	consensus Uncharacterized conserved protein [Funct	88.62
COG4105	254	ComL DNA uptake lipoprotein [General function pred	88.53
PF11848	48	DUF3368: Domain of unknown function (DUF3368); Int	88.51
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	88.48
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	88.34
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	88.0
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	87.88
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	87.48
PRK10803	263	tol-pal system protein YbgF; Provisional	86.98
PF13929	292	mRNA_stabil: mRNA stabilisation	86.98
KOG3785	557	consensus Uncharacterized conserved protein [Funct	86.92
KOG3060	289	consensus Uncharacterized conserved protein [Funct	86.89
PF13929	292	mRNA_stabil: mRNA stabilisation	86.86
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	86.54
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	86.39
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	86.38
KOG3941	406	consensus Intermediate in Toll signal transduction	86.33
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	86.32
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	86.3
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	85.74
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	85.36
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	85.31
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	85.14
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	85.0
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	84.66
PRK04841	903	transcriptional regulator MalT; Provisional	84.54
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	84.44
KOG3060	289	consensus Uncharacterized conserved protein [Funct	84.4
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	84.38
KOG2796	366	consensus Uncharacterized conserved protein [Funct	84.26
PRK10564	303	maltose regulon periplasmic protein; Provisional	84.21
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	83.99
PF14689	62	SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical do	83.92
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	83.81
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	83.77
KOG4570	418	consensus Uncharacterized conserved protein [Funct	82.98
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	82.76
KOG1915	677	consensus Cell cycle control protein (crooked neck	82.46
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	82.15
PF13431	34	TPR_17: Tetratricopeptide repeat	82.05
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	81.87
KOG2610	491	consensus Uncharacterized conserved protein [Funct	81.53
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	81.43
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	81.11
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	80.98
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	80.87
KOG4077	149	consensus Cytochrome c oxidase, subunit Va/COX6 [E	80.07

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

Probab=100.00  E-value=1.1e-32  Score=217.85  Aligned_cols=153  Identities=27%  Similarity=0.384  Sum_probs=146.8

Q ss_pred             ChhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-----hhhhhcchhhHHHHHHHHHhcCC
Q 039275            1 MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-----QIELDLSSYSLSSKTSRYAHSGR   75 (153)
Q Consensus         1 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-----~~~~~~~~~~~~~ll~~~~~~g~   75 (153)
                      ||.+|++.|++++|.++|++|.+.|+.||..||+++|.+|++.|.+++|.++     +.|+.||..+||+||.+|+++|+
T Consensus       296 li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~  375 (697)
T PLN03081        296 MLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGR  375 (697)
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCC
Confidence            5889999999999999999999999999999999999999999999999998     88899999999999999999999


Q ss_pred             ccccc---------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh--------
Q 039275           76 IRLAR---------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS--------  138 (153)
Q Consensus        76 ~~~a~---------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~--------  138 (153)
                      +++|.         |..+||+||.+|++.|+.++|.++|++|++.|++||..||+.+|++|++.|++++|.+        
T Consensus       376 ~~~A~~vf~~m~~~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~  455 (697)
T PLN03081        376 MEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSEN  455 (697)
T ss_pred             HHHHHHHHHhCCCCCeeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHh
Confidence            99998         8999999999999999999999999999999999999999999999999999999988        


Q ss_pred             -----HHHHHHHHHHHhhcC
Q 039275          139 -----NIFLTTAIIEMYAKM  153 (153)
Q Consensus       139 -----~~~~~~~li~~y~k~  153 (153)
                           +..+|+.||++|+|+
T Consensus       456 ~g~~p~~~~y~~li~~l~r~  475 (697)
T PLN03081        456 HRIKPRAMHYACMIELLGRE  475 (697)
T ss_pred             cCCCCCccchHhHHHHHHhc
Confidence                 567899999998874

>PLN03218 maturation of RBCL 1; Provisional

Probab=99.97  E-value=4.4e-31  Score=213.75  Aligned_cols=153  Identities=21%  Similarity=0.347  Sum_probs=127.1

Q ss_pred             ChhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-----h--hhhhcchhhHHHHHHHHHhc
Q 039275            1 MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-----Q--IELDLSSYSLSSKTSRYAHS   73 (153)
Q Consensus         1 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-----~--~~~~~~~~~~~~ll~~~~~~   73 (153)
                      ||++|++.|++++|.++|++|++.|+.||..||+++|.+|++.|++++|.++     .  .++.||..+|++||.+|++.
T Consensus       513 LI~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~  592 (1060)
T PLN03218        513 LIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANA  592 (1060)
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHC
Confidence            4678888888888888888888888888888888888888888888888877     1  35678888888888888888


Q ss_pred             CCccccc-------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh--
Q 039275           74 GRIRLAR-------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS--  138 (153)
Q Consensus        74 g~~~~a~-------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~--  138 (153)
                      |++++|.             +..+||++|.+|++.|++++|.++|++|.+.|+.||..||+.+|++|++.|++++|.+  
T Consensus       593 G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~  672 (1060)
T PLN03218        593 GQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEIL  672 (1060)
T ss_pred             CCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHH
Confidence            8888877             6688888888888888888888888888888888888888888888888888888887  


Q ss_pred             ----------HHHHHHHHHHHhhcC
Q 039275          139 ----------NIFLTTAIIEMYAKM  153 (153)
Q Consensus       139 ----------~~~~~~~li~~y~k~  153 (153)
                                +..+|++||++|+|+
T Consensus       673 ~eM~k~G~~pd~~tynsLI~ay~k~  697 (1060)
T PLN03218        673 QDARKQGIKLGTVSYSSLMGACSNA  697 (1060)
T ss_pred             HHHHHcCCCCCHHHHHHHHHHHHhC
Confidence                      777888888888764

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

Probab=99.97  E-value=7.6e-31  Score=207.44  Aligned_cols=153  Identities=27%  Similarity=0.433  Sum_probs=146.0

Q ss_pred             ChhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-----hhhhhcchhhHHHHHHHHHhcCC
Q 039275            1 MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-----QIELDLSSYSLSSKTSRYAHSGR   75 (153)
Q Consensus         1 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-----~~~~~~~~~~~~~ll~~~~~~g~   75 (153)
                      ||++|++.|++++|.++|++|++.|+.||..||++++.+|++.|..+.+.++     +.|+.||..+||+||.+|+++|+
T Consensus       195 li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~  274 (697)
T PLN03081        195 IIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGD  274 (697)
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHHHhcCCcHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCC
Confidence            5789999999999999999999999999999999999999999999999988     78899999999999999999999


Q ss_pred             ccccc---------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh--------
Q 039275           76 IRLAR---------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS--------  138 (153)
Q Consensus        76 ~~~a~---------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~--------  138 (153)
                      +++|.         |..+||+||.+|++.|++++|.++|++|++.|++||..||+.++++|++.|++++|.+        
T Consensus       275 ~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~  354 (697)
T PLN03081        275 IEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRT  354 (697)
T ss_pred             HHHHHHHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHh
Confidence            99998         8999999999999999999999999999999999999999999999999999999988        


Q ss_pred             ----HHHHHHHHHHHhhcC
Q 039275          139 ----NIFLTTAIIEMYAKM  153 (153)
Q Consensus       139 ----~~~~~~~li~~y~k~  153 (153)
                          +..+||+||++|+|+
T Consensus       355 g~~~d~~~~~~Li~~y~k~  373 (697)
T PLN03081        355 GFPLDIVANTALVDLYSKW  373 (697)
T ss_pred             CCCCCeeehHHHHHHHHHC
Confidence                778888899888875

>PLN03077 Protein ECB2; Provisional

Probab=99.97  E-value=8.3e-31  Score=211.10  Aligned_cols=153  Identities=35%  Similarity=0.477  Sum_probs=148.1

Q ss_pred             ChhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-----hhhhhcchhhHHHHHHHHHhcCC
Q 039275            1 MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-----QIELDLSSYSLSSKTSRYAHSGR   75 (153)
Q Consensus         1 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-----~~~~~~~~~~~~~ll~~~~~~g~   75 (153)
                      ||++|++.|++++|+++|++|.+.|+.||..||+++|.+|++.|+++.+.++     +.|+.||..+||+||.+|++.|+
T Consensus       259 li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~  338 (857)
T PLN03077        259 MISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGS  338 (857)
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCC
Confidence            5789999999999999999999999999999999999999999999999999     88899999999999999999999


Q ss_pred             ccccc---------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh--------
Q 039275           76 IRLAR---------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS--------  138 (153)
Q Consensus        76 ~~~a~---------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~--------  138 (153)
                      +++|.         |..+||+||.+|++.|++++|.++|++|++.|++||..||+.+|.+|++.|+++.|.+        
T Consensus       339 ~~~A~~vf~~m~~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~  418 (857)
T PLN03077        339 WGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERK  418 (857)
T ss_pred             HHHHHHHHhhCCCCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHh
Confidence            99999         8899999999999999999999999999999999999999999999999999999998        


Q ss_pred             ----HHHHHHHHHHHhhcC
Q 039275          139 ----NIFLTTAIIEMYAKM  153 (153)
Q Consensus       139 ----~~~~~~~li~~y~k~  153 (153)
                          +..+||+||++|+|+
T Consensus       419 g~~~~~~~~n~Li~~y~k~  437 (857)
T PLN03077        419 GLISYVVVANALIEMYSKC  437 (857)
T ss_pred             CCCcchHHHHHHHHHHHHc
Confidence                788999999999985

>PLN03218 maturation of RBCL 1; Provisional

Probab=99.97  E-value=3.8e-30  Score=208.36  Aligned_cols=152  Identities=16%  Similarity=0.259  Sum_probs=95.6

Q ss_pred             ChhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-----hhhhhcchhhHHHHHHHHHhcCC
Q 039275            1 MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-----QIELDLSSYSLSSKTSRYAHSGR   75 (153)
Q Consensus         1 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-----~~~~~~~~~~~~~ll~~~~~~g~   75 (153)
                      ||++|++.|++++|.++|++|.+.|+.||..+|+++|.+|++.|++++|.++     +.|+.||..+|++||.+|++.|+
T Consensus       443 LL~a~~k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~  522 (1060)
T PLN03218        443 LMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQ  522 (1060)
T ss_pred             HHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcC
Confidence            3556666666666666666666666666666666666666666666666666     44455666666666666666666


Q ss_pred             ccccc-------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHH--cCCCCChhhHHHHHHHhcCCCccccchh--
Q 039275           76 IRLAR-------------DPVSCKAMISGYSQAGRFNEALEPFGKLES--LGVHTDEVTMVVVLAASSGPGALDFGKS--  138 (153)
Q Consensus        76 ~~~a~-------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~g~~p~~~t~~~li~~~~~~g~~~~a~~--  138 (153)
                      +++|.             |..+||+||.+|++.|++++|.++|++|+.  .|+.||..||+++|++|++.|++++|.+  
T Consensus       523 ~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf  602 (1060)
T PLN03218        523 VAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVY  602 (1060)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            66665             556666666666666666666666666654  3566666666666666666666666655  


Q ss_pred             ----------HHHHHHHHHHHhhc
Q 039275          139 ----------NIFLTTAIIEMYAK  152 (153)
Q Consensus       139 ----------~~~~~~~li~~y~k  152 (153)
                                +..+||+||++|++
T Consensus       603 ~~M~e~gi~p~~~tynsLI~ay~k  626 (1060)
T PLN03218        603 QMIHEYNIKGTPEVYTIAVNSCSQ  626 (1060)
T ss_pred             HHHHHcCCCCChHHHHHHHHHHHh
Confidence                      44556666666554

>PLN03077 Protein ECB2; Provisional

Probab=99.97  E-value=3.6e-30  Score=207.47  Aligned_cols=153  Identities=29%  Similarity=0.472  Sum_probs=147.1

Q ss_pred             ChhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-----hhhhhcchhhHHHHHHHHHhcCC
Q 039275            1 MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-----QIELDLSSYSLSSKTSRYAHSGR   75 (153)
Q Consensus         1 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-----~~~~~~~~~~~~~ll~~~~~~g~   75 (153)
                      ||++|++.|++++|+++|++|++.|+.||..||+++|.+|++.++++.+.++     +.|+.||..++|+||.+|++.|+
T Consensus       158 li~~~~~~g~~~~A~~~f~~M~~~g~~Pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~  237 (857)
T PLN03077        158 LVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGD  237 (857)
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHhCCccchhhHHHHHHHHHHcCCCcccchHhHHHHHHhcCCC
Confidence            5789999999999999999999999999999999999999999999988888     78899999999999999999999


Q ss_pred             ccccc---------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh--------
Q 039275           76 IRLAR---------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS--------  138 (153)
Q Consensus        76 ~~~a~---------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~--------  138 (153)
                      +++|.         |..+||+||.+|++.|++++|.++|.+|++.|++||..||+.+|.+|++.|+.+.|.+        
T Consensus       238 ~~~A~~lf~~m~~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~  317 (857)
T PLN03077        238 VVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKT  317 (857)
T ss_pred             HHHHHHHHhcCCCCCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHh
Confidence            99998         8999999999999999999999999999999999999999999999999999999988        


Q ss_pred             ----HHHHHHHHHHHhhcC
Q 039275          139 ----NIFLTTAIIEMYAKM  153 (153)
Q Consensus       139 ----~~~~~~~li~~y~k~  153 (153)
                          |..+||+||++|+|+
T Consensus       318 g~~~d~~~~n~Li~~y~k~  336 (857)
T PLN03077        318 GFAVDVSVCNSLIQMYLSL  336 (857)
T ss_pred             CCccchHHHHHHHHHHHhc
Confidence                899999999999875

>PF13041 PPR_2: PPR repeat family

Probab=99.71  E-value=3.4e-17  Score=87.53  Aligned_cols=49  Identities=33%  Similarity=0.615  Sum_probs=47.4

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcC
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSG  129 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~  129 (153)
                      |..+||++|.+|++.|++++|.++|++|++.|++||..||+.+|++||+
T Consensus         2 ~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    2 DVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             chHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            5789999999999999999999999999999999999999999999986

>PF13041 PPR_2: PPR repeat family

Probab=99.45  E-value=1.7e-13  Score=73.13  Aligned_cols=42  Identities=33%  Similarity=0.654  Sum_probs=33.1

Q ss_pred             ChhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcC
Q 039275            1 MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSG   42 (153)
Q Consensus         1 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~   42 (153)
                      ||++|++.|++++|.++|++|.+.|++||..||+++|++|++
T Consensus         9 li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    9 LISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            467788888888888888888888888888888888887764

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.12  E-value=1.2e-09  Score=81.36  Aligned_cols=53  Identities=9%  Similarity=0.061  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           84 SCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        84 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +++.+...|++.|++++|.+.++++.+.  .|+...+..+...+.+.|++++|..
T Consensus       251 ~~~~l~~~~~~~g~~~~A~~~l~~~~~~--~p~~~~~~~la~~~~~~g~~~~A~~  303 (389)
T PRK11788        251 VLPKLMECYQALGDEAEGLEFLRRALEE--YPGADLLLALAQLLEEQEGPEAAQA  303 (389)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCchHHHHHHHHHHHhCCHHHHHH
Confidence            3445555555555555555555555443  2444444555555555555555555

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.09  E-value=4.4e-09  Score=78.34  Aligned_cols=136  Identities=15%  Similarity=0.098  Sum_probs=96.8

Q ss_pred             hhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHHhhh---hhcc------hhhHHHHHHHHHh
Q 039275            2 ISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIE---LDLS------SYSLSSKTSRYAH   72 (153)
Q Consensus         2 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~---~~~~------~~~~~~ll~~~~~   72 (153)
                      ...|.+.|++++|.+.|+++.+. -+++..++..+...+.+.|++++|.+....   ..|+      ...+..+...+.+
T Consensus       114 a~~~~~~g~~~~A~~~~~~~l~~-~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~  192 (389)
T PRK11788        114 GQDYLKAGLLDRAEELFLQLVDE-GDFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALA  192 (389)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHcC-CcchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHh
Confidence            34677888888888888888764 345677888888888888888888877111   1111      1234456667778


Q ss_pred             cCCccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           73 SGRIRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        73 ~g~~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .|++++|.            +...+..+...+.+.|++++|.++|+++...+......++..+..++++.|++++|.+
T Consensus       193 ~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~  270 (389)
T PRK11788        193 RGDLDAARALLKKALAADPQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLE  270 (389)
T ss_pred             CCCHHHHHHHHHHHHhHCcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHH
Confidence            88888777            4556667778888888888888888888765422334567788888888888888877

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=99.08  E-value=2.3e-10  Score=55.91  Aligned_cols=35  Identities=37%  Similarity=0.623  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCh
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDE  117 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  117 (153)
                      .+||+||.+|++.|++++|.++|++|++.|++||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            37999999999999999999999999999999984

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.

>PF12854 PPR_1: PPR repeat

Probab=98.97  E-value=7.9e-10  Score=53.84  Aligned_cols=29  Identities=41%  Similarity=0.800  Sum_probs=26.7

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLE  109 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~  109 (153)
                      |..+||+||.+||+.|++++|.++|++|+
T Consensus         6 d~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    6 DVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             cHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            56889999999999999999999999985

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.97  E-value=1.3e-09  Score=52.95  Aligned_cols=33  Identities=24%  Similarity=0.453  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESLGVHT  115 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  115 (153)
                      .+||++|.+|++.|+++.|.++|++|++.|++|
T Consensus         2 ~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    2 HTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             cHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            689999999999999999999999999999998

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.93  E-value=2.2e-08  Score=74.28  Aligned_cols=131  Identities=13%  Similarity=0.187  Sum_probs=86.8

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHH--hcCCCc--hHHHHHH-----------------------hhhhh
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTA--SSGPGA--WILAKEL-----------------------QIELD   57 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~--~~~~~~--~~~a~~~-----------------------~~~~~   57 (153)
                      ....|+++++.-+|+.|++.|+..+...--.++..  |....+  +.+-+.+                       ....+
T Consensus       125 mIS~~EvKDs~ilY~~m~~e~~~vS~kvq~~L~~LV~~~Ns~~~~~~E~~~Fv~~~~~~E~S~~sWK~G~vAdL~~E~~P  204 (625)
T KOG4422|consen  125 MISSREVKDSCILYERMRSENVDVSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFGEDSTSSWKSGAVADLLFETLP  204 (625)
T ss_pred             HHhhcccchhHHHHHHHHhcCCCCCHHHHHHHHHHHHhhcCCCCcchhHHHHhhccccccccccccccccHHHHHHhhcC
Confidence            34578899999999999999887776555555431  222221  1111111                       23345


Q ss_pred             cchhhHHHHHHHHHhcCCccccc--------------------------------------------hHHHHHHHHHHHH
Q 039275           58 LSSYSLSSKTSRYAHSGRIRLAR--------------------------------------------DPVSCKAMISGYS   93 (153)
Q Consensus        58 ~~~~~~~~ll~~~~~~g~~~~a~--------------------------------------------~~~~~~~li~~~~   93 (153)
                      .+..++.+||.+.|+....+.|.                                            |..|+|++++...
T Consensus       205 KT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~K~Lv~EMisqkm~Pnl~TfNalL~c~a  284 (625)
T KOG4422|consen  205 KTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVGKKLVAEMISQKMTPNLFTFNALLSCAA  284 (625)
T ss_pred             CCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhccHHHHHHHHHhhcCCchHhHHHHHHHHH
Confidence            56778888888888888888777                                            6777777777777


Q ss_pred             hcCChHHH----HHHHHHHHHcCCCCChhhHHHHHHHhcCCCcccc
Q 039275           94 QAGRFNEA----LEPFGKLESLGVHTDEVTMVVVLAASSGPGALDF  135 (153)
Q Consensus        94 ~~g~~~~a----~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~  135 (153)
                      +.|+++.|    .+++.+|++-|+.|+-.+|..+|.-+++-++..+
T Consensus       285 kfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k  330 (625)
T KOG4422|consen  285 KFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQK  330 (625)
T ss_pred             HhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchh
Confidence            77766543    4566677777777777777777776666666554

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.88  E-value=1.4e-08  Score=75.19  Aligned_cols=127  Identities=15%  Similarity=0.111  Sum_probs=102.3

Q ss_pred             ChhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHH-HHHHhhhhhcchhhHHHHHHHHHhcCCcccc
Q 039275            1 MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWIL-AKELQIELDLSSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         1 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~-a~~~~~~~~~~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      ||.+.|+--..++|.+++.+-+....+.+..+||.+|.+-+=...-+. ++-+.-.+.||..|+|+++++..+.|+++.|
T Consensus       213 mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~K~Lv~EMisqkm~Pnl~TfNalL~c~akfg~F~~a  292 (625)
T KOG4422|consen  213 MIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVGKKLVAEMISQKMTPNLFTFNALLSCAAKFGKFEDA  292 (625)
T ss_pred             HHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhccHHHHHHHHHhhcCCchHhHHHHHHHHHHhcchHHH
Confidence            578889999999999999999999999999999999986543332222 3333777899999999999999999999998


Q ss_pred             c-----------------hHHHHHHHHHHHHhcCChHH-HHHHHHHHHHc----CCCCChhhHHHHHHHh
Q 039275           80 R-----------------DPVSCKAMISGYSQAGRFNE-ALEPFGKLESL----GVHTDEVTMVVVLAAS  127 (153)
Q Consensus        80 ~-----------------~~~~~~~li~~~~~~g~~~~-a~~~~~~m~~~----g~~p~~~t~~~li~~~  127 (153)
                      +                 ...+|..+|.-+++.+++.+ +..+..+++..    -++|-..+-+-++..-
T Consensus       293 r~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~~FF~~A  362 (625)
T KOG4422|consen  293 RKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDNKFFQSA  362 (625)
T ss_pred             HHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchhHHHHHH
Confidence            8                 78899999999999999855 55556666543    4888888888776543

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

Probab=98.86  E-value=9.6e-08  Score=77.13  Aligned_cols=134  Identities=13%  Similarity=-0.001  Sum_probs=75.6

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hh--hh-hcchhhHHHHHHHHHhcCCccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QI--EL-DLSSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~--~~-~~~~~~~~~ll~~~~~~g~~~~   78 (153)
                      ..|.+.|++++|.++++++.+. .+.+...|..+...+.+.|++++|.+. ..  .. +.+...+..+...+.+.|++++
T Consensus       575 ~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  653 (899)
T TIGR02917       575 QYYLGKGQLKKALAILNEAADA-APDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQPDSALALLLLADAYAVMKNYAK  653 (899)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHc-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHH
Confidence            3456666677777777666543 344566666667777777777777666 11  11 2234455566666666666666


Q ss_pred             cc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           79 AR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        79 a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |.            +..+|..+...+...|++++|.++++.+.... .++...+..+...+.+.|++++|.+
T Consensus       654 A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~  724 (899)
T TIGR02917       654 AITSLKRALELKPDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQH-PKAALGFELEGDLYLRQKDYPAAIQ  724 (899)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCChHHHHHHHHHHHHCCCHHHHHH
Confidence            65            44555555555555555555555555555443 2233444444455555555555544

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.

>PF12854 PPR_1: PPR repeat

Probab=98.83  E-value=4.5e-09  Score=51.15  Aligned_cols=31  Identities=26%  Similarity=0.118  Sum_probs=26.6

Q ss_pred             cCCCccHHHHHHHHHHhcCCCchHHHHHHhh
Q 039275           24 LGVHTDEVTMVVVLTASSGPGAWILAKELQI   54 (153)
Q Consensus        24 ~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~   54 (153)
                      .|++||..||+++|+++++.|++++|.++..
T Consensus         1 ~G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~   31 (34)
T PF12854_consen    1 RGCEPDVVTYNTLIDGYCKAGRVDEAFELFD   31 (34)
T ss_pred             CCCCCcHhHHHHHHHHHHHCCCHHHHHHHHH
Confidence            4788999999999999999999999988743

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

Probab=98.82  E-value=1.6e-07  Score=75.92  Aligned_cols=133  Identities=13%  Similarity=0.088  Sum_probs=87.4

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhh---hhcchhhHHHHHHHHHhcCCccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIE---LDLSSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~---~~~~~~~~~~ll~~~~~~g~~~~   78 (153)
                      ..|.+.|++++|.+.|+++.+.. +.+...+..+...+.+.|++++|.+. +..   .+.+...+..+...+.+.|++++
T Consensus       609 ~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  687 (899)
T TIGR02917       609 RAQLAAGDLNKAVSSFKKLLALQ-PDSALALLLLADAYAVMKNYAKAITSLKRALELKPDNTEAQIGLAQLLLAAKRTES  687 (899)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHH
Confidence            45677788888888888776542 34556667777777778888887777 111   22335566677777777777777


Q ss_pred             cc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           79 AR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        79 a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |.            +...|..+...+.+.|++++|.+.|+.+...+  |+..++..+..++.+.|++++|.+
T Consensus       688 A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~A~~  757 (899)
T TIGR02917       688 AKKIAKSLQKQHPKAALGFELEGDLYLRQKDYPAAIQAYRKALKRA--PSSQNAIKLHRALLASGNTAEAVK  757 (899)
T ss_pred             HHHHHHHHHhhCcCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--CCchHHHHHHHHHHHCCCHHHHHH
Confidence            66            45556666666677777777777777766543  444556666666666666666655

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.

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

Probab=98.80  E-value=6.5e-09  Score=49.29  Aligned_cols=31  Identities=42%  Similarity=0.834  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHcCC
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESLGV  113 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  113 (153)
                      ++||+||.+|++.|++++|.++|++|++.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            4799999999999999999999999999875

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.

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

Probab=98.73  E-value=6.1e-08  Score=77.09  Aligned_cols=111  Identities=14%  Similarity=0.101  Sum_probs=94.7

Q ss_pred             HHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH----------------------------hhhhhcchhhHHHHH
Q 039275           16 EPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL----------------------------QIELDLSSYSLSSKT   67 (153)
Q Consensus        16 ~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~----------------------------~~~~~~~~~~~~~ll   67 (153)
                      +++-.+...|+.|+.+||.++|..||..|+.+.|--+                            ++.-.|...+|+.|+
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiarYc~~gdieaatif~fm~~ksLpv~e~vf~~lv~sh~~And~Enpkep~aDtyt~Ll   90 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIARYCTKGDIEAATIFPFMEIKSLPVREGVFRGLVASHKEANDAENPKEPLADTYTNLL   90 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHHHcccCCCccccchhhhhcccccccchhHHHHHhcccccccccCCCCCchhHHHHHH
Confidence            5677888999999999999999999999998887722                            122246778999999


Q ss_pred             HHHHhcCCccccc-------------------------------------------------------------------
Q 039275           68 SRYAHSGRIRLAR-------------------------------------------------------------------   80 (153)
Q Consensus        68 ~~~~~~g~~~~a~-------------------------------------------------------------------   80 (153)
                      ++|.+.||+..-.                                                                   
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            9999999976533                                                                   


Q ss_pred             --------------------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHH
Q 039275           81 --------------------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAA  126 (153)
Q Consensus        81 --------------------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~  126 (153)
                                                      ++.+|.+++.....+|+++.|..++.+|++.|+..+.+=|..++-+
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 NAPFQVFLRQNVVDNTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIRAHYFWPLLLG  248 (1088)
T ss_pred             cchHHHHHHHhccCCchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCcccccchhhhhc
Confidence                                            8899999999999999999999999999999988888888888766

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.48  E-value=1.6e-07  Score=45.47  Aligned_cols=30  Identities=40%  Similarity=0.663  Sum_probs=28.2

Q ss_pred             ChhhHhhcCChhHHHHHHHHhHHcCCCccH
Q 039275            1 MISGYSQAGRFNEALEPFGKLESLGVHTDE   30 (153)
Q Consensus         1 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~   30 (153)
                      ||++|++.|++++|.++|++|++.|++||.
T Consensus         6 li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         6 LIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            588999999999999999999999999984

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.

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.46  E-value=8.2e-06  Score=55.70  Aligned_cols=134  Identities=13%  Similarity=0.074  Sum_probs=91.5

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhh---hhcchhhHHHHHHHHHhcCCccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIE---LDLSSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~---~~~~~~~~~~ll~~~~~~g~~~~   78 (153)
                      ..|.+.|++++|.+.|++..+.. +.+...+..+-..+...|++++|.+. ..-   .+.+...+..+...+...|++++
T Consensus        39 ~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~  117 (234)
T TIGR02521        39 LGYLEQGDLEVAKENLDKALEHD-PDDYLAYLALALYYQQLGELEKAEDSFRRALTLNPNNGDVLNNYGTFLCQQGKYEQ  117 (234)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcccHHH
Confidence            35677888888888888876542 33456667777788888888888877 111   12334556666777778888877


Q ss_pred             cc--------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           79 AR--------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        79 a~--------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |.              ....+..+-..+...|++++|.+.|.+..... ..+...+..+...+.+.|++++|.+
T Consensus       118 A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~  190 (234)
T TIGR02521       118 AMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQID-PQRPESLLELAELYYLRGQYKDARA  190 (234)
T ss_pred             HHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCChHHHHHHHHHHHHcCCHHHHHH
Confidence            76              23355556667778888888888888776543 2234566677777778888887766

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.

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.42  E-value=8.3e-06  Score=55.66  Aligned_cols=134  Identities=14%  Similarity=0.152  Sum_probs=104.1

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhh-----hcchhhHHHHHHHHHhcCCc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIEL-----DLSSYSLSSKTSRYAHSGRI   76 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~-----~~~~~~~~~ll~~~~~~g~~   76 (153)
                      ..|...|++++|.+.|++..+.. +.+...+..+-..+...|++++|.+. ...+     ......+..+...+.+.|++
T Consensus        73 ~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  151 (234)
T TIGR02521        73 LYYQQLGELEKAEDSFRRALTLN-PNNGDVLNNYGTFLCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDF  151 (234)
T ss_pred             HHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCH
Confidence            35778899999999999987753 34556677777888999999999998 2211     12334566677888999999


Q ss_pred             cccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           77 RLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        77 ~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ++|.            +...|..+...+...|++++|.+.+++..+. ...+...+......+...|+.+.|..
T Consensus       152 ~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~  224 (234)
T TIGR02521       152 DKAEKYLTRALQIDPQRPESLLELAELYYLRGQYKDARAYLERYQQT-YNQTAESLWLGIRIARALGDVAAAQR  224 (234)
T ss_pred             HHHHHHHHHHHHhCcCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHHhhHHHHHH
Confidence            9887            4667888889999999999999999998876 24456667777778888888887765

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.

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

Probab=98.40  E-value=4.6e-07  Score=64.94  Aligned_cols=135  Identities=25%  Similarity=0.226  Sum_probs=74.8

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcC-CCccHHHHHHHHHHhcCCCchHHHHHH-h--hhhhc-chhhHHHHHHHHHhcCCcc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLG-VHTDEVTMVVVLTASSGPGAWILAKEL-Q--IELDL-SSYSLSSKTSRYAHSGRIR   77 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~~~~~ll~~~~~~~~~~~a~~~-~--~~~~~-~~~~~~~ll~~~~~~g~~~   77 (153)
                      ..+.+.++++++.++++...+.. .+++...|..+-..+.+.|+.++|.+. +  -...| |....+.++..+...|+.+
T Consensus       118 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~P~~~~~~~~l~~~li~~~~~~  197 (280)
T PF13429_consen  118 QLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKALELDPDDPDARNALAWLLIDMGDYD  197 (280)
T ss_dssp             H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHCTTCHHH
T ss_pred             HHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCChH
Confidence            34566677777777777765432 345666666666667777777777777 2  22334 3455666777777777766


Q ss_pred             ccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           78 LAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        78 ~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ++.            ++..|..+-.++...|+.++|...|++..... +.|......+.+++.+.|+.++|.+
T Consensus       198 ~~~~~l~~~~~~~~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~-p~d~~~~~~~a~~l~~~g~~~~A~~  269 (280)
T PF13429_consen  198 EAREALKRLLKAAPDDPDLWDALAAAYLQLGRYEEALEYLEKALKLN-PDDPLWLLAYADALEQAGRKDEALR  269 (280)
T ss_dssp             HHHHHHHHHHHH-HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHT----------
T ss_pred             HHHHHHHHHHHHCcCHHHHHHHHHHHhcccccccccccccccccccc-ccccccccccccccccccccccccc
Confidence            644            55666777777777777777777777766532 2256666666677777777777665

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

Probab=98.40  E-value=3.4e-06  Score=60.41  Aligned_cols=143  Identities=20%  Similarity=0.095  Sum_probs=86.4

Q ss_pred             hhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH------hhhhhcchhhHHHHHHHHHhcCCcccc
Q 039275            6 SQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL------QIELDLSSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         6 ~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~------~~~~~~~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      ...+++++|.++++...+..  +++..+..++..+.+.++++++.++      ....+++...|..+...+.+.|+.++|
T Consensus        88 ~~~~~~~~A~~~~~~~~~~~--~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A  165 (280)
T PF13429_consen   88 LQDGDPEEALKLAEKAYERD--GDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKA  165 (280)
T ss_dssp             --------------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHH
T ss_pred             cccccccccccccccccccc--cccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHH
Confidence            67899999999998876543  6777788899999999999999888      112345677888888999999999999


Q ss_pred             c------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh---------
Q 039275           80 R------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS---------  138 (153)
Q Consensus        80 ~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~---------  138 (153)
                      .            +....+.++..+...|+.+++.++++...+.. ..|...+..+-.++..+|+.++|..         
T Consensus       166 ~~~~~~al~~~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~  244 (280)
T PF13429_consen  166 LRDYRKALELDPDDPDARNALAWLLIDMGDYDEAREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKALKLN  244 (280)
T ss_dssp             HHHHHHHHHH-TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-cCHHHHHHHHHHHhcccccccccccccccccccc
Confidence            9            67889999999999999999999999988665 4455667888999999999999988         


Q ss_pred             --HHHHHHHHHHHhh
Q 039275          139 --NIFLTTAIIEMYA  151 (153)
Q Consensus       139 --~~~~~~~li~~y~  151 (153)
                        |+.+...+.+.+.
T Consensus       245 p~d~~~~~~~a~~l~  259 (280)
T PF13429_consen  245 PDDPLWLLAYADALE  259 (280)
T ss_dssp             TT-HHHHHHHHHHHT
T ss_pred             ccccccccccccccc
Confidence              6666666665553

>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=2.9e-06  Score=52.09  Aligned_cols=71  Identities=10%  Similarity=-0.014  Sum_probs=56.6

Q ss_pred             hhhHhhcCChhHHHHHHHHhHHcCC-CccHHHHHHHHHHhcCCCchHH--------HHHH-----hhhhhcchhhHHHHH
Q 039275            2 ISGYSQAGRFNEALEPFGKLESLGV-HTDEVTMVVVLTASSGPGAWIL--------AKEL-----QIELDLSSYSLSSKT   67 (153)
Q Consensus         2 i~~~~~~g~~~~a~~~~~~m~~~g~-~p~~~~~~~ll~~~~~~~~~~~--------a~~~-----~~~~~~~~~~~~~ll   67 (153)
                      |..+...+++.....+|..+++.|+ .|++.+|+.+|.+.++...-.+        .+.+     ..+++|+..+|+.+|
T Consensus        32 I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etYnivl  111 (120)
T PF08579_consen   32 INSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETYNIVL  111 (120)
T ss_pred             HHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHHHHHH
Confidence            4567778999999999999999999 9999999999999887653211        1111     777899998888888


Q ss_pred             HHHHh
Q 039275           68 SRYAH   72 (153)
Q Consensus        68 ~~~~~   72 (153)
                      ..+.+
T Consensus       112 ~~Llk  116 (120)
T PF08579_consen  112 GSLLK  116 (120)
T ss_pred             HHHHH
Confidence            76654

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 [, , ].

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.25  E-value=1e-06  Score=42.46  Aligned_cols=28  Identities=25%  Similarity=0.507  Sum_probs=26.6

Q ss_pred             ChhhHhhcCChhHHHHHHHHhHHcCCCc
Q 039275            1 MISGYSQAGRFNEALEPFGKLESLGVHT   28 (153)
Q Consensus         1 li~~~~~~g~~~~a~~~~~~m~~~g~~p   28 (153)
                      +|.+|++.|+++.|.++|+.|++.|++|
T Consensus         7 ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    7 LLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            5789999999999999999999999988

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=98.18  E-value=9.6e-05  Score=59.20  Aligned_cols=73  Identities=10%  Similarity=-0.009  Sum_probs=31.3

Q ss_pred             hcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH---hhhhhcc-hhhHHHHHHHHHhcCCccccc
Q 039275            7 QAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL---QIELDLS-SYSLSSKTSRYAHSGRIRLAR   80 (153)
Q Consensus         7 ~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~~-~~~~~~ll~~~~~~g~~~~a~   80 (153)
                      ..|++++|...|+++.+. -+.+...+..+-..+.+.|++++|.+.   -....|+ ...+..+...+...|++++|.
T Consensus        88 ~~g~~~~A~~~l~~~l~~-~P~~~~a~~~la~~l~~~g~~~~Ai~~l~~Al~l~P~~~~a~~~la~~l~~~g~~~eA~  164 (656)
T PRK15174         88 ASSQPDAVLQVVNKLLAV-NVCQPEDVLLVASVLLKSKQYATVADLAEQAWLAFSGNSQIFALHLRTLVLMDKELQAI  164 (656)
T ss_pred             hcCCHHHHHHHHHHHHHh-CCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCChHHHH
Confidence            345555555555555442 111223333334444555555555544   1111222 233444445555555555444

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=98.17  E-value=7.3e-05  Score=59.89  Aligned_cols=132  Identities=14%  Similarity=0.072  Sum_probs=73.2

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-h--hhh-hcchhhHHHHHHHHHhcCCcccc-
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-Q--IEL-DLSSYSLSSKTSRYAHSGRIRLA-   79 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~--~~~-~~~~~~~~~ll~~~~~~g~~~~a-   79 (153)
                      +.+.|++++|...++++.+..-.++...+..+..++.+.|++++|... .  ... +.+...+..+-..+.+.|++++| 
T Consensus       187 l~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~p~~~~~~~~Lg~~l~~~G~~~eA~  266 (656)
T PRK15174        187 FLNKSRLPEDHDLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARGLDGAALRRSLGLAYYQSGRSREAK  266 (656)
T ss_pred             HHHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhhH
Confidence            445566666666666654443223333333444555666666666665 1  111 22334555566667777777652 


Q ss_pred             ---c------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC-hhhHHHHHHHhcCCCccccchh
Q 039275           80 ---R------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTD-EVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        80 ---~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~~~~a~~  138 (153)
                         .            +...+..+-..+...|++++|...+++....  .|+ ......+..++.+.|++++|..
T Consensus       267 ~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l--~P~~~~a~~~La~~l~~~G~~~eA~~  339 (656)
T PRK15174        267 LQAAEHWRHALQFNSDNVRIVTLYADALIRTGQNEKAIPLLQQSLAT--HPDLPYVRAMYARALRQVGQYTAASD  339 (656)
T ss_pred             HHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHH
Confidence               2            4556666666666777777777776666643  232 3334445556666666666665

>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=98.09  E-value=0.00014  Score=57.80  Aligned_cols=128  Identities=18%  Similarity=0.110  Sum_probs=54.3

Q ss_pred             CChhHHHHHHHHhHHcC-CCcc-HHHHHHHHHHhcCCCchHHHHHH-hhh--hhcc-hhhHHHHHHHHHhcCCccccc--
Q 039275            9 GRFNEALEPFGKLESLG-VHTD-EVTMVVVLTASSGPGAWILAKEL-QIE--LDLS-SYSLSSKTSRYAHSGRIRLAR--   80 (153)
Q Consensus         9 g~~~~a~~~~~~m~~~g-~~p~-~~~~~~ll~~~~~~~~~~~a~~~-~~~--~~~~-~~~~~~ll~~~~~~g~~~~a~--   80 (153)
                      +++++|.+.|++....+ ..|+ ...+..+-..+...|++++|... ..-  ..|+ ...|..+...+...|++++|.  
T Consensus       308 ~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~~~  387 (615)
T TIGR00990       308 ESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELDPRVTQSYIKRASMNLELGDPDKAEED  387 (615)
T ss_pred             hhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHCCCHHHHHHH
Confidence            34555555555554432 2222 23333333444455555555555 111  1222 223334444444445544444  


Q ss_pred             ----------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           81 ----------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ----------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                                +...|..+-..+...|++++|.+.|++..+..  | +...+..+-..+.+.|++++|..
T Consensus       388 ~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~--P~~~~~~~~la~~~~~~g~~~eA~~  454 (615)
T TIGR00990       388 FDKALKLNSEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLD--PDFIFSHIQLGVTQYKEGSIASSMA  454 (615)
T ss_pred             HHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--ccCHHHHHHHHHHHHHCCCHHHHHH
Confidence                      33444444444444444444444444444321  2 22333333344444444444444

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

Probab=98.07  E-value=0.00014  Score=53.70  Aligned_cols=135  Identities=15%  Similarity=0.109  Sum_probs=110.2

Q ss_pred             hhhHhhcCChhHHHHHHHHhHHcCCCccH-------HHHHHHHHHhcCCCchHHHHHH----hhhhhcchhhHHHHHHHH
Q 039275            2 ISGYSQAGRFNEALEPFGKLESLGVHTDE-------VTMVVVLTASSGPGAWILAKEL----QIELDLSSYSLSSKTSRY   70 (153)
Q Consensus         2 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~-------~~~~~ll~~~~~~~~~~~a~~~----~~~~~~~~~~~~~ll~~~   70 (153)
                      ..+|.+.|++.+...+..+|.+.|.--|.       .+|+.++.-....+..+.-..+    ....+-+...-.+++.-+
T Consensus       194 ~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~pr~lr~~p~l~~~~a~~l  273 (400)
T COG3071         194 LRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKNQPRKLRNDPELVVAYAERL  273 (400)
T ss_pred             HHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhccHHhhcChhHHHHHHHHH
Confidence            35789999999999999999999876654       6788888877777766664444    333444556666777777


Q ss_pred             HhcCCccccc-------------------------------------------hHHHHHHHHHHHHhcCChHHHHHHHHH
Q 039275           71 AHSGRIRLAR-------------------------------------------DPVSCKAMISGYSQAGRFNEALEPFGK  107 (153)
Q Consensus        71 ~~~g~~~~a~-------------------------------------------~~~~~~~li~~~~~~g~~~~a~~~~~~  107 (153)
                      .++|+-++|.                                           ++..+.+|=.-|.+.+.|.+|.+.|+.
T Consensus       274 i~l~~~~~A~~~i~~~Lk~~~D~~L~~~~~~l~~~d~~~l~k~~e~~l~~h~~~p~L~~tLG~L~~k~~~w~kA~~~lea  353 (400)
T COG3071         274 IRLGDHDEAQEIIEDALKRQWDPRLCRLIPRLRPGDPEPLIKAAEKWLKQHPEDPLLLSTLGRLALKNKLWGKASEALEA  353 (400)
T ss_pred             HHcCChHHHHHHHHHHHHhccChhHHHHHhhcCCCCchHHHHHHHHHHHhCCCChhHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            8888877777                                           788899999999999999999999994


Q ss_pred             HHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275          108 LESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       108 m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      -.  ..+|+..+|+-+-.++-++|+..+|.+
T Consensus       354 Al--~~~~s~~~~~~la~~~~~~g~~~~A~~  382 (400)
T COG3071         354 AL--KLRPSASDYAELADALDQLGEPEEAEQ  382 (400)
T ss_pred             HH--hcCCChhhHHHHHHHHHHcCChHHHHH
Confidence            44  568999999999999999999999987

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=98.06  E-value=0.00011  Score=55.50  Aligned_cols=135  Identities=11%  Similarity=0.023  Sum_probs=83.2

Q ss_pred             hhhHhhcCChhHHHHHHHHhHHcCCCccH-----------------------------------------HHHHHHHHHh
Q 039275            2 ISGYSQAGRFNEALEPFGKLESLGVHTDE-----------------------------------------VTMVVVLTAS   40 (153)
Q Consensus         2 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~-----------------------------------------~~~~~ll~~~   40 (153)
                      ...|.+.|++++|.+++..+.+.+..++.                                         .....+..++
T Consensus       194 ~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~~~~~~~~~~~~A~~l  273 (398)
T PRK10747        194 EQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQSRKTRHQVALQVAMAEHL  273 (398)
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHHHhCCHHHHHHHHHHH
Confidence            35678889999999999999877654322                                         1122223333


Q ss_pred             cCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHH
Q 039275           41 SGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGK  107 (153)
Q Consensus        41 ~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~  107 (153)
                      ...|+.++|.+. ....+.....--.++.+....++.+++.            |...+-++-..+.+.+++++|.+.|+.
T Consensus       274 ~~~g~~~~A~~~L~~~l~~~~~~~l~~l~~~l~~~~~~~al~~~e~~lk~~P~~~~l~l~lgrl~~~~~~~~~A~~~le~  353 (398)
T PRK10747        274 IECDDHDTAQQIILDGLKRQYDERLVLLIPRLKTNNPEQLEKVLRQQIKQHGDTPLLWSTLGQLLMKHGEWQEASLAFRA  353 (398)
T ss_pred             HHCCCHHHHHHHHHHHHhcCCCHHHHHHHhhccCCChHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            334444444444 1111111111111233333334444444            666677777888888889999988888


Q ss_pred             HHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275          108 LESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       108 m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ..+.  .|+..++..+-..+.+.|+.++|.+
T Consensus       354 al~~--~P~~~~~~~La~~~~~~g~~~~A~~  382 (398)
T PRK10747        354 ALKQ--RPDAYDYAWLADALDRLHKPEEAAA  382 (398)
T ss_pred             HHhc--CCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            8754  5888888888888888888888766

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.04  E-value=0.00017  Score=60.08  Aligned_cols=130  Identities=12%  Similarity=0.047  Sum_probs=65.3

Q ss_pred             hhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH---hhhhhcchhhHHHHHHHHHhcCCccccc--
Q 039275            6 SQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL---QIELDLSSYSLSSKTSRYAHSGRIRLAR--   80 (153)
Q Consensus         6 ~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~~~~~~~~ll~~~~~~g~~~~a~--   80 (153)
                      .+.|++++|...|++..+.. +++...+..+.....+.|++++|...   -....|+...+..+-..+.+.|+.++|.  
T Consensus       553 l~~Gd~~eA~~~l~qAL~l~-P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l~P~~~a~~~LA~~l~~lG~~deA~~~  631 (987)
T PRK09782        553 QAAGNGAARDRWLQQAEQRG-LGDNALYWWLHAQRYIPGQPELALNDLTRSLNIAPSANAYVARATIYRQRHNVPAAVSD  631 (987)
T ss_pred             HHCCCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            34445555555554444332 11222222222233344555555555   1122344455555556666666666665  


Q ss_pred             ----------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           81 ----------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ----------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                                +...++.+-..+...|++++|.+.|++..+.  .| +...+..+-.++...|++++|..
T Consensus       632 l~~AL~l~Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l--~P~~~~a~~nLA~al~~lGd~~eA~~  698 (987)
T PRK09782        632 LRAALELEPNNSNYQAALGYALWDSGDIAQSREMLERAHKG--LPDDPALIRQLAYVNQRLDDMAATQH  698 (987)
T ss_pred             HHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHH
Confidence                      4555555555666666666666666665543  23 33445555556666666666655

>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=98.02  E-value=0.00019  Score=57.01  Aligned_cols=131  Identities=12%  Similarity=-0.024  Sum_probs=105.2

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCcc-HHHHHHHHHHhcCCCchHHHHHH-hh--hhh-cchhhHHHHHHHHHhcCCccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTD-EVTMVVVLTASSGPGAWILAKEL-QI--ELD-LSSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~-~~~~~~ll~~~~~~~~~~~a~~~-~~--~~~-~~~~~~~~ll~~~~~~g~~~~   78 (153)
                      .+...|++++|+..|++....  .|+ ...|..+-..+...|++++|... ..  ... .+...+..+...+...|++++
T Consensus       340 ~~~~~g~~~eA~~~~~kal~l--~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~  417 (615)
T TIGR00990       340 FKCLKGKHLEALADLSKSIEL--DPRVTQSYIKRASMNLELGDPDKAEEDFDKALKLNSEDPDIYYHRAQLHFIKGEFAQ  417 (615)
T ss_pred             HHHHcCCHHHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHH
Confidence            456789999999999998764  354 55777777788899999999988 22  222 345678888899999999999


Q ss_pred             cc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           79 AR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        79 a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |.            +...|..+-..+.+.|++++|...|++..+.  .| +...+..+-..+...|++++|..
T Consensus       418 A~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~~~~A~~  488 (615)
T TIGR00990       418 AGKDYQKSIDLDPDFIFSHIQLGVTQYKEGSIASSMATFRRCKKN--FPEAPDVYNYYGELLLDQNKFDEAIE  488 (615)
T ss_pred             HHHHHHHHHHcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHccCHHHHHH
Confidence            98            5667778888899999999999999998754  35 45678888889999999999987

>PRK12370 invasion protein regulator; Provisional

Probab=97.99  E-value=0.00036  Score=54.86  Aligned_cols=128  Identities=13%  Similarity=0.011  Sum_probs=82.7

Q ss_pred             CChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hh--hhhcc-hhhHHHHHHHHHhcCCccccc----
Q 039275            9 GRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QI--ELDLS-SYSLSSKTSRYAHSGRIRLAR----   80 (153)
Q Consensus         9 g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~--~~~~~-~~~~~~ll~~~~~~g~~~~a~----   80 (153)
                      +++++|...+++..+.. +-+...+..+-..+...|++++|.+. +.  ...|+ ...+..+-..+...|++++|.    
T Consensus       318 ~~~~~A~~~~~~Al~ld-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~G~~~eAi~~~~  396 (553)
T PRK12370        318 NAMIKAKEHAIKATELD-HNNPQALGLLGLINTIHSEYIVGSLLFKQANLLSPISADIKYYYGWNLFMAGQLEEALQTIN  396 (553)
T ss_pred             hHHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            45778888888776642 23455555555666777888888877 22  23343 345666677788888888877    


Q ss_pred             --------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChh-hHHHHHHHhcCCCccccchh
Q 039275           81 --------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEV-TMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 --------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~-t~~~li~~~~~~g~~~~a~~  138 (153)
                              +...+..+...+...|++++|.+.+++..... .|+.. .+..+-.++...|+.++|..
T Consensus       397 ~Al~l~P~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~-~p~~~~~~~~la~~l~~~G~~~eA~~  462 (553)
T PRK12370        397 ECLKLDPTRAAAGITKLWITYYHTGIDDAIRLGDELRSQH-LQDNPILLSMQVMFLSLKGKHELARK  462 (553)
T ss_pred             HHHhcCCCChhhHHHHHHHHHhccCHHHHHHHHHHHHHhc-cccCHHHHHHHHHHHHhCCCHHHHHH
Confidence                    22233344555667788888888888876443 34333 34555566777888888887

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

Probab=97.94  E-value=6.8e-06  Score=38.52  Aligned_cols=26  Identities=46%  Similarity=0.913  Sum_probs=24.2

Q ss_pred             ChhhHhhcCChhHHHHHHHHhHHcCC
Q 039275            1 MISGYSQAGRFNEALEPFGKLESLGV   26 (153)
Q Consensus         1 li~~~~~~g~~~~a~~~~~~m~~~g~   26 (153)
                      ||++|++.|++++|.++|++|.+.|+
T Consensus         6 li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    6 LISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             HHHHHHccchHHHHHHHHHHHhHCcC
Confidence            58999999999999999999999875

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.

>TIGR00540 hemY_coli hemY protein

Probab=97.91  E-value=0.00029  Score=53.37  Aligned_cols=58  Identities=17%  Similarity=0.193  Sum_probs=48.0

Q ss_pred             hH--HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 DP--VSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~--~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +.  ....++-..+.+.|++++|.+.|+........||...+..+...+.+.|+.++|.+
T Consensus       332 ~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~  391 (409)
T TIGR00540       332 KPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAA  391 (409)
T ss_pred             ChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            55  56678888889999999999999965555557888888899999999999998877

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.

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

Probab=97.88  E-value=0.0001  Score=59.46  Aligned_cols=78  Identities=14%  Similarity=0.121  Sum_probs=67.3

Q ss_pred             cchhhHHHHHHHHHhcCCccccc-------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHH
Q 039275           58 LSSYSLSSKTSRYAHSGRIRLAR-------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVL  124 (153)
Q Consensus        58 ~~~~~~~~ll~~~~~~g~~~~a~-------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li  124 (153)
                      |+..++..+++.-...|+++.|.             +.+-|..||-|   .|+......++.-|+..|+.|+..|+..-+
T Consensus       202 ~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfpir~HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyv  278 (1088)
T KOG4318|consen  202 PTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIRAHYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYV  278 (1088)
T ss_pred             CChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCcccccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHH
Confidence            46677888888888899998888             77777788877   889999999999999999999999999999


Q ss_pred             HHhcCCCccccchh
Q 039275          125 AASSGPGALDFGKS  138 (153)
Q Consensus       125 ~~~~~~g~~~~a~~  138 (153)
                      -.+.++|....++.
T Consensus       279 ip~l~N~~t~~~~e  292 (1088)
T KOG4318|consen  279 IPQLSNGQTKYGEE  292 (1088)
T ss_pred             Hhhhcchhhhhccc
Confidence            99999777666666

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

Probab=97.85  E-value=8.6e-05  Score=45.72  Aligned_cols=86  Identities=10%  Similarity=0.021  Sum_probs=63.8

Q ss_pred             HHHHHHHHHhcCCCchHHHHHH-----hhhh-hcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHH
Q 039275           31 VTMVVVLTASSGPGAWILAKEL-----QIEL-DLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEP  104 (153)
Q Consensus        31 ~~~~~ll~~~~~~~~~~~a~~~-----~~~~-~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~  104 (153)
                      .|-...|..+...+++.....+     +.++ .|+..+|+.++++.+++.-=.              ..-.++..+.+.+
T Consensus        26 ~t~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~--------------~~ie~kl~~LLtv   91 (120)
T PF08579_consen   26 ETQIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDS--------------EDIENKLTNLLTV   91 (120)
T ss_pred             HHHHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccc--------------hhHHHHHHHHHHH
Confidence            3445566677777888777776     7777 788888888877666544321              2223466778899


Q ss_pred             HHHHHHcCCCCChhhHHHHHHHhcCC
Q 039275          105 FGKLESLGVHTDEVTMVVVLAASSGP  130 (153)
Q Consensus       105 ~~~m~~~g~~p~~~t~~~li~~~~~~  130 (153)
                      +++|...+++|+..||+.++..+.+.
T Consensus        92 YqDiL~~~lKP~~etYnivl~~Llkg  117 (120)
T PF08579_consen   92 YQDILSNKLKPNDETYNIVLGSLLKG  117 (120)
T ss_pred             HHHHHHhccCCcHHHHHHHHHHHHHh
Confidence            99999999999999999999988763

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 [, , ].

>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=97.82  E-value=0.00018  Score=49.44  Aligned_cols=113  Identities=14%  Similarity=0.100  Sum_probs=78.6

Q ss_pred             HHHHHHhHHcCCCccHHHHHHHHHHhcCC-----CchH---HHHHH--hhhhhcchhhHHHHHHHHHhcCCccccchHHH
Q 039275           15 LEPFGKLESLGVHTDEVTMVVVLTASSGP-----GAWI---LAKEL--QIELDLSSYSLSSKTSRYAHSGRIRLARDPVS   84 (153)
Q Consensus        15 ~~~~~~m~~~g~~p~~~~~~~ll~~~~~~-----~~~~---~a~~~--~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~   84 (153)
                      .+.|+.....  ..|-.+|..+++.+.+.     |.++   .|++.  +.|+..|..+|+.||+.|=+ |.+-   ....
T Consensus        34 ~~~f~~~~~~--~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPK-g~fv---p~n~  107 (228)
T PF06239_consen   34 EELFERAPGQ--AKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPK-GKFV---PRNF  107 (228)
T ss_pred             HHHHHHHhhc--cccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCC-CCcc---cccH
Confidence            4455554222  34777788888777654     3333   23333  88888999999999988876 4432   2344


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCcccc
Q 039275           85 CKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDF  135 (153)
Q Consensus        85 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~  135 (153)
                      +.++...|-  -+-+-|.+++++|...|+-||..|+..+++.+++.+..-+
T Consensus       108 fQ~~F~hyp--~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~p~~  156 (228)
T PF06239_consen  108 FQAEFMHYP--RQQECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSHPMK  156 (228)
T ss_pred             HHHHhccCc--HHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccHHHH
Confidence            444444433  3568899999999999999999999999999998776543

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

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

Probab=97.81  E-value=0.0003  Score=53.29  Aligned_cols=114  Identities=7%  Similarity=0.058  Sum_probs=82.4

Q ss_pred             HHHHhHH---cCCCccHHHHHHHHHHhcCCCchHHHHHH--hhhhhc-----chhhHHHHHHHHHhcCCccccc------
Q 039275           17 PFGKLES---LGVHTDEVTMVVVLTASSGPGAWILAKEL--QIELDL-----SSYSLSSKTSRYAHSGRIRLAR------   80 (153)
Q Consensus        17 ~~~~m~~---~g~~p~~~~~~~ll~~~~~~~~~~~a~~~--~~~~~~-----~~~~~~~ll~~~~~~g~~~~a~------   80 (153)
                      ++..|.+   .+.+.+....-++++.+....+++++..+  +....|     -..|..++|+.|.+.|..+++.      
T Consensus        50 ~~~~l~~k~~~~~~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~  129 (429)
T PF10037_consen   50 LYSELDKKFERKKPVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNR  129 (429)
T ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhCh
Confidence            5555533   35667788888899999999999999888  222222     2244567788888888877777      


Q ss_pred             -------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCC
Q 039275           81 -------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGP  130 (153)
Q Consensus        81 -------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  130 (153)
                             |..++|.||..+.+.|++..|.++..+|...+...+..|+...+.+|.+-
T Consensus       130 ~~yGiF~D~~s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  130 LQYGIFPDNFSFNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             hhcccCCChhhHHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence                   78888888888888888888888888887766666667777666666655

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 [].

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=97.80  E-value=0.001  Score=55.65  Aligned_cols=129  Identities=13%  Similarity=0.070  Sum_probs=84.9

Q ss_pred             hhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhh--hcch-hhHHHHHHHHHhcCCccccc-
Q 039275            6 SQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIEL--DLSS-YSLSSKTSRYAHSGRIRLAR-   80 (153)
Q Consensus         6 ~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~--~~~~-~~~~~ll~~~~~~g~~~~a~-   80 (153)
                      .+.|++++|...|+++...  +|+...+..+...+.+.|++++|..+ +.-+  .|+. ..+..+.....+.|++++|. 
T Consensus       520 ~~~Gr~eeAi~~~rka~~~--~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~P~~~~l~~~La~~l~~~Gr~~eAl~  597 (987)
T PRK09782        520 YQVEDYATALAAWQKISLH--DMSNEDLLAAANTAQAAGNGAARDRWLQQAEQRGLGDNALYWWLHAQRYIPGQPELALN  597 (987)
T ss_pred             HHCCCHHHHHHHHHHHhcc--CCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHhCCCHHHHHH
Confidence            4778888888888877553  44444555556667778888888877 1111  2222 22222233334458888877 


Q ss_pred             ----------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCh-hhHHHHHHHhcCCCccccchh
Q 039275           81 ----------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDE-VTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ----------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~t~~~li~~~~~~g~~~~a~~  138 (153)
                                +...|..+-..+.+.|+.++|.+.|++....  .|+. ..+..+-.++.+.|++++|..
T Consensus       598 ~~~~AL~l~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l--~Pd~~~a~~nLG~aL~~~G~~eeAi~  664 (987)
T PRK09782        598 DLTRSLNIAPSANAYVARATIYRQRHNVPAAVSDLRAALEL--EPNNSNYQAALGYALWDSGDIAQSRE  664 (987)
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHH
Confidence                      5567777778888888888888888887754  4543 445555557888888888876

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=97.74  E-value=0.00088  Score=51.91  Aligned_cols=135  Identities=14%  Similarity=0.116  Sum_probs=77.2

Q ss_pred             hHhhcCChhHHHHHHHHhHHc---CCCcc----HHHHHHHHHHhcCCCchHHHHHH--------hh--h-hhcch-hhHH
Q 039275            4 GYSQAGRFNEALEPFGKLESL---GVHTD----EVTMVVVLTASSGPGAWILAKEL--------QI--E-LDLSS-YSLS   64 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~---g~~p~----~~~~~~ll~~~~~~~~~~~a~~~--------~~--~-~~~~~-~~~~   64 (153)
                      .|...+++++|+.+|+++...   ..-++    ..+++.|=.+|.+.|++++|...        +.  + -.|.+ .-.+
T Consensus       250 ~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~  329 (508)
T KOG1840|consen  250 VYRSLGKYDEAVNLYEEALTIREEVFGEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLS  329 (508)
T ss_pred             HHHHhccHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHH
Confidence            455666666666666666432   11112    23333444456666666666655        11  0 01111 1233


Q ss_pred             HHHHHHHhcCCccccc--------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc------CCCC-Ch
Q 039275           65 SKTSRYAHSGRIRLAR--------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESL------GVHT-DE  117 (153)
Q Consensus        65 ~ll~~~~~~g~~~~a~--------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~------g~~p-~~  117 (153)
                      .+...++..+.+++|.                    ...+++.|-..|...|++++|.++|++....      +..+ ..
T Consensus       330 ~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~  409 (508)
T KOG1840|consen  330 ELAAILQSMNEYEEAKKLLQKALKIYLDAPGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVG  409 (508)
T ss_pred             HHHHHHHHhcchhHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhh
Confidence            4445555555555555                    4567888888888888888888888777532      1222 24


Q ss_pred             hhHHHHHHHhcCCCccccchh
Q 039275          118 VTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       118 ~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ..++.+-..|.+.+.++.|.+
T Consensus       410 ~~l~~la~~~~~~k~~~~a~~  430 (508)
T KOG1840|consen  410 KPLNQLAEAYEELKKYEEAEQ  430 (508)
T ss_pred             HHHHHHHHHHHHhcccchHHH
Confidence            456677777777787777776

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=97.67  E-value=0.00092  Score=56.95  Aligned_cols=131  Identities=11%  Similarity=0.064  Sum_probs=100.2

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-h--hhh-hcchhhHHHHHHHHHhcCCccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-Q--IEL-DLSSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~--~~~-~~~~~~~~~ll~~~~~~g~~~~   78 (153)
                      ..+...|++++|.++++.     .++++..+..+-..+.+.|++++|.+. +  ... +.+...+..+...|...|+.++
T Consensus       581 ~~l~~~G~~~eA~~~l~~-----~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~P~~~~a~~~la~~~~~~g~~~e  655 (1157)
T PRK11447        581 NRLRDSGKEAEAEALLRQ-----QPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTREPGNADARLGLIEVDIAQGDLAA  655 (1157)
T ss_pred             HHHHHCCCHHHHHHHHHh-----CCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHH
Confidence            356788999999999872     355666777778888999999999998 1  112 3355678888999999999999


Q ss_pred             cc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCC--CC---ChhhHHHHHHHhcCCCccccchh
Q 039275           79 AR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGV--HT---DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        79 a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~--~p---~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |.            +...+..+-..+...|++++|.++|+.+....-  .|   +...+..+-..+.+.|+.++|.+
T Consensus       656 A~~~l~~ll~~~p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~~~~~~~~~~a~~~~~~a~~~~~~G~~~~A~~  732 (1157)
T PRK11447        656 ARAQLAKLPATANDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQAKSQPPSMESALVLRDAARFEAQTGQPQQALE  732 (1157)
T ss_pred             HHHHHHHHhccCCCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhhCccCCcchhhHHHHHHHHHHHHHcCCHHHHHH
Confidence            98            456666777888899999999999999886432  12   23455566778888999998887

>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=97.60  E-value=0.0021  Score=40.69  Aligned_cols=105  Identities=13%  Similarity=0.080  Sum_probs=73.4

Q ss_pred             cHHHHHHHHHHhcCCCchHHHHHH---hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHH
Q 039275           29 DEVTMVVVLTASSGPGAWILAKEL---QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPF  105 (153)
Q Consensus        29 ~~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~  105 (153)
                      |..++.++|-++++.|+++....+   .-|+.++...-..-   +.....  ...+.....+++.+|+..|++..|+++.
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~---~~~~sp--l~Pt~~lL~AIv~sf~~n~~i~~al~~v   75 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGD---YPPSSP--LYPTSRLLIAIVHSFGYNGDIFSALKLV   75 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCc---cCCCCC--CCCCHHHHHHHHHHHHhcccHHHHHHHH
Confidence            567889999999999999988888   22232222100000   000000  0016788999999999999999999999


Q ss_pred             HHHHH-cCCCCChhhHHHHHHHhcCCCccccchh
Q 039275          106 GKLES-LGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       106 ~~m~~-~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +.+.+ -++..+..+|..|++.+...-+......
T Consensus        76 d~fs~~Y~I~i~~~~W~~Ll~W~~v~s~~~~~~~  109 (126)
T PF12921_consen   76 DFFSRKYPIPIPKEFWRRLLEWAYVLSSKREDRA  109 (126)
T ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHHhcCCccccc
Confidence            99984 4888899999999998877666544433

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=97.59  E-value=0.0018  Score=55.29  Aligned_cols=100  Identities=17%  Similarity=0.040  Sum_probs=80.8

Q ss_pred             HHHhcCCCchHHHHHHhhhhhcchhhHHHHHHHHHhcCCccccc------------hHHHHHHHHHHHHhcCChHHHHHH
Q 039275           37 LTASSGPGAWILAKELQIELDLSSYSLSSKTSRYAHSGRIRLAR------------DPVSCKAMISGYSQAGRFNEALEP  104 (153)
Q Consensus        37 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~  104 (153)
                      ...+...|+.++|.++-...+.+...+..+-..+.+.|+.++|.            +...+..+...+...|+.++|.+.
T Consensus       580 a~~l~~~G~~~eA~~~l~~~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~P~~~~a~~~la~~~~~~g~~~eA~~~  659 (1157)
T PRK11447        580 ANRLRDSGKEAEAEALLRQQPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTREPGNADARLGLIEVDIAQGDLAAARAQ  659 (1157)
T ss_pred             HHHHHHCCCHHHHHHHHHhCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            45677788999999884444556667778889999999999998            678889999999999999999999


Q ss_pred             HHHHHHcCCCCC-hhhHHHHHHHhcCCCccccchh
Q 039275          105 FGKLESLGVHTD-EVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       105 ~~~m~~~g~~p~-~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ++...+.  .|+ ......+-.++.+.|++++|.+
T Consensus       660 l~~ll~~--~p~~~~~~~~la~~~~~~g~~~eA~~  692 (1157)
T PRK11447        660 LAKLPAT--ANDSLNTQRRVALAWAALGDTAAAQR  692 (1157)
T ss_pred             HHHHhcc--CCCChHHHHHHHHHHHhCCCHHHHHH
Confidence            9987653  443 4445666778889999999988

>PRK12370 invasion protein regulator; Provisional

Probab=97.53  E-value=0.0031  Score=49.69  Aligned_cols=126  Identities=11%  Similarity=-0.057  Sum_probs=87.4

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-h--hhhhcchh-hHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-Q--IELDLSSY-SLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~--~~~~~~~~-~~~~ll~~~~~~g~~~~a   79 (153)
                      .+...|++++|...|++..+.+ +.+...+..+-..+...|++++|... +  ....|+.. .+..+...+...|++++|
T Consensus       347 ~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~~~~~~~~~~~~~~~~g~~eeA  425 (553)
T PRK12370        347 INTIHSEYIVGSLLFKQANLLS-PISADIKYYYGWNLFMAGQLEEALQTINECLKLDPTRAAAGITKLWITYYHTGIDDA  425 (553)
T ss_pred             HHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCChhhHHHHHHHHHhccCHHHH
Confidence            4567899999999999998753 33456677777788999999999998 2  23344432 233344456668888877


Q ss_pred             c-------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhH-HHHHHHhcCCCc
Q 039275           80 R-------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTM-VVVLAASSGPGA  132 (153)
Q Consensus        80 ~-------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~-~~li~~~~~~g~  132 (153)
                      .             +...+..+-..+...|+.++|.+.+.++...  .|+.... +.+...+++.|+
T Consensus       426 ~~~~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~  490 (553)
T PRK12370        426 IRLGDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQ--EITGLIAVNLLYAEYCQNSE  490 (553)
T ss_pred             HHHHHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhc--cchhHHHHHHHHHHHhccHH
Confidence            6             2334566677788999999999999887644  4544443 444456677774

>PRK14574 hmsH outer membrane protein; Provisional

Probab=97.50  E-value=0.0055  Score=50.44  Aligned_cols=134  Identities=8%  Similarity=-0.006  Sum_probs=67.5

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHHhhhh----------hcchhhHHHHHHHHHhc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIEL----------DLSSYSLSSKTSRYAHS   73 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~----------~~~~~~~~~ll~~~~~~   73 (153)
                      ++...|+++++++.|+.|...|.+....+-..+-++|...+.+++|..+-..+          .++......|..+|...
T Consensus       301 aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~  380 (822)
T PRK14574        301 ALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNES  380 (822)
T ss_pred             HHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhc
Confidence            44555566666666666665555544445555566666666666666651110          11222234555555555


Q ss_pred             CCccccc--------------------------h-HHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHH
Q 039275           74 GRIRLAR--------------------------D-PVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAA  126 (153)
Q Consensus        74 g~~~~a~--------------------------~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~  126 (153)
                      +++++|.                          | ...+..++..+...|+.++|++.++++.... .-|.-.....-+.
T Consensus       381 e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~gdl~~Ae~~le~l~~~a-P~n~~l~~~~A~v  459 (822)
T PRK14574        381 EQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVALNDLPTAQKKLEDLSSTA-PANQNLRIALASI  459 (822)
T ss_pred             ccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence            5555555                          0 1112233444555566666666666654321 1144444455555


Q ss_pred             hcCCCccccchh
Q 039275          127 SSGPGALDFGKS  138 (153)
Q Consensus       127 ~~~~g~~~~a~~  138 (153)
                      +...|.+.+|++
T Consensus       460 ~~~Rg~p~~A~~  471 (822)
T PRK14574        460 YLARDLPRKAEQ  471 (822)
T ss_pred             HHhcCCHHHHHH
Confidence            555555555555

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

Probab=97.47  E-value=0.0016  Score=49.12  Aligned_cols=104  Identities=20%  Similarity=0.166  Sum_probs=75.2

Q ss_pred             hhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhc---chhhHHHHHHHHHhcCCcc
Q 039275            2 ISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDL---SSYSLSSKTSRYAHSGRIR   77 (153)
Q Consensus         2 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~---~~~~~~~ll~~~~~~g~~~   77 (153)
                      ++.+...++++.|+++|+++.+..  |+..  ..+...+...+.-.+|.++ ...+..   |......-.+.+.+.++.+
T Consensus       176 l~~l~~t~~~~~ai~lle~L~~~~--pev~--~~LA~v~l~~~~E~~AI~ll~~aL~~~p~d~~LL~~Qa~fLl~k~~~~  251 (395)
T PF09295_consen  176 LKYLSLTQRYDEAIELLEKLRERD--PEVA--VLLARVYLLMNEEVEAIRLLNEALKENPQDSELLNLQAEFLLSKKKYE  251 (395)
T ss_pred             HHHHhhcccHHHHHHHHHHHHhcC--CcHH--HHHHHHHHhcCcHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHH
Confidence            456677789999999999998875  5543  3466666666666667777 444432   3334444456678888888


Q ss_pred             ccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 039275           78 LAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLE  109 (153)
Q Consensus        78 ~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~  109 (153)
                      .|.            +-.+|..|...|...|++++|+..+..+.
T Consensus       252 lAL~iAk~av~lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  252 LALEIAKKAVELSPSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             HHHHHHHHHHHhCchhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            887            77788889999999999999988887775

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

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=97.41  E-value=0.0061  Score=49.92  Aligned_cols=49  Identities=6%  Similarity=-0.117  Sum_probs=21.5

Q ss_pred             HHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           89 ISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        89 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ...+...|+.++|.++++++.... .-+...+..+...+...|++++|.+
T Consensus       366 a~~l~~~g~~~eA~~~l~~al~~~-P~n~~l~~~lA~l~~~~g~~~~A~~  414 (765)
T PRK10049        366 SQVAKYSNDLPQAEMRARELAYNA-PGNQGLRIDYASVLQARGWPRAAEN  414 (765)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCHHHHHH
Confidence            334444455555555555544321 1123334444444444454444444

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

Probab=97.38  E-value=0.0032  Score=49.70  Aligned_cols=131  Identities=13%  Similarity=0.153  Sum_probs=101.6

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCcc-HHHHHHHHHHhcCCCchHHHHHH-hh--hhhc-chhhHHHHHHHHHhcCCccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTD-EVTMVVVLTASSGPGAWILAKEL-QI--ELDL-SSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~-~~~~~~ll~~~~~~~~~~~a~~~-~~--~~~~-~~~~~~~ll~~~~~~g~~~~   78 (153)
                      .|.+.|.++.|++.|++...  +.|+ +..|+-|-+++-..|++.+|.+. ..  .+.| .....+.|-..|.+.|.+++
T Consensus       295 iYyeqG~ldlAI~~Ykral~--~~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l~p~hadam~NLgni~~E~~~~e~  372 (966)
T KOG4626|consen  295 IYYEQGLLDLAIDTYKRALE--LQPNFPDAYNNLANALKDKGSVTEAVDCYNKALRLCPNHADAMNNLGNIYREQGKIEE  372 (966)
T ss_pred             EEeccccHHHHHHHHHHHHh--cCCCchHHHhHHHHHHHhccchHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhccchH
Confidence            46778999999999998766  3454 57899999999999999999988 22  1222 34567778888889999888


Q ss_pred             cc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC-hhhHHHHHHHhcCCCccccchh
Q 039275           79 AR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTD-EVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        79 a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |.            -....|.|-..|-..|+.++|...+++..+  ++|+ +..|+.+-+.|-..|+.+.|.+
T Consensus       373 A~~ly~~al~v~p~~aaa~nNLa~i~kqqgnl~~Ai~~Ykealr--I~P~fAda~~NmGnt~ke~g~v~~A~q  443 (966)
T KOG4626|consen  373 ATRLYLKALEVFPEFAAAHNNLASIYKQQGNLDDAIMCYKEALR--IKPTFADALSNMGNTYKEMGDVSAAIQ  443 (966)
T ss_pred             HHHHHHHHHhhChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHh--cCchHHHHHHhcchHHHHhhhHHHHHH
Confidence            87            456778888888899999999999888764  5674 4567777777777888887777

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

Probab=97.38  E-value=0.007  Score=42.62  Aligned_cols=111  Identities=11%  Similarity=-0.019  Sum_probs=93.6

Q ss_pred             CccHHHHHHHHHHhcCCCchHHHHHH----hhhhhcchhhHHHHHHHHHhcCCccccc------------hHHHHHHHHH
Q 039275           27 HTDEVTMVVVLTASSGPGAWILAKEL----QIELDLSSYSLSSKTSRYAHSGRIRLAR------------DPVSCKAMIS   90 (153)
Q Consensus        27 ~p~~~~~~~ll~~~~~~~~~~~a~~~----~~~~~~~~~~~~~ll~~~~~~g~~~~a~------------~~~~~~~li~   90 (153)
                      +-|....+.......+.|++.+|...    -..-++|...|+-+--.|.+.|+.++|.            +....|.|-.
T Consensus        97 ~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~~~~p~~~nNlgm  176 (257)
T COG5010          97 PKDRELLAAQGKNQIRNGNFGEAVSVLRKAARLAPTDWEAWNLLGAALDQLGRFDEARRAYRQALELAPNEPSIANNLGM  176 (257)
T ss_pred             cccHHHHHHHHHHHHHhcchHHHHHHHHHHhccCCCChhhhhHHHHHHHHccChhHHHHHHHHHHHhccCCchhhhhHHH
Confidence            33455666678888899999999888    3334678889999999999999999999            8899999999


Q ss_pred             HHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           91 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        91 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .+.-.|+.+.|..++..-...+ .-|...-..+--+....|++++|+.
T Consensus       177 s~~L~gd~~~A~~lll~a~l~~-~ad~~v~~NLAl~~~~~g~~~~A~~  223 (257)
T COG5010         177 SLLLRGDLEDAETLLLPAYLSP-AADSRVRQNLALVVGLQGDFREAED  223 (257)
T ss_pred             HHHHcCCHHHHHHHHHHHHhCC-CCchHHHHHHHHHHhhcCChHHHHh
Confidence            9999999999999999988765 3366677788888999999999998

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=97.38  E-value=0.0038  Score=48.49  Aligned_cols=135  Identities=15%  Similarity=0.141  Sum_probs=101.9

Q ss_pred             hHhhcCChhHHHHHHHHhHH---c---CCCccHHHH-HHHHHHhcCCCchHHHHHH--------hhhhhcc----hhhHH
Q 039275            4 GYSQAGRFNEALEPFGKLES---L---GVHTDEVTM-VVVLTASSGPGAWILAKEL--------QIELDLS----SYSLS   64 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~---~---g~~p~~~~~-~~ll~~~~~~~~~~~a~~~--------~~~~~~~----~~~~~   64 (153)
                      .|.+.|++++|...+++...   .   -..|.+... +.+...+...+.+++|..+        ..-+.++    ..+++
T Consensus       292 ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g~~~~~~a~~~~  371 (508)
T KOG1840|consen  292 LYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDAPGEDNVNLAKIYA  371 (508)
T ss_pred             HHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhccccchHHHHHHH
Confidence            58999999999999987643   2   233444333 3444566777899999988        2112222    35788


Q ss_pred             HHHHHHHhcCCccccc--------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc--CCCC----Chh
Q 039275           65 SKTSRYAHSGRIRLAR--------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESL--GVHT----DEV  118 (153)
Q Consensus        65 ~ll~~~~~~g~~~~a~--------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~--g~~p----~~~  118 (153)
                      .|-..|.+.|++++|.                    .....|.|-..|.+.++..+|.++|.+-..-  -+.|    ...
T Consensus       372 nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~~~~g~~~~~~~~  451 (508)
T KOG1840|consen  372 NLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDIMKLCGPDHPDVTY  451 (508)
T ss_pred             HHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHhCCCCCchHH
Confidence            9999999999999999                    4677888889999999999999999876532  2334    457


Q ss_pred             hHHHHHHHhcCCCccccchh
Q 039275          119 TMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       119 t~~~li~~~~~~g~~~~a~~  138 (153)
                      +|..|...|.+.|+++.|.+
T Consensus       452 ~~~nL~~~Y~~~g~~e~a~~  471 (508)
T KOG1840|consen  452 TYLNLAALYRAQGNYEAAEE  471 (508)
T ss_pred             HHHHHHHHHHHcccHHHHHH
Confidence            89999999999999999998

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

Probab=97.36  E-value=0.0034  Score=45.53  Aligned_cols=98  Identities=13%  Similarity=0.061  Sum_probs=68.4

Q ss_pred             HHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccc----------hHHHHHHH----HHHHHhcCChHHHH
Q 039275           38 TASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLAR----------DPVSCKAM----ISGYSQAGRFNEAL  102 (153)
Q Consensus        38 ~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~----------~~~~~~~l----i~~~~~~g~~~~a~  102 (153)
                      ..+...|++++|.++ ..+  .+.......+..|.+.++++.|.          +..+-..+    +......+.+.+|.
T Consensus       110 ~i~~~~~~~~~AL~~l~~~--~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~eD~~l~qLa~awv~l~~g~e~~~~A~  187 (290)
T PF04733_consen  110 TILFHEGDYEEALKLLHKG--GSLELLALAVQILLKMNRPDLAEKELKNMQQIDEDSILTQLAEAWVNLATGGEKYQDAF  187 (290)
T ss_dssp             HHHCCCCHHHHHHCCCTTT--TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHTTTCCCHHH
T ss_pred             HHHHHcCCHHHHHHHHHcc--CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhCchhHHHHH
Confidence            567888999999999 333  44555667788888999998888          22222223    33333345789999


Q ss_pred             HHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275          103 EPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       103 ~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .+|+++.+ .+.++..+.+.+..+...+|++++|++
T Consensus       188 y~f~El~~-~~~~t~~~lng~A~~~l~~~~~~eAe~  222 (290)
T PF04733_consen  188 YIFEELSD-KFGSTPKLLNGLAVCHLQLGHYEEAEE  222 (290)
T ss_dssp             HHHHHHHC-CS--SHHHHHHHHHHHHHCT-HHHHHH
T ss_pred             HHHHHHHh-ccCCCHHHHHHHHHHHHHhCCHHHHHH
Confidence            99999764 456788888999999999999999988

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.

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

Probab=97.32  E-value=0.0009  Score=50.78  Aligned_cols=80  Identities=15%  Similarity=0.172  Sum_probs=65.8

Q ss_pred             chhhHHHHHHHHHhcCCccccc---------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHH
Q 039275           59 SSYSLSSKTSRYAHSGRIRLAR---------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVV  123 (153)
Q Consensus        59 ~~~~~~~ll~~~~~~g~~~~a~---------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l  123 (153)
                      +......+++......+++++.               ...|.+++|..|.+.|..+++.++++.=...|+=||.+||+.+
T Consensus        65 S~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~n~L  144 (429)
T PF10037_consen   65 SSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSFNLL  144 (429)
T ss_pred             cHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhHHHH
Confidence            3444445555555555555554               4556679999999999999999999999999999999999999


Q ss_pred             HHHhcCCCccccchh
Q 039275          124 LAASSGPGALDFGKS  138 (153)
Q Consensus       124 i~~~~~~g~~~~a~~  138 (153)
                      ++.+.+.|++..|.+
T Consensus       145 md~fl~~~~~~~A~~  159 (429)
T PF10037_consen  145 MDHFLKKGNYKSAAK  159 (429)
T ss_pred             HHHHhhcccHHHHHH
Confidence            999999999999988

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 [].

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=97.30  E-value=0.0095  Score=48.83  Aligned_cols=132  Identities=14%  Similarity=0.048  Sum_probs=99.9

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hh--hhhc-chhhHHHHHHHHHhcCCccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QI--ELDL-SSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~--~~~~-~~~~~~~ll~~~~~~g~~~~   78 (153)
                      ....-.|+.++|+++|.+.... -+.+...+..+-..+...|++++|.++ +.  ...| +...+..+...+.+.|++++
T Consensus        23 ~ia~~~g~~~~A~~~~~~~~~~-~~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~l~~~g~~~e  101 (765)
T PRK10049         23 QIALWAGQDAEVITVYNRYRVH-MQLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLEPQNDDYQRGLILTLADAGQYDE  101 (765)
T ss_pred             HHHHHcCCHHHHHHHHHHHHhh-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHH
Confidence            3456789999999999998762 244556688888899999999999998 22  2334 34556678888999999999


Q ss_pred             cc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCh-hhHHHHHHHhcCCCccccchh
Q 039275           79 AR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDE-VTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        79 a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |.            +.. |..+-..+...|+.++|...+++..+.  .|+. ..+..+...+...+..+.|.+
T Consensus       102 A~~~l~~~l~~~P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~--~P~~~~~~~~la~~l~~~~~~e~Al~  171 (765)
T PRK10049        102 ALVKAKQLVSGAPDKAN-LLALAYVYKRAGRHWDELRAMTQALPR--APQTQQYPTEYVQALRNNRLSAPALG  171 (765)
T ss_pred             HHHHHHHHHHhCCCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCChHHHHH
Confidence            98            555 888888999999999999999999875  3533 334455666767777776554

>PRK14574 hmsH outer membrane protein; Provisional

Probab=97.23  E-value=0.014  Score=48.24  Aligned_cols=130  Identities=13%  Similarity=-0.010  Sum_probs=89.2

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccH--HHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHH-HH--HHHHHhcCCcc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDE--VTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLS-SK--TSRYAHSGRIR   77 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~--~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~-~l--l~~~~~~g~~~   77 (153)
                      ...+.|+++.|++.|++..+.  .|+.  ..+ -++..+...|+.++|... +.-+.|+...+. .+  ...|...|+++
T Consensus        43 i~~r~Gd~~~Al~~L~qaL~~--~P~~~~av~-dll~l~~~~G~~~~A~~~~eka~~p~n~~~~~llalA~ly~~~gdyd  119 (822)
T PRK14574         43 IRARAGDTAPVLDYLQEESKA--GPLQSGQVD-DWLQIAGWAGRDQEVIDVYERYQSSMNISSRGLASAARAYRNEKRWD  119 (822)
T ss_pred             HHHhCCCHHHHHHHHHHHHhh--CccchhhHH-HHHHHHHHcCCcHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHH
Confidence            357889999999999998774  3443  344 777777888999999998 333455433333 33  45777779999


Q ss_pred             ccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           78 LAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        78 ~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +|.            +...+..++..+...++.++|++.++++...  .|+...+..++..+...++..+|.+
T Consensus       120 ~Aiely~kaL~~dP~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~--dp~~~~~l~layL~~~~~~~~~AL~  190 (822)
T PRK14574        120 QALALWQSSLKKDPTNPDLISGMIMTQADAGRGGVVLKQATELAER--DPTVQNYMTLSYLNRATDRNYDALQ  190 (822)
T ss_pred             HHHHHHHHHHhhCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHhccc--CcchHHHHHHHHHHHhcchHHHHHH
Confidence            888            6677778888888999999999999888754  4666666444333333344433433

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

Probab=97.20  E-value=0.012  Score=45.03  Aligned_cols=80  Identities=14%  Similarity=0.102  Sum_probs=48.0

Q ss_pred             hcchhhHHHHHHHHHhcCCccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHH
Q 039275           57 DLSSYSLSSKTSRYAHSGRIRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVL  124 (153)
Q Consensus        57 ~~~~~~~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li  124 (153)
                      +-|..+.+.|-..|-+.|+-.+|+            +..+-.=|-.-|....-++++.++|++--  =+.|+.+-|..+|
T Consensus       589 p~dp~ilskl~dlydqegdksqafq~~ydsyryfp~nie~iewl~ayyidtqf~ekai~y~ekaa--liqp~~~kwqlmi  666 (840)
T KOG2003|consen  589 PNDPAILSKLADLYDQEGDKSQAFQCHYDSYRYFPCNIETIEWLAAYYIDTQFSEKAINYFEKAA--LIQPNQSKWQLMI  666 (840)
T ss_pred             CCCHHHHHHHHHHhhcccchhhhhhhhhhcccccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHH--hcCccHHHHHHHH
Confidence            335567777888888888877777            33333334444555555566666665432  3456666666666


Q ss_pred             HHhc-CCCccccchh
Q 039275          125 AASS-GPGALDFGKS  138 (153)
Q Consensus       125 ~~~~-~~g~~~~a~~  138 (153)
                      ..|. +.|++++|.+
T Consensus       667 asc~rrsgnyqka~d  681 (840)
T KOG2003|consen  667 ASCFRRSGNYQKAFD  681 (840)
T ss_pred             HHHHHhcccHHHHHH
Confidence            5443 3466666655

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=97.17  E-value=0.018  Score=43.57  Aligned_cols=105  Identities=13%  Similarity=0.144  Sum_probs=72.5

Q ss_pred             cCChhHHHHHHHHhHHcCCCccHHH-HHHHHHHhcCCCchHHHHHH---hhhhhcchhhHH--HHHHHHHhcCCccccc-
Q 039275            8 AGRFNEALEPFGKLESLGVHTDEVT-MVVVLTASSGPGAWILAKEL---QIELDLSSYSLS--SKTSRYAHSGRIRLAR-   80 (153)
Q Consensus         8 ~g~~~~a~~~~~~m~~~g~~p~~~~-~~~ll~~~~~~~~~~~a~~~---~~~~~~~~~~~~--~ll~~~~~~g~~~~a~-   80 (153)
                      .|++++|.+....-.+..  +++.. |-..-.+..+.|+++.+.+.   -....|+.....  .....+...|++++|. 
T Consensus        97 eGd~~~A~k~l~~~~~~~--~~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~~~~~~~~~~l~~a~l~l~~g~~~~Al~  174 (398)
T PRK10747         97 EGDYQQVEKLMTRNADHA--EQPVVNYLLAAEAAQQRGDEARANQHLERAAELADNDQLPVEITRVRIQLARNENHAARH  174 (398)
T ss_pred             CCCHHHHHHHHHHHHhcc--cchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHCCCHHHHHH
Confidence            588888887777654432  22222 22223444778888888888   233345544333  3356778888888888 


Q ss_pred             -----------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCC
Q 039275           81 -----------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVH  114 (153)
Q Consensus        81 -----------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~  114 (153)
                                 ++.....+...|.+.|++++|.+++..+.+.+..
T Consensus       175 ~l~~~~~~~P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~  219 (398)
T PRK10747        175 GVDKLLEVAPRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVG  219 (398)
T ss_pred             HHHHHHhcCCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCC
Confidence                       6777888889999999999999999999877644

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

Probab=97.17  E-value=0.011  Score=43.53  Aligned_cols=133  Identities=14%  Similarity=0.058  Sum_probs=87.0

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCccHHHHHH---HHHHhcCCCchHHHHHH-hh--hhhcc-hhhHHHHHHHHHhcCCcc
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTDEVTMVV---VLTASSGPGAWILAKEL-QI--ELDLS-SYSLSSKTSRYAHSGRIR   77 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~---ll~~~~~~~~~~~a~~~-~~--~~~~~-~~~~~~ll~~~~~~g~~~   77 (153)
                      +...|++++|.+.+++..+. .+.|...+..   ........+..+.+.+. ..  ...|+ ......+-..+...|+++
T Consensus        53 ~~~~g~~~~A~~~~~~~l~~-~P~~~~a~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~a~~~~~~G~~~  131 (355)
T cd05804          53 AWIAGDLPKALALLEQLLDD-YPRDLLALKLHLGAFGLGDFSGMRDHVARVLPLWAPENPDYWYLLGMLAFGLEEAGQYD  131 (355)
T ss_pred             HHHcCCHHHHHHHHHHHHHH-CCCcHHHHHHhHHHHHhcccccCchhHHHHHhccCcCCCCcHHHHHHHHHHHHHcCCHH
Confidence            46778999999999988765 3334434431   22222234444544444 11  12222 223344556778899999


Q ss_pred             ccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCC-CCCh--hhHHHHHHHhcCCCccccchh
Q 039275           78 LAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGV-HTDE--VTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        78 ~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~-~p~~--~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +|.            +...+..+-..+...|++++|.+.+++.....- .|+.  ..|..+...+...|++++|..
T Consensus       132 ~A~~~~~~al~~~p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~  207 (355)
T cd05804         132 RAEEAARRALELNPDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALA  207 (355)
T ss_pred             HHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHH
Confidence            887            566778888889999999999999998775432 2332  345577788899999999887

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.

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=97.08  E-value=0.021  Score=36.97  Aligned_cols=85  Identities=13%  Similarity=-0.065  Sum_probs=49.1

Q ss_pred             HHHHHhcCCCchHHHHHH-hh--hhhc-chhhHHHHHHHHHhcCCccccc------------hHHHHHHHHHHHHhcCCh
Q 039275           35 VVLTASSGPGAWILAKEL-QI--ELDL-SSYSLSSKTSRYAHSGRIRLAR------------DPVSCKAMISGYSQAGRF   98 (153)
Q Consensus        35 ~ll~~~~~~~~~~~a~~~-~~--~~~~-~~~~~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~~~~~g~~   98 (153)
                      ..-..+...|++++|... ..  ...| +...+..+-..+.+.|++++|.            +...|..+-..+...|+.
T Consensus        29 ~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p~~~~a~~~lg~~l~~~g~~  108 (144)
T PRK15359         29 ASGYASWQEGDYSRAVIDFSWLVMAQPWSWRAHIALAGTWMMLKEYTTAINFYGHALMLDASHPEPVYQTGVCLKMMGEP  108 (144)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHcCCH
Confidence            344455566666666555 11  1222 3334444444455555555554            556677777778888888


Q ss_pred             HHHHHHHHHHHHcCCCCChhhHH
Q 039275           99 NEALEPFGKLESLGVHTDEVTMV  121 (153)
Q Consensus        99 ~~a~~~~~~m~~~g~~p~~~t~~  121 (153)
                      ++|...|+.....  .|+...+.
T Consensus       109 ~eAi~~~~~Al~~--~p~~~~~~  129 (144)
T PRK15359        109 GLAREAFQTAIKM--SYADASWS  129 (144)
T ss_pred             HHHHHHHHHHHHh--CCCChHHH
Confidence            8888888877653  46554443

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

Probab=97.07  E-value=0.019  Score=36.21  Aligned_cols=97  Identities=15%  Similarity=0.126  Sum_probs=58.0

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDP   82 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~   82 (153)
                      .+.+.|++++|.+.|+.....+ +.+...+..+-..+.+.|++++|... ...+..+..                   +.
T Consensus        26 ~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~-------------------~~   85 (135)
T TIGR02552        26 NLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALDPD-------------------DP   85 (135)
T ss_pred             HHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-------------------Ch
Confidence            4556677777777776665532 33555555666666666777766665 222222111                   23


Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHH
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVV  122 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~  122 (153)
                      ..|..+-..+...|++++|.+.|+...+.  .|+...+..
T Consensus        86 ~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~  123 (135)
T TIGR02552        86 RPYFHAAECLLALGEPESALKALDLAIEI--CGENPEYSE  123 (135)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHh--ccccchHHH
Confidence            44555666777888888888888877754  355555443

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

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

Probab=97.05  E-value=0.019  Score=40.05  Aligned_cols=133  Identities=17%  Similarity=0.116  Sum_probs=83.9

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-h--hhhhc-chhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-Q--IELDL-SSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~--~~~~~-~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      +|.+.|+...|.+-+++..++. +-+..++..+-..|-+.|..+.|.+- +  -.+.| +..+-|..=-.+|..|.+++|
T Consensus        44 ~YL~~gd~~~A~~nlekAL~~D-Ps~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p~~GdVLNNYG~FLC~qg~~~eA  122 (250)
T COG3063          44 GYLQQGDYAQAKKNLEKALEHD-PSYYLAHLVRAHYYQKLGENDLADESYRKALSLAPNNGDVLNNYGAFLCAQGRPEEA  122 (250)
T ss_pred             HHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCCCccchhhhhhHHHHhCCChHHH
Confidence            5778888888888888887752 23446666777777888877777666 2  22223 344555555566777777777


Q ss_pred             c--------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           80 R--------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        80 ~--------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .              ...+|..+-....+.|+++.|.+.|+.-.+..-. ...+...+..--.+.|++-.|..
T Consensus       123 ~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~-~~~~~l~~a~~~~~~~~y~~Ar~  194 (250)
T COG3063         123 MQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQ-FPPALLELARLHYKAGDYAPARL  194 (250)
T ss_pred             HHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcC-CChHHHHHHHHHHhcccchHHHH
Confidence            7              5667777777777778888887777766543211 12234444444455555555544

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=96.98  E-value=0.0069  Score=35.21  Aligned_cols=82  Identities=18%  Similarity=0.289  Sum_probs=54.8

Q ss_pred             hcCChhHHHHHHHHhHHcCC-CccHHHHHHHHHHhcCCCchHHHHHHhhhhhcchhhHHHHHHHHHhcCCccccchHHHH
Q 039275            7 QAGRFNEALEPFGKLESLGV-HTDEVTMVVVLTASSGPGAWILAKELQIELDLSSYSLSSKTSRYAHSGRIRLARDPVSC   85 (153)
Q Consensus         7 ~~g~~~~a~~~~~~m~~~g~-~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~   85 (153)
                      +.|++++|+.+|+++....- .|+...+-.+-.++.+.|++++|..+-...+.+....                  ...|
T Consensus         1 ~~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~~~~~~~~~------------------~~~~   62 (84)
T PF12895_consen    1 DQGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQKLKLDPSNP------------------DIHY   62 (84)
T ss_dssp             HTT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHCHTHHHCHH------------------HHHH
T ss_pred             CCccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHHhCCCCCCH------------------HHHH
Confidence            36899999999999977543 2355555567889999999999999932222222111                  1222


Q ss_pred             HHHHHHHHhcCChHHHHHHHHH
Q 039275           86 KAMISGYSQAGRFNEALEPFGK  107 (153)
Q Consensus        86 ~~li~~~~~~g~~~~a~~~~~~  107 (153)
                       .+-.++.+.|++++|.++|++
T Consensus        63 -l~a~~~~~l~~y~eAi~~l~~   83 (84)
T PF12895_consen   63 -LLARCLLKLGKYEEAIKALEK   83 (84)
T ss_dssp             -HHHHHHHHTT-HHHHHHHHHH
T ss_pred             -HHHHHHHHhCCHHHHHHHHhc
Confidence             335778888888888888865

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

Probab=96.96  E-value=0.0036  Score=45.86  Aligned_cols=132  Identities=11%  Similarity=-0.002  Sum_probs=92.5

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhh--cchhhH-HHHHHHHHhcCCccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELD--LSSYSL-SSKTSRYAHSGRIRL   78 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~--~~~~~~-~~ll~~~~~~g~~~~   78 (153)
                      +.|.+.|.+.+|.+.|..-...  .|-+.||--+-.+|-+...++.|..+ ..|++  |-.+|+ .-+.+-+-..++.++
T Consensus       231 kCylrLgm~r~AekqlqssL~q--~~~~dTfllLskvY~ridQP~~AL~~~~~gld~fP~~VT~l~g~ARi~eam~~~~~  308 (478)
T KOG1129|consen  231 KCYLRLGMPRRAEKQLQSSLTQ--FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDSFPFDVTYLLGQARIHEAMEQQED  308 (478)
T ss_pred             HHHHHhcChhhhHHHHHHHhhc--CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhcCCchhhhhhhhHHHHHHHHhHHH
Confidence            4789999999999999887665  56777888888999999999999998 44432  333333 334455566666666


Q ss_pred             cc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccch
Q 039275           79 AR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGK  137 (153)
Q Consensus        79 a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~  137 (153)
                      |.            ++..-.++-.+|...|+++-|++++..+.+.|+.-- ..|..+--+|.-.+.+|.+.
T Consensus       309 a~~lYk~vlk~~~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~sp-eLf~NigLCC~yaqQ~D~~L  378 (478)
T KOG1129|consen  309 ALQLYKLVLKLHPINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQSP-ELFCNIGLCCLYAQQIDLVL  378 (478)
T ss_pred             HHHHHHHHHhcCCccceeeeeeeeccccCCChHHHHHHHHHHHHhcCCCh-HHHhhHHHHHHhhcchhhhH
Confidence            65            444555556678888888888888888888885433 34555555665555555443

>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=96.95  E-value=0.03  Score=42.37  Aligned_cols=123  Identities=16%  Similarity=-0.004  Sum_probs=88.7

Q ss_pred             HHHHHHHhHHcCCCc------------cHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccc
Q 039275           14 ALEPFGKLESLGVHT------------DEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLAR   80 (153)
Q Consensus        14 a~~~~~~m~~~g~~p------------~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~   80 (153)
                      .++.+.++-..|...            +.....+++..+...++++.|.++ +.=.+.+......+++.+...++-.+|.
T Consensus       141 fi~~~~~~~~~G~~lG~~~~i~~~t~~~NyLv~~Ll~~l~~t~~~~~ai~lle~L~~~~pev~~~LA~v~l~~~~E~~AI  220 (395)
T PF09295_consen  141 FIKLFPKLFERGWKLGSDPEIQVPTIVNNYLVDTLLKYLSLTQRYDEAIELLEKLRERDPEVAVLLARVYLLMNEEVEAI  220 (395)
T ss_pred             HHHHHHHHhhcccccCCCCccCCCCCcchHHHHHHHHHHhhcccHHHHHHHHHHHHhcCCcHHHHHHHHHHhcCcHHHHH
Confidence            455666665555332            234455667777788999999999 2222333445556778887777766666


Q ss_pred             ------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChh-hHHHHHHHhcCCCccccchh
Q 039275           81 ------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEV-TMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~-t~~~li~~~~~~g~~~~a~~  138 (153)
                                  +....+.-...+.+.++.+.|.++.++....  .|+.. +|..|..+|.+.|+++.|.-
T Consensus       221 ~ll~~aL~~~p~d~~LL~~Qa~fLl~k~~~~lAL~iAk~av~l--sP~~f~~W~~La~~Yi~~~d~e~ALl  289 (395)
T PF09295_consen  221 RLLNEALKENPQDSELLNLQAEFLLSKKKYELALEIAKKAVEL--SPSEFETWYQLAECYIQLGDFENALL  289 (395)
T ss_pred             HHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh--CchhHHHHHHHHHHHHhcCCHHHHHH
Confidence                        5555555567789999999999999998864  68655 99999999999999999876

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

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

Probab=96.94  E-value=0.038  Score=37.75  Aligned_cols=108  Identities=10%  Similarity=0.027  Sum_probs=63.3

Q ss_pred             ChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH---hhhhhc-chhhHHHHHHH-HHhcCCc--cccc--
Q 039275           10 RFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL---QIELDL-SSYSLSSKTSR-YAHSGRI--RLAR--   80 (153)
Q Consensus        10 ~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~-~~~~~~~ll~~-~~~~g~~--~~a~--   80 (153)
                      +.++++..+++..+. -+.|...|..+-..+...|++++|...   -..+.| +...+..+-.+ +.+.|+.  ++|.  
T Consensus        54 ~~~~~i~~l~~~L~~-~P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~  132 (198)
T PRK10370         54 TPEAQLQALQDKIRA-NPQNSEQWALLGEYYLWRNDYDNALLAYRQALQLRGENAELYAALATVLYYQAGQHMTPQTREM  132 (198)
T ss_pred             hHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCCCcHHHHHH
Confidence            334444444433332 244566666666677777888877777   222233 44455555554 3555653  4444  


Q ss_pred             ----------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhh
Q 039275           81 ----------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVT  119 (153)
Q Consensus        81 ----------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t  119 (153)
                                +...+..+-..+.+.|++++|...|+++.+.. .|+..-
T Consensus       133 l~~al~~dP~~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l~-~~~~~r  180 (198)
T PRK10370        133 IDKALALDANEVTALMLLASDAFMQADYAQAIELWQKVLDLN-SPRVNR  180 (198)
T ss_pred             HHHHHHhCCCChhHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCccH
Confidence                      66777777777788888888888888876543 344433

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

Probab=96.83  E-value=0.029  Score=42.99  Aligned_cols=124  Identities=12%  Similarity=0.101  Sum_probs=83.3

Q ss_pred             CChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH----hhhhhcchhhHHHHHHHHHhcCCccccc----
Q 039275            9 GRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL----QIELDLSSYSLSSKTSRYAHSGRIRLAR----   80 (153)
Q Consensus         9 g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~----~~~~~~~~~~~~~ll~~~~~~g~~~~a~----   80 (153)
                      .++.+|++++.+..+ -++-|+.+...|-..|-+.|+-.+|.+.    -+-++.|..+..=|-..|....=.+++.    
T Consensus       572 ed~aqaie~~~q~~s-lip~dp~ilskl~dlydqegdksqafq~~ydsyryfp~nie~iewl~ayyidtqf~ekai~y~e  650 (840)
T KOG2003|consen  572 EDPAQAIELLMQANS-LIPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRYFPCNIETIEWLAAYYIDTQFSEKAINYFE  650 (840)
T ss_pred             hCHHHHHHHHHHhcc-cCCCCHHHHHHHHHHhhcccchhhhhhhhhhcccccCcchHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            344445554443322 2666889999999999999998888888    2223444444444444444333333333    


Q ss_pred             -------hHHHHHHHHHHH-HhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccc
Q 039275           81 -------DPVSCKAMISGY-SQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALD  134 (153)
Q Consensus        81 -------~~~~~~~li~~~-~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~  134 (153)
                             +.+-|..||..| .+.|+..+|++++++..+ .+.-|.....-++.-|..+|..+
T Consensus       651 kaaliqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hr-kfpedldclkflvri~~dlgl~d  711 (840)
T KOG2003|consen  651 KAALIQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHR-KFPEDLDCLKFLVRIAGDLGLKD  711 (840)
T ss_pred             HHHhcCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHH-hCccchHHHHHHHHHhccccchh
Confidence                   789999999665 567999999999999874 45567777777777888877654

>PF12921 ATP13: Mitochondrial ATPase expression; InterPro: IPR024319 ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase

Probab=96.79  E-value=0.0092  Score=37.81  Aligned_cols=58  Identities=9%  Similarity=0.044  Sum_probs=49.6

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHH---------------HcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLE---------------SLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~---------------~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |..++.++|.++++.|+++....+.+..=               .....|+..+..+++.+|+..|++..|.+
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~~~~~spl~Pt~~lL~AIv~sf~~n~~i~~al~   73 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGDYPPSSPLYPTSRLLIAIVHSFGYNGDIFSALK   73 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCccCCCCCCCCCHHHHHHHHHHHHhcccHHHHHH
Confidence            45688899999999999999999987651               12356899999999999999999999998

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=96.77  E-value=0.058  Score=37.44  Aligned_cols=135  Identities=16%  Similarity=0.100  Sum_probs=87.8

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccH---HHHHHHHHHhcCCCchHHHHHH-h--hhhhcchh----hHHHHHHHHHh
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDE---VTMVVVLTASSGPGAWILAKEL-Q--IELDLSSY----SLSSKTSRYAH   72 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~---~~~~~ll~~~~~~~~~~~a~~~-~--~~~~~~~~----~~~~ll~~~~~   72 (153)
                      ..+.+.|++++|...|+++.... +.+.   ..+..+-.++.+.|++++|... +  ....|+..    .+..+-..+.+
T Consensus        41 ~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~~g~~~~~  119 (235)
T TIGR03302        41 KEALDSGDYTEAIKYFEALESRY-PFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAYYLRGLSNYN  119 (235)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-CCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHHHHHHHHHHH
Confidence            35678899999999999986642 1122   3556667788899999999999 1  12233222    22222222322


Q ss_pred             c--------CCccccc------------hHHHH-----------------HHHHHHHHhcCChHHHHHHHHHHHHcCC-C
Q 039275           73 S--------GRIRLAR------------DPVSC-----------------KAMISGYSQAGRFNEALEPFGKLESLGV-H  114 (153)
Q Consensus        73 ~--------g~~~~a~------------~~~~~-----------------~~li~~~~~~g~~~~a~~~~~~m~~~g~-~  114 (153)
                      .        |+.++|.            +...+                 -.+-..+.+.|++++|...+++..+..- .
T Consensus       120 ~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~  199 (235)
T TIGR03302       120 QIDRVDRDQTAAREAFEAFQELIRRYPNSEYAPDAKKRMDYLRNRLAGKELYVARFYLKRGAYVAAINRFETVVENYPDT  199 (235)
T ss_pred             hcccccCCHHHHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHCCCC
Confidence            2        3444444            11111                 1334567888999999999999986532 2


Q ss_pred             C-ChhhHHHHHHHhcCCCccccchh
Q 039275          115 T-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       115 p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      | ....+..+..++.+.|++++|..
T Consensus       200 ~~~~~a~~~l~~~~~~lg~~~~A~~  224 (235)
T TIGR03302       200 PATEEALARLVEAYLKLGLKDLAQD  224 (235)
T ss_pred             cchHHHHHHHHHHHHHcCCHHHHHH
Confidence            3 35678899999999999998876

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).

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

Probab=96.76  E-value=0.013  Score=46.15  Aligned_cols=50  Identities=20%  Similarity=0.210  Sum_probs=33.1

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHHcCCCCChhh-HHHHHHHhcCCCccccchh
Q 039275           87 AMISGYSQAGRFNEALEPFGKLESLGVHTDEVT-MVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        87 ~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t-~~~li~~~~~~g~~~~a~~  138 (153)
                      .....+...++.++|++.++++++  +.|++.+ |..+-..|-+.|+.+.|..
T Consensus       562 ~~~~il~~~~~~~eal~~LEeLk~--~vP~es~v~~llgki~k~~~~~~~Al~  612 (638)
T KOG1126|consen  562 HRASILFSLGRYVEALQELEELKE--LVPQESSVFALLGKIYKRLGNTDLALL  612 (638)
T ss_pred             HHHHHHHhhcchHHHHHHHHHHHH--hCcchHHHHHHHHHHHHHHccchHHHH
Confidence            445556667777777777777774  4575554 4444457777777777765

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

Probab=96.74  E-value=0.046  Score=41.87  Aligned_cols=103  Identities=19%  Similarity=0.147  Sum_probs=60.3

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCccHHHHH-HHHHHhcCCCchHHHHHH---hhhhhcc-hhhHHHHHHHHHhcCCcccc
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTDEVTMV-VVLTASSGPGAWILAKEL---QIELDLS-SYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~-~ll~~~~~~~~~~~a~~~---~~~~~~~-~~~~~~ll~~~~~~g~~~~a   79 (153)
                      +...|++++|.+.++.+.+.  .||..-|. ....-+.+.++.++|.+.   -....|+ ....-.+-.+|.+.|++.+|
T Consensus       316 ~~~~~~~d~A~~~l~~L~~~--~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l~P~~~~l~~~~a~all~~g~~~ea  393 (484)
T COG4783         316 TYLAGQYDEALKLLQPLIAA--QPDNPYYLELAGDILLEANKAKEAIERLKKALALDPNSPLLQLNLAQALLKGGKPQEA  393 (484)
T ss_pred             HHHhcccchHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCCccHHHHHHHHHHHhcCChHHH
Confidence            44566677777777776553  34433333 444455666666666666   2223344 33444455666667776666


Q ss_pred             c------------hHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 039275           80 R------------DPVSCKAMISGYSQAGRFNEALEPFGKLE  109 (153)
Q Consensus        80 ~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~  109 (153)
                      .            |+..|+.|-.+|...|+..++.....+.-
T Consensus       394 i~~L~~~~~~~p~dp~~w~~LAqay~~~g~~~~a~~A~AE~~  435 (484)
T COG4783         394 IRILNRYLFNDPEDPNGWDLLAQAYAELGNRAEALLARAEGY  435 (484)
T ss_pred             HHHHHHHhhcCCCCchHHHHHHHHHHHhCchHHHHHHHHHHH
Confidence            6            66677777777776666666666665554

>PRK11189 lipoprotein NlpI; Provisional

Probab=96.69  E-value=0.078  Score=38.50  Aligned_cols=104  Identities=18%  Similarity=0.080  Sum_probs=66.3

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhh--hhcc-hhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIE--LDLS-SYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~--~~~~-~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .|.+.|+.++|...|++..+.. +.+...|+.+-..+...|++++|.+. ..-  +.|+ ...+..+-..+...|++++|
T Consensus        73 ~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~g~~~eA  151 (296)
T PRK11189         73 LYDSLGLRALARNDFSQALALR-PDMADAYNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAYLNRGIALYYGGRYELA  151 (296)
T ss_pred             HHHHCCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHH
Confidence            3566788888888888776642 33567777777788888888888877 222  3343 34566666777777888887


Q ss_pred             c------------hHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 039275           80 R------------DPVSCKAMISGYSQAGRFNEALEPFGKLE  109 (153)
Q Consensus        80 ~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~  109 (153)
                      .            +.. ...........+++++|.+.|.+..
T Consensus       152 ~~~~~~al~~~P~~~~-~~~~~~l~~~~~~~~~A~~~l~~~~  192 (296)
T PRK11189        152 QDDLLAFYQDDPNDPY-RALWLYLAESKLDPKQAKENLKQRY  192 (296)
T ss_pred             HHHHHHHHHhCCCCHH-HHHHHHHHHccCCHHHHHHHHHHHH
Confidence            7            111 1111122345667888888886644

>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=96.65  E-value=0.0066  Score=39.14  Aligned_cols=59  Identities=20%  Similarity=0.305  Sum_probs=39.1

Q ss_pred             HHHHHHHHHhcCCccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHH-----HcCCCCChhhHH
Q 039275           63 LSSKTSRYAHSGRIRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLE-----SLGVHTDEVTMV  121 (153)
Q Consensus        63 ~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~-----~~g~~p~~~t~~  121 (153)
                      ...++..+...|++++|.            +...|-.+|.++...|+..+|.++|+.+.     +-|+.|+..+-.
T Consensus        65 ~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~~  140 (146)
T PF03704_consen   65 LERLAEALLEAGDYEEALRLLQRALALDPYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETRA  140 (146)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHHH
T ss_pred             HHHHHHHHHhccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHHH
Confidence            344555556666666666            77899999999999999999999998885     338999877643

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

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

Probab=96.63  E-value=0.039  Score=42.28  Aligned_cols=118  Identities=18%  Similarity=0.082  Sum_probs=87.7

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCcc-HHHHHHHHHHhcCCCchHHHHHH----hhhhhcchhhHHHHHHHHHhcCCcc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTD-EVTMVVVLTASSGPGAWILAKEL----QIELDLSSYSLSSKTSRYAHSGRIR   77 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~~~~~ll~~~~~~~~~~~a~~~----~~~~~~~~~~~~~ll~~~~~~g~~~   77 (153)
                      +-+.+.++.++|.+.++++...  .|+ ....-.+-.++.+.|.+.+|..+    ....+.|...|..|-.+|.+.|+..
T Consensus       348 ~i~~~~nk~~~A~e~~~kal~l--~P~~~~l~~~~a~all~~g~~~eai~~L~~~~~~~p~dp~~w~~LAqay~~~g~~~  425 (484)
T COG4783         348 DILLEANKAKEAIERLKKALAL--DPNSPLLQLNLAQALLKGGKPQEAIRILNRYLFNDPEDPNGWDLLAQAYAELGNRA  425 (484)
T ss_pred             HHHHHcCChHHHHHHHHHHHhc--CCCccHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCCchHHHHHHHHHHHhCchH
Confidence            3567889999999999999874  566 34444555788899999988888    4445667888999999999999988


Q ss_pred             ccchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcC--CCCChhhHHHHHHHh
Q 039275           78 LARDPVSCKAMISGYSQAGRFNEALEPFGKLESLG--VHTDEVTMVVVLAAS  127 (153)
Q Consensus        78 ~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g--~~p~~~t~~~li~~~  127 (153)
                      ++.     .+.-.++...|++++|...+..-++..  -.|+..-+...|+..
T Consensus       426 ~a~-----~A~AE~~~~~G~~~~A~~~l~~A~~~~~~~~~~~aR~dari~~~  472 (484)
T COG4783         426 EAL-----LARAEGYALAGRLEQAIIFLMRASQQVKLGFPDWARADARIDQL  472 (484)
T ss_pred             HHH-----HHHHHHHHhCCCHHHHHHHHHHHHHhccCCcHHHHHHHHHHHHH
Confidence            866     345577889999999999888877542  234444444555443

>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=96.61  E-value=0.032  Score=40.50  Aligned_cols=124  Identities=15%  Similarity=0.077  Sum_probs=80.4

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHHhhhhh--cchhhHHHHHHHHHh----cCCcc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIELD--LSSYSLSSKTSRYAH----SGRIR   77 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~--~~~~~~~~ll~~~~~----~g~~~   77 (153)
                      .+...|++++|+++++.-      .+.......+..+.+.++++.|.+.-..++  .+..+...|..++..    .+.+.
T Consensus       111 i~~~~~~~~~AL~~l~~~------~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~eD~~l~qLa~awv~l~~g~e~~~  184 (290)
T PF04733_consen  111 ILFHEGDYEEALKLLHKG------GSLELLALAVQILLKMNRPDLAEKELKNMQQIDEDSILTQLAEAWVNLATGGEKYQ  184 (290)
T ss_dssp             HHCCCCHHHHHHCCCTTT------TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHTTTCCC
T ss_pred             HHHHcCCHHHHHHHHHcc------CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhCchhHH
Confidence            356678888888887642      456667777788888888888888822221  222334444444432    23455


Q ss_pred             ccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccc
Q 039275           78 LAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALD  134 (153)
Q Consensus        78 ~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~  134 (153)
                      +|.            ++.+.|.+.......|++++|.+++++-.... .-+..+...++.+....|+..
T Consensus       185 ~A~y~f~El~~~~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~-~~~~d~LaNliv~~~~~gk~~  252 (290)
T PF04733_consen  185 DAFYIFEELSDKFGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKD-PNDPDTLANLIVCSLHLGKPT  252 (290)
T ss_dssp             HHHHHHHHHHCCS--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC--CCHHHHHHHHHHHHHHTT-TC
T ss_pred             HHHHHHHHHHhccCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhc-cCCHHHHHHHHHHHHHhCCCh
Confidence            665            67778888888999999999999988866433 225567777888878888773

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006890 retrograde vesicle-mediated transport, Golgi to ER, 0030126 COPI vesicle coat; PDB: 3MV2_B 3MV3_F 3MKR_A.

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

Probab=96.57  E-value=0.037  Score=47.54  Aligned_cols=130  Identities=13%  Similarity=0.028  Sum_probs=97.6

Q ss_pred             hhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhh--hc---chhhHHHHHHHHHhcCC
Q 039275            2 ISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIEL--DL---SSYSLSSKTSRYAHSGR   75 (153)
Q Consensus         2 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~--~~---~~~~~~~ll~~~~~~g~   75 (153)
                      ..-|.+.+++++|.++++.|.+. +.....+|......+.+...-+.|..+ .+-+  -|   ........+..=-+.|+
T Consensus      1537 ~~iy~k~ek~~~A~ell~~m~KK-F~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv~~IskfAqLEFk~GD 1615 (1710)
T KOG1070|consen 1537 LGIYEKSEKNDEADELLRLMLKK-FGQTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVEFISKFAQLEFKYGD 1615 (1710)
T ss_pred             HHHHHHhhcchhHHHHHHHHHHH-hcchhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHHHHHHHHHHHhhcCC
Confidence            45688899999999999999665 337788999999999999998888888 2221  12   33445555555667888


Q ss_pred             ccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCh--hhHHHHHHHhcCCCc
Q 039275           76 IRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDE--VTMVVVLAASSGPGA  132 (153)
Q Consensus        76 ~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~--~t~~~li~~~~~~g~  132 (153)
                      .+.++            ....|+..|..-.++|+.+.+..+|++....++.|..  ..|.--+..=-+.|+
T Consensus      1616 aeRGRtlfEgll~ayPKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~kkmKfffKkwLeyEk~~Gd 1686 (1710)
T KOG1070|consen 1616 AERGRTLFEGLLSAYPKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSIKKMKFFFKKWLEYEKSHGD 1686 (1710)
T ss_pred             chhhHHHHHHHHhhCccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCChhHhHHHHHHHHHHHHhcCc
Confidence            88866            6788999999999999999999999999999988854  334444443333343

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

Probab=96.55  E-value=0.037  Score=39.11  Aligned_cols=105  Identities=19%  Similarity=0.123  Sum_probs=86.4

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH---hhhhhc-chhhHHHHHHHHHhcCCccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL---QIELDL-SSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~-~~~~~~~ll~~~~~~g~~~~   78 (153)
                      ....+.|++.+|+..|++..+- -+||...|+-+=-+|.+.|++++|..-   -..+.| +....|.|.-.|.-.|+++.
T Consensus       108 k~~~~~g~~~~A~~~~rkA~~l-~p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~~~~p~~~nNlgms~~L~gd~~~  186 (257)
T COG5010         108 KNQIRNGNFGEAVSVLRKAARL-APTDWEAWNLLGAALDQLGRFDEARRAYRQALELAPNEPSIANNLGMSLLLRGDLED  186 (257)
T ss_pred             HHHHHhcchHHHHHHHHHHhcc-CCCChhhhhHHHHHHHHccChhHHHHHHHHHHHhccCCchhhhhHHHHHHHcCCHHH
Confidence            4567899999999999988653 568889999888999999999998877   333444 34568888888999999999


Q ss_pred             cc------------hHHHHHHHHHHHHhcCChHHHHHHHHHH
Q 039275           79 AR------------DPVSCKAMISGYSQAGRFNEALEPFGKL  108 (153)
Q Consensus        79 a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m  108 (153)
                      |.            |...-+.+-..-...|++++|..+-..-
T Consensus       187 A~~lll~a~l~~~ad~~v~~NLAl~~~~~g~~~~A~~i~~~e  228 (257)
T COG5010         187 AETLLLPAYLSPAADSRVRQNLALVVGLQGDFREAEDIAVQE  228 (257)
T ss_pred             HHHHHHHHHhCCCCchHHHHHHHHHHhhcCChHHHHhhcccc
Confidence            99            7888888989999999999999876543

>TIGR00540 hemY_coli hemY protein

Probab=96.53  E-value=0.097  Score=39.78  Aligned_cols=108  Identities=15%  Similarity=0.143  Sum_probs=77.1

Q ss_pred             hhcCChhHHHHHHHHhHHcCCCccHHHHHH-HHHHhcCCCchHHHHHHh---hhhhcchh--hHHHHHHHHHhcCCcccc
Q 039275            6 SQAGRFNEALEPFGKLESLGVHTDEVTMVV-VLTASSGPGAWILAKELQ---IELDLSSY--SLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         6 ~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~-ll~~~~~~~~~~~a~~~~---~~~~~~~~--~~~~ll~~~~~~g~~~~a   79 (153)
                      ...|+++.|.+.+.+..+.  .|++..+-. .-.+..+.|+.+.+.+.-   ....|+..  ..-.....+.+.|+++.|
T Consensus        95 ~~~g~~~~A~~~l~~~~~~--~~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~~~~~~~A  172 (409)
T TIGR00540        95 LAEGDYAKAEKLIAKNADH--AAEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRILLAQNELHAA  172 (409)
T ss_pred             HhCCCHHHHHHHHHHHhhc--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHHHHCCCHHHH
Confidence            4578999999999776553  455444333 335667778999988881   12234443  333346777888888888


Q ss_pred             c------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC
Q 039275           80 R------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT  115 (153)
Q Consensus        80 ~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  115 (153)
                      .            +...+..+...+...|+++++.+++..+.+.++.+
T Consensus       173 l~~l~~l~~~~P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~  220 (409)
T TIGR00540       173 RHGVDKLLEMAPRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFD  220 (409)
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCC
Confidence            7            67778888899999999999999999998886543

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.

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

Probab=96.52  E-value=0.099  Score=39.09  Aligned_cols=102  Identities=11%  Similarity=0.041  Sum_probs=70.9

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDP   82 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~   82 (153)
                      .+...|++++|++.|++..+.. +-+...|..+-.++.+.|++++|... ..-+..+..                   +.
T Consensus        11 ~a~~~~~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~-------------------~~   70 (356)
T PLN03088         11 EAFVDDDFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANKAIELDPS-------------------LA   70 (356)
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcC-------------------CH
Confidence            4567899999999999998742 23556677777788899999999888 333332221                   23


Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHh
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAAS  127 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~  127 (153)
                      ..|..+-..|...|++++|.+.|++....  .|+...+...+.-|
T Consensus        71 ~a~~~lg~~~~~lg~~~eA~~~~~~al~l--~P~~~~~~~~l~~~  113 (356)
T PLN03088         71 KAYLRKGTACMKLEEYQTAKAALEKGASL--APGDSRFTKLIKEC  113 (356)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHH
Confidence            45666677778888888888888887753  46555555555444

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A

Probab=96.51  E-value=0.015  Score=32.07  Aligned_cols=46  Identities=20%  Similarity=0.228  Sum_probs=38.4

Q ss_pred             hhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH
Q 039275            6 SQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL   52 (153)
Q Consensus         6 ~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~   52 (153)
                      .+.|++++|++.|+++.+. .+-+....-.+..++.+.|++++|.++
T Consensus         2 l~~~~~~~A~~~~~~~l~~-~p~~~~~~~~la~~~~~~g~~~~A~~~   47 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQR-NPDNPEARLLLAQCYLKQGQYDEAEEL   47 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHH-TTTSHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            5789999999999999775 233677777889999999999999999

...

>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=96.46  E-value=0.0096  Score=38.22  Aligned_cols=122  Identities=17%  Similarity=0.145  Sum_probs=82.2

Q ss_pred             ChhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHHhhhhhcchhhHHHHHHHHHhcCCccccc
Q 039275            1 MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIELDLSSYSLSSKTSRYAHSGRIRLAR   80 (153)
Q Consensus         1 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~ll~~~~~~g~~~~a~   80 (153)
                      +|+.+.+.+.++.+..+++.+...+...+....+.++..|++.++.+...++-.  ..+......+++.+-+.|.+++  
T Consensus        13 vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~--~~~~yd~~~~~~~c~~~~l~~~--   88 (143)
T PF00637_consen   13 VISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLK--TSNNYDLDKALRLCEKHGLYEE--   88 (143)
T ss_dssp             CHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTT--SSSSS-CTHHHHHHHTTTSHHH--
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcc--cccccCHHHHHHHHHhcchHHH--
Confidence            467788889999999999999988777889999999999999998888888822  1122333445555555554433  


Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc-------CCCCChhhHHHHHHHhcCCCcc
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESL-------GVHTDEVTMVVVLAASSGPGAL  133 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-------g~~p~~~t~~~li~~~~~~g~~  133 (153)
                             .+.-|.+.|++++|.++...+..-       .-.++...|..+++.|...+..
T Consensus        89 -------a~~Ly~~~~~~~~al~i~~~~~~~~~a~e~~~~~~~~~l~~~l~~~~l~~~~~  141 (143)
T PF00637_consen   89 -------AVYLYSKLGNHDEALEILHKLKDYEEAIEYAKKVDDPELWEQLLKYCLDSKPF  141 (143)
T ss_dssp             -------HHHHHHCCTTHTTCSSTSSSTHCSCCCTTTGGGCSSSHHHHHHHHHHCTSTCT
T ss_pred             -------HHHHHHHcccHHHHHHHHHHHccHHHHHHHHHhcCcHHHHHHHHHHHHhcCcc
Confidence                   334667777777777754433211       1134677888888888876653

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.

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

Probab=96.43  E-value=0.034  Score=41.55  Aligned_cols=109  Identities=14%  Similarity=0.006  Sum_probs=82.0

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchH----HHHHHhhhhhcchhhHHHHHHHHHhcCCccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWI----LAKELQIELDLSSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~----~a~~~~~~~~~~~~~~~~ll~~~~~~g~~~~   78 (153)
                      .-+.+.|+.++|.++.++-.++++.|...++   +.. .+.++.+    .++++-..++-+...+.+|=..|.+.+.+.+
T Consensus       271 ~~li~l~~~~~A~~~i~~~Lk~~~D~~L~~~---~~~-l~~~d~~~l~k~~e~~l~~h~~~p~L~~tLG~L~~k~~~w~k  346 (400)
T COG3071         271 ERLIRLGDHDEAQEIIEDALKRQWDPRLCRL---IPR-LRPGDPEPLIKAAEKWLKQHPEDPLLLSTLGRLALKNKLWGK  346 (400)
T ss_pred             HHHHHcCChHHHHHHHHHHHHhccChhHHHH---Hhh-cCCCCchHHHHHHHHHHHhCCCChhHHHHHHHHHHHhhHHHH
Confidence            4567899999999999999999888883333   332 3444333    3333333344455778888899999999999


Q ss_pred             cc-----------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC
Q 039275           79 AR-----------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT  115 (153)
Q Consensus        79 a~-----------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  115 (153)
                      |.           +..+|+-+-..+.+.|++.+|.+++++-...-..|
T Consensus       347 A~~~leaAl~~~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L~~~~~~  394 (400)
T COG3071         347 ASEALEAALKLRPSASDYAELADALDQLGEPEEAEQVRREALLLTRQP  394 (400)
T ss_pred             HHHHHHHHHhcCCChhhHHHHHHHHHHcCChHHHHHHHHHHHHHhcCC
Confidence            98           88999999999999999999999999876443333

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

Probab=96.42  E-value=0.08  Score=34.11  Aligned_cols=101  Identities=17%  Similarity=0.112  Sum_probs=60.8

Q ss_pred             hcCChhHHHHHHHHhHHcCCCccHHHHHH--HHHHhcCCCchHHHHHH-----hhhhhcch--hhHHHHHHHHHhcCCcc
Q 039275            7 QAGRFNEALEPFGKLESLGVHTDEVTMVV--VLTASSGPGAWILAKEL-----QIELDLSS--YSLSSKTSRYAHSGRIR   77 (153)
Q Consensus         7 ~~g~~~~a~~~~~~m~~~g~~p~~~~~~~--ll~~~~~~~~~~~a~~~-----~~~~~~~~--~~~~~ll~~~~~~g~~~   77 (153)
                      ..++...+...++.+.+..-.-.......  +-..+...|++++|...     .....|+.  ...-.|...+...|+++
T Consensus        23 ~~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~~d  102 (145)
T PF09976_consen   23 QAGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRLARILLQQGQYD  102 (145)
T ss_pred             HCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHH
Confidence            46677777777777765422111222222  23566677777777776     11111111  12223456666777777


Q ss_pred             ccc-----------hHHHHHHHHHHHHhcCChHHHHHHHHH
Q 039275           78 LAR-----------DPVSCKAMISGYSQAGRFNEALEPFGK  107 (153)
Q Consensus        78 ~a~-----------~~~~~~~li~~~~~~g~~~~a~~~~~~  107 (153)
                      +|.           ....+...=..+.+.|+.++|...|+.
T Consensus       103 ~Al~~L~~~~~~~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen  103 EALATLQQIPDEAFKALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHHHhccCcchHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            766           455666777889999999999999875

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

Probab=96.42  E-value=0.02  Score=41.93  Aligned_cols=133  Identities=17%  Similarity=0.191  Sum_probs=64.1

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHH-HHHH-------hcCC
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKT-SRYA-------HSGR   75 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll-~~~~-------~~g~   75 (153)
                      |..+|-+++|.++|..+...+- .-......++.-|-+..+|+.|.+. +.=.+.+...++.-| ..||       ...+
T Consensus       117 ym~aGl~DRAE~~f~~L~de~e-fa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~  195 (389)
T COG2956         117 YMAAGLLDRAEDIFNQLVDEGE-FAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSD  195 (389)
T ss_pred             HHHhhhhhHHHHHHHHHhcchh-hhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhh
Confidence            4455556666666655544321 1222334555555566666666655 222233333333322 1222       2223


Q ss_pred             ccccc---------hHH--HHH-HHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           76 IRLAR---------DPV--SCK-AMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        76 ~~~a~---------~~~--~~~-~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ++.|.         |..  --+ .+=..+...|++.+|.+.++...+.+...-..+...+..+|.++|+.+.+..
T Consensus       196 ~d~A~~~l~kAlqa~~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~  270 (389)
T COG2956         196 VDRARELLKKALQADKKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLN  270 (389)
T ss_pred             HHHHHHHHHHHHhhCccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHH
Confidence            33332         111  111 1224455666777777777766665544444556666667777766665554

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

Probab=96.41  E-value=0.068  Score=43.81  Aligned_cols=132  Identities=16%  Similarity=0.059  Sum_probs=94.4

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH---hhhh-hcchhhHHHHHHHHHhcCCccccc
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL---QIEL-DLSSYSLSSKTSRYAHSGRIRLAR   80 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~---~~~~-~~~~~~~~~ll~~~~~~g~~~~a~   80 (153)
                      +++ |++++|.+++.+..+. -+-+..-|-+|-..+-..|+.+++...   -..+ +.|.-.|..+-....+.|++++|.
T Consensus       150 far-g~~eeA~~i~~EvIkq-dp~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~p~d~e~W~~ladls~~~~~i~qA~  227 (895)
T KOG2076|consen  150 FAR-GDLEEAEEILMEVIKQ-DPRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLNPKDYELWKRLADLSEQLGNINQAR  227 (895)
T ss_pred             HHh-CCHHHHHHHHHHHHHh-CccchhhHHHHHHHHHHcccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHhcccHHHHH
Confidence            455 9999999999999775 345677888999999999999999888   3333 345567888889999999999998


Q ss_pred             ------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC----ChhhHHHHHHHhcCCCccccchh
Q 039275           81 ------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT----DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p----~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                                  +...+---+.-|-+.|+..+|++.|.+|.+..-..    -..+.-.++..+...++.+.|.+
T Consensus       228 ~cy~rAI~~~p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~~e~a~~  301 (895)
T KOG2076|consen  228 YCYSRAIQANPSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNERERAAK  301 (895)
T ss_pred             HHHHHHHhcCCcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence                        22222233456788899999999999998653211    22333444556666666666555

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=96.39  E-value=0.13  Score=41.86  Aligned_cols=111  Identities=15%  Similarity=0.033  Sum_probs=88.3

Q ss_pred             CCccHHHHHHHHHHhcCCCchHHHHHH---hhhhhcch-hhHHHHHHHHHhcCCccccc------------hHHHHHHHH
Q 039275           26 VHTDEVTMVVVLTASSGPGAWILAKEL---QIELDLSS-YSLSSKTSRYAHSGRIRLAR------------DPVSCKAMI   89 (153)
Q Consensus        26 ~~p~~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~~~-~~~~~ll~~~~~~g~~~~a~------------~~~~~~~li   89 (153)
                      ++.++..+--|-....+.|.+++|..+   -..+.|+. .....+...+.+.+.+++|.            +......+-
T Consensus        82 ~~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~p~~~~~~~~~a  161 (694)
T PRK15179         82 YPHTELFQVLVARALEAAHRSDEGLAVWRGIHQRFPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGGSSSAREILLEA  161 (694)
T ss_pred             ccccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcCCCCHHHHHHHH
Confidence            455677777777788888999999988   33345544 45666778888999999988            666777777


Q ss_pred             HHHHhcCChHHHHHHHHHHHHcCCCCC-hhhHHHHHHHhcCCCccccchh
Q 039275           90 SGYSQAGRFNEALEPFGKLESLGVHTD-EVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        90 ~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ..+.+.|+.++|.++|++....  .|+ ...+...-.++-+.|+.++|..
T Consensus       162 ~~l~~~g~~~~A~~~y~~~~~~--~p~~~~~~~~~a~~l~~~G~~~~A~~  209 (694)
T PRK15179        162 KSWDEIGQSEQADACFERLSRQ--HPEFENGYVGWAQSLTRRGALWRARD  209 (694)
T ss_pred             HHHHHhcchHHHHHHHHHHHhc--CCCcHHHHHHHHHHHHHcCCHHHHHH
Confidence            8899999999999999999873  344 7788888889999999999887

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

Probab=96.39  E-value=0.099  Score=36.55  Aligned_cols=132  Identities=15%  Similarity=0.057  Sum_probs=104.2

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCcc-HHHHHHHHHHhcCCCchHHHHHHhhh--hhc----chhhHHHHHHHHHhcCCc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTD-EVTMVVVLTASSGPGAWILAKELQIE--LDL----SSYSLSSKTSRYAHSGRI   76 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~--~~~----~~~~~~~ll~~~~~~g~~   76 (153)
                      .|-+.|+.+.|.+-|++..+.  .|+ -.+.|-.=.-+|..|.+++|......  ..|    -..+|..+.-+..+.|+.
T Consensus        78 ~Yq~~Ge~~~A~e~YrkAlsl--~p~~GdVLNNYG~FLC~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~  155 (250)
T COG3063          78 YYQKLGENDLADESYRKALSL--APNNGDVLNNYGAFLCAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQF  155 (250)
T ss_pred             HHHHcCChhhHHHHHHHHHhc--CCCccchhhhhhHHHHhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCc
Confidence            577889999999999988764  343 35556666677889999999998221  222    235677777888889999


Q ss_pred             cccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           77 RLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        77 ~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +.|.            ...+.-.+-....+.|+...|..+++.....+. ++..+...-|.---..|+.+.+.+
T Consensus       156 ~~A~~~l~raL~~dp~~~~~~l~~a~~~~~~~~y~~Ar~~~~~~~~~~~-~~A~sL~L~iriak~~gd~~~a~~  228 (250)
T COG3063         156 DQAEEYLKRALELDPQFPPALLELARLHYKAGDYAPARLYLERYQQRGG-AQAESLLLGIRIAKRLGDRAAAQR  228 (250)
T ss_pred             hhHHHHHHHHHHhCcCCChHHHHHHHHHHhcccchHHHHHHHHHHhccc-ccHHHHHHHHHHHHHhccHHHHHH
Confidence            9998            667777888999999999999999999887765 999999999998888888876655

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

Probab=96.37  E-value=0.047  Score=42.66  Aligned_cols=124  Identities=15%  Similarity=0.128  Sum_probs=92.4

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhh------hc----chhhHHHHHHHHHh
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIEL------DL----SSYSLSSKTSRYAH   72 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~------~~----~~~~~~~ll~~~~~   72 (153)
                      -|.+.++.+.|.++|.+.... .+-|+.+.+-+=-...+.+.+.+|..+ +.-+      .+    -.-+++.|-..|.+
T Consensus       389 ey~~t~n~kLAe~Ff~~A~ai-~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rk  467 (611)
T KOG1173|consen  389 EYMRTNNLKLAEKFFKQALAI-APSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRK  467 (611)
T ss_pred             HHHHhccHHHHHHHHHHHHhc-CCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHH
Confidence            366788899999999876553 344566666665566777888888888 1111      11    11235666788889


Q ss_pred             cCCccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCC
Q 039275           73 SGRIRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGP  130 (153)
Q Consensus        73 ~g~~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  130 (153)
                      .+.+++|.            +..++.++--.|...|+++.|.+.|++-.  .++||..+-..+++.+...
T Consensus       468 l~~~~eAI~~~q~aL~l~~k~~~~~asig~iy~llgnld~Aid~fhKaL--~l~p~n~~~~~lL~~aie~  535 (611)
T KOG1173|consen  468 LNKYEEAIDYYQKALLLSPKDASTHASIGYIYHLLGNLDKAIDHFHKAL--ALKPDNIFISELLKLAIED  535 (611)
T ss_pred             HhhHHHHHHHHHHHHHcCCCchhHHHHHHHHHHHhcChHHHHHHHHHHH--hcCCccHHHHHHHHHHHHh
Confidence            99988888            88899999999999999999999999765  5789998888888866554

>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=96.33  E-value=0.13  Score=40.48  Aligned_cols=107  Identities=16%  Similarity=0.070  Sum_probs=81.4

Q ss_pred             HHHHHHHHhcCCCchHHHHHH-hhhh--hcch-hhHHHHHHHHHhcCCccccc------------hHHHHHHHHHHHHhc
Q 039275           32 TMVVVLTASSGPGAWILAKEL-QIEL--DLSS-YSLSSKTSRYAHSGRIRLAR------------DPVSCKAMISGYSQA   95 (153)
Q Consensus        32 ~~~~ll~~~~~~~~~~~a~~~-~~~~--~~~~-~~~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~~~~~   95 (153)
                      ++.-+-..+...|++++|.++ ...+  .|+. ..|-.-.+-|-+.|++.+|.            |...-+-...-+.++
T Consensus       196 ~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD~~DRyiNsK~aKy~LRa  275 (517)
T PF12569_consen  196 TLYFLAQHYDYLGDYEKALEYIDKAIEHTPTLVELYMTKARILKHAGDLKEAAEAMDEARELDLADRYINSKCAKYLLRA  275 (517)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHC
Confidence            444555667889999999999 4444  4443 35667778889999999988            888888888999999


Q ss_pred             CChHHHHHHHHHHHHcCCCCChhhH--------HHHHHHhcCCCccccchh
Q 039275           96 GRFNEALEPFGKLESLGVHTDEVTM--------VVVLAASSGPGALDFGKS  138 (153)
Q Consensus        96 g~~~~a~~~~~~m~~~g~~p~~~t~--------~~li~~~~~~g~~~~a~~  138 (153)
                      |++++|.+++..+-+.+..|-...+        .-.-.+|.+.|++..|..
T Consensus       276 ~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~r~~~~~~ALk  326 (517)
T PF12569_consen  276 GRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYLRQGDYGLALK  326 (517)
T ss_pred             CCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence            9999999999999877765543332        344557888888888877

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 [], [].

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=96.33  E-value=0.14  Score=32.74  Aligned_cols=73  Identities=5%  Similarity=0.028  Sum_probs=46.5

Q ss_pred             ChhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHHhhhhhcchhhHHHHHHHHHhcCCc
Q 039275            1 MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIELDLSSYSLSSKTSRYAHSGRI   76 (153)
Q Consensus         1 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~ll~~~~~~g~~   76 (153)
                      +|..+.+.+.++....+++.+...+ ..+...++.++..+++..+-+...-+..  .++.......++.+.+.+.+
T Consensus        13 vv~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~ly~~~~~~~ll~~l~~--~~~~yd~~~~~~~c~~~~l~   85 (140)
T smart00299       13 VVELFEKRNLLEELIPYLESALKLN-SENPALQTKLIELYAKYDPQKEIERLDN--KSNHYDIEKVGKLCEKAKLY   85 (140)
T ss_pred             HHHHHHhCCcHHHHHHHHHHHHccC-ccchhHHHHHHHHHHHHCHHHHHHHHHh--ccccCCHHHHHHHHHHcCcH
Confidence            3566777889999999999998877 4788899999999987654332222231  12333333345544444433

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

Probab=96.32  E-value=0.074  Score=34.25  Aligned_cols=105  Identities=16%  Similarity=0.181  Sum_probs=64.7

Q ss_pred             HHHHHHHHHhcCCCchHHHHHH----hhhhhcchhh-HH--HHHHHHHhcCCccccc---------------hHHHHHHH
Q 039275           31 VTMVVVLTASSGPGAWILAKEL----QIELDLSSYS-LS--SKTSRYAHSGRIRLAR---------------DPVSCKAM   88 (153)
Q Consensus        31 ~~~~~ll~~~~~~~~~~~a~~~----~~~~~~~~~~-~~--~ll~~~~~~g~~~~a~---------------~~~~~~~l   88 (153)
                      ..|..++..+. .++...+.+.    ....+.+... ..  .+-+.+...|++++|.               .....-.|
T Consensus        13 ~~y~~~~~~~~-~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~L   91 (145)
T PF09976_consen   13 ALYEQALQALQ-AGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRL   91 (145)
T ss_pred             HHHHHHHHHHH-CCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHH
Confidence            34555555543 5665655553    2222222122 11  2336777888888887               23344456


Q ss_pred             HHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           89 ISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        89 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      -..+...|++++|...++......+.|  ..+...-+.+.+.|+.++|..
T Consensus        92 A~~~~~~~~~d~Al~~L~~~~~~~~~~--~~~~~~Gdi~~~~g~~~~A~~  139 (145)
T PF09976_consen   92 ARILLQQGQYDEALATLQQIPDEAFKA--LAAELLGDIYLAQGDYDEARA  139 (145)
T ss_pred             HHHHHHcCCHHHHHHHHHhccCcchHH--HHHHHHHHHHHHCCCHHHHHH
Confidence            677888999999999997755444433  345566778888999888875

>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C

Probab=96.29  E-value=0.055  Score=30.53  Aligned_cols=88  Identities=24%  Similarity=0.283  Sum_probs=60.4

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccch
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARD   81 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~   81 (153)
                      ..+.+.|++++|.+.|++..+.. +.+...+..+-..+...+++++|.+. .........                   +
T Consensus         8 ~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~-------------------~   67 (100)
T cd00189           8 NLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALELDPD-------------------N   67 (100)
T ss_pred             HHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc-------------------c
Confidence            35677899999999999887652 23345666677777778888888887 222211110                   2


Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHHH
Q 039275           82 PVSCKAMISGYSQAGRFNEALEPFGKLES  110 (153)
Q Consensus        82 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~  110 (153)
                      ...+..+...+...|+.++|...+....+
T Consensus        68 ~~~~~~~~~~~~~~~~~~~a~~~~~~~~~   96 (100)
T cd00189          68 AKAYYNLGLAYYKLGKYEEALEAYEKALE   96 (100)
T ss_pred             hhHHHHHHHHHHHHHhHHHHHHHHHHHHc
Confidence            24566777778888889999888887664

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

Probab=96.27  E-value=0.036  Score=40.81  Aligned_cols=70  Identities=16%  Similarity=0.058  Sum_probs=32.9

Q ss_pred             HHhcCCCchHHHHHHhhhh-hcchhhHHHHHHHHHhcCCccccc-------hHHHHHHHHHHHHhcCChHHHHHHHHH
Q 039275           38 TASSGPGAWILAKELQIEL-DLSSYSLSSKTSRYAHSGRIRLAR-------DPVSCKAMISGYSQAGRFNEALEPFGK  107 (153)
Q Consensus        38 ~~~~~~~~~~~a~~~~~~~-~~~~~~~~~ll~~~~~~g~~~~a~-------~~~~~~~li~~~~~~g~~~~a~~~~~~  107 (153)
                      .-+...|....|.++.... .|+..-|...|+++++.+++++-.       .+.-|...+..|.+.|+..+|..+...
T Consensus       185 ~~li~~~~~k~A~kl~k~Fkv~dkrfw~lki~aLa~~~~w~eL~~fa~skKsPIGyepFv~~~~~~~~~~eA~~yI~k  262 (319)
T PF04840_consen  185 RKLIEMGQEKQAEKLKKEFKVPDKRFWWLKIKALAENKDWDELEKFAKSKKSPIGYEPFVEACLKYGNKKEASKYIPK  262 (319)
T ss_pred             HHHHHCCCHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCCHHHHHHHHhCCCCCCChHHHHHHHHHCCCHHHHHHHHHh
Confidence            3334444444444442222 234444444455555555544443       444555555555555555555555444

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

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

Probab=96.26  E-value=0.054  Score=41.81  Aligned_cols=123  Identities=15%  Similarity=0.152  Sum_probs=89.9

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCcc-HHHHHHHHHHhcCCCchHHHHHH---hhhhhcch-hhHHHHHHHHHhcCCccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTD-EVTMVVVLTASSGPGAWILAKEL---QIELDLSS-YSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~-~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~~~-~~~~~ll~~~~~~g~~~~   78 (153)
                      -|.++|++++|++.|.+...  ..|| +..|.-.--+|...|+|+++.+.   .-.+.|+- ..+.---+++-+.|++++
T Consensus       124 ~~f~~kkY~eAIkyY~~AI~--l~p~epiFYsNraAcY~~lgd~~~Vied~TkALEl~P~Y~KAl~RRA~A~E~lg~~~e  201 (606)
T KOG0547|consen  124 KFFRNKKYDEAIKYYTQAIE--LCPDEPIFYSNRAACYESLGDWEKVIEDCTKALELNPDYVKALLRRASAHEQLGKFDE  201 (606)
T ss_pred             hhhhcccHHHHHHHHHHHHh--cCCCCchhhhhHHHHHHHHhhHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHhhccHHH
Confidence            47889999999999999877  5788 77777777788899999998888   33344443 244455588899999999


Q ss_pred             cchHHHHHHHHHHHHhcCChHHHHHHHHHHH--------H-c--CCCCChhhHHHHHHHhc
Q 039275           79 ARDPVSCKAMISGYSQAGRFNEALEPFGKLE--------S-L--GVHTDEVTMVVVLAASS  128 (153)
Q Consensus        79 a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~--------~-~--g~~p~~~t~~~li~~~~  128 (153)
                      |...+|-.+++.+|....-.--+.+++++.-        . .  .+-|+.....+.+..+-
T Consensus       202 al~D~tv~ci~~~F~n~s~~~~~eR~Lkk~a~~ka~e~~k~nr~p~lPS~~fi~syf~sF~  262 (606)
T KOG0547|consen  202 ALFDVTVLCILEGFQNASIEPMAERVLKKQAMKKAKEKLKENRPPVLPSATFIASYFGSFH  262 (606)
T ss_pred             HHHhhhHHHHhhhcccchhHHHHHHHHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHhhcc
Confidence            9977888888888887777777777775531        1 1  23466666666555543

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=96.24  E-value=0.029  Score=36.25  Aligned_cols=75  Identities=9%  Similarity=0.031  Sum_probs=63.8

Q ss_pred             HHHHHHHHHhcCCccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCC
Q 039275           63 LSSKTSRYAHSGRIRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGP  130 (153)
Q Consensus        63 ~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  130 (153)
                      +..+-..+.+.|++++|.            +...|..+-..+.+.|++++|...|+...... ..+...+..+-.++.+.
T Consensus        27 ~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~-p~~~~a~~~lg~~l~~~  105 (144)
T PRK15359         27 VYASGYASWQEGDYSRAVIDFSWLVMAQPWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD-ASHPEPVYQTGVCLKMM  105 (144)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHc
Confidence            445667778899988887            78888889999999999999999999998643 33777788888899999


Q ss_pred             Cccccchh
Q 039275          131 GALDFGKS  138 (153)
Q Consensus       131 g~~~~a~~  138 (153)
                      |++++|..
T Consensus       106 g~~~eAi~  113 (144)
T PRK15359        106 GEPGLARE  113 (144)
T ss_pred             CCHHHHHH
Confidence            99999988

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

Probab=96.19  E-value=0.089  Score=40.40  Aligned_cols=132  Identities=15%  Similarity=0.034  Sum_probs=70.2

Q ss_pred             HhhcCChhHHHHHHHHhHHcC--CCccHHHHHHHHHHhcC-------------------------------CCchHHHHH
Q 039275            5 YSQAGRFNEALEPFGKLESLG--VHTDEVTMVVVLTASSG-------------------------------PGAWILAKE   51 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g--~~p~~~~~~~ll~~~~~-------------------------------~~~~~~a~~   51 (153)
                      .-...++++|+++|++++++.  -.-|..+|.-+|-..-.                               .+.-+.|..
T Consensus       272 ~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~skLs~LA~~v~~idKyR~ETCCiIaNYYSlr~eHEKAv~  351 (559)
T KOG1155|consen  272 SYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSKLSYLAQNVSNIDKYRPETCCIIANYYSLRSEHEKAVM  351 (559)
T ss_pred             HhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHHHHHHHHHHHHhccCCccceeeehhHHHHHHhHHHHHH
Confidence            345678999999999998873  11255677665543322                               111222222


Q ss_pred             H-hhhhhcch---hhHHHHHHHHHhcCCccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC
Q 039275           52 L-QIELDLSS---YSLSSKTSRYAHSGRIRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT  115 (153)
Q Consensus        52 ~-~~~~~~~~---~~~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  115 (153)
                      . ++.++.|.   ..|+-+=.-|....+...|.            |-..|=.|=++|...+.+.-|+-.|++-..  ++|
T Consensus       352 YFkRALkLNp~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~--~kP  429 (559)
T KOG1155|consen  352 YFKRALKLNPKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDINPRDYRAWYGLGQAYEIMKMHFYALYYFQKALE--LKP  429 (559)
T ss_pred             HHHHHHhcCcchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcCchhHHHHhhhhHHHHHhcchHHHHHHHHHHHh--cCC
Confidence            2 33333333   34554445555555555554            444555555555555555555555554432  344


Q ss_pred             -ChhhHHHHHHHhcCCCccccchh
Q 039275          116 -DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       116 -~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                       |...|.+|-++|.+.++.++|+.
T Consensus       430 nDsRlw~aLG~CY~kl~~~~eAiK  453 (559)
T KOG1155|consen  430 NDSRLWVALGECYEKLNRLEEAIK  453 (559)
T ss_pred             CchHHHHHHHHHHHHhccHHHHHH
Confidence             45555555555555555555555

>PRK11189 lipoprotein NlpI; Provisional

Probab=96.10  E-value=0.34  Score=35.20  Aligned_cols=131  Identities=17%  Similarity=0.022  Sum_probs=74.1

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCcc-HHHHHHHHHHhcCCCchHHHHHH---hhhhhcchhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTD-EVTMVVVLTASSGPGAWILAKEL---QIELDLSSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~-~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .|...|++++|.+.|++..+.  .|+ ...+..+-.++...|++++|.+.   -....|+..............++.++|
T Consensus       107 ~~~~~g~~~~A~~~~~~Al~l--~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~~P~~~~~~~~~~l~~~~~~~~~A  184 (296)
T PRK11189        107 YLTQAGNFDAAYEAFDSVLEL--DPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQDDPNDPYRALWLYLAESKLDPKQA  184 (296)
T ss_pred             HHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHccCCHHHH
Confidence            467788999999998888763  343 45666666777788888888887   222334332112222223344555555


Q ss_pred             c----------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcC---C--CC-ChhhHHHHHHHhcCCCccccchh
Q 039275           80 R----------DPVSCKAMISGYSQAGRFNEALEPFGKLESLG---V--HT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        80 ~----------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g---~--~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .          +...|.. -......|+.+++ +.++.+.+..   +  .| ....|..+-..+.+.|++++|..
T Consensus       185 ~~~l~~~~~~~~~~~~~~-~~~~~~lg~~~~~-~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~  257 (296)
T PRK11189        185 KENLKQRYEKLDKEQWGW-NIVEFYLGKISEE-TLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAA  257 (296)
T ss_pred             HHHHHHHHhhCCccccHH-HHHHHHccCCCHH-HHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHH
Confidence            4          2222321 2223345566554 3555554221   1  11 23467777778888888888877

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

Probab=96.07  E-value=0.14  Score=41.02  Aligned_cols=133  Identities=14%  Similarity=0.101  Sum_probs=102.1

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhh--hhcc-hhhHHHHHHHHHhcCCccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIE--LDLS-SYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~--~~~~-~~~~~~ll~~~~~~g~~~~   78 (153)
                      .++-+.|++.+|.+.|++...-.. --....+-|-+.+...|.+++|..+ +.-  +-|. ....|.|-..|-+.|++++
T Consensus       328 nALkd~G~V~ea~~cYnkaL~l~p-~hadam~NLgni~~E~~~~e~A~~ly~~al~v~p~~aaa~nNLa~i~kqqgnl~~  406 (966)
T KOG4626|consen  328 NALKDKGSVTEAVDCYNKALRLCP-NHADAMNNLGNIYREQGKIEEATRLYLKALEVFPEFAAAHNNLASIYKQQGNLDD  406 (966)
T ss_pred             HHHHhccchHHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHhccchHHHHHHHHHHhhChhhhhhhhhHHHHHHhcccHHH
Confidence            355677999999999998877532 2345677788888999999999988 222  2333 3467888899999999999


Q ss_pred             cc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC-hhhHHHHHHHhcCCCccccchh
Q 039275           79 AR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTD-EVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        79 a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |.            -...|+.|=..|-..|+.+.|.+.+.+-..  +.|. +..++.+-+.+-..|++.+|.+
T Consensus       407 Ai~~YkealrI~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~--~nPt~AeAhsNLasi~kDsGni~~AI~  477 (966)
T KOG4626|consen  407 AIMCYKEALRIKPTFADALSNMGNTYKEMGDVSAAIQCYTRAIQ--INPTFAEAHSNLASIYKDSGNIPEAIQ  477 (966)
T ss_pred             HHHHHHHHHhcCchHHHHHHhcchHHHHhhhHHHHHHHHHHHHh--cCcHHHHHHhhHHHHhhccCCcHHHHH
Confidence            98            455677888888889999999998887765  3463 4457888889999999999988

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

Probab=95.97  E-value=0.052  Score=39.99  Aligned_cols=67  Identities=10%  Similarity=0.029  Sum_probs=36.4

Q ss_pred             HHHHHHhcCCccccc---------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccc
Q 039275           66 KTSRYAHSGRIRLAR---------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFG  136 (153)
Q Consensus        66 ll~~~~~~g~~~~a~---------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a  136 (153)
                      -|.-+...|+...|.         +..-|...|.+++..++|++-.++-+.      +-+..-|..++.+|.+.|+..+|
T Consensus       183 Ti~~li~~~~~k~A~kl~k~Fkv~dkrfw~lki~aLa~~~~w~eL~~fa~s------kKsPIGyepFv~~~~~~~~~~eA  256 (319)
T PF04840_consen  183 TIRKLIEMGQEKQAEKLKKEFKVPDKRFWWLKIKALAENKDWDELEKFAKS------KKSPIGYEPFVEACLKYGNKKEA  256 (319)
T ss_pred             HHHHHHHCCCHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCCHHHHHHHHhC------CCCCCChHHHHHHHHHCCCHHHH
Confidence            344445555555555         556666666666666666655544322      11124456666666666666555


Q ss_pred             hh
Q 039275          137 KS  138 (153)
Q Consensus       137 ~~  138 (153)
                      ..
T Consensus       257 ~~  258 (319)
T PF04840_consen  257 SK  258 (319)
T ss_pred             HH
Confidence            55

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

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=95.97  E-value=0.07  Score=43.47  Aligned_cols=134  Identities=18%  Similarity=0.146  Sum_probs=70.5

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH---hhhhhcchhhHHHHHHHHHhcCCcccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL---QIELDLSSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      +.|+..|+++.|.++|-+-         ..++-.|..|.+.|.|+.|.++   -.+.+...+.|-+-..-.-+.|.+.+|
T Consensus       773 dhyan~~dfe~ae~lf~e~---------~~~~dai~my~k~~kw~da~kla~e~~~~e~t~~~yiakaedldehgkf~ea  843 (1636)
T KOG3616|consen  773 DHYANKGDFEIAEELFTEA---------DLFKDAIDMYGKAGKWEDAFKLAEECHGPEATISLYIAKAEDLDEHGKFAEA  843 (1636)
T ss_pred             HHhccchhHHHHHHHHHhc---------chhHHHHHHHhccccHHHHHHHHHHhcCchhHHHHHHHhHHhHHhhcchhhh
Confidence            3455666666666666421         2345556677777777777777   333344444555555555666666666


Q ss_pred             c----hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC--hhhHHHHHHHhcCCCccccchh---HHHHHHHHHHHh
Q 039275           80 R----DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTD--EVTMVVVLAASSGPGALDFGKS---NIFLTTAIIEMY  150 (153)
Q Consensus        80 ~----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~--~~t~~~li~~~~~~g~~~~a~~---~~~~~~~li~~y  150 (153)
                      .    +.-.=..-|..|-+.|.-|.+.++.++--     ||  ..|-.-+-.-+-..|++..|++   ...-|.+-+++|
T Consensus       844 eqlyiti~~p~~aiqmydk~~~~ddmirlv~k~h-----~d~l~dt~~~f~~e~e~~g~lkaae~~flea~d~kaavnmy  918 (1636)
T KOG3616|consen  844 EQLYITIGEPDKAIQMYDKHGLDDDMIRLVEKHH-----GDHLHDTHKHFAKELEAEGDLKAAEEHFLEAGDFKAAVNMY  918 (1636)
T ss_pred             hheeEEccCchHHHHHHHhhCcchHHHHHHHHhC-----hhhhhHHHHHHHHHHHhccChhHHHHHHHhhhhHHHHHHHh
Confidence            6    11112233455555566555555554321     21  1233334445555666666666   444455555554

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=95.94  E-value=0.14  Score=31.14  Aligned_cols=92  Identities=12%  Similarity=-0.014  Sum_probs=65.1

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcC--CCccHHHHHHHHHHhcCCCchHHHHHH-hhh--hhcchhhHHHHHHHHHhcCCcc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLG--VHTDEVTMVVVLTASSGPGAWILAKEL-QIE--LDLSSYSLSSKTSRYAHSGRIR   77 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g--~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~--~~~~~~~~~~ll~~~~~~g~~~   77 (153)
                      ..+.+.|++++|.+.|.++.+..  -+.....+..+-..+.+.|++++|.+. +.-  ..|+...               
T Consensus        10 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~---------------   74 (119)
T TIGR02795        10 LLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPK---------------   74 (119)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCc---------------
Confidence            35678899999999999997642  111234566678889999999999998 222  2232210               


Q ss_pred             ccchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 039275           78 LARDPVSCKAMISGYSQAGRFNEALEPFGKLESLG  112 (153)
Q Consensus        78 ~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  112 (153)
                         ....+..+-..+.+.|+.++|.+.++++.+..
T Consensus        75 ---~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~  106 (119)
T TIGR02795        75 ---APDALLKLGMSLQELGDKEKAKATLQQVIKRY  106 (119)
T ss_pred             ---ccHHHHHHHHHHHHhCChHHHHHHHHHHHHHC
Confidence               12345566677788999999999999998764

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.

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=95.94  E-value=0.11  Score=37.63  Aligned_cols=75  Identities=13%  Similarity=0.078  Sum_probs=55.1

Q ss_pred             hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCc
Q 039275           53 QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGA  132 (153)
Q Consensus        53 ~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~  132 (153)
                      +.|++.|..+|+.||+.+=+-.-+    ....+....-.|=+  +-.-+..++++|...|+.||..+-..+++++++.+-
T Consensus       100 eyGVerDl~vYk~LlnvfPKgkfi----P~nvfQ~~F~HYP~--QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~  173 (406)
T KOG3941|consen  100 EYGVERDLDVYKGLLNVFPKGKFI----PQNVFQKVFLHYPQ--QQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNF  173 (406)
T ss_pred             HhcchhhHHHHHHHHHhCcccccc----cHHHHHHHHhhCch--hhhHHHHHHHHHHHcCCCCchHHHHHHHHHhccccc
Confidence            667777777777777766554333    33445555555544  345688999999999999999999999999998765


Q ss_pred             c
Q 039275          133 L  133 (153)
Q Consensus       133 ~  133 (153)
                      .
T Consensus       174 p  174 (406)
T KOG3941|consen  174 P  174 (406)
T ss_pred             c
Confidence            4

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

Probab=95.93  E-value=0.053  Score=43.54  Aligned_cols=134  Identities=14%  Similarity=0.054  Sum_probs=90.5

Q ss_pred             hhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH------h--hhh---hcchhhHH------
Q 039275            2 ISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL------Q--IEL---DLSSYSLS------   64 (153)
Q Consensus         2 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~------~--~~~---~~~~~~~~------   64 (153)
                      |-.|+..|+.++|..+..+-.+  -+||+.-|..+.+.....-.++.|.++      +  +..   ..+...|.      
T Consensus       431 i~CY~~lg~~~kaeei~~q~le--k~~d~~lyc~LGDv~~d~s~yEkawElsn~~sarA~r~~~~~~~~~~~fs~~~~hl  508 (777)
T KOG1128|consen  431 ILCYLLLGQHGKAEEINRQELE--KDPDPRLYCLLGDVLHDPSLYEKAWELSNYISARAQRSLALLILSNKDFSEADKHL  508 (777)
T ss_pred             HHHHHHhcccchHHHHHHHHhc--CCCcchhHHHhhhhccChHHHHHHHHHhhhhhHHHHHhhccccccchhHHHHHHHH
Confidence            5678888888888888777665  578999999999988888888888888      1  100   00111111      


Q ss_pred             ---------------HHHHHHHhcCCccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCh
Q 039275           65 ---------------SKTSRYAHSGRIRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDE  117 (153)
Q Consensus        65 ---------------~ll~~~~~~g~~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  117 (153)
                                     .+=.+..+.+++..|.            +...||++-.+|.+.++-.+|...+++-.+-+..| -
T Consensus       509 e~sl~~nplq~~~wf~~G~~ALqlek~q~av~aF~rcvtL~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn~~~-w  587 (777)
T KOG1128|consen  509 ERSLEINPLQLGTWFGLGCAALQLEKEQAAVKAFHRCVTLEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCNYQH-W  587 (777)
T ss_pred             HHHhhcCccchhHHHhccHHHHHHhhhHHHHHHHHHHhhcCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcCCCC-C
Confidence                           1112233444444444            67899999999999999999999999987766333 3


Q ss_pred             hhHHHHHHHhcCCCccccchh
Q 039275          118 VTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       118 ~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ..|...+-...+.|.++.|.+
T Consensus       588 ~iWENymlvsvdvge~eda~~  608 (777)
T KOG1128|consen  588 QIWENYMLVSVDVGEFEDAIK  608 (777)
T ss_pred             eeeechhhhhhhcccHHHHHH
Confidence            335555555666677776666

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=95.92  E-value=0.19  Score=34.88  Aligned_cols=109  Identities=17%  Similarity=0.095  Sum_probs=70.9

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCC-CccH-HHHHHHHHHhcCC--------CchHHHHHHh---hhhhcchh-hH-----
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGV-HTDE-VTMVVVLTASSGP--------GAWILAKELQ---IELDLSSY-SL-----   63 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~-~p~~-~~~~~ll~~~~~~--------~~~~~a~~~~---~~~~~~~~-~~-----   63 (153)
                      ..+.+.|++++|.+.|+++.+..- .|.. ..+..+-.++.+.        |++++|.+..   ....|+.. .+     
T Consensus        78 ~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~  157 (235)
T TIGR03302        78 YAYYKSGDYAEAIAAADRFIRLHPNHPDADYAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYPNSEYAPDAKKR  157 (235)
T ss_pred             HHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHCCCChhHHHHHHH
Confidence            357788999999999999976421 1221 1232222333332        6677777771   11123221 11     


Q ss_pred             ------------HHHHHHHHhcCCccccc---------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 039275           64 ------------SSKTSRYAHSGRIRLAR---------------DPVSCKAMISGYSQAGRFNEALEPFGKLESL  111 (153)
Q Consensus        64 ------------~~ll~~~~~~g~~~~a~---------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  111 (153)
                                  -.+-..|.+.|++++|.               ....|..+...+.+.|+.++|..+++.+...
T Consensus       158 ~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       158 MDYLRNRLAGKELYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence                        13345677889988888               2367889999999999999999999998754

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).

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=95.92  E-value=0.22  Score=36.12  Aligned_cols=102  Identities=16%  Similarity=0.178  Sum_probs=71.8

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCc-cHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchH
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDP   82 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~   82 (153)
                      ..+++++++|++.|.+...  +.| |.+-|.-=-.+|++.|.++.|.+= +..+.-|...+                   
T Consensus        91 ~m~~~~Y~eAv~kY~~AI~--l~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iDp~ys-------------------  149 (304)
T KOG0553|consen   91 LMKNKDYQEAVDKYTEAIE--LDPTNAVYYCNRAAAYSKLGEYEDAVKDCESALSIDPHYS-------------------  149 (304)
T ss_pred             HHHhhhHHHHHHHHHHHHh--cCCCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcChHHH-------------------
Confidence            3567778888888877766  344 344444555677777777776665 66666655544                   


Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcC
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSG  129 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~  129 (153)
                      .+|..|=.+|...|++.+|.+.|++-.  .+.|+-.+|-.=++.--+
T Consensus       150 kay~RLG~A~~~~gk~~~A~~aykKaL--eldP~Ne~~K~nL~~Ae~  194 (304)
T KOG0553|consen  150 KAYGRLGLAYLALGKYEEAIEAYKKAL--ELDPDNESYKSNLKIAEQ  194 (304)
T ss_pred             HHHHHHHHHHHccCcHHHHHHHHHhhh--ccCCCcHHHHHHHHHHHH
Confidence            778888899999999999999988765  367888888777765443

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

Probab=95.90  E-value=0.098  Score=41.18  Aligned_cols=107  Identities=18%  Similarity=0.141  Sum_probs=74.3

Q ss_pred             hhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHH--HHH--HHHhcCCc
Q 039275            2 ISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSS--KTS--RYAHSGRI   76 (153)
Q Consensus         2 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~--ll~--~~~~~g~~   76 (153)
                      ++-+...|++++|.+.-.++...+ +-|...+..=+-++.+.+.+++|+++ +.....  .+++.  +=+  ...+.+.+
T Consensus        19 ln~~~~~~e~e~a~k~~~Kil~~~-pdd~~a~~cKvValIq~~ky~~ALk~ikk~~~~--~~~~~~~fEKAYc~Yrlnk~   95 (652)
T KOG2376|consen   19 LNRHGKNGEYEEAVKTANKILSIV-PDDEDAIRCKVVALIQLDKYEDALKLIKKNGAL--LVINSFFFEKAYCEYRLNKL   95 (652)
T ss_pred             HHHhccchHHHHHHHHHHHHHhcC-CCcHhhHhhhHhhhhhhhHHHHHHHHHHhcchh--hhcchhhHHHHHHHHHcccH
Confidence            345678899999999999999977 44555555666677999999999988 222111  12222  234  44577888


Q ss_pred             cccc---------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 039275           77 RLAR---------DPVSCKAMISGYSQAGRFNEALEPFGKLESL  111 (153)
Q Consensus        77 ~~a~---------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  111 (153)
                      ++|.         |..+-..=-..+.+.|++++|+.+|+.+.+.
T Consensus        96 Dealk~~~~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn  139 (652)
T KOG2376|consen   96 DEALKTLKGLDRLDDKLLELRAQVLYRLERYDEALDIYQHLAKN  139 (652)
T ss_pred             HHHHHHHhcccccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            8887         2234444446778999999999999988433

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

Probab=95.87  E-value=0.25  Score=35.34  Aligned_cols=119  Identities=9%  Similarity=0.076  Sum_probs=75.2

Q ss_pred             HHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhh--hcchhhHHHHHHHHHhcCCccccc----------h
Q 039275           15 LEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIEL--DLSSYSLSSKTSRYAHSGRIRLAR----------D   81 (153)
Q Consensus        15 ~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~--~~~~~~~~~ll~~~~~~g~~~~a~----------~   81 (153)
                      -++.+++......-+....-.-..-|.+.+++++|++. +.+.  +.-...-.++|    +..+++-|.          +
T Consensus        93 ~~l~E~~a~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~~~~lE~~Al~VqI~l----k~~r~d~A~~~lk~mq~ide  168 (299)
T KOG3081|consen   93 ASLYELVADSTDGSNLIDLLLAAIIYMHDGDFDEALKALHLGENLEAAALNVQILL----KMHRFDLAEKELKKMQQIDE  168 (299)
T ss_pred             HHHHHHHHhhccchhHHHHHHhhHHhhcCCChHHHHHHHhccchHHHHHHHHHHHH----HHHHHHHHHHHHHHHHccch
Confidence            34455555555555544444555677889999999988 2222  21111112222    222222222          3


Q ss_pred             HHHHH----HHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           82 PVSCK----AMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        82 ~~~~~----~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ..|.+    +.|......++...|+-+|++|-+ +..|+..+.+....++..+|++++|+.
T Consensus       169 d~tLtQLA~awv~la~ggek~qdAfyifeE~s~-k~~~T~~llnG~Av~~l~~~~~eeAe~  228 (299)
T KOG3081|consen  169 DATLTQLAQAWVKLATGGEKIQDAFYIFEELSE-KTPPTPLLLNGQAVCHLQLGRYEEAES  228 (299)
T ss_pred             HHHHHHHHHHHHHHhccchhhhhHHHHHHHHhc-ccCCChHHHccHHHHHHHhcCHHHHHH
Confidence            44444    344445556789999999999863 468999999999999999999999998

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

Probab=95.86  E-value=0.037  Score=43.74  Aligned_cols=28  Identities=21%  Similarity=0.252  Sum_probs=12.9

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHH
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKL  108 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m  108 (153)
                      .+.+|-++=..|.-.++.+.|.+.|++-
T Consensus       420 sPesWca~GNcfSLQkdh~~Aik~f~RA  447 (638)
T KOG1126|consen  420 SPESWCALGNCFSLQKDHDTAIKCFKRA  447 (638)
T ss_pred             CcHHHHHhcchhhhhhHHHHHHHHHHHh
Confidence            3444444444444444444444444443

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

Probab=95.79  E-value=0.043  Score=34.55  Aligned_cols=86  Identities=10%  Similarity=0.035  Sum_probs=61.6

Q ss_pred             HHHHHHHHHhcCCCchHHHHHHhhh-h--hcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHH
Q 039275           31 VTMVVVLTASSGPGAWILAKELQIE-L--DLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGK  107 (153)
Q Consensus        31 ~~~~~ll~~~~~~~~~~~a~~~~~~-~--~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~  107 (153)
                      .....+...+.+.|++++|.+.... .  .|+                     +...|..+-..+.+.|++++|...|+.
T Consensus        18 ~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~---------------------~~~~~~~la~~~~~~~~~~~A~~~~~~   76 (135)
T TIGR02552        18 EQIYALAYNLYQQGRYDEALKLFQLLAAYDPY---------------------NSRYWLGLAACCQMLKEYEEAIDAYAL   76 (135)
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHhCCC---------------------cHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344555666777888888777211 1  121                     446777888889999999999999998


Q ss_pred             HHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275          108 LESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       108 m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ..... ..+...+..+-..+...|+++.|.+
T Consensus        77 ~~~~~-p~~~~~~~~la~~~~~~g~~~~A~~  106 (135)
T TIGR02552        77 AAALD-PDDPRPYFHAAECLLALGEPESALK  106 (135)
T ss_pred             HHhcC-CCChHHHHHHHHHHHHcCCHHHHHH
Confidence            87654 3355666677778899999999877

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

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

Probab=95.77  E-value=0.37  Score=32.92  Aligned_cols=122  Identities=11%  Similarity=0.023  Sum_probs=82.7

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhh---hhcchhhHHHHHHHHHhcCCccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIE---LDLSSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~---~~~~~~~~~~ll~~~~~~g~~~~   78 (153)
                      -.|...|+++.+......+..    |. .       .+...++.+++... +..   -+.|...|..|-..|...|++++
T Consensus        24 ~~Y~~~g~~~~v~~~~~~~~~----~~-~-------~~~~~~~~~~~i~~l~~~L~~~P~~~~~w~~Lg~~~~~~g~~~~   91 (198)
T PRK10370         24 GSYLLSPKWQAVRAEYQRLAD----PL-H-------QFASQQTPEAQLQALQDKIRANPQNSEQWALLGEYYLWRNDYDN   91 (198)
T ss_pred             HHHHHcchHHHHHHHHHHHhC----cc-c-------cccCchhHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHH
Confidence            367888888886544422211    11 0       11223444444333 222   24456678888899999999999


Q ss_pred             cc------------hHHHHHHHHHHH-HhcCC--hHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           79 AR------------DPVSCKAMISGY-SQAGR--FNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        79 a~------------~~~~~~~li~~~-~~~g~--~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |.            +...+..+-..+ ...|+  .++|.+++++..+..  | +...+..+-..+.+.|++++|..
T Consensus        92 A~~a~~~Al~l~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~d--P~~~~al~~LA~~~~~~g~~~~Ai~  165 (198)
T PRK10370         92 ALLAYRQALQLRGENAELYAALATVLYYQAGQHMTPQTREMIDKALALD--ANEVTALMLLASDAFMQADYAQAIE  165 (198)
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhC--CCChhHHHHHHHHHHHcCCHHHHHH
Confidence            98            777777777664 67777  599999999998764  4 55667777788899999999998

>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=95.62  E-value=0.36  Score=32.13  Aligned_cols=93  Identities=15%  Similarity=0.079  Sum_probs=68.6

Q ss_pred             HHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccc--------hHH-
Q 039275           14 ALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLAR--------DPV-   83 (153)
Q Consensus        14 a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~--------~~~-   83 (153)
                      ..+..+.+.+.|++|+...|.-+++.+.+.|++..-..+ ..++-+|.......+-.+....  ..+.        ... 
T Consensus        13 llEYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~L~qllq~~Vi~DSk~lA~~LLs~~~~~--~~~~Ql~lDMLkRL~~   90 (167)
T PF07035_consen   13 LLEYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQLHQLLQYHVIPDSKPLACQLLSLGNQY--PPAYQLGLDMLKRLGT   90 (167)
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHHHHHHHhhcccCCcHHHHHHHHHhHccC--hHHHHHHHHHHHHhhh
Confidence            355667777889999999999999999999999988888 7776666655444432222211  1111        334 


Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHH
Q 039275           84 SCKAMISGYSQAGRFNEALEPFGKL  108 (153)
Q Consensus        84 ~~~~li~~~~~~g~~~~a~~~~~~m  108 (153)
                      .++.++..+...|++-+|.++....
T Consensus        91 ~~~~iievLL~~g~vl~ALr~ar~~  115 (167)
T PF07035_consen   91 AYEEIIEVLLSKGQVLEALRYARQY  115 (167)
T ss_pred             hHHHHHHHHHhCCCHHHHHHHHHHc
Confidence            7888889999999999999998775

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=95.56  E-value=0.39  Score=31.79  Aligned_cols=118  Identities=14%  Similarity=0.131  Sum_probs=63.1

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCcc--HHHHHHHHHHhcCCCchHHHHHH-hhhh--hc-chhhHHHHHHHHHhcCCcc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTD--EVTMVVVLTASSGPGAWILAKEL-QIEL--DL-SSYSLSSKTSRYAHSGRIR   77 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~--~~~~~~ll~~~~~~~~~~~a~~~-~~~~--~~-~~~~~~~ll~~~~~~g~~~   77 (153)
                      .+...|++++|...|++..+....|+  ...+..+-..+.+.|++++|... ...+  .| +...+..+...+...|+..
T Consensus        44 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~  123 (172)
T PRK02603         44 SAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELNPKQPSALNNIAVIYHKRGEKA  123 (172)
T ss_pred             HHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCChH
Confidence            45667888888888887765432222  35566666777788888888877 2222  22 2223333344444444433


Q ss_pred             ccchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCcc
Q 039275           78 LARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGAL  133 (153)
Q Consensus        78 ~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~  133 (153)
                      .+..  -+..-      ...+++|.+++++...  ..|+.  +..++..+...|+.
T Consensus       124 ~a~~--~~~~A------~~~~~~A~~~~~~a~~--~~p~~--~~~~~~~~~~~~~~  167 (172)
T PRK02603        124 EEAG--DQDEA------EALFDKAAEYWKQAIR--LAPNN--YIEAQNWLKTTGRS  167 (172)
T ss_pred             hHhh--CHHHH------HHHHHHHHHHHHHHHh--hCchh--HHHHHHHHHhcCcc
Confidence            3220  00000      0125667777766553  33554  66666666655543

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A

Probab=95.56  E-value=0.053  Score=29.80  Aligned_cols=44  Identities=16%  Similarity=0.220  Sum_probs=28.8

Q ss_pred             HhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           93 SQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        93 ~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ...|++++|.++|++.....  | +......+..++.+.|++++|.+
T Consensus         2 l~~~~~~~A~~~~~~~l~~~--p~~~~~~~~la~~~~~~g~~~~A~~   46 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQRN--PDNPEARLLLAQCYLKQGQYDEAEE   46 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHHT--TTSHHHHHHHHHHHHHTT-HHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            45677777777777776543  3 55555567777777777777776

...

>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=95.56  E-value=0.038  Score=31.23  Aligned_cols=55  Identities=18%  Similarity=0.199  Sum_probs=41.5

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ..+..+...+...|++++|.+.|+...... ..+..++..+...+...|+.+.|..
T Consensus        35 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~   89 (100)
T cd00189          35 DAYYNLAAAYYKLGKYEEALEDYEKALELD-PDNAKAYYNLGLAYYKLGKYEEALE   89 (100)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CcchhHHHHHHHHHHHHHhHHHHHH
Confidence            455667777788899999999999887654 2233577778888888888887765

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

Probab=95.54  E-value=0.5  Score=34.06  Aligned_cols=74  Identities=14%  Similarity=0.194  Sum_probs=42.0

Q ss_pred             hHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCC-----CCChh--hHHHHHHHhcCCCccc
Q 039275           62 SLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGV-----HTDEV--TMVVVLAASSGPGALD  134 (153)
Q Consensus        62 ~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~-----~p~~~--t~~~li~~~~~~g~~~  134 (153)
                      .|..-+..|...|....  -..++..+...+.+.|++++|.++|++....-.     +++..  .+..+| ++...|+..
T Consensus       137 ~Y~~A~~~y~~e~~~~~--a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l-~~L~~~D~v  213 (282)
T PF14938_consen  137 YYQKAAELYEQEGSPHS--AAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAIL-CHLAMGDYV  213 (282)
T ss_dssp             HHHHHHHHHHHTT-HHH--HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHH-HHHHTT-HH
T ss_pred             HHHHHHHHHHHCCChhh--HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHH-HHHHcCCHH
Confidence            34444444444443333  346777888888999999999999988865422     22222  233433 444457777


Q ss_pred             cchh
Q 039275          135 FGKS  138 (153)
Q Consensus       135 ~a~~  138 (153)
                      .|.+
T Consensus       214 ~A~~  217 (282)
T PF14938_consen  214 AARK  217 (282)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6666

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=95.51  E-value=0.4  Score=39.19  Aligned_cols=105  Identities=10%  Similarity=0.054  Sum_probs=81.6

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCccHHHH-HHHHHHhcCCCchHHHHHH---hhhhhc-chhhHHHHHHHHHhcCCcccc
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTDEVTM-VVVLTASSGPGAWILAKEL---QIELDL-SSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~~~~~-~~ll~~~~~~~~~~~a~~~---~~~~~~-~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      -.+.|.+++|..+++...+  +.||..-. ..+...+.+.+++++|...   -....| +......+-.++.+.|+.++|
T Consensus        96 ~~~~g~~~ea~~~l~~~~~--~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~p~~~~~~~~~a~~l~~~g~~~~A  173 (694)
T PRK15179         96 LEAAHRSDEGLAVWRGIHQ--RFPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGGSSSAREILLEAKSWDEIGQSEQA  173 (694)
T ss_pred             HHHcCCcHHHHHHHHHHHh--hCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHhcchHHH
Confidence            4567899999999999887  56766544 4566788999999999998   222334 344556677889999999999


Q ss_pred             c------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 039275           80 R------------DPVSCKAMISGYSQAGRFNEALEPFGKLESL  111 (153)
Q Consensus        80 ~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  111 (153)
                      .            +..+|-.+-..+-..|+.++|...|..-.+.
T Consensus       174 ~~~y~~~~~~~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~  217 (694)
T PRK15179        174 DACFERLSRQHPEFENGYVGWAQSLTRRGALWRARDVLQAGLDA  217 (694)
T ss_pred             HHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            8            5677777778888899999999999888643

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

Probab=95.40  E-value=0.6  Score=34.39  Aligned_cols=76  Identities=13%  Similarity=0.169  Sum_probs=50.9

Q ss_pred             HHHHHhcCCCchHHHHHH-hhh--hhc-chhhHHHHHHHHHhcCCccccc----------------hHHHHHHHHHHHHh
Q 039275           35 VVLTASSGPGAWILAKEL-QIE--LDL-SSYSLSSKTSRYAHSGRIRLAR----------------DPVSCKAMISGYSQ   94 (153)
Q Consensus        35 ~ll~~~~~~~~~~~a~~~-~~~--~~~-~~~~~~~ll~~~~~~g~~~~a~----------------~~~~~~~li~~~~~   94 (153)
                      .+-..+...|++++|.+. +..  ..| +...+..+-..+...|++++|.                ....|..+...+..
T Consensus       119 ~~a~~~~~~G~~~~A~~~~~~al~~~p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~  198 (355)
T cd05804         119 MLAFGLEEAGQYDRAEEAARRALELNPDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLE  198 (355)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHH
Confidence            344456677777777777 211  222 3345556666777777777776                12345567788899


Q ss_pred             cCChHHHHHHHHHHHH
Q 039275           95 AGRFNEALEPFGKLES  110 (153)
Q Consensus        95 ~g~~~~a~~~~~~m~~  110 (153)
                      .|++++|.+++++...
T Consensus       199 ~G~~~~A~~~~~~~~~  214 (355)
T cd05804         199 RGDYEAALAIYDTHIA  214 (355)
T ss_pred             CCCHHHHHHHHHHHhc
Confidence            9999999999999853

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.

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=95.40  E-value=0.048  Score=29.80  Aligned_cols=49  Identities=14%  Similarity=0.137  Sum_probs=40.1

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL   52 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~   52 (153)
                      ..+.+.|++++|.+.|++..+.. +-+...+..+-..+.+.|++++|...
T Consensus         5 ~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~   53 (65)
T PF13432_consen    5 RALYQQGDYDEAIAAFEQALKQD-PDNPEAWYLLGRILYQQGRYDEALAY   53 (65)
T ss_dssp             HHHHHCTHHHHHHHHHHHHHCCS-TTHHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            35788999999999999998875 33667777777888999999999988

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

Probab=95.37  E-value=0.48  Score=36.83  Aligned_cols=128  Identities=12%  Similarity=0.005  Sum_probs=100.9

Q ss_pred             cCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH----hhhhhcchhhHHHHHHHHHhcCCccccc---
Q 039275            8 AGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL----QIELDLSSYSLSSKTSRYAHSGRIRLAR---   80 (153)
Q Consensus         8 ~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~----~~~~~~~~~~~~~ll~~~~~~g~~~~a~---   80 (153)
                      .+++.+|.++|++..... .-++..|-..+.+=.+.+.+..|..+    -.-++.-...|-..+.+=-..|++..|.   
T Consensus        86 q~e~~RARSv~ERALdvd-~r~itLWlkYae~Emknk~vNhARNv~dRAvt~lPRVdqlWyKY~ymEE~LgNi~gaRqif  164 (677)
T KOG1915|consen   86 QKEIQRARSVFERALDVD-YRNITLWLKYAEFEMKNKQVNHARNVWDRAVTILPRVDQLWYKYIYMEEMLGNIAGARQIF  164 (677)
T ss_pred             HHHHHHHHHHHHHHHhcc-cccchHHHHHHHHHHhhhhHhHHHHHHHHHHHhcchHHHHHHHHHHHHHHhcccHHHHHHH
Confidence            456788999999887654 35666676777777788888888888    2223333456777777778888988888   


Q ss_pred             --------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 --------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 --------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                              +.-+|++.|..-.+-..++.|..+++..+-  +.|+..+|.--...=-+.|.+..+.+
T Consensus       165 erW~~w~P~eqaW~sfI~fElRykeieraR~IYerfV~--~HP~v~~wikyarFE~k~g~~~~aR~  228 (677)
T KOG1915|consen  165 ERWMEWEPDEQAWLSFIKFELRYKEIERARSIYERFVL--VHPKVSNWIKYARFEEKHGNVALARS  228 (677)
T ss_pred             HHHHcCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhe--ecccHHHHHHHHHHHHhcCcHHHHHH
Confidence                    889999999999999999999999999885  45999999888888888888877776

>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=95.25  E-value=0.033  Score=38.54  Aligned_cols=41  Identities=17%  Similarity=0.193  Sum_probs=34.4

Q ss_pred             hHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCc-hHHHHHH
Q 039275           12 NEALEPFGKLESLGVHTDEVTMVVVLTASSGPGA-WILAKEL   52 (153)
Q Consensus        12 ~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~-~~~a~~~   52 (153)
                      +-|++++++|..+|+.||..|+..+++.+.+.+. +.....+
T Consensus       120 ~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~p~~K~~rm  161 (228)
T PF06239_consen  120 ECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSHPMKKYRRM  161 (228)
T ss_pred             HHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccHHHHHHHHH
Confidence            5689999999999999999999999999998875 3333333

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

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=95.24  E-value=0.51  Score=31.08  Aligned_cols=48  Identities=17%  Similarity=0.200  Sum_probs=29.7

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCc--cHHHHHHHHHHhcCCCchHHHHHH
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHT--DEVTMVVVLTASSGPGAWILAKEL   52 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p--~~~~~~~ll~~~~~~~~~~~a~~~   52 (153)
                      +...|++++|...|++.....-.|  ...++..+-..+.+.|++++|.+.
T Consensus        45 ~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~   94 (168)
T CHL00033         45 AQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEY   94 (168)
T ss_pred             HHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHH
Confidence            455677777777777765442221  123555666666777777777776

>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production

Probab=95.19  E-value=0.052  Score=34.88  Aligned_cols=59  Identities=20%  Similarity=0.263  Sum_probs=38.5

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH----------hhhhhcchhh
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL----------QIELDLSSYS   62 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~----------~~~~~~~~~~   62 (153)
                      ..+...|++++|.++.+++... -+.|...|..+|.++...|+..+|.+.          +.|+.|+..+
T Consensus        70 ~~~~~~~~~~~a~~~~~~~l~~-dP~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~  138 (146)
T PF03704_consen   70 EALLEAGDYEEALRLLQRALAL-DPYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPET  138 (146)
T ss_dssp             HHHHHTT-HHHHHHHHHHHHHH-STT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHH
T ss_pred             HHHHhccCHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHH
Confidence            3566788888888888888664 345677888888888888888888777          4566676544

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

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

Probab=95.19  E-value=0.89  Score=33.64  Aligned_cols=111  Identities=16%  Similarity=0.124  Sum_probs=74.3

Q ss_pred             ChhhHhhcCChhHHHHHHHHhHHcCCCccH----HHHHHHHHHhcCCCchHHHHHH-hhhhhcch--hhHHHHH-HHHHh
Q 039275            1 MISGYSQAGRFNEALEPFGKLESLGVHTDE----VTMVVVLTASSGPGAWILAKEL-QIELDLSS--YSLSSKT-SRYAH   72 (153)
Q Consensus         1 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~----~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~--~~~~~ll-~~~~~   72 (153)
                      |+.-|-...+|++|++.=+++.+.+-++..    ..|.-+-.......+++.|..+ .+....|.  +--+.++ +.+..
T Consensus       147 Ll~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~kAlqa~~~cvRAsi~lG~v~~~  226 (389)
T COG2956         147 LLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLKKALQADKKCVRASIILGRVELA  226 (389)
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhhCccceehhhhhhHHHHh
Confidence            356677888999999999888776554442    3344455555566778887777 44443333  2233322 56677


Q ss_pred             cCCccccc-------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 039275           73 SGRIRLAR-------------DPVSCKAMISGYSQAGRFNEALEPFGKLESL  111 (153)
Q Consensus        73 ~g~~~~a~-------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  111 (153)
                      .|+++.|.             -+.+.+.|..+|...|++++....+..+.+.
T Consensus       227 ~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~  278 (389)
T COG2956         227 KGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMET  278 (389)
T ss_pred             ccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHc
Confidence            77777776             5667777888888888888888887776654

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=95.18  E-value=0.41  Score=30.03  Aligned_cols=103  Identities=15%  Similarity=0.067  Sum_probs=67.1

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccH--HHHHHHHHHhcCCCchHHHHHH-hhhh--hcchhhHHHHHHHHHhcCCccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDE--VTMVVVLTASSGPGAWILAKEL-QIEL--DLSSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~--~~~~~ll~~~~~~~~~~~a~~~-~~~~--~~~~~~~~~ll~~~~~~g~~~~   78 (153)
                      ++-..|+.++|+.+|++-...|...+.  ..+-.+-+.+...|++++|..+ +...  .|+......             
T Consensus        10 a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~~~~-------------   76 (120)
T PF12688_consen   10 AHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDDELNAA-------------   76 (120)
T ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHH-------------
Confidence            456789999999999999999877663  3444555678889999999999 2222  243221111             


Q ss_pred             cchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhc
Q 039275           79 ARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASS  128 (153)
Q Consensus        79 a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~  128 (153)
                         ...+  +-.++...|+.++|.+.+-....    ++...|.--|..|.
T Consensus        77 ---l~~f--~Al~L~~~gr~~eAl~~~l~~la----~~~~~y~ra~~~ya  117 (120)
T PF12688_consen   77 ---LRVF--LALALYNLGRPKEALEWLLEALA----ETLPRYRRAIRFYA  117 (120)
T ss_pred             ---HHHH--HHHHHHHCCCHHHHHHHHHHHHH----HHHHHHHHHHHHHH
Confidence               1222  22366777888888877765542    44446666666654

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

Probab=94.75  E-value=0.75  Score=39.12  Aligned_cols=123  Identities=15%  Similarity=0.111  Sum_probs=91.4

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHHhhhhhcchhhHHHHHHHHHhcCCccccc----
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIELDLSSYSLSSKTSRYAHSGRIRLAR----   80 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~ll~~~~~~g~~~~a~----   80 (153)
                      +..++-+++|..+|++..-     +....+.+|.   ..++++.|.++...+. ...+|+.+.++..+.|.+.+|.    
T Consensus      1058 ai~~~LyEEAF~ifkkf~~-----n~~A~~VLie---~i~~ldRA~efAe~~n-~p~vWsqlakAQL~~~~v~dAieSyi 1128 (1666)
T KOG0985|consen 1058 AIENQLYEEAFAIFKKFDM-----NVSAIQVLIE---NIGSLDRAYEFAERCN-EPAVWSQLAKAQLQGGLVKDAIESYI 1128 (1666)
T ss_pred             HhhhhHHHHHHHHHHHhcc-----cHHHHHHHHH---HhhhHHHHHHHHHhhC-ChHHHHHHHHHHHhcCchHHHHHHHH
Confidence            3456667888888875432     4444444444   3456777777732221 2356999999999999998888    


Q ss_pred             ---hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 ---DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                         |+..|.-+|....+.|.+++-.+++..-++..-.|...  +.+|-+|++.+++.+-++
T Consensus      1129 kadDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id--~eLi~AyAkt~rl~elE~ 1187 (1666)
T KOG0985|consen 1129 KADDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYID--SELIFAYAKTNRLTELEE 1187 (1666)
T ss_pred             hcCCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccch--HHHHHHHHHhchHHHHHH
Confidence               99999999999999999999999988777766667655  468888998888887776

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

Probab=94.69  E-value=0.62  Score=33.65  Aligned_cols=123  Identities=10%  Similarity=-0.012  Sum_probs=87.3

Q ss_pred             hhhHhhcCChhHHHHHHHHhHHcC-CCccHHHHHHHHHHhcCCCchHHHHHH-hhh---hhcchhhHHHHHHHHHhcCCc
Q 039275            2 ISGYSQAGRFNEALEPFGKLESLG-VHTDEVTMVVVLTASSGPGAWILAKEL-QIE---LDLSSYSLSSKTSRYAHSGRI   76 (153)
Q Consensus         2 i~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~---~~~~~~~~~~ll~~~~~~g~~   76 (153)
                      |...-+.+..+.|.++|.+.++.+ ....++....+|.-.+ .++.+.|.++ +.|   ...+...|...|..+.+.++.
T Consensus         8 m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E~~~-~~d~~~A~~Ife~glk~f~~~~~~~~~Y~~~l~~~~d~   86 (280)
T PF05843_consen    8 MRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALMEYYC-NKDPKRARKIFERGLKKFPSDPDFWLEYLDFLIKLNDI   86 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHHHHT-CS-HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-H
T ss_pred             HHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHh-CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHhCcH
Confidence            445567777999999999998654 4566777667776543 4556667777 444   355667788888999999998


Q ss_pred             cccc---------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHh
Q 039275           77 RLAR---------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAAS  127 (153)
Q Consensus        77 ~~a~---------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~  127 (153)
                      +.++               -...|...+..=.+.|+.+.+.++.+.+.+.  -|+..++..+++-|
T Consensus        87 ~~aR~lfer~i~~l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~--~~~~~~~~~f~~ry  150 (280)
T PF05843_consen   87 NNARALFERAISSLPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL--FPEDNSLELFSDRY  150 (280)
T ss_dssp             HHHHHHHHHHCCTSSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH--TTTS-HHHHHHCCT
T ss_pred             HHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--hhhhhHHHHHHHHh
Confidence            8888               2358999999999999999999999888864  46666666666655

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.

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=94.65  E-value=0.35  Score=29.25  Aligned_cols=89  Identities=11%  Similarity=0.030  Sum_probs=59.1

Q ss_pred             HHHHHHHHhcCCCchHHHHHHhhhh---hcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHH
Q 039275           32 TMVVVLTASSGPGAWILAKELQIEL---DLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKL  108 (153)
Q Consensus        32 ~~~~ll~~~~~~~~~~~a~~~~~~~---~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m  108 (153)
                      ++-.....+.+.|++++|.+.....   .|+.. +                 ....+-.+...+.+.|++++|.+.|+.+
T Consensus         4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~-~-----------------~~~~~~~l~~~~~~~~~~~~A~~~~~~~   65 (119)
T TIGR02795         4 AYYDAALLVLKAGDYADAIQAFQAFLKKYPKST-Y-----------------APNAHYWLGEAYYAQGKYADAAKAFLAV   65 (119)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcc-c-----------------cHHHHHHHHHHHHhhccHHHHHHHHHHH
Confidence            3444555667778888877771111   12110 0                 1234556788899999999999999998


Q ss_pred             HHcCCC--CChhhHHHHHHHhcCCCccccchh
Q 039275          109 ESLGVH--TDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       109 ~~~g~~--p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ....-.  .....+..+..++.+.|+.+.|.+
T Consensus        66 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~A~~   97 (119)
T TIGR02795        66 VKKYPKSPKAPDALLKLGMSLQELGDKEKAKA   97 (119)
T ss_pred             HHHCCCCCcccHHHHHHHHHHHHhCChHHHHH
Confidence            864311  124557777788889999998887

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.

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.49  E-value=1.2  Score=32.75  Aligned_cols=130  Identities=13%  Similarity=0.100  Sum_probs=86.1

Q ss_pred             hhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-----hhhhhc-------------chh------
Q 039275            6 SQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-----QIELDL-------------SSY------   61 (153)
Q Consensus         6 ~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-----~~~~~~-------------~~~------   61 (153)
                      .+.|.++.|++-|....+-+--.....||..+.-| +.++.++|.+.     .+|++-             |..      
T Consensus       155 ykegqyEaAvqkFqaAlqvsGyqpllAYniALaHy-~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsvgNt~  233 (459)
T KOG4340|consen  155 YKEGQYEAAVQKFQAALQVSGYQPLLAYNLALAHY-SSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSVGNTL  233 (459)
T ss_pred             eccccHHHHHHHHHHHHhhcCCCchhHHHHHHHHH-hhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcccchH
Confidence            57899999999999887654334456788877664 56778888877     444321             111      


Q ss_pred             --hHHHHHHHH-------HhcCCccccc--------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChh
Q 039275           62 --SLSSKTSRY-------AHSGRIRLAR--------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEV  118 (153)
Q Consensus        62 --~~~~ll~~~-------~~~g~~~~a~--------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  118 (153)
                        .-+.++.++       .+.++++.|.              |++|.+.+-.. -..+++.+..+-++.+.....- -..
T Consensus       234 ~lh~Sal~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~-n~~~~p~~g~~KLqFLL~~nPf-P~E  311 (459)
T KOG4340|consen  234 VLHQSALVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALM-NMDARPTEGFEKLQFLLQQNPF-PPE  311 (459)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHh-cccCCccccHHHHHHHHhcCCC-ChH
Confidence              122344333       4555555555              78888776554 3345677777777777755432 456


Q ss_pred             hHHHHHHHhcCCCccccchh
Q 039275          119 TMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       119 t~~~li~~~~~~g~~~~a~~  138 (153)
                      ||..++--||+..-++.|.+
T Consensus       312 TFANlLllyCKNeyf~lAAD  331 (459)
T KOG4340|consen  312 TFANLLLLYCKNEYFDLAAD  331 (459)
T ss_pred             HHHHHHHHHhhhHHHhHHHH
Confidence            89999999999999888877

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

Probab=94.42  E-value=0.62  Score=36.01  Aligned_cols=133  Identities=16%  Similarity=0.088  Sum_probs=91.1

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccH-HHHHHHHHHhcCCCchHHHHHH-hhhhhcch---hhHHHHHHHHHhcCCcc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDE-VTMVVVLTASSGPGAWILAKEL-QIELDLSS---YSLSSKTSRYAHSGRIR   77 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~---~~~~~ll~~~~~~g~~~   77 (153)
                      +.|+-.++.++|+..|++..+-  -|.. ..|+-+=+-|...++-..|.+- ++-++.+.   ..|-.|=.+|.-.+...
T Consensus       338 NYYSlr~eHEKAv~YFkRALkL--Np~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~p~DyRAWYGLGQaYeim~Mh~  415 (559)
T KOG1155|consen  338 NYYSLRSEHEKAVMYFKRALKL--NPKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDINPRDYRAWYGLGQAYEIMKMHF  415 (559)
T ss_pred             hHHHHHHhHHHHHHHHHHHHhc--CcchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcCchhHHHHhhhhHHHHHhcchH
Confidence            3466778899999999988774  2333 3344444577777776666655 43333322   34444555555555544


Q ss_pred             ccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           78 LAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        78 ~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      -|.            |...|.+|=..|.+.++.++|.+.|+.-..-| ......+..+-+.+-+.++.++|.+
T Consensus       416 YaLyYfqkA~~~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~-dte~~~l~~LakLye~l~d~~eAa~  487 (559)
T KOG1155|consen  416 YALYYFQKALELKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLG-DTEGSALVRLAKLYEELKDLNEAAQ  487 (559)
T ss_pred             HHHHHHHHHHhcCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhcc-ccchHHHHHHHHHHHHHHhHHHHHH
Confidence            444            88888888888888888888888888877655 3356778888888888888888877

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

Probab=94.36  E-value=1.3  Score=34.98  Aligned_cols=75  Identities=16%  Similarity=0.025  Sum_probs=46.8

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHH----HHHHhhhhhcchhhHHHHHHHHHhcCCccccc
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWIL----AKELQIELDLSSYSLSSKTSRYAHSGRIRLAR   80 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~----a~~~~~~~~~~~~~~~~ll~~~~~~g~~~~a~   80 (153)
                      |...+++++..++++..... .++...++..=|.++.+.|+..+    +.++-...+....+|=++--.|.-.|...+|+
T Consensus       254 ~y~~c~f~~c~kit~~lle~-dpfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~yP~~a~sW~aVg~YYl~i~k~seAR  332 (611)
T KOG1173|consen  254 LYYGCRFKECLKITEELLEK-DPFHLPCLPLHIACLYELGKSNKLFLLSHKLVDLYPSKALSWFAVGCYYLMIGKYSEAR  332 (611)
T ss_pred             HHHcChHHHHHHHhHHHHhh-CCCCcchHHHHHHHHHHhcccchHHHHHHHHHHhCCCCCcchhhHHHHHHHhcCcHHHH
Confidence            45667888888888877543 34444455555556666665444    33334444556667777666666667777777

>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=94.20  E-value=1.9  Score=34.17  Aligned_cols=28  Identities=7%  Similarity=-0.012  Sum_probs=14.0

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 039275           82 PVSCKAMISGYSQAGRFNEALEPFGKLE  109 (153)
Q Consensus        82 ~~~~~~li~~~~~~g~~~~a~~~~~~m~  109 (153)
                      +..|+.|-.-|....+..-..+++....
T Consensus       143 PslF~~lk~Ly~d~~K~~~i~~l~~~~~  170 (517)
T PF12569_consen  143 PSLFSNLKPLYKDPEKAAIIESLVEEYV  170 (517)
T ss_pred             chHHHHHHHHHcChhHHHHHHHHHHHHH
Confidence            4555555555554444444444444443

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 [], [].

>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=94.16  E-value=0.14  Score=29.02  Aligned_cols=55  Identities=22%  Similarity=0.307  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHHc----C-CCCC-hhhHHHHHHHhcCCCccccchh
Q 039275           84 SCKAMISGYSQAGRFNEALEPFGKLESL----G-VHTD-EVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        84 ~~~~li~~~~~~g~~~~a~~~~~~m~~~----g-~~p~-~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +|+.+-..|...|++++|.+.|++..+.    | -.|+ ..++..+-..+...|++++|.+
T Consensus         7 ~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~   67 (78)
T PF13424_consen    7 AYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALE   67 (78)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            3444444455555555555555444321    1 0111 3344444445555555554444

...

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=94.06  E-value=0.74  Score=37.90  Aligned_cols=61  Identities=13%  Similarity=0.186  Sum_probs=32.8

Q ss_pred             HHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh---HHHHHHHHHHHhhc
Q 039275           90 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS---NIFLTTAIIEMYAK  152 (153)
Q Consensus        90 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~---~~~~~~~li~~y~k  152 (153)
                      .+..+..+|.+|..+++.+++.+...  --|..+-+.|...|+++.|++   ....++--|++|.+
T Consensus       740 eaai~akew~kai~ildniqdqk~~s--~yy~~iadhyan~~dfe~ae~lf~e~~~~~dai~my~k  803 (1636)
T KOG3616|consen  740 EAAIGAKEWKKAISILDNIQDQKTAS--GYYGEIADHYANKGDFEIAEELFTEADLFKDAIDMYGK  803 (1636)
T ss_pred             HHHhhhhhhhhhHhHHHHhhhhcccc--ccchHHHHHhccchhHHHHHHHHHhcchhHHHHHHHhc
Confidence            34455566666666666666554221  124555566666666666666   33334444455543

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=93.85  E-value=0.16  Score=24.36  Aligned_cols=26  Identities=19%  Similarity=0.319  Sum_probs=22.1

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHH
Q 039275           84 SCKAMISGYSQAGRFNEALEPFGKLE  109 (153)
Q Consensus        84 ~~~~li~~~~~~g~~~~a~~~~~~m~  109 (153)
                      +|+.|-..|.+.|++++|.++|++..
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            57888899999999999999999854

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

Probab=93.84  E-value=0.68  Score=39.33  Aligned_cols=49  Identities=10%  Similarity=0.030  Sum_probs=27.5

Q ss_pred             hhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH
Q 039275            2 ISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL   52 (153)
Q Consensus         2 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~   52 (153)
                      |+...+.|++++.++.+.-.++...+|.+.+  .+|-+|++.+++.+.+++
T Consensus      1140 i~~a~~~~~~edLv~yL~MaRkk~~E~~id~--eLi~AyAkt~rl~elE~f 1188 (1666)
T KOG0985|consen 1140 IDVASRTGKYEDLVKYLLMARKKVREPYIDS--ELIFAYAKTNRLTELEEF 1188 (1666)
T ss_pred             HHHHHhcCcHHHHHHHHHHHHHhhcCccchH--HHHHHHHHhchHHHHHHH
Confidence            4455566666666665544455555554443  455666666666665555

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=93.72  E-value=0.86  Score=28.97  Aligned_cols=108  Identities=10%  Similarity=0.010  Sum_probs=65.6

Q ss_pred             HHHHHhcCCCchHHHHHH-----hhhhhcchhhHHHHHHHHHhcCCccccc------hHHHHHHHHHHHHhcCChHHHHH
Q 039275           35 VVLTASSGPGAWILAKEL-----QIELDLSSYSLSSKTSRYAHSGRIRLAR------DPVSCKAMISGYSQAGRFNEALE  103 (153)
Q Consensus        35 ~ll~~~~~~~~~~~a~~~-----~~~~~~~~~~~~~ll~~~~~~g~~~~a~------~~~~~~~li~~~~~~g~~~~a~~  103 (153)
                      .++..+.+.+.......+     ..+ ..+....|.++..|++...-+.-.      +.......+..|.+.+.++++..
T Consensus        12 ~vv~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~ly~~~~~~~ll~~l~~~~~~yd~~~~~~~c~~~~l~~~~~~   90 (140)
T smart00299       12 EVVELFEKRNLLEELIPYLESALKLN-SENPALQTKLIELYAKYDPQKEIERLDNKSNHYDIEKVGKLCEKAKLYEEAVE   90 (140)
T ss_pred             HHHHHHHhCCcHHHHHHHHHHHHccC-ccchhHHHHHHHHHHHHCHHHHHHHHHhccccCCHHHHHHHHHHcCcHHHHHH
Confidence            445555555555655555     222 245668888998888764432211      22334447778888888888888


Q ss_pred             HHHHHHHcCCCCChhhHHHHHHHhcCC-Cccccchh------HHHHHHHHHHHhhc
Q 039275          104 PFGKLESLGVHTDEVTMVVVLAASSGP-GALDFGKS------NIFLTTAIIEMYAK  152 (153)
Q Consensus       104 ~~~~m~~~g~~p~~~t~~~li~~~~~~-g~~~~a~~------~~~~~~~li~~y~k  152 (153)
                      ++..+..         +...++.+.+. ++++.|.+      +...|..+++.+..
T Consensus        91 l~~k~~~---------~~~Al~~~l~~~~d~~~a~~~~~~~~~~~lw~~~~~~~l~  137 (140)
T smart00299       91 LYKKDGN---------FKDAIVTLIEHLGNYEKAIEYFVKQNNPELWAEVLKALLD  137 (140)
T ss_pred             HHHhhcC---------HHHHHHHHHHcccCHHHHHHHHHhCCCHHHHHHHHHHHHc
Confidence            8877642         22233333333 66777776      77899888887753

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=93.69  E-value=0.19  Score=27.66  Aligned_cols=55  Identities=20%  Similarity=0.136  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCC-ccccchh
Q 039275           82 PVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPG-ALDFGKS  138 (153)
Q Consensus        82 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g-~~~~a~~  138 (153)
                      ...|..+=..+...|++++|.+.|++..+..  | +...|..+-.++.+.| ++++|.+
T Consensus         3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~--p~~~~~~~~~g~~~~~~~~~~~~A~~   59 (69)
T PF13414_consen    3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIELD--PNNAEAYYNLGLAYMKLGKDYEEAIE   59 (69)
T ss_dssp             HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHS--TTHHHHHHHHHHHHHHTTTHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHhCccHHHHHH
Confidence            4577788888899999999999999888754  4 5556777777888888 6877766

...

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H

Probab=93.55  E-value=0.1  Score=29.53  Aligned_cols=43  Identities=21%  Similarity=0.278  Sum_probs=30.6

Q ss_pred             hhhHHHHHHHHHhcCCccccc-------------------hHHHHHHHHHHHHhcCChHHHH
Q 039275           60 SYSLSSKTSRYAHSGRIRLAR-------------------DPVSCKAMISGYSQAGRFNEAL  102 (153)
Q Consensus        60 ~~~~~~ll~~~~~~g~~~~a~-------------------~~~~~~~li~~~~~~g~~~~a~  102 (153)
                      ..+++.+-..|.+.|++++|.                   ...+++.+-..+...|++++|.
T Consensus         5 a~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~   66 (78)
T PF13424_consen    5 ANAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEAL   66 (78)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            356788889999999999998                   2455666666666666666665

...

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=93.50  E-value=0.77  Score=30.25  Aligned_cols=82  Identities=13%  Similarity=0.079  Sum_probs=45.3

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHh-cCCCchHHHHHH-hhh--hhcchhhHHHHHHHHHhcCCccccc
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTAS-SGPGAWILAKEL-QIE--LDLSSYSLSSKTSRYAHSGRIRLAR   80 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~-~~~~~~~~a~~~-~~~--~~~~~~~~~~ll~~~~~~g~~~~a~   80 (153)
                      +...|++++|.++|+.+-..  .|....|-.=|.++ -..|++++|... ...  +.||                     
T Consensus        45 ly~~G~l~~A~~~f~~L~~~--Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~d---------------------  101 (157)
T PRK15363         45 LMEVKEFAGAARLFQLLTIY--DAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKID---------------------  101 (157)
T ss_pred             HHHCCCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC---------------------
Confidence            45677888888888777663  34444444334433 334677777666 111  2222                     


Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLE  109 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~  109 (153)
                      |+.++-.+=..+...|+.+.|.+.|+.-.
T Consensus       102 dp~~~~~ag~c~L~lG~~~~A~~aF~~Ai  130 (157)
T PRK15363        102 APQAPWAAAECYLACDNVCYAIKALKAVV  130 (157)
T ss_pred             CchHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            33444445555555666666666555444

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=93.23  E-value=0.27  Score=26.72  Aligned_cols=46  Identities=15%  Similarity=0.172  Sum_probs=20.2

Q ss_pred             HHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           91 GYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        91 ~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .+...|++++|.+.|++..+..  | +...+..+-.++.+.|++++|..
T Consensus         6 ~~~~~g~~~~A~~~~~~~l~~~--P~~~~a~~~lg~~~~~~g~~~~A~~   52 (65)
T PF13432_consen    6 ALYQQGDYDEAIAAFEQALKQD--PDNPEAWYLLGRILYQQGRYDEALA   52 (65)
T ss_dssp             HHHHCTHHHHHHHHHHHHHCCS--TTHHHHHHHHHHHHHHTT-HHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            3444455555555555544333  2 33333444444444455544443

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

Probab=92.99  E-value=0.87  Score=37.75  Aligned_cols=122  Identities=16%  Similarity=0.080  Sum_probs=78.9

Q ss_pred             HHHHHHHhHHcC--CCccHHHHHHHHHHhcCCCchHHHHHH-----hhhhhcchhhHHHHHHHHHhcCCccccc------
Q 039275           14 ALEPFGKLESLG--VHTDEVTMVVVLTASSGPGAWILAKEL-----QIELDLSSYSLSSKTSRYAHSGRIRLAR------   80 (153)
Q Consensus        14 a~~~~~~m~~~g--~~p~~~~~~~ll~~~~~~~~~~~a~~~-----~~~~~~~~~~~~~ll~~~~~~g~~~~a~------   80 (153)
                      ..-+........  ..-+...|--+-+++...|.+.+|..+     ....--+..+|-.+-++|-..|..++|.      
T Consensus       396 ~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~l~e~e~A~e~y~kv  475 (895)
T KOG2076|consen  396 LEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYMELGEYEEAIEFYEKV  475 (895)
T ss_pred             HHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHHHHhhHHHHHHHHHHH
Confidence            333344444444  333456777777888888888888888     2222234557888888888888888887      


Q ss_pred             ---hHHHHH---HHHHHHHhcCChHHHHHHHHHHH--------HcCCCCChhhHHHHHHHhcCCCcccc
Q 039275           81 ---DPVSCK---AMISGYSQAGRFNEALEPFGKLE--------SLGVHTDEVTMVVVLAASSGPGALDF  135 (153)
Q Consensus        81 ---~~~~~~---~li~~~~~~g~~~~a~~~~~~m~--------~~g~~p~~~t~~~li~~~~~~g~~~~  135 (153)
                         ++.+++   +|-.-+-+.|++++|.++++.|.        ..+..|+...-.-..+-+.+.|+.++
T Consensus       476 l~~~p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~~D~~~~e~~a~~~e~ri~~~r~d~l~~~gk~E~  544 (895)
T KOG2076|consen  476 LILAPDNLDARITLASLYQQLGNHEKALETLEQIINPDGRNAEACAWEPERRILAHRCDILFQVGKREE  544 (895)
T ss_pred             HhcCCCchhhhhhHHHHHHhcCCHHHHHHHHhcccCCCccchhhccccHHHHHHHHHHHHHHHhhhHHH
Confidence               223333   33456678899999999999864        23455666655555566666666654

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=92.94  E-value=0.7  Score=33.43  Aligned_cols=69  Identities=16%  Similarity=0.228  Sum_probs=55.3

Q ss_pred             hhHHHHHHHHHhcCCccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHH-----cCCCCChhhHHHH
Q 039275           61 YSLSSKTSRYAHSGRIRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLES-----LGVHTDEVTMVVV  123 (153)
Q Consensus        61 ~~~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~~~t~~~l  123 (153)
                      .+...+++.+...|+.+.+.            +...|..+|.+|.+.|+...|.+.|+.+.+     .|+.|...+....
T Consensus       154 ~~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~y  233 (280)
T COG3629         154 KALTKLAEALIACGRADAVIEHLERLIELDPYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRALY  233 (280)
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHHH
Confidence            34556777777777766666            889999999999999999999999999875     4899988887777


Q ss_pred             HHHhcC
Q 039275          124 LAASSG  129 (153)
Q Consensus       124 i~~~~~  129 (153)
                      .....+
T Consensus       234 ~~~~~~  239 (280)
T COG3629         234 EEILRQ  239 (280)
T ss_pred             HHHhcc
Confidence            766433

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

Probab=92.94  E-value=1.9  Score=34.92  Aligned_cols=47  Identities=11%  Similarity=0.070  Sum_probs=33.9

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcC
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSG  129 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~  129 (153)
                      -...|.+|-.=|.+.|++++|..+|++-.+.-  .+..-|..+.++|.+
T Consensus       247 ~g~Lw~SLAdYYIr~g~~ekarDvyeeai~~v--~tvrDFt~ifd~Ya~  293 (835)
T KOG2047|consen  247 LGFLWCSLADYYIRSGLFEKARDVYEEAIQTV--MTVRDFTQIFDAYAQ  293 (835)
T ss_pred             HHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhh--eehhhHHHHHHHHHH
Confidence            45778899999999999999999998876542  344445566665543

>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=92.79  E-value=0.022  Score=36.56  Aligned_cols=107  Identities=10%  Similarity=-0.014  Sum_probs=69.4

Q ss_pred             HHHHhcCCCchHHHHHH-----hhhhhcchhhHHHHHHHHHhcCCccccc------hHHHHHHHHHHHHhcCChHHHHHH
Q 039275           36 VLTASSGPGAWILAKEL-----QIELDLSSYSLSSKTSRYAHSGRIRLAR------DPVSCKAMISGYSQAGRFNEALEP  104 (153)
Q Consensus        36 ll~~~~~~~~~~~a~~~-----~~~~~~~~~~~~~ll~~~~~~g~~~~a~------~~~~~~~li~~~~~~g~~~~a~~~  104 (153)
                      +++.+.+.+.++....+     ..+...+....+.++..|++.+..++..      +..-...++..+.+.|.++++.-+
T Consensus        13 vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~~~~yd~~~~~~~c~~~~l~~~a~~L   92 (143)
T PF00637_consen   13 VISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKTSNNYDLDKALRLCEKHGLYEEAVYL   92 (143)
T ss_dssp             CHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTSSSSS-CTHHHHHHHTTTSHHHHHHH
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcccccccCHHHHHHHHHhcchHHHHHHH
Confidence            45566666666666555     2223355777888999999988766665      334556777888888888888888


Q ss_pred             HHHHHHcCCCCChhhHHHHHHHhcCCCccccchh------HHHHHHHHHHHhh
Q 039275          105 FGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS------NIFLTTAIIEMYA  151 (153)
Q Consensus       105 ~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~------~~~~~~~li~~y~  151 (153)
                      +.++....-         .+..+.+.++++.|.+      +..+|..+++.|.
T Consensus        93 y~~~~~~~~---------al~i~~~~~~~~~a~e~~~~~~~~~l~~~l~~~~l  136 (143)
T PF00637_consen   93 YSKLGNHDE---------ALEILHKLKDYEEAIEYAKKVDDPELWEQLLKYCL  136 (143)
T ss_dssp             HHCCTTHTT---------CSSTSSSTHCSCCCTTTGGGCSSSHHHHHHHHHHC
T ss_pred             HHHcccHHH---------HHHHHHHHccHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            887653321         1112445566666666      7889999988775

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.

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=92.79  E-value=0.09  Score=30.41  Aligned_cols=53  Identities=15%  Similarity=0.159  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCh-hhHHHHHHHhcCCCccccchh
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDE-VTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ..|-.+-..+.+.|++++|.++++. ..  ..|+. ...-.+-.++.++|++++|.+
T Consensus        26 ~~~~~la~~~~~~~~y~~A~~~~~~-~~--~~~~~~~~~~l~a~~~~~l~~y~eAi~   79 (84)
T PF12895_consen   26 AYLYNLAQCYFQQGKYEEAIELLQK-LK--LDPSNPDIHYLLARCLLKLGKYEEAIK   79 (84)
T ss_dssp             HHHHHHHHHHHHTTHHHHHHHHHHC-HT--HHHCHHHHHHHHHHHHHHTT-HHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHH-hC--CCCCCHHHHHHHHHHHHHhCCHHHHHH
Confidence            3444588999999999999999988 32  22322 333344778999999999875

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=92.78  E-value=0.94  Score=25.02  Aligned_cols=50  Identities=22%  Similarity=0.084  Sum_probs=40.2

Q ss_pred             hhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH
Q 039275            2 ISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL   52 (153)
Q Consensus         2 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~   52 (153)
                      -..|.+.+++++|.+.++.+... .+.++..+...=..+.+.|++++|.+.
T Consensus         2 ~~~~~~~~~~~~A~~~~~~~l~~-~p~~~~~~~~~a~~~~~~g~~~~A~~~   51 (73)
T PF13371_consen    2 KQIYLQQEDYEEALEVLERALEL-DPDDPELWLQRARCLFQLGRYEEALED   51 (73)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHh-CcccchhhHHHHHHHHHhccHHHHHHH
Confidence            35788999999999999999886 233556666666788999999999888

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

Probab=92.76  E-value=0.59  Score=39.08  Aligned_cols=103  Identities=17%  Similarity=0.166  Sum_probs=64.7

Q ss_pred             cCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHHhhhhhc----chhhHHHHHHHHHhcCCccccc---
Q 039275            8 AGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIELDL----SSYSLSSKTSRYAHSGRIRLAR---   80 (153)
Q Consensus         8 ~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~----~~~~~~~ll~~~~~~g~~~~a~---   80 (153)
                      .+..++|+++|.+..+. -+-|.+.-|=+=-.++..|++.+|.++.+.+..    +..+|-.+-..|...|++..|.   
T Consensus       625 kk~~~KAlq~y~kvL~~-dpkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~~~~dv~lNlah~~~e~~qy~~AIqmY  703 (1018)
T KOG2002|consen  625 KKHQEKALQLYGKVLRN-DPKNMYAANGIGIVLAEKGRFSEARDIFSQVREATSDFEDVWLNLAHCYVEQGQYRLAIQMY  703 (1018)
T ss_pred             HHHHHHHHHHHHHHHhc-CcchhhhccchhhhhhhccCchHHHHHHHHHHHHHhhCCceeeeHHHHHHHHHHHHHHHHHH
Confidence            34567788888777664 334555555555567788888888888444432    3345556666666666666665   


Q ss_pred             -----------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 039275           81 -----------DPVSCKAMISGYSQAGRFNEALEPFGKLESL  111 (153)
Q Consensus        81 -----------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  111 (153)
                                 ++...+.|-.++.+.|++.+|.+....-...
T Consensus       704 e~~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~ll~a~~~  745 (1018)
T KOG2002|consen  704 ENCLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEALLKARHL  745 (1018)
T ss_pred             HHHHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHHHHHHHHh
Confidence                       4555556666666667766666666554433

>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=92.49  E-value=0.37  Score=26.44  Aligned_cols=63  Identities=17%  Similarity=0.194  Sum_probs=42.0

Q ss_pred             cHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcC-ChHHHHHHHH
Q 039275           29 DEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAG-RFNEALEPFG  106 (153)
Q Consensus        29 ~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g-~~~~a~~~~~  106 (153)
                      ++.+|..+=..+...|++++|... ...+..|..                   +...|..+-..+.+.| ++++|.+.|+
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~-------------------~~~~~~~~g~~~~~~~~~~~~A~~~~~   62 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELDPN-------------------NAEAYYNLGLAYMKLGKDYEEAIEDFE   62 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTT-------------------HHHHHHHHHHHHHHTTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-------------------CHHHHHHHHHHHHHhCccHHHHHHHHH
Confidence            345566666666777777777776 333333322                   3466777888888888 7999999888


Q ss_pred             HHHH
Q 039275          107 KLES  110 (153)
Q Consensus       107 ~m~~  110 (153)
                      +-.+
T Consensus        63 ~al~   66 (69)
T PF13414_consen   63 KALK   66 (69)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7654

...

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=92.40  E-value=0.52  Score=22.79  Aligned_cols=29  Identities=24%  Similarity=0.429  Sum_probs=24.6

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHHH
Q 039275           82 PVSCKAMISGYSQAGRFNEALEPFGKLES  110 (153)
Q Consensus        82 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~  110 (153)
                      ..+++.|-..|...|++++|.+++++...
T Consensus         2 a~~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    2 ASALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            36789999999999999999999998863

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=92.34  E-value=1.2  Score=31.92  Aligned_cols=86  Identities=9%  Similarity=-0.079  Sum_probs=54.2

Q ss_pred             hhcCChhHHHHHHHHhHHcCCCccH----HHHHHHHHHhcCCCchHHHHHHhhhh---hcc-hhhHHHHHHHHHhcCCcc
Q 039275            6 SQAGRFNEALEPFGKLESLGVHTDE----VTMVVVLTASSGPGAWILAKELQIEL---DLS-SYSLSSKTSRYAHSGRIR   77 (153)
Q Consensus         6 ~~~g~~~~a~~~~~~m~~~g~~p~~----~~~~~ll~~~~~~~~~~~a~~~~~~~---~~~-~~~~~~ll~~~~~~g~~~   77 (153)
                      .+.|++++|+..|+.+.+.-  |+.    ..+-.+-..+...|++++|......+   .|+ ....              
T Consensus       154 ~~~~~y~~Ai~af~~fl~~y--P~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~--------------  217 (263)
T PRK10803        154 QDKSRQDDAIVAFQNFVKKY--PDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAA--------------  217 (263)
T ss_pred             HhcCCHHHHHHHHHHHHHHC--cCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchh--------------
Confidence            45688888888888887642  322    34445667778888888888772222   122 1122              


Q ss_pred             ccchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 039275           78 LARDPVSCKAMISGYSQAGRFNEALEPFGKLESLG  112 (153)
Q Consensus        78 ~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  112 (153)
                           ..+-.+...+...|+.++|.++|+++.+.-
T Consensus       218 -----dAl~klg~~~~~~g~~~~A~~~~~~vi~~y  247 (263)
T PRK10803        218 -----DAMFKVGVIMQDKGDTAKAKAVYQQVIKKY  247 (263)
T ss_pred             -----HHHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence                 223334455667888888888888887653

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

Probab=92.17  E-value=0.6  Score=33.68  Aligned_cols=126  Identities=15%  Similarity=0.161  Sum_probs=80.3

Q ss_pred             ChhHHHHHHHHhHH-----cCCCccHHHHHHHHHHhcCCCchHHHHHH---------hhhhhcchhhHHHHHHHHHhcCC
Q 039275           10 RFNEALEPFGKLES-----LGVHTDEVTMVVVLTASSGPGAWILAKEL---------QIELDLSSYSLSSKTSRYAHSGR   75 (153)
Q Consensus        10 ~~~~a~~~~~~m~~-----~g~~p~~~~~~~ll~~~~~~~~~~~a~~~---------~~~~~~~~~~~~~ll~~~~~~g~   75 (153)
                      ++++|.++|++.-.     ..+..-...|......+.+.++...+-..         +.....-...|...+..|.+.|+
T Consensus        30 ~~e~Aa~~y~~Aa~~fk~~~~~~~A~~ay~kAa~~~~~~~~~~~Aa~~~~~Aa~~~k~~~~~~Ai~~~~~A~~~y~~~G~  109 (282)
T PF14938_consen   30 DYEEAADLYEKAANCFKLAKDWEKAAEAYEKAADCYEKLGDKFEAAKAYEEAANCYKKGDPDEAIECYEKAIEIYREAGR  109 (282)
T ss_dssp             HHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHCT-
T ss_pred             CHHHHHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHHHhcCc
Confidence            66777777766522     22444456666666666666553332222         22222223467778899999999


Q ss_pred             ccccchHHHHHHHHHHHHhc-CChHHHHHHHHHHHHc----CCCC--ChhhHHHHHHHhcCCCccccchh
Q 039275           76 IRLARDPVSCKAMISGYSQA-GRFNEALEPFGKLESL----GVHT--DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        76 ~~~a~~~~~~~~li~~~~~~-g~~~~a~~~~~~m~~~----g~~p--~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +..|-  .++..+-..|-.. |++++|.+.|++-.+.    | .|  -...+..+...+.+.|++++|.+
T Consensus       110 ~~~aA--~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~-~~~~a~~~~~~~A~l~~~l~~y~~A~~  176 (282)
T PF14938_consen  110 FSQAA--KCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEG-SPHSAAECLLKAADLYARLGRYEEAIE  176 (282)
T ss_dssp             HHHHH--HHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHH
T ss_pred             HHHHH--HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCC-ChhhHHHHHHHHHHHHHHhCCHHHHHH
Confidence            98866  7888888888888 9999999999887532    3 33  24556778888999999999988

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=92.16  E-value=0.76  Score=27.72  Aligned_cols=58  Identities=10%  Similarity=-0.040  Sum_probs=43.0

Q ss_pred             ChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHHhhh----hhcchhhHHHHH
Q 039275           10 RFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIE----LDLSSYSLSSKT   67 (153)
Q Consensus        10 ~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~----~~~~~~~~~~ll   67 (153)
                      +.=++.+-++.+....+.|++.+....|.||-+.+++..|..+..+    ...+...|..++
T Consensus        22 D~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~~~~~~~y~~~l   83 (103)
T cd00923          22 DGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKCGAHKEIYPYIL   83 (103)
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccCchhhHHHHH
Confidence            3345666667777788999999999999999999999999998333    333444555554

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=92.06  E-value=0.74  Score=28.05  Aligned_cols=55  Identities=11%  Similarity=0.019  Sum_probs=36.7

Q ss_pred             HHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH----hhhhhcchhhHHHHH
Q 039275           13 EALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL----QIELDLSSYSLSSKT   67 (153)
Q Consensus        13 ~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~----~~~~~~~~~~~~~ll   67 (153)
                      +..+-++.+-...+.|++.+....|.+|-+.+++..|..+    +.........|..++
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~~~~~~Y~~~l   86 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKCGNKKEIYPYIL   86 (108)
T ss_dssp             HHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTTT-TTHHHHHH
T ss_pred             HHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccChHHHHHHHH
Confidence            4555566666778999999999999999999999999998    333333333565554

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 ....

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

Probab=92.05  E-value=2.8  Score=36.93  Aligned_cols=55  Identities=7%  Similarity=-0.003  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccch
Q 039275           82 PVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGK  137 (153)
Q Consensus        82 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~  137 (153)
                      -..|..|...|.+.+++++|.++|+.|.+. ++-....|...+.++.++..-+.|.
T Consensus      1530 ~~V~~~L~~iy~k~ek~~~A~ell~~m~KK-F~q~~~vW~~y~~fLl~~ne~~aa~ 1584 (1710)
T KOG1070|consen 1530 YTVHLKLLGIYEKSEKNDEADELLRLMLKK-FGQTRKVWIMYADFLLRQNEAEAAR 1584 (1710)
T ss_pred             HHHHHHHHHHHHHhhcchhHHHHHHHHHHH-hcchhhHHHHHHHHHhcccHHHHHH
Confidence            355666666666666666666666666533 2233445555555555555544333

>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised

Probab=92.03  E-value=0.87  Score=23.54  Aligned_cols=38  Identities=13%  Similarity=0.160  Sum_probs=32.6

Q ss_pred             HHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHH
Q 039275           89 ISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAA  126 (153)
Q Consensus        89 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~  126 (153)
                      +.-.-+.|-++++..++++|++.|+..+...+..++.-
T Consensus         9 L~~Ak~~GlI~~~~~~l~~l~~~g~~is~~l~~~~L~~   46 (48)
T PF11848_consen    9 LLLAKRRGLISEVKPLLDRLQQAGFRISPKLIEEILRR   46 (48)
T ss_pred             HHHHHHcCChhhHHHHHHHHHHcCcccCHHHHHHHHHH
Confidence            44457889999999999999999999999999888764

This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.

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

Probab=92.03  E-value=4.3  Score=34.35  Aligned_cols=131  Identities=8%  Similarity=0.015  Sum_probs=72.7

Q ss_pred             hhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHH-HHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCcccc
Q 039275            2 ISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVL-TASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         2 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll-~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      ++.|-+.+++++|.++.+.-..  ..|+...+-.++ ..+.+.++.+.+-.+ --+..+...-|+.+-..|.+.++.-. 
T Consensus        38 i~~~~~~~~~deai~i~~~~l~--~~P~~i~~yy~~G~l~~q~~~~~~~~lv~~l~~~~~~~~~~~ve~~~~~i~~~~~-  114 (906)
T PRK14720         38 IDAYKSENLTDEAKDICEEHLK--EHKKSISALYISGILSLSRRPLNDSNLLNLIDSFSQNLKWAIVEHICDKILLYGE-  114 (906)
T ss_pred             HHHHHhcCCHHHHHHHHHHHHH--hCCcceehHHHHHHHHHhhcchhhhhhhhhhhhcccccchhHHHHHHHHHHhhhh-
Confidence            4455566666666666653332  233332222111 133444444444444 11112222223333333334444333 


Q ss_pred             chHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           80 RDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        80 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                       +...+-.+-..|-+.|+.+++..+|++..+.. .-+....+.+--.+... ++++|.+
T Consensus       115 -~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-dL~KA~~  170 (906)
T PRK14720        115 -NKLALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-DKEKAIT  170 (906)
T ss_pred             -hhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-hHHHHHH
Confidence             33566677788888899999999999998765 23666677777777777 8888888

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=91.65  E-value=0.96  Score=22.58  Aligned_cols=34  Identities=21%  Similarity=0.290  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChh
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEV  118 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  118 (153)
                      .+|..+-..|.+.|++++|.++|++..+.  .|+..
T Consensus         2 ~~~~~la~~~~~~G~~~~A~~~~~~~l~~--~P~~~   35 (44)
T PF13428_consen    2 AAWLALARAYRRLGQPDEAERLLRRALAL--DPDDP   35 (44)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CcCCH
Confidence            35778889999999999999999999875  46544

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

Probab=91.64  E-value=3.4  Score=31.83  Aligned_cols=47  Identities=6%  Similarity=-0.034  Sum_probs=36.0

Q ss_pred             HHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           90 SGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        90 ~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ..+...|++++|.-.|.+-+.  +.| +-.+|..++.+|...|++.+|.-
T Consensus       342 ~lL~~~~R~~~A~IaFR~Aq~--Lap~rL~~Y~GL~hsYLA~~~~kEA~~  389 (564)
T KOG1174|consen  342 RLLIALERHTQAVIAFRTAQM--LAPYRLEIYRGLFHSYLAQKRFKEANA  389 (564)
T ss_pred             HHHHhccchHHHHHHHHHHHh--cchhhHHHHHHHHHHHHhhchHHHHHH
Confidence            445677888888888877664  454 67788889998888888888776

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.60  E-value=1.9  Score=32.49  Aligned_cols=133  Identities=15%  Similarity=0.121  Sum_probs=74.1

Q ss_pred             hhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHH-HhcCC----CchHHHHHH-----hhhhhcchh-hHHHHHHHH
Q 039275            2 ISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLT-ASSGP----GAWILAKEL-----QIELDLSSY-SLSSKTSRY   70 (153)
Q Consensus         2 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~-~~~~~----~~~~~a~~~-----~~~~~~~~~-~~~~ll~~~   70 (153)
                      +-.|.+.+++++|..+.+.+..  ..|-.....-+.. ++.+.    .++.-|..+     .++.+.|.+ -..++..++
T Consensus       292 ~iYyL~q~dVqeA~~L~Kdl~P--ttP~EyilKgvv~aalGQe~gSreHlKiAqqffqlVG~Sa~ecDTIpGRQsmAs~f  369 (557)
T KOG3785|consen  292 IIYYLNQNDVQEAISLCKDLDP--TTPYEYILKGVVFAALGQETGSREHLKIAQQFFQLVGESALECDTIPGRQSMASYF  369 (557)
T ss_pred             eeeecccccHHHHHHHHhhcCC--CChHHHHHHHHHHHHhhhhcCcHHHHHHHHHHHHHhcccccccccccchHHHHHHH
Confidence            4467888999999988776533  2333333333332 22222    123334444     333332221 112233333


Q ss_pred             HhcCCccccc-------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHH-HHhcCCCccccc
Q 039275           71 AHSGRIRLAR-------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVL-AASSGPGALDFG  136 (153)
Q Consensus        71 ~~~g~~~~a~-------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li-~~~~~~g~~~~a  136 (153)
                      --..++++..             |...| .+-++.+..|...+|+++|-.+....++ +..+|-+++ .++.+.++.+.|
T Consensus       370 FL~~qFddVl~YlnSi~sYF~NdD~Fn~-N~AQAk~atgny~eaEelf~~is~~~ik-n~~~Y~s~LArCyi~nkkP~lA  447 (557)
T KOG3785|consen  370 FLSFQFDDVLTYLNSIESYFTNDDDFNL-NLAQAKLATGNYVEAEELFIRISGPEIK-NKILYKSMLARCYIRNKKPQLA  447 (557)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCcchhhh-HHHHHHHHhcChHHHHHHHhhhcChhhh-hhHHHHHHHHHHHHhcCCchHH
Confidence            3333333333             33333 4678888899999999999776644433 555665555 588899999988


Q ss_pred             hh
Q 039275          137 KS  138 (153)
Q Consensus       137 ~~  138 (153)
                      ++
T Consensus       448 W~  449 (557)
T KOG3785|consen  448 WD  449 (557)
T ss_pred             HH
Confidence            88

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

Probab=91.42  E-value=1.2  Score=37.36  Aligned_cols=57  Identities=14%  Similarity=0.153  Sum_probs=44.2

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +..+-|-+-..++..|++.+|..+|...++..- -...+|..+-.+|...|.+..|.+
T Consensus       645 N~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~-~~~dv~lNlah~~~e~~qy~~AIq  701 (1018)
T KOG2002|consen  645 NMYAANGIGIVLAEKGRFSEARDIFSQVREATS-DFEDVWLNLAHCYVEQGQYRLAIQ  701 (1018)
T ss_pred             hhhhccchhhhhhhccCchHHHHHHHHHHHHHh-hCCceeeeHHHHHHHHHHHHHHHH
Confidence            445556666777888999999999999887653 344567888888888888888888

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

Probab=90.99  E-value=1  Score=33.53  Aligned_cols=111  Identities=12%  Similarity=0.033  Sum_probs=65.0

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-------hhhhhcchhhHHHHHHHHHhcCCc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-------QIELDLSSYSLSSKTSRYAHSGRI   76 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-------~~~~~~~~~~~~~ll~~~~~~g~~   76 (153)
                      .|.=.++++.|...++++.+-|+. ++..|+-+--+|.-.+.+|-+.--       -.....-..+|-.|-....-.|++
T Consensus       333 ~yfY~~~PE~AlryYRRiLqmG~~-speLf~NigLCC~yaqQ~D~~L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~  411 (478)
T KOG1129|consen  333 GYFYDNNPEMALRYYRRILQMGAQ-SPELFCNIGLCCLYAQQIDLVLPSFQRALSTATQPGQAADVWYNLGFVAVTIGDF  411 (478)
T ss_pred             ccccCCChHHHHHHHHHHHHhcCC-ChHHHhhHHHHHHhhcchhhhHHHHHHHHhhccCcchhhhhhhccceeEEeccch
Confidence            455567899999999999999885 445555444444444554443322       110011112232222222333333


Q ss_pred             cccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCh
Q 039275           77 RLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDE  117 (153)
Q Consensus        77 ~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  117 (153)
                      .-|.            ....+|.|----.+.|++++|..+++.-...  .|+.
T Consensus       412 nlA~rcfrlaL~~d~~h~ealnNLavL~~r~G~i~~Arsll~~A~s~--~P~m  462 (478)
T KOG1129|consen  412 NLAKRCFRLALTSDAQHGEALNNLAVLAARSGDILGARSLLNAAKSV--MPDM  462 (478)
T ss_pred             HHHHHHHHHHhccCcchHHHHHhHHHHHhhcCchHHHHHHHHHhhhh--Cccc
Confidence            3333            5678888888888999999999999886643  4543

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

Probab=90.98  E-value=0.88  Score=34.06  Aligned_cols=57  Identities=14%  Similarity=0.035  Sum_probs=46.7

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +...|..+-..|.+.|++++|...+++..... ..+...|..+-.+|.+.|++++|..
T Consensus        35 ~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~-P~~~~a~~~lg~~~~~lg~~~eA~~   91 (356)
T PLN03088         35 NAELYADRAQANIKLGNFTEAVADANKAIELD-PSLAKAYLRKGTACMKLEEYQTAKA   91 (356)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhCCHHHHHH
Confidence            34567777888899999999999999998653 2256678888889999999999988

>PF10366 Vps39_1: Vacuolar sorting protein 39 domain 1; InterPro: IPR019452 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1

Probab=90.96  E-value=0.76  Score=28.26  Aligned_cols=30  Identities=23%  Similarity=0.336  Sum_probs=27.3

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHH
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLES  110 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  110 (153)
                      ...-|..|+.-|..+|..++|.+++.++..
T Consensus        38 ~~~~~~eL~~lY~~kg~h~~AL~ll~~l~~   67 (108)
T PF10366_consen   38 EHGKYQELVDLYQGKGLHRKALELLKKLAD   67 (108)
T ss_pred             HcCCHHHHHHHHHccCccHHHHHHHHHHhc
Confidence            456789999999999999999999999987

Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised.

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

Probab=90.70  E-value=7  Score=33.19  Aligned_cols=78  Identities=12%  Similarity=0.035  Sum_probs=50.5

Q ss_pred             HHHHHHHHHhcCCCchHHHHHH-hhhh---hcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHH
Q 039275           31 VTMVVVLTASSGPGAWILAKEL-QIEL---DLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFG  106 (153)
Q Consensus        31 ~~~~~ll~~~~~~~~~~~a~~~-~~~~---~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~  106 (153)
                      ..+.++-.+|.+.|+.+++.+. ++-+   +.|..+.|.+-..|... ++++|.  ..+...+..+....++.++.++|.
T Consensus       117 ~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D~~n~~aLNn~AY~~ae~-dL~KA~--~m~~KAV~~~i~~kq~~~~~e~W~  193 (906)
T PRK14720        117 LALRTLAEAYAKLNENKKLKGVWERLVKADRDNPEIVKKLATSYEEE-DKEKAI--TYLKKAIYRFIKKKQYVGIEEIWS  193 (906)
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHh-hHHHHH--HHHHHHHHHHHhhhcchHHHHHHH
Confidence            4555666666777777777766 1111   34555667777777777 777766  666666666777777777777777


Q ss_pred             HHHHc
Q 039275          107 KLESL  111 (153)
Q Consensus       107 ~m~~~  111 (153)
                      ++...
T Consensus       194 k~~~~  198 (906)
T PRK14720        194 KLVHY  198 (906)
T ss_pred             HHHhc
Confidence            76644

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

Probab=90.67  E-value=3.2  Score=34.86  Aligned_cols=38  Identities=21%  Similarity=0.341  Sum_probs=26.6

Q ss_pred             hhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH
Q 039275            6 SQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL   52 (153)
Q Consensus         6 ~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~   52 (153)
                      .+.|.+++|..+|++-++..+      .|.+   |-..|+|++|.++
T Consensus       811 ieLgMlEeA~~lYr~ckR~DL------lNKl---yQs~g~w~eA~ei  848 (1416)
T KOG3617|consen  811 IELGMLEEALILYRQCKRYDL------LNKL---YQSQGMWSEAFEI  848 (1416)
T ss_pred             HHHhhHHHHHHHHHHHHHHHH------HHHH---HHhcccHHHHHHH
Confidence            456888899999988877532      3333   3446888888888

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=90.58  E-value=2.4  Score=27.99  Aligned_cols=75  Identities=15%  Similarity=0.067  Sum_probs=50.9

Q ss_pred             hHHHHHHHHHhcCCccccc-----------h----HHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHH
Q 039275           62 SLSSKTSRYAHSGRIRLAR-----------D----PVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLA  125 (153)
Q Consensus        62 ~~~~ll~~~~~~g~~~~a~-----------~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~  125 (153)
                      .+..+-..+...|++++|.           +    ...|..+-..+.+.|++++|.+.+++....  .| +...+..+..
T Consensus        37 ~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~  114 (172)
T PRK02603         37 VYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALEL--NPKQPSALNNIAV  114 (172)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CcccHHHHHHHHH
Confidence            4555666677778877777           1    246777778888888888888888887754  34 3444555566


Q ss_pred             HhcCCCccccchh
Q 039275          126 ASSGPGALDFGKS  138 (153)
Q Consensus       126 ~~~~~g~~~~a~~  138 (153)
                      .+...|+...+..
T Consensus       115 ~~~~~g~~~~a~~  127 (172)
T PRK02603        115 IYHKRGEKAEEAG  127 (172)
T ss_pred             HHHHcCChHhHhh
Confidence            7777777665554

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

Probab=90.45  E-value=4.9  Score=29.06  Aligned_cols=128  Identities=16%  Similarity=0.102  Sum_probs=79.2

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhc-chhhHHHHHHHH----HhcCCcc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDL-SSYSLSSKTSRY----AHSGRIR   77 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~-~~~~~~~ll~~~----~~~g~~~   77 (153)
                      .|+..|++++|.+..+..  .    +.....-=+..+.+..+++.|.+. +..... +..+-+.|..++    .-.+.+.
T Consensus       117 i~~~~~~~deAl~~~~~~--~----~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~ided~tLtQLA~awv~la~ggek~q  190 (299)
T KOG3081|consen  117 IYMHDGDFDEALKALHLG--E----NLEAAALNVQILLKMHRFDLAEKELKKMQQIDEDATLTQLAQAWVKLATGGEKIQ  190 (299)
T ss_pred             HhhcCCChHHHHHHHhcc--c----hHHHHHHHHHHHHHHHHHHHHHHHHHHHHccchHHHHHHHHHHHHHHhccchhhh
Confidence            478889999999988762  1    222222223344566677777766 222222 223444343333    3344455


Q ss_pred             ccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           78 LAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        78 ~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +|.            +..+.|-+...+...|++++|..++++...+. .-|..|...+|.+--..|.-.++..
T Consensus       191 dAfyifeE~s~k~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd-~~dpetL~Nliv~a~~~Gkd~~~~~  262 (299)
T KOG3081|consen  191 DAFYIFEELSEKTPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKD-AKDPETLANLIVLALHLGKDAEVTE  262 (299)
T ss_pred             hHHHHHHHHhcccCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhcc-CCCHHHHHHHHHHHHHhCCChHHHH
Confidence            555            66777777788889999999999999988654 2245566666666666666654443

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=90.42  E-value=0.57  Score=25.94  Aligned_cols=48  Identities=19%  Similarity=0.113  Sum_probs=27.7

Q ss_pred             HHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           90 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        90 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ..|.+.+++++|.++++.+.... ..+...+...-.++.+.|++++|.+
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~g~~~~A~~   50 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELD-PDDPELWLQRARCLFQLGRYEEALE   50 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC-cccchhhHHHHHHHHHhccHHHHHH
Confidence            34566666666666666666543 1144444445556666666666665

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

Probab=90.19  E-value=3.4  Score=32.45  Aligned_cols=129  Identities=9%  Similarity=-0.012  Sum_probs=86.6

Q ss_pred             cCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH---hhhhh-cchhhHHHHHHHHHhcCCccccc---
Q 039275            8 AGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL---QIELD-LSSYSLSSKTSRYAHSGRIRLAR---   80 (153)
Q Consensus         8 ~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~---~~~~~-~~~~~~~~ll~~~~~~g~~~~a~---   80 (153)
                      .|+...|.+-|+......-.++.- |-.+-..|....+.++..+.   -..+. -|..+|-.--.++--.+++++|.   
T Consensus       339 ~g~~~~a~~d~~~~I~l~~~~~~l-yI~~a~~y~d~~~~~~~~~~F~~A~~ldp~n~dvYyHRgQm~flL~q~e~A~aDF  417 (606)
T KOG0547|consen  339 KGDSLGAQEDFDAAIKLDPAFNSL-YIKRAAAYADENQSEKMWKDFNKAEDLDPENPDVYYHRGQMRFLLQQYEEAIADF  417 (606)
T ss_pred             cCCchhhhhhHHHHHhcCcccchH-HHHHHHHHhhhhccHHHHHHHHHHHhcCCCCCchhHhHHHHHHHHHHHHHHHHHH
Confidence            466777777777776654333331 55555567777776666666   22222 24456665555555566666665   


Q ss_pred             ---------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 ---------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ---------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                               +...|-.+-.+..+.+++++++..|++-++. +.--...|+-+-..+..+++++.|.+
T Consensus       418 ~Kai~L~pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkk-FP~~~Evy~~fAeiLtDqqqFd~A~k  483 (606)
T KOG0547|consen  418 QKAISLDPENAYAYIQLCCALYRQHKIAESMKTFEEAKKK-FPNCPEVYNLFAEILTDQQQFDKAVK  483 (606)
T ss_pred             HHHhhcChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCchHHHHHHHHHhhHHhHHHHHH
Confidence                     5566666666778899999999999998865 33345567888889999999999887

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

Probab=90.06  E-value=8.7  Score=30.88  Aligned_cols=108  Identities=13%  Similarity=-0.039  Sum_probs=71.0

Q ss_pred             hhHhhcCChhHHHHHHH--------HhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-------hhhhhcchhhHHHHH
Q 039275            3 SGYSQAGRFNEALEPFG--------KLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-------QIELDLSSYSLSSKT   67 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~--------~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-------~~~~~~~~~~~~~ll   67 (153)
                      .--...|+++.|++++.        .+...+..|-.+  ..++..+.+.++-+.|.++       .+.-.+..   ..  
T Consensus       384 Ql~is~gn~~~A~~il~~~~~~~~ss~~~~~~~P~~V--~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s---~~--  456 (652)
T KOG2376|consen  384 QLKISQGNPEVALEILSLFLESWKSSILEAKHLPGTV--GAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGS---IA--  456 (652)
T ss_pred             HHHHhcCCHHHHHHHHHHHhhhhhhhhhhhccChhHH--HHHHHHHHhccCCccHHHHHHHHHHHHHHhcccc---hH--
Confidence            34567899999999998        555555655554  4455555666554444433       22212211   11  


Q ss_pred             HHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCC
Q 039275           68 SRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPG  131 (153)
Q Consensus        68 ~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g  131 (153)
                                   -..+|.-....-.+.|+.++|..+++++.+.+ .+|..+...++.+|++..
T Consensus       457 -------------l~~~~~~aa~f~lr~G~~~ea~s~leel~k~n-~~d~~~l~~lV~a~~~~d  506 (652)
T KOG2376|consen  457 -------------LLSLMREAAEFKLRHGNEEEASSLLEELVKFN-PNDTDLLVQLVTAYARLD  506 (652)
T ss_pred             -------------HHhHHHHHhHHHHhcCchHHHHHHHHHHHHhC-CchHHHHHHHHHHHHhcC
Confidence                         12445555556677899999999999998654 689999999999998763

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=90.00  E-value=3.3  Score=25.96  Aligned_cols=68  Identities=19%  Similarity=0.143  Sum_probs=47.3

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC---hhhHHHH-HHHhcCCCccccchh--------HHHHHHHHHHHh
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESLGVHTD---EVTMVVV-LAASSGPGALDFGKS--------NIFLTTAIIEMY  150 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~---~~t~~~l-i~~~~~~g~~~~a~~--------~~~~~~~li~~y  150 (153)
                      ..+-.+-+++...|++++|..+|++.....  |+   ......+ --++...|+.++|.+        +..-|..-|..|
T Consensus        39 ~a~i~lastlr~LG~~deA~~~L~~~~~~~--p~~~~~~~l~~f~Al~L~~~gr~~eAl~~~l~~la~~~~~y~ra~~~y  116 (120)
T PF12688_consen   39 RALIQLASTLRNLGRYDEALALLEEALEEF--PDDELNAALRVFLALALYNLGRPKEALEWLLEALAETLPRYRRAIRFY  116 (120)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCccccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344467788899999999999999988653  43   2222222 236678899999888        555677777766


Q ss_pred             hc
Q 039275          151 AK  152 (153)
Q Consensus       151 ~k  152 (153)
                      +.
T Consensus       117 a~  118 (120)
T PF12688_consen  117 AD  118 (120)
T ss_pred             Hh
Confidence            53

>PRK04841 transcriptional regulator MalT; Provisional

Probab=89.89  E-value=6.8  Score=32.91  Aligned_cols=134  Identities=16%  Similarity=-0.001  Sum_probs=80.1

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCccH----HHHHHHHHHhcCCCchHHHHHH-hhh------h-hc--chhhHHHHHHHH
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTDE----VTMVVVLTASSGPGAWILAKEL-QIE------L-DL--SSYSLSSKTSRY   70 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~~----~~~~~ll~~~~~~~~~~~a~~~-~~~------~-~~--~~~~~~~ll~~~   70 (153)
                      +...|++++|...+++....--..+.    ...+.+-..+...|++++|... ...      . .+  -......+-..+
T Consensus       462 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~  541 (903)
T PRK04841        462 AINDGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEIL  541 (903)
T ss_pred             HHhCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHH
Confidence            45688999999999887653111111    2334444556778898888777 111      1 11  122344555677


Q ss_pred             HhcCCccccc--------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc--CCCC--ChhhHHHHHHH
Q 039275           71 AHSGRIRLAR--------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESL--GVHT--DEVTMVVVLAA  126 (153)
Q Consensus        71 ~~~g~~~~a~--------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~--g~~p--~~~t~~~li~~  126 (153)
                      ...|++++|.                    ....+..+-..+...|++++|...+.+....  ...|  ....+..+-..
T Consensus       542 ~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~  621 (903)
T PRK04841        542 FAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKI  621 (903)
T ss_pred             HHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHH
Confidence            7889888886                    0112333344567779999999998887532  1122  23334445556


Q ss_pred             hcCCCccccchh
Q 039275          127 SSGPGALDFGKS  138 (153)
Q Consensus       127 ~~~~g~~~~a~~  138 (153)
                      ....|+.+.|.+
T Consensus       622 ~~~~G~~~~A~~  633 (903)
T PRK04841        622 SLARGDLDNARR  633 (903)
T ss_pred             HHHcCCHHHHHH
Confidence            677888888876

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

Probab=89.82  E-value=3.8  Score=32.53  Aligned_cols=105  Identities=12%  Similarity=0.069  Sum_probs=66.3

Q ss_pred             hhHHHHHHHHh-HHcCCCccHHHHHHHHHHhcCCCchHHHHHH---hhhhhcchhhHHHHHHHHHhcCCccccchHHHHH
Q 039275           11 FNEALEPFGKL-ESLGVHTDEVTMVVVLTASSGPGAWILAKEL---QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCK   86 (153)
Q Consensus        11 ~~~a~~~~~~m-~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~   86 (153)
                      +.+..++|-++ .+.+.++|+.++..|=--|--.|.++.|.+.   --.++|+                     |-..||
T Consensus       410 l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdraiDcf~~AL~v~Pn---------------------d~~lWN  468 (579)
T KOG1125|consen  410 LAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAVDCFEAALQVKPN---------------------DYLLWN  468 (579)
T ss_pred             HHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHHHHHHHHHhcCCc---------------------hHHHHH
Confidence            34455555555 3444445555555444445555666665555   2223333                     558899


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHHcCCCCChh-hHHHHHHHhcCCCccccchh
Q 039275           87 AMISGYSQAGRFNEALEPFGKLESLGVHTDEV-TMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        87 ~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~-t~~~li~~~~~~g~~~~a~~  138 (153)
                      -|=.+++...+..+|...|++-.+  ++|.-+ ..-.|--+|..+|.+++|..
T Consensus       469 RLGAtLAN~~~s~EAIsAY~rALq--LqP~yVR~RyNlgIS~mNlG~ykEA~~  519 (579)
T KOG1125|consen  469 RLGATLANGNRSEEAISAYNRALQ--LQPGYVRVRYNLGISCMNLGAYKEAVK  519 (579)
T ss_pred             HhhHHhcCCcccHHHHHHHHHHHh--cCCCeeeeehhhhhhhhhhhhHHHHHH
Confidence            999999999999999999998875  456432 23334456788888888877

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

Probab=89.73  E-value=2.1  Score=30.94  Aligned_cols=107  Identities=12%  Similarity=0.022  Sum_probs=67.6

Q ss_pred             HHHHHHHHHhcCCCchHHHHHHhhh-hhc---chhhHHHHHHH-HHhcCCccccc------------hHHHHHHHHHHHH
Q 039275           31 VTMVVVLTASSGPGAWILAKELQIE-LDL---SSYSLSSKTSR-YAHSGRIRLAR------------DPVSCKAMISGYS   93 (153)
Q Consensus        31 ~~~~~ll~~~~~~~~~~~a~~~~~~-~~~---~~~~~~~ll~~-~~~~g~~~~a~------------~~~~~~~li~~~~   93 (153)
                      .+|..++..+-+.+..+.|.++... ...   +..+|...... |...++.+.|.            +...|..-+..+.
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~f~~~~~~~~~Y~~~l~   81 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALMEYYCNKDPKRARKIFERGLKKFPSDPDFWLEYLDFLI   81 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH
Confidence            4677777777777778888888111 111   22233333233 22234444455            7888999999999


Q ss_pred             hcCChHHHHHHHHHHHHcCCCCC---hhhHHHHHHHhcCCCccccchh
Q 039275           94 QAGRFNEALEPFGKLESLGVHTD---EVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        94 ~~g~~~~a~~~~~~m~~~g~~p~---~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +.|+.+.|..+|++.... +.++   ...|...++.=.+.|+.+....
T Consensus        82 ~~~d~~~aR~lfer~i~~-l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~  128 (280)
T PF05843_consen   82 KLNDINNARALFERAISS-LPKEKQSKKIWKKFIEFESKYGDLESVRK  128 (280)
T ss_dssp             HTT-HHHHHHHHHHHCCT-SSCHHHCHHHHHHHHHHHHHHS-HHHHHH
T ss_pred             HhCcHHHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            999999999999998855 3222   3478888887777777776555

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.

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=89.52  E-value=6.6  Score=30.51  Aligned_cols=47  Identities=15%  Similarity=0.091  Sum_probs=36.0

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccH----HHHHHHHHHhcCCCchHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDE----VTMVVVLTASSGPGAWILAKEL   52 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~----~~~~~ll~~~~~~~~~~~a~~~   52 (153)
                      +|.+.|++++|+..|++-...  .|+.    ..|..+-.+|.+.|+.++|.+.
T Consensus        84 AL~~lGryeEAIa~f~rALeL--~Pd~aeA~~A~yNLAcaya~LGr~dEAla~  134 (453)
T PLN03098         84 SLFSKGRVKDALAQFETALEL--NPNPDEAQAAYYNKACCHAYREEGKKAADC  134 (453)
T ss_pred             HHHHcCCHHHHHHHHHHHHhh--CCCchHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            577888888888888886663  4554    3477778888888888888877

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

Probab=89.45  E-value=8.9  Score=31.46  Aligned_cols=130  Identities=10%  Similarity=-0.022  Sum_probs=71.2

Q ss_pred             hhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhh--cch-hhHHHHHHHHHhcCCccccc-
Q 039275            6 SQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELD--LSS-YSLSSKTSRYAHSGRIRLAR-   80 (153)
Q Consensus         6 ~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~--~~~-~~~~~ll~~~~~~g~~~~a~-   80 (153)
                      .++..+++|..+|.+-+.  ..|+..+|-.-.+.---.++.++|.++ +..++  |+- ..|-.+=.-+-+.++++.|+ 
T Consensus       629 ~en~e~eraR~llakar~--~sgTeRv~mKs~~~er~ld~~eeA~rllEe~lk~fp~f~Kl~lmlGQi~e~~~~ie~aR~  706 (913)
T KOG0495|consen  629 FENDELERARDLLAKARS--ISGTERVWMKSANLERYLDNVEEALRLLEEALKSFPDFHKLWLMLGQIEEQMENIEMARE  706 (913)
T ss_pred             hccccHHHHHHHHHHHhc--cCCcchhhHHHhHHHHHhhhHHHHHHHHHHHHHhCCchHHHHHHHhHHHHHHHHHHHHHH
Confidence            455667777777776655  456666666555555556667777776 22221  111 12222223334444444444 


Q ss_pred             -----------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 -----------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 -----------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                                 .+..|-.|-.---+.|++-+|..+|+.-+..+ .-+...|...|..=.+.|+.++|+.
T Consensus       707 aY~~G~k~cP~~ipLWllLakleEk~~~~~rAR~ildrarlkN-Pk~~~lwle~Ir~ElR~gn~~~a~~  774 (913)
T KOG0495|consen  707 AYLQGTKKCPNSIPLWLLLAKLEEKDGQLVRARSILDRARLKN-PKNALLWLESIRMELRAGNKEQAEL  774 (913)
T ss_pred             HHHhccccCCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhcC-CCcchhHHHHHHHHHHcCCHHHHHH
Confidence                       34444444444455666666766666655443 2255556666666666666666655

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=89.07  E-value=10  Score=30.19  Aligned_cols=56  Identities=14%  Similarity=0.086  Sum_probs=46.5

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +...|.++-......|++++|...+++.....  |+...|..+-..+...|+.++|.+
T Consensus       419 ~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~  474 (517)
T PRK10153        419 LPRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAAD  474 (517)
T ss_pred             ChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHH
Confidence            44667777666667899999999999988665  788889999999999999999888

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=88.62  E-value=6.1  Score=29.41  Aligned_cols=44  Identities=11%  Similarity=0.069  Sum_probs=33.9

Q ss_pred             cCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           95 AGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        95 ~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .-+++++.-++..=.+.|+-||.+|+..+|+.+.+.+++..|.+
T Consensus       113 ky~pq~~i~~l~npIqYGiF~dqf~~c~l~D~flk~~n~~~aa~  156 (418)
T KOG4570|consen  113 KYDPQKAIYTLVNPIQYGIFPDQFTFCLLMDSFLKKENYKDAAS  156 (418)
T ss_pred             ccChHHHHHHHhCcchhccccchhhHHHHHHHHHhcccHHHHHH
Confidence            33677777777777777888888888888888888888877776

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=88.53  E-value=7.2  Score=27.88  Aligned_cols=133  Identities=18%  Similarity=0.116  Sum_probs=88.5

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCcc---HHHHHHHHHHhcCCCchHHHHHH---hhhhhc--chhhHHHHHHHHHhcCCc
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTD---EVTMVVVLTASSGPGAWILAKEL---QIELDL--SSYSLSSKTSRYAHSGRI   76 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~---~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~--~~~~~~~ll~~~~~~g~~   76 (153)
                      -.+.|++++|.+-|+.+.+. .+-+   ..+.--++-+..+.+++++|...   ....-|  ...-|..-|++++..-.+
T Consensus        44 ~L~~gn~~~A~~~fe~l~~~-~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~~n~dY~~YlkgLs~~~~i  122 (254)
T COG4105          44 ELQKGNYEEAIKYFEALDSR-HPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTHPNADYAYYLKGLSYFFQI  122 (254)
T ss_pred             HHhcCCHHHHHHHHHHHHHc-CCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCCCChhHHHHHHHHHHhccC
Confidence            35789999999999999754 2222   33344455678899999998887   111112  223455566666655555


Q ss_pred             cccc-------------------------------------hHHHHHH--HHHHHHhcCChHHHHHHHHHHHHcC--CCC
Q 039275           77 RLAR-------------------------------------DPVSCKA--MISGYSQAGRFNEALEPFGKLESLG--VHT  115 (153)
Q Consensus        77 ~~a~-------------------------------------~~~~~~~--li~~~~~~g~~~~a~~~~~~m~~~g--~~p  115 (153)
                      +...                                     |.....-  +-.-|.+.|.+-.|..-+++|.+.=  ..-
T Consensus       123 ~~~~rDq~~~~~A~~~f~~~i~ryPnS~Ya~dA~~~i~~~~d~LA~~Em~IaryY~kr~~~~AA~nR~~~v~e~y~~t~~  202 (254)
T COG4105         123 DDVTRDQSAARAAFAAFKELVQRYPNSRYAPDAKARIVKLNDALAGHEMAIARYYLKRGAYVAAINRFEEVLENYPDTSA  202 (254)
T ss_pred             CccccCHHHHHHHHHHHHHHHHHCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHhccccccc
Confidence            5544                                     2222222  2356789999999999999999771  122


Q ss_pred             ChhhHHHHHHHhcCCCccccchh
Q 039275          116 DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       116 ~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .....-.+..+|.+.|..++|..
T Consensus       203 ~~eaL~~l~eaY~~lgl~~~a~~  225 (254)
T COG4105         203 VREALARLEEAYYALGLTDEAKK  225 (254)
T ss_pred             hHHHHHHHHHHHHHhCChHHHHH
Confidence            33456677789999999998887

>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised

Probab=88.51  E-value=1.5  Score=22.59  Aligned_cols=37  Identities=14%  Similarity=0.143  Sum_probs=31.3

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHH
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTA   39 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~   39 (153)
                      ...-+.|-..++...+++|.+.|+-.+...|..++.-
T Consensus        10 ~~Ak~~GlI~~~~~~l~~l~~~g~~is~~l~~~~L~~   46 (48)
T PF11848_consen   10 LLAKRRGLISEVKPLLDRLQQAGFRISPKLIEEILRR   46 (48)
T ss_pred             HHHHHcCChhhHHHHHHHHHHcCcccCHHHHHHHHHH
Confidence            3445778888999999999999999999999888764

This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=88.48  E-value=4.7  Score=26.40  Aligned_cols=27  Identities=15%  Similarity=-0.022  Sum_probs=15.2

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHH
Q 039275           84 SCKAMISGYSQAGRFNEALEPFGKLES  110 (153)
Q Consensus        84 ~~~~li~~~~~~g~~~~a~~~~~~m~~  110 (153)
                      +|..+-..+...|++++|.+.++....
T Consensus        74 ~~~~lg~~~~~~g~~~eA~~~~~~Al~  100 (168)
T CHL00033         74 ILYNIGLIHTSNGEHTKALEYYFQALE  100 (168)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            455555555556666666666555543

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=88.34  E-value=6.5  Score=30.65  Aligned_cols=124  Identities=14%  Similarity=-0.020  Sum_probs=73.0

Q ss_pred             hhcCChhHHHHHHHHhHHcC----CCcc-HHHHHHHHHHhcCCCchHHHHHH---hhhhhcchhhHHHHHHHH--HhcCC
Q 039275            6 SQAGRFNEALEPFGKLESLG----VHTD-EVTMVVVLTASSGPGAWILAKEL---QIELDLSSYSLSSKTSRY--AHSGR   75 (153)
Q Consensus         6 ~~~g~~~~a~~~~~~m~~~g----~~p~-~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~~~~~~~~ll~~~--~~~g~   75 (153)
                      -+.+++.++.++|.++-+..    .... .+.-+.+|+||...+ .+.....   -+...| ...|-.|..+.  .+.++
T Consensus        17 qkq~~~~esEkifskI~~e~~~~~f~lkeEvl~grilnAffl~n-ld~Me~~l~~l~~~~~-~s~~l~LF~~L~~Y~~k~   94 (549)
T PF07079_consen   17 QKQKKFQESEKIFSKIYDEKESSPFLLKEEVLGGRILNAFFLNN-LDLMEKQLMELRQQFG-KSAYLPLFKALVAYKQKE   94 (549)
T ss_pred             HHHhhhhHHHHHHHHHHHHhhcchHHHHHHHHhhHHHHHHHHhh-HHHHHHHHHHHHHhcC-CchHHHHHHHHHHHHhhh
Confidence            46789999999999985542    1111 244557888877544 3333333   111112 11222222221  23333


Q ss_pred             ccccc---------------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCC----CChhhHHHHH
Q 039275           76 IRLAR---------------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVH----TDEVTMVVVL  124 (153)
Q Consensus        76 ~~~a~---------------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~----p~~~t~~~li  124 (153)
                      +.+|.                           |-.-=+..+..+...|+++++..++++|...=++    .+..+|+.++
T Consensus        95 ~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~yd~~v  174 (549)
T PF07079_consen   95 YRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMYDRAV  174 (549)
T ss_pred             HHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHHHHHH
Confidence            33333                           3334456678889999999999999988765444    8888998866


Q ss_pred             HHhcCCC
Q 039275          125 AASSGPG  131 (153)
Q Consensus       125 ~~~~~~g  131 (153)
                      -.++++-
T Consensus       175 lmlsrSY  181 (549)
T PF07079_consen  175 LMLSRSY  181 (549)
T ss_pred             HHHhHHH
Confidence            6666543

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

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

Probab=88.00  E-value=12  Score=29.90  Aligned_cols=112  Identities=14%  Similarity=0.038  Sum_probs=56.3

Q ss_pred             hcCChhHHHHHHHHhHHcCCCc-cHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHH
Q 039275            7 QAGRFNEALEPFGKLESLGVHT-DEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVS   84 (153)
Q Consensus         7 ~~g~~~~a~~~~~~m~~~g~~p-~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~   84 (153)
                      +..-++.|..+|.+.++.+..+ ++.+++.+|.-+|. ++.+-|.++ +.|++.-.              +     ++.-
T Consensus       378 R~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~cs-kD~~~AfrIFeLGLkkf~--------------d-----~p~y  437 (656)
T KOG1914|consen  378 RAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCS-KDKETAFRIFELGLKKFG--------------D-----SPEY  437 (656)
T ss_pred             HhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhc-CChhHHHHHHHHHHHhcC--------------C-----ChHH
Confidence            3444555566666665555555 55555555555442 333334444 33332100              0     2222


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC--hhhHHHHHHHhcCCCccccchh
Q 039275           85 CKAMISGYSQAGRFNEALEPFGKLESLGVHTD--EVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        85 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~--~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      -..-+.-+...|+-..+.-+|+.....++.||  ..+|..+|+.=..-|++..+..
T Consensus       438 v~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~  493 (656)
T KOG1914|consen  438 VLKYLDFLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILK  493 (656)
T ss_pred             HHHHHHHHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHH
Confidence            23445555566666666666666665555443  3456666666555565554433

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=87.88  E-value=2  Score=33.17  Aligned_cols=56  Identities=11%  Similarity=0.035  Sum_probs=37.6

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCh----hhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDE----VTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~----~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +...|+.+-..|.+.|++++|...|++-.+.  .|+.    .+|..+-.+|.++|++++|.+
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALeL--~Pd~aeA~~A~yNLAcaya~LGr~dEAla  133 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALEL--NPNPDEAQAAYYNKACCHAYREEGKKAAD  133 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCchHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            5666777777777777777777777765543  3543    346777777777777777766

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=87.48  E-value=14  Score=31.14  Aligned_cols=72  Identities=19%  Similarity=0.098  Sum_probs=32.5

Q ss_pred             hhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhh--hhcchhhHHHHHHHHHhcCCccc
Q 039275            6 SQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIE--LDLSSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         6 ~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~--~~~~~~~~~~ll~~~~~~g~~~~   78 (153)
                      .+.|+.++|..+++....-+.. |..|..++-..|-..+..+++..+ ++.  .-|+......+..+|.|.+++.+
T Consensus        54 ~r~gk~~ea~~~Le~~~~~~~~-D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~~~P~eell~~lFmayvR~~~yk~  128 (932)
T KOG2053|consen   54 FRLGKGDEALKLLEALYGLKGT-DDLTLQFLQNVYRDLGKLDEAVHLYERANQKYPSEELLYHLFMAYVREKSYKK  128 (932)
T ss_pred             HHhcCchhHHHHHhhhccCCCC-chHHHHHHHHHHHHHhhhhHHHHHHHHHHhhCCcHHHHHHHHHHHHHHHHHHH
Confidence            3445555555555444433332 455555555555555555555555 222  22333333334444444444433

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=86.98  E-value=6.7  Score=28.17  Aligned_cols=64  Identities=14%  Similarity=0.039  Sum_probs=44.2

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHHcC-CCC-ChhhHHHHHHHhcCCCccccchhHHHHHHHHHHHh
Q 039275           84 SCKAMISGYSQAGRFNEALEPFGKLESLG-VHT-DEVTMVVVLAASSGPGALDFGKSNIFLTTAIIEMY  150 (153)
Q Consensus        84 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p-~~~t~~~li~~~~~~g~~~~a~~~~~~~~~li~~y  150 (153)
                      .+--+-..|...|++++|...|+.+...- -.| ....+-.+...+...|+.+.|..   +|..+++-|
T Consensus       182 A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg~~~~~~g~~~~A~~---~~~~vi~~y  247 (263)
T PRK10803        182 ANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVGVIMQDKGDTAKAKA---VYQQVIKKY  247 (263)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHHHHHHHcCCHHHHHH---HHHHHHHHC
Confidence            33456677889999999999999998542 111 22233444556778899999988   666666655

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=86.98  E-value=5.6  Score=28.98  Aligned_cols=58  Identities=5%  Similarity=0.006  Sum_probs=30.5

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc-CCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESL-GVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +..+--.+|..+++.+++.+-++++..-... +..-|..-|..+|+...+.|+..-.+.
T Consensus       201 ~~~vi~~Il~~L~~~~dW~kl~~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~k  259 (292)
T PF13929_consen  201 TRNVIISILEILAESRDWNKLFQFWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRK  259 (292)
T ss_pred             ChhHHHHHHHHHHhcccHHHHHHHHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHH
Confidence            3344445555556666666555555554432 334455556666665555555544433

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=86.92  E-value=6.1  Score=29.96  Aligned_cols=107  Identities=21%  Similarity=0.265  Sum_probs=69.4

Q ss_pred             cCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH---hhhhh-cchhhHHHHH-HHHHhcCCccccc--
Q 039275            8 AGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL---QIELD-LSSYSLSSKT-SRYAHSGRIRLAR--   80 (153)
Q Consensus         8 ~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~---~~~~~-~~~~~~~~ll-~~~~~~g~~~~a~--   80 (153)
                      ...+++.+-.++.+++.=.--|..-| -+-.+.+..|++.+|+++   -++.+ .|..+|-+++ ++|.+++.++-|-  
T Consensus       372 ~~qFddVl~YlnSi~sYF~NdD~Fn~-N~AQAk~atgny~eaEelf~~is~~~ikn~~~Y~s~LArCyi~nkkP~lAW~~  450 (557)
T KOG3785|consen  372 SFQFDDVLTYLNSIESYFTNDDDFNL-NLAQAKLATGNYVEAEELFIRISGPEIKNKILYKSMLARCYIRNKKPQLAWDM  450 (557)
T ss_pred             HHHHHHHHHHHHHHHHHhcCcchhhh-HHHHHHHHhcChHHHHHHHhhhcChhhhhhHHHHHHHHHHHHhcCCchHHHHH
Confidence            34567777777776665333333333 345677778888888888   33343 5667776654 7778888877665  


Q ss_pred             --------hHHHHHHHH-HHHHhcCChHHHHHHHHHHHHcCCCC
Q 039275           81 --------DPVSCKAMI-SGYSQAGRFNEALEPFGKLESLGVHT  115 (153)
Q Consensus        81 --------~~~~~~~li-~~~~~~g~~~~a~~~~~~m~~~g~~p  115 (153)
                              +..+.-.+| .-|.+.+++.-|-+.|+++......|
T Consensus       451 ~lk~~t~~e~fsLLqlIAn~CYk~~eFyyaaKAFd~lE~lDP~p  494 (557)
T KOG3785|consen  451 MLKTNTPSERFSLLQLIANDCYKANEFYYAAKAFDELEILDPTP  494 (557)
T ss_pred             HHhcCCchhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHccCCCc
Confidence                    333333334 66788999999999999988654333

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=86.89  E-value=9.5  Score=27.47  Aligned_cols=30  Identities=20%  Similarity=0.202  Sum_probs=21.7

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHH
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLES  110 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  110 (153)
                      |...|.-+-..|...|++++|--.++++.-
T Consensus       153 D~EAW~eLaeiY~~~~~f~kA~fClEE~ll  182 (289)
T KOG3060|consen  153 DQEAWHELAEIYLSEGDFEKAAFCLEELLL  182 (289)
T ss_pred             cHHHHHHHHHHHHhHhHHHHHHHHHHHHHH
Confidence            677777777777777777777777777764

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=86.86  E-value=2.2  Score=31.05  Aligned_cols=57  Identities=9%  Similarity=0.075  Sum_probs=41.8

Q ss_pred             cCCCccHHHHHHHHHHhcCCCchHHHHHH------hhhhhcchhhHHHHHHHHHhcCCccccc
Q 039275           24 LGVHTDEVTMVVVLTASSGPGAWILAKEL------QIELDLSSYSLSSKTSRYAHSGRIRLAR   80 (153)
Q Consensus        24 ~g~~p~~~~~~~ll~~~~~~~~~~~a~~~------~~~~~~~~~~~~~ll~~~~~~g~~~~a~   80 (153)
                      .|-.++..+..++|+.+++.++|..-.++      ..+...|...|..+|+...+.|+..-..
T Consensus       196 ~~~~l~~~vi~~Il~~L~~~~dW~kl~~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~  258 (292)
T PF13929_consen  196 FSKSLTRNVIISILEILAESRDWNKLFQFWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMR  258 (292)
T ss_pred             cccCCChhHHHHHHHHHHhcccHHHHHHHHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHH
Confidence            35667788888888888888888888888      2233446677888888888888764433

>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=86.54  E-value=2  Score=33.35  Aligned_cols=94  Identities=18%  Similarity=0.141  Sum_probs=52.0

Q ss_pred             hhcCChhHHHHHHH--HhHHcCCCccHHHHHHHHHHhcCCCchHHHHHHhhhhhcchhhHHHHHHHHHhcCCccccc---
Q 039275            6 SQAGRFNEALEPFG--KLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIELDLSSYSLSSKTSRYAHSGRIRLAR---   80 (153)
Q Consensus         6 ~~~g~~~~a~~~~~--~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~ll~~~~~~g~~~~a~---   80 (153)
                      .-.++++++.++..  ++. ..++  ....+.++.-+-+.|-.+.|+++-...       ..-.+...+.|+++.|.   
T Consensus       272 v~~~d~~~v~~~i~~~~ll-~~i~--~~~~~~i~~fL~~~G~~e~AL~~~~D~-------~~rFeLAl~lg~L~~A~~~a  341 (443)
T PF04053_consen  272 VLRGDFEEVLRMIAASNLL-PNIP--KDQGQSIARFLEKKGYPELALQFVTDP-------DHRFELALQLGNLDIALEIA  341 (443)
T ss_dssp             HHTT-HHH-----HHHHTG-GG----HHHHHHHHHHHHHTT-HHHHHHHSS-H-------HHHHHHHHHCT-HHHHHHHC
T ss_pred             HHcCChhhhhhhhhhhhhc-ccCC--hhHHHHHHHHHHHCCCHHHHHhhcCCh-------HHHhHHHHhcCCHHHHHHHH
Confidence            34567777666664  111 1122  445778888888889899888881111       11122334566666666   


Q ss_pred             ----hHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 039275           81 ----DPVSCKAMISGYSQAGRFNEALEPFGKLE  109 (153)
Q Consensus        81 ----~~~~~~~li~~~~~~g~~~~a~~~~~~m~  109 (153)
                          +...|..|-....+.|+++-|++.|++..
T Consensus       342 ~~~~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~  374 (443)
T PF04053_consen  342 KELDDPEKWKQLGDEALRQGNIELAEECYQKAK  374 (443)
T ss_dssp             CCCSTHHHHHHHHHHHHHTTBHHHHHHHHHHCT
T ss_pred             HhcCcHHHHHHHHHHHHHcCCHHHHHHHHHhhc
Confidence                56677777777777777777777776654

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.

>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=86.39  E-value=6.9  Score=25.35  Aligned_cols=124  Identities=11%  Similarity=0.057  Sum_probs=74.3

Q ss_pred             hhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH--hhhhhcchhh---HHHHHHHHHhcCCccccc
Q 039275            6 SQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL--QIELDLSSYS---LSSKTSRYAHSGRIRLAR   80 (153)
Q Consensus         6 ~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~--~~~~~~~~~~---~~~ll~~~~~~g~~~~a~   80 (153)
                      .-.|.+++..++..+....   .+..-||.+|--....-+.+-..+.  .-|---|...   .-.++..|.+.+-.    
T Consensus        13 ildG~V~qGveii~k~v~S---sni~E~NWvICNiiDaa~C~yvv~~LdsIGkiFDis~C~NlKrVi~C~~~~n~~----   85 (161)
T PF09205_consen   13 ILDGDVKQGVEIIEKTVNS---SNIKEYNWVICNIIDAADCDYVVETLDSIGKIFDISKCGNLKRVIECYAKRNKL----   85 (161)
T ss_dssp             HHTT-HHHHHHHHHHHHHH---S-HHHHTHHHHHHHHH--HHHHHHHHHHHGGGS-GGG-S-THHHHHHHHHTT------
T ss_pred             HHhchHHHHHHHHHHHcCc---CCccccceeeeecchhhchhHHHHHHHHHhhhcCchhhcchHHHHHHHHHhcch----
Confidence            3467888888888887553   3455555555444444444443333  2222222222   23467777777764    


Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                       ....+.-+..+...|+-|+-.++..++.+. -+|+......+-+||.+.|+..++.+
T Consensus        86 -se~vD~ALd~lv~~~kkDqLdki~~~l~kn-~~~~p~~L~kia~Ay~klg~~r~~~e  141 (161)
T PF09205_consen   86 -SEYVDLALDILVKQGKKDQLDKIYNELKKN-EEINPEFLVKIANAYKKLGNTREANE  141 (161)
T ss_dssp             --HHHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHH
T ss_pred             -HHHHHHHHHHHHHhccHHHHHHHHHHHhhc-cCCCHHHHHHHHHHHHHhcchhhHHH
Confidence             346677888999999999999999998863 37888888899999999999988776

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=86.38  E-value=8.5  Score=30.41  Aligned_cols=101  Identities=15%  Similarity=0.085  Sum_probs=64.3

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH---hhhhhcchhhHHHHHHHHHhcCCccccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL---QIELDLSSYSLSSKTSRYAHSGRIRLAR   80 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~~~~~~~~ll~~~~~~g~~~~a~   80 (153)
                      +.+..|+++.|+..|-+-..-. ++|.+-|.-=..++++.|++++|.+=   ...+.|+.                    
T Consensus        11 aa~s~~d~~~ai~~~t~ai~l~-p~nhvlySnrsaa~a~~~~~~~al~da~k~~~l~p~w--------------------   69 (539)
T KOG0548|consen   11 AAFSSGDFETAIRLFTEAIMLS-PTNHVLYSNRSAAYASLGSYEKALKDATKTRRLNPDW--------------------   69 (539)
T ss_pred             hhcccccHHHHHHHHHHHHccC-CCccchhcchHHHHHHHhhHHHHHHHHHHHHhcCCch--------------------
Confidence            3466788888888887665532 33666677777777888888777666   34445543                    


Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAAS  127 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~  127 (153)
                       ...|+-.=.++.-.|++++|..-|.+=.+.- .-+...++.+.++.
T Consensus        70 -~kgy~r~Gaa~~~lg~~~eA~~ay~~GL~~d-~~n~~L~~gl~~a~  114 (539)
T KOG0548|consen   70 -AKGYSRKGAALFGLGDYEEAILAYSEGLEKD-PSNKQLKTGLAQAY  114 (539)
T ss_pred             -hhHHHHhHHHHHhcccHHHHHHHHHHHhhcC-CchHHHHHhHHHhh
Confidence             2456666666777788888888877644321 22455566666665

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=86.33  E-value=6.7  Score=28.81  Aligned_cols=51  Identities=14%  Similarity=0.095  Sum_probs=44.3

Q ss_pred             hHHHHHHHHHHHHhc-----CChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCC
Q 039275           81 DPVSCKAMISGYSQA-----GRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPG  131 (153)
Q Consensus        81 ~~~~~~~li~~~~~~-----g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g  131 (153)
                      |..+|-+++..|..+     +.++-....++.|++-|+..|..+|..||+.+=+..
T Consensus        66 dK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgk  121 (406)
T KOG3941|consen   66 DKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGK  121 (406)
T ss_pred             cHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccc
Confidence            778888888888654     888888999999999999999999999999987654

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=86.32  E-value=1.8  Score=21.97  Aligned_cols=35  Identities=17%  Similarity=0.228  Sum_probs=25.5

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHH
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVL   37 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll   37 (153)
                      .+|.+.|+.+.|.+++++....|-.|-..--..|+
T Consensus         7 ~ayie~Gd~e~Ar~lL~evl~~~~~~q~~eA~~LL   41 (44)
T TIGR03504         7 RAYIEMGDLEGARELLEEVIEEGDEAQRQEARALL   41 (44)
T ss_pred             HHHHHcCChHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            57999999999999999998765544443333333

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.

>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=86.30  E-value=2.1  Score=33.16  Aligned_cols=96  Identities=18%  Similarity=0.148  Sum_probs=64.4

Q ss_pred             HHHHhcCCCchHHHHHHhhhhhcchhhHHHHHHHHHhcCCccccc----hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 039275           36 VLTASSGPGAWILAKELQIELDLSSYSLSSKTSRYAHSGRIRLAR----DPVSCKAMISGYSQAGRFNEALEPFGKLESL  111 (153)
Q Consensus        36 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~ll~~~~~~g~~~~a~----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  111 (153)
                      -++...+.|+++.|.++-.... +...|..|-+...+.|+++-|.    ...-|..|+--|.-.|+.++-.++-+.-...
T Consensus       324 rFeLAl~lg~L~~A~~~a~~~~-~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d~~~L~lLy~~~g~~~~L~kl~~~a~~~  402 (443)
T PF04053_consen  324 RFELALQLGNLDIALEIAKELD-DPEKWKQLGDEALRQGNIELAEECYQKAKDFSGLLLLYSSTGDREKLSKLAKIAEER  402 (443)
T ss_dssp             HHHHHHHCT-HHHHHHHCCCCS-THHHHHHHHHHHHHTTBHHHHHHHHHHCT-HHHHHHHHHHCT-HHHHHHHHHHHHHT
T ss_pred             HhHHHHhcCCHHHHHHHHHhcC-cHHHHHHHHHHHHHcCCHHHHHHHHHhhcCccccHHHHHHhCCHHHHHHHHHHHHHc
Confidence            3555677888888888822222 5568889999999999988888    6667788888888888887777777666655


Q ss_pred             CCCCChhhHHHHHHHhcCCCccccchh
Q 039275          112 GVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       112 g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |      -++..+.++.-.|++++..+
T Consensus       403 ~------~~n~af~~~~~lgd~~~cv~  423 (443)
T PF04053_consen  403 G------DINIAFQAALLLGDVEECVD  423 (443)
T ss_dssp             T-------HHHHHHHHHHHT-HHHHHH
T ss_pred             c------CHHHHHHHHHHcCCHHHHHH
Confidence            5      35555555555666665554

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.

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=85.74  E-value=7.2  Score=32.77  Aligned_cols=72  Identities=25%  Similarity=0.225  Sum_probs=43.2

Q ss_pred             hhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHh--cCCCchHHHHHH---hhhhhc-chhhHHHHHHHHHhcCCcccc
Q 039275            6 SQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTAS--SGPGAWILAKEL---QIELDL-SSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         6 ~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~--~~~~~~~~a~~~---~~~~~~-~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      ...+++++|..-..++.+.  .|+ ..|..++.++  .+.|+.++|..+   ..+.++ |..|-..+-..|...+..++|
T Consensus        20 ld~~qfkkal~~~~kllkk--~Pn-~~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~D~~tLq~l~~~y~d~~~~d~~   96 (932)
T KOG2053|consen   20 LDSSQFKKALAKLGKLLKK--HPN-ALYAKVLKALSLFRLGKGDEALKLLEALYGLKGTDDLTLQFLQNVYRDLGKLDEA   96 (932)
T ss_pred             hhhHHHHHHHHHHHHHHHH--CCC-cHHHHHHHHHHHHHhcCchhHHHHHhhhccCCCCchHHHHHHHHHHHHHhhhhHH
Confidence            4567888888888877553  233 3455556655  567888888877   333333 344455555555555555554


Q ss_pred             c
Q 039275           80 R   80 (153)
Q Consensus        80 ~   80 (153)
                      .
T Consensus        97 ~   97 (932)
T KOG2053|consen   97 V   97 (932)
T ss_pred             H
Confidence            4

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

Probab=85.36  E-value=6.8  Score=30.29  Aligned_cols=97  Identities=16%  Similarity=0.115  Sum_probs=59.9

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccH----HHHHHHHHHhcCCCchHHHHHH--------------------------
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDE----VTMVVVLTASSGPGAWILAKEL--------------------------   52 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~----~~~~~ll~~~~~~~~~~~a~~~--------------------------   52 (153)
                      +.+...|+.++|+..|++-...  .|+.    ..|..++   .+.|+++...++                          
T Consensus       240 k~~~~~Gdn~~a~~~Fe~~~~~--dpy~i~~MD~Ya~LL---~~eg~~e~~~~L~~~Lf~~~~~ta~~wfV~~~~l~~~K  314 (564)
T KOG1174|consen  240 KCLYYNGDYFQAEDIFSSTLCA--NPDNVEAMDLYAVLL---GQEGGCEQDSALMDYLFAKVKYTASHWFVHAQLLYDEK  314 (564)
T ss_pred             hhhhhhcCchHHHHHHHHHhhC--ChhhhhhHHHHHHHH---HhccCHhhHHHHHHHHHhhhhcchhhhhhhhhhhhhhh
Confidence            4678899999999999877653  2322    2333333   233444433333                          


Q ss_pred             ---------hhhhhcchhhHHHHH---HHHHhcCCccccc------------hHHHHHHHHHHHHhcCChHHHHHH
Q 039275           53 ---------QIELDLSSYSLSSKT---SRYAHSGRIRLAR------------DPVSCKAMISGYSQAGRFNEALEP  104 (153)
Q Consensus        53 ---------~~~~~~~~~~~~~ll---~~~~~~g~~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~  104 (153)
                               ...+..+......+|   ..+...++.++|.            +..+|.-|+..|...|++.+|.-.
T Consensus       315 ~~~rAL~~~eK~I~~~~r~~~alilKG~lL~~~~R~~~A~IaFR~Aq~Lap~rL~~Y~GL~hsYLA~~~~kEA~~~  390 (564)
T KOG1174|consen  315 KFERALNFVEKCIDSEPRNHEALILKGRLLIALERHTQAVIAFRTAQMLAPYRLEIYRGLFHSYLAQKRFKEANAL  390 (564)
T ss_pred             hHHHHHHHHHHHhccCcccchHHHhccHHHHhccchHHHHHHHHHHHhcchhhHHHHHHHHHHHHhhchHHHHHHH
Confidence                     222333333333333   4455666666666            888999999999999999998743

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=85.31  E-value=11  Score=26.68  Aligned_cols=131  Identities=11%  Similarity=0.057  Sum_probs=79.5

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCccH-HHH---HHHHHHhcCCCchHHHHHH---hhhhhcch--hhHHHHHHHHH----
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTDE-VTM---VVVLTASSGPGAWILAKEL---QIELDLSS--YSLSSKTSRYA----   71 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~~-~~~---~~ll~~~~~~~~~~~a~~~---~~~~~~~~--~~~~~ll~~~~----   71 (153)
                      +.+.|++++|++.|+.+...-  |+. ...   -.+..++.+.+++++|...   .-...|+.  .-+.-.+.+.+    
T Consensus        42 ~~~~g~y~~Ai~~f~~l~~~y--P~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~~g~~~~~~  119 (243)
T PRK10866         42 KLQDGNWKQAITQLEALDNRY--PFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLYMRGLTNMAL  119 (243)
T ss_pred             HHHCCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHHHHHHhhhhc
Confidence            456799999999999998742  332 222   2344677889999998877   11111211  12222223322    


Q ss_pred             ------------------------------------hcCCccccc-------h---HHHHHHHHHHHHhcCChHHHHHHH
Q 039275           72 ------------------------------------HSGRIRLAR-------D---PVSCKAMISGYSQAGRFNEALEPF  105 (153)
Q Consensus        72 ------------------------------------~~g~~~~a~-------~---~~~~~~li~~~~~~g~~~~a~~~~  105 (153)
                                                          .+.-..+|.       +   ..-+ .+-.-|.+.|.+.-|..-|
T Consensus       120 ~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~~yP~S~ya~~A~~rl~~l~~~la~~e~-~ia~~Y~~~~~y~AA~~r~  198 (243)
T PRK10866        120 DDSALQGFFGVDRSDRDPQHARAAFRDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEL-SVAEYYTKRGAYVAVVNRV  198 (243)
T ss_pred             chhhhhhccCCCccccCHHHHHHHHHHHHHHHHHCcCChhHHHHHHHHHHHHHHHHHHHH-HHHHHHHHcCchHHHHHHH
Confidence                                                111111111       1   1111 3335578889999999999


Q ss_pred             HHHHHc--CCCCChhhHHHHHHHhcCCCccccchh
Q 039275          106 GKLESL--GVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       106 ~~m~~~--g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +.+.+.  +.+........++.++.++|..++|.+
T Consensus       199 ~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~  233 (243)
T PRK10866        199 EQMLRDYPDTQATRDALPLMENAYRQLQLNAQADK  233 (243)
T ss_pred             HHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHH
Confidence            988865  344466667788899999999998876

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=85.14  E-value=7.1  Score=28.63  Aligned_cols=111  Identities=16%  Similarity=0.220  Sum_probs=62.7

Q ss_pred             hhHHHHHHHHhHHcCCCccHHHHHHHHHHhcC--CCc----hHHHHHH----hhhh----hcchhhHHHHHHHHHhcCCc
Q 039275           11 FNEALEPFGKLESLGVHTDEVTMVVVLTASSG--PGA----WILAKEL----QIEL----DLSSYSLSSKTSRYAHSGRI   76 (153)
Q Consensus        11 ~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~--~~~----~~~a~~~----~~~~----~~~~~~~~~ll~~~~~~g~~   76 (153)
                      +++.+++++.|++.|+.-+..+|-+.......  ..+    ...+.++    +..+    .++.+.+..|+..  ...++
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--~~~~~  155 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--TSEDV  155 (297)
T ss_pred             HHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc--ccccH
Confidence            56778889999999999999888764444333  222    3334444    1111    3455666666543  22222


Q ss_pred             cccc--hHHHHHHHHH----------------HHHh-cCC--hHHHHHHHHHHHHcCCCCChhhHHHH
Q 039275           77 RLAR--DPVSCKAMIS----------------GYSQ-AGR--FNEALEPFGKLESLGVHTDEVTMVVV  123 (153)
Q Consensus        77 ~~a~--~~~~~~~li~----------------~~~~-~g~--~~~a~~~~~~m~~~g~~p~~~t~~~l  123 (153)
                      +.-.  -..+|+.|-.                +++. ..+  +.++.++++.+++.|+++....|..+
T Consensus       156 e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~l  223 (297)
T PF13170_consen  156 EELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYPTL  223 (297)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccccHH
Confidence            2221  1222222222                2222 112  34788999999999998877766544

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=85.00  E-value=4.7  Score=31.70  Aligned_cols=49  Identities=18%  Similarity=0.067  Sum_probs=39.8

Q ss_pred             hHhhcCChhHHHHHHHHhHHcC-CCccHHHHHHHHHHhcCCCchHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESLG-VHTDEVTMVVVLTASSGPGAWILAKEL   52 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g-~~p~~~~~~~ll~~~~~~~~~~~a~~~   52 (153)
                      ..-+.|+.++|+++|++|.+.. ..-+.-+...|++++...+.+.++..+
T Consensus       268 CarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~l  317 (539)
T PF04184_consen  268 CARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQAL  317 (539)
T ss_pred             HHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHH
Confidence            3457799999999999997653 222345777899999999999999999

The molecular function of this protein is uncertain.

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=84.66  E-value=2.8  Score=34.18  Aligned_cols=69  Identities=17%  Similarity=0.224  Sum_probs=46.8

Q ss_pred             HHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 039275           35 VVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLESLG  112 (153)
Q Consensus        35 ~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  112 (153)
                      +++..-...++|++|..+ ++..+.-..+|-.--..++...++++|.         .+|-++|+-.+|.++++++-...
T Consensus       778 siVqlHve~~~W~eAFalAe~hPe~~~dVy~pyaqwLAE~DrFeEAq---------kAfhkAGr~~EA~~vLeQLtnna  847 (1081)
T KOG1538|consen  778 SLVQLHVETQRWDEAFALAEKHPEFKDDVYMPYAQWLAENDRFEEAQ---------KAFHKAGRQREAVQVLEQLTNNA  847 (1081)
T ss_pred             HHhhheeecccchHhHhhhhhCccccccccchHHHHhhhhhhHHHHH---------HHHHHhcchHHHHHHHHHhhhhh
Confidence            445555667788888888 3333322333444556667777777766         67789999999999999987553

>PRK04841 transcriptional regulator MalT; Provisional

Probab=84.54  E-value=11  Score=31.70  Aligned_cols=107  Identities=16%  Similarity=0.110  Sum_probs=68.3

Q ss_pred             hHhhcCChhHHHHHHHHhHHc----CC-CccHHHHHHHHHHhcCCCchHHHHHH---------hhhhh--c-chhhHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESL----GV-HTDEVTMVVVLTASSGPGAWILAKEL---------QIELD--L-SSYSLSSK   66 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~----g~-~p~~~~~~~ll~~~~~~~~~~~a~~~---------~~~~~--~-~~~~~~~l   66 (153)
                      .+...|++++|...+++....    |- .+....+..+-..+...|++++|...         ..+..  + ....+..+
T Consensus       500 ~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l  579 (903)
T PRK04841        500 VHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIR  579 (903)
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHH
Confidence            356789999999999887542    11 11223444555567788999998887         11111  1 12233444


Q ss_pred             HHHHHhcCCccccc-----------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHH
Q 039275           67 TSRYAHSGRIRLAR-----------------DPVSCKAMISGYSQAGRFNEALEPFGKLES  110 (153)
Q Consensus        67 l~~~~~~g~~~~a~-----------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  110 (153)
                      -..+...|++++|.                 ....+..+-..+...|+.++|.+.+.+...
T Consensus       580 a~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~l~~a~~  640 (903)
T PRK04841        580 AQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISLARGDLDNARRYLNRLEN  640 (903)
T ss_pred             HHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            55667778888886                 123344455677889999999999888753

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=84.44  E-value=6  Score=26.12  Aligned_cols=57  Identities=5%  Similarity=-0.034  Sum_probs=45.7

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +..-|-.|=..+-..|++.+|.+.|....... .-|...+-.+-.++...|+.+.|++
T Consensus        68 ~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~-~ddp~~~~~ag~c~L~lG~~~~A~~  124 (157)
T PRK15363         68 SFDYWFRLGECCQAQKHWGEAIYAYGRAAQIK-IDAPQAPWAAAECYLACDNVCYAIK  124 (157)
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCchHHHHHHHHHHHcCCHHHHHH
Confidence            34556678888889999999999999987655 2366667777888899999999888

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=84.40  E-value=13  Score=26.81  Aligned_cols=72  Identities=19%  Similarity=0.142  Sum_probs=35.4

Q ss_pred             cCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH----hhhhhcchhhHHHHHHHHHhcCCccccc
Q 039275            8 AGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL----QIELDLSSYSLSSKTSRYAHSGRIRLAR   80 (153)
Q Consensus         8 ~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~----~~~~~~~~~~~~~ll~~~~~~g~~~~a~   80 (153)
                      .|++++|.+.++.+.+.. +.|.+++..=+-..-..|.--+|.+-    -..+.-|...|.-+-+.|...|++++|.
T Consensus        99 ~~~~~~A~e~y~~lL~dd-pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~F~~D~EAW~eLaeiY~~~~~f~kA~  174 (289)
T KOG3060|consen   99 TGNYKEAIEYYESLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDKFMNDQEAWHELAEIYLSEGDFEKAA  174 (289)
T ss_pred             hhchhhHHHHHHHHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhHhHHHHHH
Confidence            455566666666655554 44455554333333333322222222    3334445555666666666666666655

>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=84.38  E-value=2.1  Score=18.71  Aligned_cols=22  Identities=18%  Similarity=0.077  Sum_probs=17.3

Q ss_pred             HHHHHHHHHhcCChHHHHHHHH
Q 039275           85 CKAMISGYSQAGRFNEALEPFG  106 (153)
Q Consensus        85 ~~~li~~~~~~g~~~~a~~~~~  106 (153)
                      ...+-..+...|++++|.++++
T Consensus         4 ~~~la~~~~~~G~~~eA~~~l~   25 (26)
T PF07721_consen    4 RLALARALLAQGDPDEAERLLR   25 (26)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHh
Confidence            3456678889999999998875

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

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=84.26  E-value=14  Score=26.98  Aligned_cols=116  Identities=11%  Similarity=0.081  Sum_probs=73.8

Q ss_pred             hhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHHh-----hhhhcchhhHHHHH---HHHHhcCCcc
Q 039275            6 SQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQ-----IELDLSSYSLSSKT---SRYAHSGRIR   77 (153)
Q Consensus         6 ~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~-----~~~~~~~~~~~~ll---~~~~~~g~~~   77 (153)
                      ..-|++.-..+++++..+..-+.++.....+...-.+.|+.+.|....     ..-+.|...++.++   .++...|.-+
T Consensus       188 lG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~a~i~lg~nn  267 (366)
T KOG2796|consen  188 LGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNSAFLHLGQNN  267 (366)
T ss_pred             hcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhhhhheecccc
Confidence            345566777778888877766777888888888888889988887772     33344444554443   2333333333


Q ss_pred             ccc--------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHH
Q 039275           78 LAR--------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVV  123 (153)
Q Consensus        78 ~a~--------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l  123 (153)
                      .|.              ++..-|+---.....|+...|.+.++.|+..  -|...+-+++
T Consensus       268 ~a~a~r~~~~i~~~D~~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~--~P~~~l~es~  325 (366)
T KOG2796|consen  268 FAEAHRFFTEILRMDPRNAVANNNKALCLLYLGKLKDALKQLEAMVQQ--DPRHYLHESV  325 (366)
T ss_pred             hHHHHHHHhhccccCCCchhhhchHHHHHHHHHHHHHHHHHHHHHhcc--CCccchhhhH
Confidence            333              4445555555556678999999999999865  3544444433

>PRK10564 maltose regulon periplasmic protein; Provisional

Probab=84.21  E-value=3  Score=30.53  Aligned_cols=45  Identities=18%  Similarity=0.252  Sum_probs=37.4

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHH
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLA  125 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~  125 (153)
                      +..-||.-|....+.||+++|+++++|-++.|+.-=..+|..-++
T Consensus       256 Te~Yy~~aI~~AVk~gDi~KAL~LldEAe~LG~~~Ar~tFik~V~  300 (303)
T PRK10564        256 TESYFNQAIKQAVKKGDVDKALKLLDEAERLGSTSARSTFISSVK  300 (303)
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCchHHHHHHHHhh
Confidence            556689999999999999999999999999998766666655443

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=83.99  E-value=4.9  Score=27.43  Aligned_cols=49  Identities=20%  Similarity=0.132  Sum_probs=33.4

Q ss_pred             hHhhcCChhHHHHHHHHhHHcC--CCccHHHHHHHHHHhcCCCchHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESLG--VHTDEVTMVVVLTASSGPGAWILAKEL   52 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g--~~p~~~~~~~ll~~~~~~~~~~~a~~~   52 (153)
                      .+.+.|++++|++.|+.+...-  -+--....-.+..++.+.|++++|...
T Consensus        14 ~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~   64 (203)
T PF13525_consen   14 EALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAA   64 (203)
T ss_dssp             HHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            4578899999999999997651  111223334566788899999888877

>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B

Probab=83.92  E-value=2.2  Score=23.30  Aligned_cols=25  Identities=32%  Similarity=0.434  Sum_probs=20.8

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHH
Q 039275           86 KAMISGYSQAGRFNEALEPFGKLES  110 (153)
Q Consensus        86 ~~li~~~~~~g~~~~a~~~~~~m~~  110 (153)
                      -.+|.|+...|++++|.++.+++..
T Consensus        27 LqvI~gllqlg~~~~a~eYi~~~~~   51 (62)
T PF14689_consen   27 LQVIYGLLQLGKYEEAKEYIKELSK   51 (62)
T ss_dssp             HHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3678999999999999999988864

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=83.81  E-value=5.5  Score=32.84  Aligned_cols=52  Identities=13%  Similarity=0.065  Sum_probs=22.9

Q ss_pred             ccHHHHHHHHHHhcCCCchHHHHHHhhhhhcchhhHHHHHHHHHhcCCccccc
Q 039275           28 TDEVTMVVVLTASSGPGAWILAKELQIELDLSSYSLSSKTSRYAHSGRIRLAR   80 (153)
Q Consensus        28 p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~ll~~~~~~g~~~~a~   80 (153)
                      ||-..|---+.+++..++|++-+++...-++ ..-|--.+.++.+.|+.++|.
T Consensus       713 pdKr~~wLk~~aLa~~~kweeLekfAkskks-PIGy~PFVe~c~~~~n~~EA~  764 (829)
T KOG2280|consen  713 PDKRLWWLKLTALADIKKWEELEKFAKSKKS-PIGYLPFVEACLKQGNKDEAK  764 (829)
T ss_pred             cchhhHHHHHHHHHhhhhHHHHHHHHhccCC-CCCchhHHHHHHhcccHHHHh
Confidence            4444444444455555555554444111111 233444444444555544444

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=83.77  E-value=3.1  Score=19.07  Aligned_cols=29  Identities=28%  Similarity=0.372  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESL  111 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~  111 (153)
                      .+|..+-..+...|++++|.+.|++..+.
T Consensus         2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~   30 (34)
T PF00515_consen    2 EAYYNLGNAYFQLGDYEEALEYYQRALEL   30 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHH
Confidence            46788889999999999999999988753

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 ....

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=82.98  E-value=1.9  Score=31.93  Aligned_cols=44  Identities=11%  Similarity=0.102  Sum_probs=31.5

Q ss_pred             CChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH
Q 039275            9 GRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL   52 (153)
Q Consensus         9 g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~   52 (153)
                      =++++++.+...=.+.|+-||..+++.+|+.+.+.+++.+|-.+
T Consensus       114 y~pq~~i~~l~npIqYGiF~dqf~~c~l~D~flk~~n~~~aa~v  157 (418)
T KOG4570|consen  114 YDPQKAIYTLVNPIQYGIFPDQFTFCLLMDSFLKKENYKDAASV  157 (418)
T ss_pred             cChHHHHHHHhCcchhccccchhhHHHHHHHHHhcccHHHHHHH
Confidence            35666666666666777777777777777777777777776666

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=82.76  E-value=6.5  Score=27.11  Aligned_cols=67  Identities=19%  Similarity=0.060  Sum_probs=39.3

Q ss_pred             hHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH--------hhhhhcchhhHHHHHHHHHhcCCcccc
Q 039275           12 NEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL--------QIELDLSSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus        12 ~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~--------~~~~~~~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      ++|..-|-++...+..-++...-.+-+-|. ..+.+.+..+        ..+-.+|...+.+|...|-+.++++.|
T Consensus       123 ~~A~~~fL~~E~~~~l~t~elq~aLAtyY~-krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~e~A  197 (203)
T PF11207_consen  123 QEALRRFLQLEGTPELETAELQYALATYYT-KRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNYEQA  197 (203)
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcchhhh
Confidence            567778888887776655555555444444 5555556555        222245555566666666666555543

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

Probab=82.46  E-value=23  Score=28.13  Aligned_cols=131  Identities=8%  Similarity=-0.013  Sum_probs=71.3

Q ss_pred             hcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhc----CCCchHHHHHH---hhhhhcchhhHHHHHHHHHhcCCcccc
Q 039275            7 QAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASS----GPGAWILAKEL---QIELDLSSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         7 ~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~----~~~~~~~a~~~---~~~~~~~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      ...+++.+.++|..... =++....||..+=-.++    +..++..|.++   .-|..|-..+|-..|..=.+.++++..
T Consensus       378 e~ed~ertr~vyq~~l~-lIPHkkFtFaKiWlmyA~feIRq~~l~~ARkiLG~AIG~cPK~KlFk~YIelElqL~efDRc  456 (677)
T KOG1915|consen  378 EAEDVERTRQVYQACLD-LIPHKKFTFAKIWLMYAQFEIRQLNLTGARKILGNAIGKCPKDKLFKGYIELELQLREFDRC  456 (677)
T ss_pred             HhhhHHHHHHHHHHHHh-hcCcccchHHHHHHHHHHHHHHHcccHHHHHHHHHHhccCCchhHHHHHHHHHHHHhhHHHH
Confidence            34567777788877766 35666667765444333    23456666666   556666666666666666666666666


Q ss_pred             c------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcC-CCCChhhHHHHHHHhcCCCccccchh
Q 039275           80 R------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLG-VHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        80 ~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .            +..+|...-..--..|+.|.|..+|.--.+.. +.--...|-+-|+.=...|.++.|..
T Consensus       457 RkLYEkfle~~Pe~c~~W~kyaElE~~LgdtdRaRaifelAi~qp~ldmpellwkaYIdFEi~~~E~ekaR~  528 (677)
T KOG1915|consen  457 RKLYEKFLEFSPENCYAWSKYAELETSLGDTDRARAIFELAISQPALDMPELLWKAYIDFEIEEGEFEKARA  528 (677)
T ss_pred             HHHHHHHHhcChHhhHHHHHHHHHHHHhhhHHHHHHHHHHHhcCcccccHHHHHHHhhhhhhhcchHHHHHH
Confidence            6            44444444444445555555555555544321 11223333444444444444444444

>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=82.15  E-value=7.2  Score=26.18  Aligned_cols=56  Identities=13%  Similarity=0.188  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC--ChhhHHHHHHHhcCCCccccchh
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESLGVHT--DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p--~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ..+..+-..|++.|+.++|.+.|.++.+.-..|  -...+-.+|..+.-.+++..+..
T Consensus        37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~   94 (177)
T PF10602_consen   37 MALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEK   94 (177)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHH
Confidence            445555555566666666666666555443333  22334444555555555554444

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.

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=82.05  E-value=1.7  Score=20.49  Aligned_cols=22  Identities=18%  Similarity=0.418  Sum_probs=12.8

Q ss_pred             hHHHHHHHHHHHHhcCChHHHH
Q 039275           81 DPVSCKAMISGYSQAGRFNEAL  102 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~  102 (153)
                      +...|+.+-..|...|++++|.
T Consensus        12 n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen   12 NAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             CHHHHHHHHHHHHHCcCHHhhc
Confidence            3455566666666666666554

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=81.87  E-value=4.4  Score=20.53  Aligned_cols=25  Identities=20%  Similarity=0.331  Sum_probs=21.5

Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHcC
Q 039275           88 MISGYSQAGRFNEALEPFGKLESLG  112 (153)
Q Consensus        88 li~~~~~~g~~~~a~~~~~~m~~~g  112 (153)
                      |-.+|...|+.+.|.+++++....|
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~~~   29 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIEEG   29 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHcC
Confidence            5578999999999999999998655

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.

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=81.53  E-value=21  Score=27.05  Aligned_cols=136  Identities=18%  Similarity=0.009  Sum_probs=73.6

Q ss_pred             cCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHHhh--------hhhcchhhHHHHHHHHHhcCCcccc
Q 039275            8 AGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQI--------ELDLSSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         8 ~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~--------~~~~~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .|++.+|-..++++.+. ++.|.-.++..=++++-.|+.+.......        +.+...++-..+.-++..+|-+++|
T Consensus       116 ~g~~h~a~~~wdklL~d-~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~wn~dlp~~sYv~GmyaFgL~E~g~y~dA  194 (491)
T KOG2610|consen  116 RGKHHEAAIEWDKLLDD-YPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPKWNADLPCYSYVHGMYAFGLEECGIYDDA  194 (491)
T ss_pred             cccccHHHHHHHHHHHh-CchhhhhhhhhhhHHHhccchhhhhhHHHHhccccCCCCcHHHHHHHHHHhhHHHhccchhH
Confidence            56677777777777664 66666666666667776676555444411        2222233334444555677888877


Q ss_pred             c------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc---CCCCChhhHHHHHHHhcCCCccccchh--HHHH
Q 039275           80 R------------DPVSCKAMISGYSQAGRFNEALEPFGKLESL---GVHTDEVTMVVVLAASSGPGALDFGKS--NIFL  142 (153)
Q Consensus        80 ~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~---g~~p~~~t~~~li~~~~~~g~~~~a~~--~~~~  142 (153)
                      +            |.=.-.++-..+-..|++.++.+++++-...   +.-.-.+-|.-.--.+...+.++.|.+  |.++
T Consensus       195 Ek~A~ralqiN~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~s~mlasHNyWH~Al~~iE~aeye~aleIyD~ei  274 (491)
T KOG2610|consen  195 EKQADRALQINRFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWMLASHNYWHTALFHIEGAEYEKALEIYDREI  274 (491)
T ss_pred             HHHHHhhccCCCcchHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHHHhhhhHHHHHhhhcccchhHHHHHHHHHH
Confidence            7            3333345555566677777777666553321   111111123333333444466666666  4444


Q ss_pred             HH
Q 039275          143 TT  144 (153)
Q Consensus       143 ~~  144 (153)
                      |.
T Consensus       275 ~k  276 (491)
T KOG2610|consen  275 WK  276 (491)
T ss_pred             HH
Confidence            43

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=81.43  E-value=3.1  Score=34.64  Aligned_cols=132  Identities=14%  Similarity=0.073  Sum_probs=70.5

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHHhhhhhcchh--hHHHHHHHHHhcCCccccc--
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIELDLSSY--SLSSKTSRYAHSGRIRLAR--   80 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~--~~~~ll~~~~~~g~~~~a~--   80 (153)
                      |.+..+..+....++.+.+.|+. +...-..||++|.+.++.+.-.++-.+.+....  -.-..++-+.+.+-.++|.  
T Consensus       407 fLdaq~IknLt~YLe~L~~~gla-~~dhttlLLncYiKlkd~~kL~efI~~~~~g~~~fd~e~al~Ilr~snyl~~a~~L  485 (933)
T KOG2114|consen  407 FLDAQRIKNLTSYLEALHKKGLA-NSDHTTLLLNCYIKLKDVEKLTEFISKCDKGEWFFDVETALEILRKSNYLDEAELL  485 (933)
T ss_pred             hcCHHHHHHHHHHHHHHHHcccc-cchhHHHHHHHHHHhcchHHHHHHHhcCCCcceeeeHHHHHHHHHHhChHHHHHHH
Confidence            33334444444555555566653 445556778888888888877777222221111  1234455555555555555  


Q ss_pred             ---hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCC-------------CChhhHHHHHHHhcCCCccccch
Q 039275           81 ---DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVH-------------TDEVTMVVVLAASSGPGALDFGK  137 (153)
Q Consensus        81 ---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~-------------p~~~t~~~li~~~~~~g~~~~a~  137 (153)
                         -..+=+.+---+-..+++++|.++++.|.-...-             .-..|...++..|...++.....
T Consensus       486 A~k~~~he~vl~ille~~~ny~eAl~yi~slp~~e~l~~l~kyGk~Ll~h~P~~t~~ili~~~t~~~~~~~~~  558 (933)
T KOG2114|consen  486 ATKFKKHEWVLDILLEDLHNYEEALRYISSLPISELLRTLNKYGKILLEHDPEETMKILIELITELNSQGKGK  558 (933)
T ss_pred             HHHhccCHHHHHHHHHHhcCHHHHHHHHhcCCHHHHHHHHHHHHHHHHhhChHHHHHHHHHHHhhcCCCCCCc
Confidence               1112234444456678888888888776422111             12334566666666665444433

>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=81.11  E-value=14  Score=24.80  Aligned_cols=89  Identities=15%  Similarity=0.155  Sum_probs=57.2

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCcc--HHHHHHHHHHhcCCCchHHHHHH----hhhhh--cchhhHHHHHHHHHhcC
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTD--EVTMVVVLTASSGPGAWILAKEL----QIELD--LSSYSLSSKTSRYAHSG   74 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~--~~~~~~ll~~~~~~~~~~~a~~~----~~~~~--~~~~~~~~ll~~~~~~g   74 (153)
                      +.|++.|+.++|++.|.+++.....|.  ...+-.+|....-.+++..+...    +.-+.  .|...-|          
T Consensus        44 ~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~n----------  113 (177)
T PF10602_consen   44 DHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWERRN----------  113 (177)
T ss_pred             HHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHHHH----------
Confidence            568999999999999999988765554  35556777777777888777766    11111  1111111          


Q ss_pred             CccccchHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 039275           75 RIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLE  109 (153)
Q Consensus        75 ~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  109 (153)
                            ....|..|..  ...+++.+|-+.|-+..
T Consensus       114 ------rlk~~~gL~~--l~~r~f~~AA~~fl~~~  140 (177)
T PF10602_consen  114 ------RLKVYEGLAN--LAQRDFKEAAELFLDSL  140 (177)
T ss_pred             ------HHHHHHHHHH--HHhchHHHHHHHHHccC
Confidence                  1244544433  34578888888887765

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.

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=80.98  E-value=2.1  Score=19.31  Aligned_cols=24  Identities=29%  Similarity=0.512  Sum_probs=19.8

Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHc
Q 039275           88 MISGYSQAGRFNEALEPFGKLESL  111 (153)
Q Consensus        88 li~~~~~~g~~~~a~~~~~~m~~~  111 (153)
                      +-..+.+.|++++|.+.|+++.+.
T Consensus         6 ~a~~~~~~g~~~~A~~~~~~~~~~   29 (33)
T PF13174_consen    6 LARCYYKLGDYDEAIEYFQRLIKR   29 (33)
T ss_dssp             HHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHH
Confidence            445677889999999999998865

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

Probab=80.87  E-value=20  Score=29.25  Aligned_cols=87  Identities=18%  Similarity=0.150  Sum_probs=57.2

Q ss_pred             CccH--HHHHHHHHHhcCCCchHHHHHH---hhhhhcchh-hHHHHHHHHHhcCCccccc------------hHHHHHHH
Q 039275           27 HTDE--VTMVVVLTASSGPGAWILAKEL---QIELDLSSY-SLSSKTSRYAHSGRIRLAR------------DPVSCKAM   88 (153)
Q Consensus        27 ~p~~--~~~~~ll~~~~~~~~~~~a~~~---~~~~~~~~~-~~~~ll~~~~~~g~~~~a~------------~~~~~~~l   88 (153)
                      +|.+  +|+--+...+-+.|+++.|..+   .-+..|+.+ .|-.-.+.+...|++++|.            |...-.--
T Consensus       366 ~PttllWt~y~laqh~D~~g~~~~A~~yId~AIdHTPTliEly~~KaRI~kH~G~l~eAa~~l~ea~elD~aDR~INsKc  445 (700)
T KOG1156|consen  366 PPTTLLWTLYFLAQHYDKLGDYEVALEYIDLAIDHTPTLIELYLVKARIFKHAGLLDEAAAWLDEAQELDTADRAINSKC  445 (700)
T ss_pred             CchHHHHHHHHHHHHHHHcccHHHHHHHHHHHhccCchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhccchhHHHHHHH
Confidence            4444  3444566777888999999988   333444443 3444457888899988887            33333233


Q ss_pred             HHHHHhcCChHHHHHHHHHHHHcCC
Q 039275           89 ISGYSQAGRFNEALEPFGKLESLGV  113 (153)
Q Consensus        89 i~~~~~~g~~~~a~~~~~~m~~~g~  113 (153)
                      ..=..+++++++|.++....-+.|.
T Consensus       446 AKYmLrAn~i~eA~~~~skFTr~~~  470 (700)
T KOG1156|consen  446 AKYMLRANEIEEAEEVLSKFTREGF  470 (700)
T ss_pred             HHHHHHccccHHHHHHHHHhhhccc
Confidence            3444677899999988888877775

>KOG4077 consensus Cytochrome c oxidase, subunit Va/COX6 [Energy production and conversion]

Probab=80.07  E-value=8.9  Score=24.54  Aligned_cols=34  Identities=12%  Similarity=0.097  Sum_probs=23.5

Q ss_pred             HHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH
Q 039275           19 GKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL   52 (153)
Q Consensus        19 ~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~   52 (153)
                      +.+....+.|++.+....|.+|-+.+++..|..+
T Consensus        73 N~l~~yDlVP~pkvIEaaLRA~RRvNDfa~aVRi  106 (149)
T KOG4077|consen   73 NNLFDYDLVPSPKVIEAALRACRRVNDFATAVRI  106 (149)
T ss_pred             HhhhccccCCChHHHHHHHHHHHHhccHHHHHHH
Confidence            3344456777777777777777777777777776

---

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

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	153
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.95
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.85
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.77
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.58
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.56
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.18
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.17
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.07
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.07
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.06
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.01
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	98.99
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	98.93
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	98.89
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	98.86
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	98.83
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	98.83
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	98.83
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	98.82
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	98.82
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	98.8
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	98.78
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	98.77
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	98.75
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	98.73
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	98.72
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	98.72
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	98.71
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.7
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	98.68
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	98.66
2gw1_A	514	Mitochondrial precursor proteins import receptor;	98.63
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	98.63
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	98.6
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	98.58
2gw1_A	514	Mitochondrial precursor proteins import receptor;	98.57
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	98.56
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	98.56
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	98.5
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.48
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	98.48
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	98.47
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.46
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	98.44
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	98.44
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.4
3u4t_A	272	TPR repeat-containing protein; structural genomics	98.4
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	98.4
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.36
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	98.32
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.3
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.3
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.29
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	98.28
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.27
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	98.24
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	98.2
3u4t_A	272	TPR repeat-containing protein; structural genomics	98.18
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.17
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	98.15
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	98.14
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.11
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	98.07
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	98.04
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.02
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.01
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	97.97
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	97.96
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	97.96
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	97.94
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	97.93
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	97.92
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	97.91
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	97.9
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	97.9
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	97.9
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	97.88
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	97.88
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	97.88
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	97.87
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	97.86
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	97.86
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	97.85
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	97.83
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	97.83
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	97.82
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	97.82
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	97.82
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	97.8
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	97.78
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	97.73
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	97.67
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	97.67
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	97.64
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.64
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	97.62
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	97.61
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	97.6
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	97.6
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	97.59
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	97.58
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.58
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	97.58
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	97.57
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.53
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	97.52
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	97.52
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	97.51
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	97.47
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	97.47
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	97.47
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.46
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	97.46
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	97.46
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	97.45
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	97.39
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	97.39
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	97.38
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	97.38
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.36
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	97.34
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	97.33
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	97.33
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	97.32
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	97.31
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	97.31
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	97.29
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.26
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	97.25
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	97.23
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	97.22
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	97.22
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	97.22
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	97.16
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	97.15
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	97.14
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	97.14
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	97.09
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.03
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	97.02
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	97.01
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	96.98
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	96.94
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	96.92
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	96.92
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	96.89
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	96.86
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	96.86
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	96.83
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	96.82
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	96.82
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	96.82
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	96.81
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	96.8
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	96.74
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	96.7
4g1t_A	472	Interferon-induced protein with tetratricopeptide	96.66
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	96.65
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	96.61
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	96.58
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.58
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	96.54
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	96.47
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	96.45
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.45
2l6j_A	111	TPR repeat-containing protein associated with HSP;	96.35
2l6j_A	111	TPR repeat-containing protein associated with HSP;	96.29
3k9i_A	117	BH0479 protein; putative protein binding protein,	96.27
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	96.21
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	96.2
4g1t_A	472	Interferon-induced protein with tetratricopeptide	96.11
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	96.09
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	96.07
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	96.02
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	96.01
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	95.8
2kat_A	115	Uncharacterized protein; NESG, structure, structur	95.72
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	95.72
1klx_A	138	Cysteine rich protein B; structural genomics, heli	95.71
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	95.66
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	95.61
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	95.55
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	95.35
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	95.04
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	94.81
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	94.74
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	94.34
2kat_A	115	Uncharacterized protein; NESG, structure, structur	94.21
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	94.19
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	94.17
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	94.06
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	93.77
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	93.76
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	93.39
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	93.13
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	93.04
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	92.82
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	92.6
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	92.17
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	92.14
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	91.97
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	91.86
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	91.62
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	90.85
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	90.64
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	90.07
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	89.92
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	89.62
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	89.38
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	87.59
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	86.16
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	85.69
1pc2_A	152	Mitochondria fission protein; unknown function; NM	85.04
3lpz_A	336	GET4 (YOR164C homolog); protein targeting, tail-an	84.56
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	83.42
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	83.23
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	82.54
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	81.71
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	81.27
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	80.41

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=100.00  E-value=6e-34  Score=216.57  Aligned_cols=152  Identities=16%  Similarity=0.099  Sum_probs=144.0

Q ss_pred             ChhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCc---------hHHHHHH-----hhhhhcchhhHHHH
Q 039275            1 MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGA---------WILAKEL-----QIELDLSSYSLSSK   66 (153)
Q Consensus         1 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~---------~~~a~~~-----~~~~~~~~~~~~~l   66 (153)
                      +|++|++.|++++|.++|++|++.|++||..|||++|.+|++.+.         ++.|.++     ..|+.||..+||+|
T Consensus        32 ~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~~Pd~~tyn~l  111 (501)
T 4g26_A           32 KLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEATFTNG  111 (501)
T ss_dssp             HHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTCCCCHHHHHHH
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCCCCCHHHHHHH
Confidence            378999999999999999999999999999999999999987664         6777777     77899999999999


Q ss_pred             HHHHHhcCCccccc-------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCcc
Q 039275           67 TSRYAHSGRIRLAR-------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGAL  133 (153)
Q Consensus        67 l~~~~~~g~~~~a~-------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~  133 (153)
                      |.+|++.|++++|.             |..+||+||.+|++.|++++|.++|++|.+.|+.||..||++||++|++.|+.
T Consensus       112 I~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~~~g~~  191 (501)
T 4g26_A          112 ARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNA  191 (501)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhhCCCH
Confidence            99999999999998             89999999999999999999999999999999999999999999999999999


Q ss_pred             ccchh------------HHHHHHHHHHHhhc
Q 039275          134 DFGKS------------NIFLTTAIIEMYAK  152 (153)
Q Consensus       134 ~~a~~------------~~~~~~~li~~y~k  152 (153)
                      ++|.+            +..+|++|++.|++
T Consensus       192 d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s  222 (501)
T 4g26_A          192 DKVYKTLQRLRDLVRQVSKSTFDMIEEWFKS  222 (501)
T ss_dssp             HHHHHHHHHHHHHTSSBCHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHhCCCcCHHHHHHHHHHHhc
Confidence            99998            88999999998875

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=99.95  E-value=1.3e-27  Score=181.80  Aligned_cols=138  Identities=12%  Similarity=0.067  Sum_probs=127.4

Q ss_pred             ChhhHhhcCC---------hhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-----hhhhhcchhhHHHH
Q 039275            1 MISGYSQAGR---------FNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-----QIELDLSSYSLSSK   66 (153)
Q Consensus         1 li~~~~~~g~---------~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-----~~~~~~~~~~~~~l   66 (153)
                      ||++|++.+.         +++|.++|++|.+.|+.||..||+++|.+|++.|++++|.++     ..|+.||..+||+|
T Consensus        67 Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~l  146 (501)
T 4g26_A           67 LLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPA  146 (501)
T ss_dssp             HHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHH
T ss_pred             HHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHH
Confidence            4667776654         688999999999999999999999999999999999999999     77899999999999


Q ss_pred             HHHHHhcCCccccc-------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCcc
Q 039275           67 TSRYAHSGRIRLAR-------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGAL  133 (153)
Q Consensus        67 l~~~~~~g~~~~a~-------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~  133 (153)
                      |.+|++.|++++|.             |..||++||.+|++.|++++|.++|++|++.|+.|+..||+.++.+|+..+..
T Consensus       147 I~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s~~a~  226 (501)
T 4g26_A          147 LFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSEVAT  226 (501)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHSHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhcCcch
Confidence            99999999999998             99999999999999999999999999999999999999999999999986655


Q ss_pred             ccchh
Q 039275          134 DFGKS  138 (153)
Q Consensus       134 ~~a~~  138 (153)
                      +.+..
T Consensus       227 ~~g~~  231 (501)
T 4g26_A          227 KTGVK  231 (501)
T ss_dssp             TCCBS
T ss_pred             hhhhh
Confidence            55444

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.85  E-value=2e-22  Score=160.69  Aligned_cols=116  Identities=10%  Similarity=0.009  Sum_probs=97.8

Q ss_pred             ChhhHhhcCChhHHHHHHHHhH---HcCCCccHHHHHHHHHHhcCCCchHHHHHH-----hhhhhcchhhHHHHHHHHHh
Q 039275            1 MISGYSQAGRFNEALEPFGKLE---SLGVHTDEVTMVVVLTASSGPGAWILAKEL-----QIELDLSSYSLSSKTSRYAH   72 (153)
Q Consensus         1 li~~~~~~g~~~~a~~~~~~m~---~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-----~~~~~~~~~~~~~ll~~~~~   72 (153)
                      ||++||+.|++++|.++|++|.   +.|+.||++|||+||++|++.|++++|.++     ..|+.|              
T Consensus       133 LIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~P--------------  198 (1134)
T 3spa_A          133 FFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTP--------------  198 (1134)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCC--------------
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCC--------------
Confidence            4788999999999999998775   458899999999999999999999999998     677788              


Q ss_pred             cCCccccchHHHHHHHHHHHHhcCCh-HHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           73 SGRIRLARDPVSCKAMISGYSQAGRF-NEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        73 ~g~~~~a~~~~~~~~li~~~~~~g~~-~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                              |..|||+||.++|+.|+. ++|.++|++|.+.|+.||..||+++++++.+.+-++..++
T Consensus       199 --------DvvTYntLI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~~vL~~Vrk  257 (1134)
T 3spa_A          199 --------DLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHK  257 (1134)
T ss_dssp             --------CHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHHHHHHHHGG
T ss_pred             --------cHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHHHHHHHHHH
Confidence                    558888899999999985 7899999999999999999999988877766555544443

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.77  E-value=2e-19  Score=143.67  Aligned_cols=102  Identities=13%  Similarity=0.144  Sum_probs=87.6

Q ss_pred             cHHHHHHHHHHhcCCCchHHHHHHh--------hhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHH
Q 039275           29 DEVTMVVVLTASSGPGAWILAKELQ--------IELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNE  100 (153)
Q Consensus        29 ~~~~~~~ll~~~~~~~~~~~a~~~~--------~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~  100 (153)
                      -..|||++|++|++.|++++|.++.        .|+.|                      |..|||+||.|||+.|++++
T Consensus       126 ~~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~P----------------------dvvTYNtLI~Glck~G~~~e  183 (1134)
T 3spa_A          126 QQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLL----------------------TLDMYNAVMLGWARQGAFKE  183 (1134)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTC----------------------CHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCC----------------------CHhHHHHHHHHHHhCCCHHH
Confidence            4578999999999999999998882        35566                      56889999999999999999


Q ss_pred             HHHHHHHHHHcCCCCChhhHHHHHHHhcCCCcc-ccchh------------HHHHHHHHHHHhhc
Q 039275          101 ALEPFGKLESLGVHTDEVTMVVVLAASSGPGAL-DFGKS------------NIFLTTAIIEMYAK  152 (153)
Q Consensus       101 a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~-~~a~~------------~~~~~~~li~~y~k  152 (153)
                      |.++|++|++.|++||..||+++|+++|+.|+. +.|.+            |..+|++++..+.|
T Consensus       184 A~~Lf~eM~~~G~~PDvvTYntLI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR  248 (1134)
T 3spa_A          184 LVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDR  248 (1134)
T ss_dssp             HHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHH
T ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhH
Confidence            999999999999999999999999999999985 56655            88999977766543

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.58  E-value=2.1e-14  Score=109.95  Aligned_cols=149  Identities=15%  Similarity=0.036  Sum_probs=111.7

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-h---hhhhcchhhHHHHHHHHHhcCCccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-Q---IELDLSSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~---~~~~~~~~~~~~ll~~~~~~g~~~~   78 (153)
                      ..|.+.|++++|.+.|+++.+. -+.+..+|+.+...+.+.|++++|.++ +   ...+.+..+|+.+..+|.+.|++++
T Consensus       381 ~~~~~~g~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  459 (597)
T 2xpi_A          381 IYYLCVNKISEARRYFSKSSTM-DPQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLFQGTHLPYLFLGMQHMQLGNILL  459 (597)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTTTCSHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHHhccHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCCHHH
Confidence            4667777777777777777653 223566777777777777777777777 1   1123366677778888888888777


Q ss_pred             cc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc----CCCCC--hhhHHHHHHHhcCCCccccchh--
Q 039275           79 AR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESL----GVHTD--EVTMVVVLAASSGPGALDFGKS--  138 (153)
Q Consensus        79 a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~--~~t~~~li~~~~~~g~~~~a~~--  138 (153)
                      |.            +..+|+.+...+.+.|++++|.++|+++.+.    +..|+  ..+|..+..+|.+.|++++|.+  
T Consensus       460 A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~  539 (597)
T 2xpi_A          460 ANEYLQSSYALFQYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDAL  539 (597)
T ss_dssp             HHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHH
Confidence            77            6778888888888888888888888888765    67787  6788888888888888888887  


Q ss_pred             ---------HHHHHHHHHHHhhc
Q 039275          139 ---------NIFLTTAIIEMYAK  152 (153)
Q Consensus       139 ---------~~~~~~~li~~y~k  152 (153)
                               +..+|..+...|.+
T Consensus       540 ~~~~~~~p~~~~~~~~l~~~~~~  562 (597)
T 2xpi_A          540 NQGLLLSTNDANVHTAIALVYLH  562 (597)
T ss_dssp             HHHHHHSSCCHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCChHHHHHHHHHHHH
Confidence                     56777777777654

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.56  E-value=1.6e-14  Score=110.57  Aligned_cols=148  Identities=10%  Similarity=0.039  Sum_probs=99.0

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH----hhhhhcchhhHHHHHHHHHhcCCccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL----QIELDLSSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~----~~~~~~~~~~~~~ll~~~~~~g~~~~   78 (153)
                      ..|.+.|++++|.++|+++.+.+ +.+..+++.++.++.+.|++++|.++    ....+.+..+++.+..+|.+.|++++
T Consensus       313 ~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  391 (597)
T 2xpi_A          313 DTLFVRSRFIDVLAITTKILEID-PYNLDVYPLHLASLHESGEKNKLYLISNDLVDRHPEKAVTWLAVGIYYLCVNKISE  391 (597)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHhccHHH
Confidence            34555555555555555555433 22444555555555555555555555    11123355677777788888888877


Q ss_pred             cc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh--------
Q 039275           79 AR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS--------  138 (153)
Q Consensus        79 a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~--------  138 (153)
                      |.            +..+|+.++.+|.+.|++++|.++|+++.+.+ ..+..+|..+..+|.+.|++++|.+        
T Consensus       392 A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  470 (597)
T 2xpi_A          392 ARRYFSKSSTMDPQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLF-QGTHLPYLFLGMQHMQLGNILLANEYLQSSYAL  470 (597)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            77            56688888888888888888888888887553 3467778888888888888888877        


Q ss_pred             ---HHHHHHHHHHHhhc
Q 039275          139 ---NIFLTTAIIEMYAK  152 (153)
Q Consensus       139 ---~~~~~~~li~~y~k  152 (153)
                         +..+|+.+...|.+
T Consensus       471 ~~~~~~~~~~l~~~~~~  487 (597)
T 2xpi_A          471 FQYDPLLLNELGVVAFN  487 (597)
T ss_dssp             CCCCHHHHHHHHHHHHH
T ss_pred             CCCChHHHHHHHHHHHH
Confidence               56777777777764

>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=99.18  E-value=6.8e-12  Score=93.57  Aligned_cols=126  Identities=10%  Similarity=0.064  Sum_probs=47.5

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHHhhhhhcchhhHHHHHHHHHhcCCccccc--
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIELDLSSYSLSSKTSRYAHSGRIRLAR--   80 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~ll~~~~~~g~~~~a~--   80 (153)
                      +++.+.|++++|++.++..++.  .+++.+.+.++.+|.+.|+++++.++..+  |+..+|+.+...|...|.+++|.  
T Consensus        69 ~~ae~~g~~EeAi~yl~~ark~--~~~~~i~~~Li~~Y~Klg~l~e~e~f~~~--pn~~a~~~IGd~~~~~g~yeeA~~~  144 (449)
T 1b89_A           69 QAANTSGNWEELVKYLQMARKK--ARESYVETELIFALAKTNRLAELEEFING--PNNAHIQQVGDRCYDEKMYDAAKLL  144 (449)
T ss_dssp             ------------------------------------------CHHHHTTTTTC--C----------------CTTTHHHH
T ss_pred             HHHHhCCCHHHHHHHHHHHHHh--CccchhHHHHHHHHHHhCCHHHHHHHHcC--CcHHHHHHHHHHHHHcCCHHHHHHH
Confidence            4455566666666644433332  34456666666666666666666666332  45556666666666666666666  


Q ss_pred             --hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 --DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 --~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                        ....|..|..++.+.|++++|.+.+.+.      -+..+|..++.+|...|+++.|..
T Consensus       145 Y~~a~n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~  198 (449)
T 1b89_A          145 YNNVSNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQM  198 (449)
T ss_dssp             HHHTTCHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHhhhHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHH
Confidence              5566777777777777777777777766      256677777777777777777766

>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=99.17  E-value=2.6e-11  Score=90.47  Aligned_cols=137  Identities=12%  Similarity=0.105  Sum_probs=47.8

Q ss_pred             ChhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH---hhhhhcchhhHHHHHHHHHhcCCcc
Q 039275            1 MISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL---QIELDLSSYSLSSKTSRYAHSGRIR   77 (153)
Q Consensus         1 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~~~~~~~~ll~~~~~~g~~~   77 (153)
                      |..++.+.|++++|++.|.+      .+|..+|..++.++...|++++|.+.   -..-.++..+.+.|+.+|.+.|+++
T Consensus        38 La~A~l~~g~~~eAIdsfik------a~D~~~y~~V~~~ae~~g~~EeAi~yl~~ark~~~~~~i~~~Li~~Y~Klg~l~  111 (449)
T 1b89_A           38 LAKAQLQKGMVKEAIDSYIK------ADDPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYVETELIFALAKTNRLA  111 (449)
T ss_dssp             -----------------------------------------------------------------------------CHH
T ss_pred             HHHHHHHcCCHHHHHHHHHc------CCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCccchhHHHHHHHHHHhCCHH
Confidence            34678899999999999965      37888999999999999999999998   1112455788999999999999999


Q ss_pred             ccc------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh------HHHHHHH
Q 039275           78 LAR------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS------NIFLTTA  145 (153)
Q Consensus        78 ~a~------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~------~~~~~~~  145 (153)
                      ++.      +..+|+.+...|...|++++|..+|..+         ..|..+.+++.++|+++.|.+      ++.+|..
T Consensus       112 e~e~f~~~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a---------~n~~~LA~~L~~Lg~yq~AVea~~KA~~~~~Wk~  182 (449)
T 1b89_A          112 ELEEFINGPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKANSTRTWKE  182 (449)
T ss_dssp             HHTTTTTCC----------------CTTTHHHHHHHT---------TCHHHHHHHHHTTTCHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHcCCcHHHHHHHHHHHHHcCCHHHHHHHHHHh---------hhHHHHHHHHHHhccHHHHHHHHHHcCCchhHHH
Confidence            988      5679999999999999999999999977         479999999999999999999      8999999


Q ss_pred             HHHHhhc
Q 039275          146 IIEMYAK  152 (153)
Q Consensus       146 li~~y~k  152 (153)
                      ++.+|..
T Consensus       183 v~~aCv~  189 (449)
T 1b89_A          183 VCFACVD  189 (449)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9888864

>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=99.07  E-value=4.4e-09  Score=77.72  Aligned_cols=148  Identities=14%  Similarity=0.031  Sum_probs=118.2

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hh--hh-hcchhhHHHHHHHHHhcCCccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QI--EL-DLSSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~--~~-~~~~~~~~~ll~~~~~~g~~~~   78 (153)
                      ..|.+.|++++|++.|+++.+. .+.+...+..+..++.+.|++++|.+. ..  .. +.+...+..+...|.+.|++++
T Consensus        34 ~~~~~~g~~~~A~~~~~~~l~~-~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~  112 (450)
T 2y4t_A           34 KKLLAAGQLADALSQFHAAVDG-DPDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLKMDFTAARLQRGHLLLKQGKLDE  112 (450)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHh-CCccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHH
Confidence            4678899999999999999765 345788899999999999999999998 21  12 3345678889999999999999


Q ss_pred             cc------------hH---HHHHHHHHH------------HHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCC
Q 039275           79 AR------------DP---VSCKAMISG------------YSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPG  131 (153)
Q Consensus        79 a~------------~~---~~~~~li~~------------~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g  131 (153)
                      |.            +.   ..|..+...            +...|++++|.+.|+++.+.. ..+...+..+..++.+.|
T Consensus       113 A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g  191 (450)
T 2y4t_A          113 AEDDFKKVLKSNPSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVC-VWDAELRELRAECFIKEG  191 (450)
T ss_dssp             HHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHCC
Confidence            98            33   666666444            899999999999999998653 346778888999999999


Q ss_pred             ccccchh-----------HHHHHHHHHHHhhc
Q 039275          132 ALDFGKS-----------NIFLTTAIIEMYAK  152 (153)
Q Consensus       132 ~~~~a~~-----------~~~~~~~li~~y~k  152 (153)
                      ++++|.+           +...|..+...|.+
T Consensus       192 ~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~  223 (450)
T 2y4t_A          192 EPRKAISDLKAASKLKNDNTEAFYKISTLYYQ  223 (450)
T ss_dssp             CGGGGHHHHHHHHHHHCSCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence            9999988           56677777766653

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.07  E-value=2.5e-09  Score=75.91  Aligned_cols=146  Identities=12%  Similarity=0.037  Sum_probs=108.1

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHH-HHHHHHhcCCCchHHHHHHhhhhhcchhhHHHHHHHHHhcCCccccc-
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTM-VVVLTASSGPGAWILAKELQIELDLSSYSLSSKTSRYAHSGRIRLAR-   80 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~-~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~ll~~~~~~g~~~~a~-   80 (153)
                      ..+.+.|+.++|++.++++...+..|+...+ ..+-..+.+.|++++|.+.-.. +.+...+..+...|.+.|++++|. 
T Consensus        73 ~~~~~~~~~~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~-~~~~~~~~~l~~~~~~~g~~~~A~~  151 (291)
T 3mkr_A           73 EYLASHSRRDAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ-GDSLECMAMTVQILLKLDRLDLARK  151 (291)
T ss_dssp             HHHHCSTTHHHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT-CCSHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHcCCCcHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            4567788899999999999887766654444 4444788899999999998333 566778888889999999999988 


Q ss_pred             --------h-HHHHH----HHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh---------
Q 039275           81 --------D-PVSCK----AMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS---------  138 (153)
Q Consensus        81 --------~-~~~~~----~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~---------  138 (153)
                              + ..+..    ..+..+...|++++|..+|+++.+. ...+...++.+-.++.+.|++++|..         
T Consensus       152 ~l~~~~~~~p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~-~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~  230 (291)
T 3mkr_A          152 ELKKMQDQDEDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADK-CSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKD  230 (291)
T ss_dssp             HHHHHHHHCTTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH-SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHhhCcCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHh-CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence                    1 11112    2233344558999999999999876 34577788888899999999999988         


Q ss_pred             --HHHHHHHHHHHh
Q 039275          139 --NIFLTTAIIEMY  150 (153)
Q Consensus       139 --~~~~~~~li~~y  150 (153)
                        ++.++..++..+
T Consensus       231 p~~~~~l~~l~~~~  244 (291)
T 3mkr_A          231 SGHPETLINLVVLS  244 (291)
T ss_dssp             TTCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH
Confidence              555666655444

>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=99.06  E-value=5.8e-09  Score=75.94  Aligned_cols=77  Identities=16%  Similarity=0.135  Sum_probs=37.5

Q ss_pred             hhHHHHHHHHHhcCCccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhc
Q 039275           61 YSLSSKTSRYAHSGRIRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASS  128 (153)
Q Consensus        61 ~~~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~  128 (153)
                      .++..+...|.+.|++++|.            +..+|..+...+.+.|++++|.+.|+++.+.. .++..++..+...+.
T Consensus       238 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~  316 (388)
T 1w3b_A          238 VVHGNLACVYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLANIKR  316 (388)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHH
Confidence            34444445555555555444            33445555555555555555555555554332 224444555555555


Q ss_pred             CCCccccchh
Q 039275          129 GPGALDFGKS  138 (153)
Q Consensus       129 ~~g~~~~a~~  138 (153)
                      +.|++++|.+
T Consensus       317 ~~g~~~~A~~  326 (388)
T 1w3b_A          317 EQGNIEEAVR  326 (388)
T ss_dssp             TTTCHHHHHH
T ss_pred             HcCCHHHHHH
Confidence            5555555544

>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=99.01  E-value=1.8e-08  Score=73.36  Aligned_cols=145  Identities=13%  Similarity=0.041  Sum_probs=100.2

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hh--hhhc-chhhHHHHHHHHHhcCCccccc
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QI--ELDL-SSYSLSSKTSRYAHSGRIRLAR   80 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~--~~~~-~~~~~~~ll~~~~~~g~~~~a~   80 (153)
                      |.+.|++++|.+.|+++.+. -+-+..+|..+-..+.+.|++++|.+. +.  ...| +...+..+-..+...|++++|.
T Consensus       145 ~~~~g~~~~A~~~~~~al~~-~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~  223 (388)
T 1w3b_A          145 LKALGRLEEAKACYLKAIET-QPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAV  223 (388)
T ss_dssp             HHTTSCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHH
T ss_pred             HHHccCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHH
Confidence            44556666666666666553 122355666666666777777766666 11  1222 2345666667777777777776


Q ss_pred             ------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh---------
Q 039275           81 ------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS---------  138 (153)
Q Consensus        81 ------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~---------  138 (153)
                                  +..+|..+...+.+.|++++|.+.|+++.+..  | +..++..+...+.+.|++++|.+         
T Consensus       224 ~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  301 (388)
T 1w3b_A          224 AAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ--PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC  301 (388)
T ss_dssp             HHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC--SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHhhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence                        56788888999999999999999999988653  4 45678888899999999999888         


Q ss_pred             --HHHHHHHHHHHhhc
Q 039275          139 --NIFLTTAIIEMYAK  152 (153)
Q Consensus       139 --~~~~~~~li~~y~k  152 (153)
                        +..+++.+...|.+
T Consensus       302 p~~~~~~~~l~~~~~~  317 (388)
T 1w3b_A          302 PTHADSLNNLANIKRE  317 (388)
T ss_dssp             TTCHHHHHHHHHHHHT
T ss_pred             cccHHHHHHHHHHHHH
Confidence              55667777666543

>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=98.99  E-value=1.3e-08  Score=75.16  Aligned_cols=145  Identities=11%  Similarity=0.011  Sum_probs=102.8

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-h---hhhhcchhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-Q---IELDLSSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~---~~~~~~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .+.+.|++++|++.|+++.+. .+.+...+..+...+.+.|++++|.+. .   ...+.+..++..+...|.+.|++++|
T Consensus       152 ~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  230 (450)
T 2y4t_A          152 NAFGSGDYTAAIAFLDKILEV-CVWDAELRELRAECFIKEGEPRKAISDLKAASKLKNDNTEAFYKISTLYYQLGDHELS  230 (450)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHCSCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHh-CCCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHH
Confidence            367788888888888888764 234677778888888888888888887 1   11234566788888888888888888


Q ss_pred             c------------hHHHHHHH------------HHHHHhcCChHHHHHHHHHHHHcCCCCC-----hhhHHHHHHHhcCC
Q 039275           80 R------------DPVSCKAM------------ISGYSQAGRFNEALEPFGKLESLGVHTD-----EVTMVVVLAASSGP  130 (153)
Q Consensus        80 ~------------~~~~~~~l------------i~~~~~~g~~~~a~~~~~~m~~~g~~p~-----~~t~~~li~~~~~~  130 (153)
                      .            +...+..+            ...+.+.|++++|.+.|+++...  .|+     ...+..+...+.+.
T Consensus       231 ~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~~~~~~l~~~~~~~  308 (450)
T 2y4t_A          231 LSEVRECLKLDQDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKT--EPSIAEYTVRSKERICHCFSKD  308 (450)
T ss_dssp             HHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CCSSHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHHHHC
Confidence            7            33344443            67778888888888888888763  354     34677777888888


Q ss_pred             Cccccchh-----------HHHHHHHHHHHhh
Q 039275          131 GALDFGKS-----------NIFLTTAIIEMYA  151 (153)
Q Consensus       131 g~~~~a~~-----------~~~~~~~li~~y~  151 (153)
                      |++++|.+           +...|..+...|.
T Consensus       309 g~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~~  340 (450)
T 2y4t_A          309 EKPVEAIRVCSEVLQMEPDNVNALKDRAEAYL  340 (450)
T ss_dssp             TCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhCcccHHHHHHHHHHHH
Confidence            88888877           4455555555543

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=98.93  E-value=3.5e-08  Score=67.26  Aligned_cols=132  Identities=16%  Similarity=0.139  Sum_probs=78.6

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-h--hhhhcc--------hhhHHHHHHHHHh
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-Q--IELDLS--------SYSLSSKTSRYAH   72 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~--~~~~~~--------~~~~~~ll~~~~~   72 (153)
                      .+.+.|++++|++.|++..+..  ++...+..+-..+...|++++|.+. .  ....|+        ...+..+...|.+
T Consensus        14 ~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~   91 (258)
T 3uq3_A           14 KFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFARIGNAYHK   91 (258)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHHHHHH
Confidence            4556677777777777766655  5666666666666777777766666 1  111121        3555666666666


Q ss_pred             cCCccccc--------------------------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCC
Q 039275           73 SGRIRLAR--------------------------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVH  114 (153)
Q Consensus        73 ~g~~~~a~--------------------------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~  114 (153)
                      .|++++|.                                      +...|..+...+...|++++|.+.|++..... .
T Consensus        92 ~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~  170 (258)
T 3uq3_A           92 LGDLKKTIEYYQKSLTEHRTADILTKLRNAEKELKKAEAEAYVNPEKAEEARLEGKEYFTKSDWPNAVKAYTEMIKRA-P  170 (258)
T ss_dssp             TTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-T
T ss_pred             cccHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-c
Confidence            66666665                                      23345555556666666666666666665443 2


Q ss_pred             CChhhHHHHHHHhcCCCccccchh
Q 039275          115 TDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       115 p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .+...+..+...+.+.|++++|.+
T Consensus       171 ~~~~~~~~l~~~~~~~~~~~~A~~  194 (258)
T 3uq3_A          171 EDARGYSNRAAALAKLMSFPEAIA  194 (258)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhCCHHHHHH
Confidence            244556666666666666666665

>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=98.89  E-value=6.3e-08  Score=66.15  Aligned_cols=132  Identities=10%  Similarity=-0.044  Sum_probs=59.5

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhh----hhc-chhhHHHHHHHHHhcCCccc
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIE----LDL-SSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~----~~~-~~~~~~~ll~~~~~~g~~~~   78 (153)
                      |.+.|++++|.+.|++..+.. +.+...+..+...+...|++++|.++ ..-    ..| +...+..+...+.+.|++++
T Consensus        81 ~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~  159 (252)
T 2ho1_A           81 FQTEMEPKLADEEYRKALASD-SRNARVLNNYGGFLYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQ  159 (252)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHH
Confidence            344455555555554444331 12334444444444455555555544 111    111 22334444445555555554


Q ss_pred             cc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           79 AR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        79 a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |.            +...|..+...+...|++++|.+.|++..+.. ..+...+..+...+.+.|+.++|.+
T Consensus       160 A~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~  230 (252)
T 2ho1_A          160 AKEYFEKSLRLNRNQPSVALEMADLLYKEREYVPARQYYDLFAQGG-GQNARSLLLGIRLAKVFEDRDTAAS  230 (252)
T ss_dssp             HHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-CCCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHhcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHccCHHHHHH
Confidence            44            34444455555555555555555555544321 1233344444445555555555544

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=98.86  E-value=5.6e-08  Score=65.81  Aligned_cols=132  Identities=14%  Similarity=0.010  Sum_probs=100.0

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hh--hhhc-chhhHHHHHHHHHhc------
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QI--ELDL-SSYSLSSKTSRYAHS------   73 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~--~~~~-~~~~~~~ll~~~~~~------   73 (153)
                      .+.+.|++++|+..|++..+. -+.+...+..+-..+.+.|++++|... +.  ...| +...+..+-..+.+.      
T Consensus        14 ~~~~~g~~~~A~~~~~~al~~-~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~~   92 (217)
T 2pl2_A           14 QLYALGRYDAALTLFERALKE-NPQDPEALYWLARTQLKLGLVNPALENGKTLVARTPRYLGGYMVLSEAYVALYRQAED   92 (217)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTT-SSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHTCSS
T ss_pred             HHHHcCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhhhhhhh
Confidence            567888999999999888764 234566777777788888888888887 22  2334 334666777777777      


Q ss_pred             -----CCccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccc
Q 039275           74 -----GRIRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFG  136 (153)
Q Consensus        74 -----g~~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a  136 (153)
                           |++++|.            +...|..+-..+...|++++|.+.|++..+..  .+...+..+-.++...|++++|
T Consensus        93 ~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~la~~~~~~g~~~~A  170 (217)
T 2pl2_A           93 RERGKGYLEQALSVLKDAERVNPRYAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRSALAELYLSMGRLDEA  170 (217)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHH
T ss_pred             hcccccCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHHHHHHHHHHcCCHHHH
Confidence                 8888887            56677777788888888888888888887766  6777778888888888888888


Q ss_pred             hh
Q 039275          137 KS  138 (153)
Q Consensus       137 ~~  138 (153)
                      ..
T Consensus       171 ~~  172 (217)
T 2pl2_A          171 LA  172 (217)
T ss_dssp             HH
T ss_pred             HH
Confidence            77

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=98.83  E-value=1e-07  Score=68.66  Aligned_cols=76  Identities=12%  Similarity=-0.047  Sum_probs=38.2

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hh--hhh-cchhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QI--ELD-LSSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~--~~~-~~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .+.+.|++++|++.|+++.+.. +.+...+..+-..+.+.|++++|.+. ..  ... .+...+..+...|.+.|++++|
T Consensus        74 ~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A  152 (365)
T 4eqf_A           74 KRLKEGDLPVTILFMEAAILQD-PGDAEAWQFLGITQAENENEQAAIVALQRCLELQPNNLKALMALAVSYTNTSHQQDA  152 (365)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHccccHHHH
Confidence            3455556666666666555432 23445555555555555655555555 11  111 2234455555555555555554


Q ss_pred             c
Q 039275           80 R   80 (153)
Q Consensus        80 ~   80 (153)
                      .
T Consensus       153 ~  153 (365)
T 4eqf_A          153 C  153 (365)
T ss_dssp             H
T ss_pred             H
Confidence            4

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=98.83  E-value=1.1e-07  Score=64.41  Aligned_cols=133  Identities=11%  Similarity=-0.014  Sum_probs=93.7

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-h---hhhhcchhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-Q---IELDLSSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~---~~~~~~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .|.+.|++++|.+.|++..+.. +.+...+..+...+...|++++|.+. .   ...+.+...+..+...+.+.|++++|
T Consensus        66 ~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A  144 (243)
T 2q7f_A           66 LLSSVNELERALAFYDKALELD-SSAATAYYGAGNVYVVKEMYKEAKDMFEKALRAGMENGDLFYMLGTVLVKLEQPKLA  144 (243)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHTSCHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHcC-CcchHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccHHHH
Confidence            5667778888888887776542 33566677777777777888887777 1   11223455667777777888887777


Q ss_pred             c------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           80 R------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        80 ~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .            +...|..+...+.+.|++++|.+.|++..+.. ..+..++..+...+.+.|++++|.+
T Consensus       145 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~  214 (243)
T 2q7f_A          145 LPYLQRAVELNENDTEARFQFGMCLANEGMLDEALSQFAAVTEQD-PGHADAFYNAGVTYAYKENREKALE  214 (243)
T ss_dssp             HHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTHHHH
T ss_pred             HHHHHHHHHhCCccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHccCHHHHHH
Confidence            7            56677777778888888888888888776543 2345667777778888888887776

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=98.83  E-value=5.2e-08  Score=62.98  Aligned_cols=134  Identities=16%  Similarity=0.074  Sum_probs=110.9

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hh--hh-hcchhhHHHHHHHHHhcCCccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QI--EL-DLSSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~--~~-~~~~~~~~~ll~~~~~~g~~~~   78 (153)
                      ..+...|++++|.+.|+++.+. .+.+...+..+...+...|++++|.+. ..  .. +.+...+..+...+...|++++
T Consensus        16 ~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~   94 (186)
T 3as5_A           16 ISHAKAGRYSQAVMLLEQVYDA-DAFDVDVALHLGIAYVKTGAVDRGTELLERSLADAPDNVKVATVLGLTYVQVQKYDL   94 (186)
T ss_dssp             HHHHHHTCHHHHHHHHTTTCCT-TSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHh-CccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcCHHH
Confidence            3577889999999999988764 335678888888999999999999998 22  12 3356678888899999999999


Q ss_pred             cc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           79 AR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        79 a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |.            +...|..+...+...|++++|.+.+++..+.. ..+...+..+...+.+.|++++|.+
T Consensus        95 A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~  165 (186)
T 3as5_A           95 AVPLLIKVAEANPINFNVRFRLGVALDNLGRFDEAIDSFKIALGLR-PNEGKVHRAIAFSYEQMGRHEEALP  165 (186)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHhcCcHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCHHHHHH
Confidence            88            67788888899999999999999999988664 3356788889999999999999887

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=98.82  E-value=1.1e-07  Score=62.11  Aligned_cols=133  Identities=17%  Similarity=0.055  Sum_probs=108.2

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH---hhhhh-cchhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL---QIELD-LSSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~---~~~~~-~~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .|.+.|++++|++.|++..+.. +-+...+..+-..+.+.|++++|.+.   -.... .+...+..+...+...++++.+
T Consensus        14 ~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a   92 (184)
T 3vtx_A           14 KKRTKGDFDGAIRAYKKVLKAD-PNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLDTTSAEAYYILGSANFMIDEKQAA   92 (184)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHcCCHHHH
Confidence            5778999999999999987752 34677888888899999999999988   22223 3445566667788888888888


Q ss_pred             c------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           80 R------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        80 ~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .            +...|..+-..+.+.|++++|.+.|++..+.. .-+...+..+-.++.+.|++++|.+
T Consensus        93 ~~~~~~a~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~lg~~~~~~g~~~~A~~  162 (184)
T 3vtx_A           93 IDALQRAIALNTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIK-PGFIRAYQSIGLAYEGKGLRDEAVK  162 (184)
T ss_dssp             HHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHhCccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhc-chhhhHHHHHHHHHHHCCCHHHHHH
Confidence            7            67788889999999999999999999988653 2356778889999999999999988

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=98.82  E-value=3.4e-08  Score=66.92  Aligned_cols=146  Identities=15%  Similarity=0.037  Sum_probs=109.8

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhh--h-hcchhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIE--L-DLSSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~--~-~~~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .+.+.|++++|.+.|++..+. .+.+...+..+...+.+.|++++|.+. +..  . +.+...+..+...|.+.|++++|
T Consensus        32 ~~~~~~~~~~A~~~~~~~l~~-~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A  110 (243)
T 2q7f_A           32 RGSEFGDYEKAAEAFTKAIEE-NKEDAIPYINFANLLSSVNELERALAFYDKALELDSSAATAYYGAGNVYVVKEMYKEA  110 (243)
T ss_dssp             ----------CCTTHHHHHTT-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHhhCHHHHHHHHHHHHHh-CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHhccHHHH
Confidence            567889999999999999874 344678888888899999999999998 221  2 33567788888999999999999


Q ss_pred             c------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh---------
Q 039275           80 R------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS---------  138 (153)
Q Consensus        80 ~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~---------  138 (153)
                      .            +...|..+...+.+.|++++|.+.+++..+.. ..+...+..+...+.+.|++++|.+         
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~  189 (243)
T 2q7f_A          111 KDMFEKALRAGMENGDLFYMLGTVLVKLEQPKLALPYLQRAVELN-ENDTEARFQFGMCLANEGMLDEALSQFAAVTEQD  189 (243)
T ss_dssp             HHHHHHHHHHTCCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            8            67788889999999999999999999988653 3367788888999999999999988         


Q ss_pred             --HHHHHHHHHHHhh
Q 039275          139 --NIFLTTAIIEMYA  151 (153)
Q Consensus       139 --~~~~~~~li~~y~  151 (153)
                        +...+..+...|.
T Consensus       190 ~~~~~~~~~la~~~~  204 (243)
T 2q7f_A          190 PGHADAFYNAGVTYA  204 (243)
T ss_dssp             TTCHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHH
Confidence              4555665555553

>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=98.80  E-value=8.5e-08  Score=65.50  Aligned_cols=134  Identities=14%  Similarity=0.002  Sum_probs=111.3

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hh--hh-hcchhhHHHHHHHHHhcCCccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QI--EL-DLSSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~--~~-~~~~~~~~~ll~~~~~~g~~~~   78 (153)
                      ..|...|++++|.+.|++..+.. +.+...+..+-..+.+.|++++|.+. ..  .. +.+...+..+...|.+.|++++
T Consensus        45 ~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~  123 (252)
T 2ho1_A           45 LGYLQRGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTEMEPKLADEEYRKALASDSRNARVLNNYGGFLYEQKRYEE  123 (252)
T ss_dssp             HHHHHTTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHcCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHHhHHHH
Confidence            45788999999999999997753 44678888888999999999999998 21  12 2356678888899999999988


Q ss_pred             cc--------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           79 AR--------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        79 a~--------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |.              +...|..+...+...|++++|.+.|++..+.. ..+...+..+...+.+.|++++|.+
T Consensus       124 A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~A~~  196 (252)
T 2ho1_A          124 AYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLLYKEREYVPARQ  196 (252)
T ss_dssp             HHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCCHHHHHH
Confidence            87              45678888899999999999999999988654 2357788899999999999999988

>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=98.78  E-value=1.9e-07  Score=67.03  Aligned_cols=78  Identities=12%  Similarity=-0.012  Sum_probs=47.6

Q ss_pred             hhhHHHHHHHHHhcCCccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHh
Q 039275           60 SYSLSSKTSRYAHSGRIRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAAS  127 (153)
Q Consensus        60 ~~~~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~  127 (153)
                      ..++..+...|.+.|++++|.            +...|..+...+...|++++|.+.|++..+.. ..+...+..+...+
T Consensus       217 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~  295 (368)
T 1fch_A          217 PDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQ-PGYIRSRYNLGISC  295 (368)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHH
Confidence            345555566666666666665            45566666666666666666666666665432 22345566666666


Q ss_pred             cCCCccccchh
Q 039275          128 SGPGALDFGKS  138 (153)
Q Consensus       128 ~~~g~~~~a~~  138 (153)
                      .+.|++++|..
T Consensus       296 ~~~g~~~~A~~  306 (368)
T 1fch_A          296 INLGAHREAVE  306 (368)
T ss_dssp             HHHTCHHHHHH
T ss_pred             HHCCCHHHHHH
Confidence            66666666665

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=98.77  E-value=1.6e-07  Score=62.64  Aligned_cols=133  Identities=10%  Similarity=-0.068  Sum_probs=81.7

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hh--hh-hcchhhHHHHHHHHHhc-CCccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QI--EL-DLSSYSLSSKTSRYAHS-GRIRL   78 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~--~~-~~~~~~~~~ll~~~~~~-g~~~~   78 (153)
                      .+...|++++|.+.|++..+.. +.+...+..+...+...|++++|.+. ..  .. +.+...+..+...+... |++++
T Consensus        17 ~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~~   95 (225)
T 2vq2_A           17 EYMRGQDYRQATASIEDALKSD-PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIKPDSAEINNNYGWFLCGRLNRPAE   95 (225)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCCHHH
T ss_pred             HHHHHhhHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhcCcHHH
Confidence            4566677777777777665542 23455666666666777777777666 11  11 22344566666666677 77666


Q ss_pred             cc--------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           79 AR--------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        79 a~--------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |.              +...|..+...+...|++++|.+.|++..+.. ..+...+..+...+.+.|++++|.+
T Consensus        96 A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~  168 (225)
T 2vq2_A           96 SMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQ-PQFPPAFKELARTKMLAGQLGDADY  168 (225)
T ss_dssp             HHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCchHHHHHHHHHHHcCCHHHHHH
Confidence            65              24556666666777777777777777666542 1235556666666667777766665

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=98.75  E-value=1.6e-07  Score=62.63  Aligned_cols=135  Identities=16%  Similarity=0.014  Sum_probs=110.5

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCC-CchHHHHHH-hhhhh----c-chhhHHHHHHHHHhcCC
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGP-GAWILAKEL-QIELD----L-SSYSLSSKTSRYAHSGR   75 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~-~~~~~a~~~-~~~~~----~-~~~~~~~ll~~~~~~g~   75 (153)
                      ..|...|++++|.+.|++..+.. +.+...+..+...+... |++++|.+. ...+.    | +...+..+...+.+.|+
T Consensus        50 ~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  128 (225)
T 2vq2_A           50 EIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYGWFLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQ  128 (225)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCC
Confidence            45788999999999999997753 34677888889999999 999999998 22222    2 24678888899999999


Q ss_pred             ccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           76 IRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        76 ~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +++|.            +...|..+...+.+.|++++|.+.|++..+.....+...+..+...+...|+.+.+..
T Consensus       129 ~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~  203 (225)
T 2vq2_A          129 FGLAEAYLKRSLAAQPQFPPAFKELARTKMLAGQLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYE  203 (225)
T ss_dssp             HHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHH
Confidence            99998            5788889999999999999999999998865432466677788888889999988876

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=98.73  E-value=2e-07  Score=67.12  Aligned_cols=133  Identities=11%  Similarity=-0.002  Sum_probs=90.1

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-------------------------------
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-------------------------------   52 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-------------------------------   52 (153)
                      .|.+.|++++|++.|++..+.. +.+...+..+...+.+.|++++|.+.                               
T Consensus       108 ~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~  186 (365)
T 4eqf_A          108 TQAENENEQAAIVALQRCLELQ-PNNLKALMALAVSYTNTSHQQDACEALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKS  186 (365)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCHHHHCC-----------------
T ss_pred             HHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHccccHHHHHHHHHHHHHhCccchHHHhhhccchHHHHHHHHH
Confidence            4556666666666666665532 23355566666666666666665555                               


Q ss_pred             ----------------hhhhhc---chhhHHHHHHHHHhcCCccccc------------hHHHHHHHHHHHHhcCChHHH
Q 039275           53 ----------------QIELDL---SSYSLSSKTSRYAHSGRIRLAR------------DPVSCKAMISGYSQAGRFNEA  101 (153)
Q Consensus        53 ----------------~~~~~~---~~~~~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~~~~~g~~~~a  101 (153)
                                      -....|   +..++..+...|.+.|++++|.            +..+|..+...+...|++++|
T Consensus       187 ~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A  266 (365)
T 4eqf_A          187 PVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLGVLFHLSGEFNRAIDAFNAALTVRPEDYSLWNRLGATLANGDRSEEA  266 (365)
T ss_dssp             --CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHH
Confidence                            001112   4556777778888888888877            567788888888888888888


Q ss_pred             HHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275          102 LEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       102 ~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .+.|++..+.. ..+...+..+...+.+.|++++|..
T Consensus       267 ~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~  302 (365)
T 4eqf_A          267 VEAYTRALEIQ-PGFIRSRYNLGISCINLGAYREAVS  302 (365)
T ss_dssp             HHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCHHHHH
T ss_pred             HHHHHHHHhcC-CCchHHHHHHHHHHHHCCCHHHHHH
Confidence            88888877653 2246677778888888888888877

>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=98.72  E-value=1.8e-07  Score=65.96  Aligned_cols=58  Identities=14%  Similarity=-0.083  Sum_probs=28.3

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcC--------CCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLG--------VHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g--------~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +...|..+...+...|++++|.+.|++..+..        ...+...+..+...+.+.|++++|.+
T Consensus       192 ~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  257 (330)
T 3hym_B          192 DPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALD  257 (330)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHH
T ss_pred             ChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHHHH
Confidence            34455555555555555555555555554321        01123445555555555555555554

>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=98.72  E-value=1.9e-07  Score=65.79  Aligned_cols=133  Identities=9%  Similarity=-0.062  Sum_probs=66.6

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH----hhhhhcchhhHHHHHHHHHhcC-Cccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL----QIELDLSSYSLSSKTSRYAHSG-RIRL   78 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~----~~~~~~~~~~~~~ll~~~~~~g-~~~~   78 (153)
                      .+...|++++|.++|+++.+.. +.+...+..+...+.+.|++++|..+    ....+.+...+..+...+...| ++++
T Consensus        31 ~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  109 (330)
T 3hym_B           31 RHYYNCDFKMCYKLTSVVMEKD-PFHASCLPVHIGTLVELNKANELFYLSHKLVDLYPSNPVSWFAVGCYYLMVGHKNEH  109 (330)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTHHHHHHHHHHHHSCSCHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHcC-CCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhhhhHHH
Confidence            3455566666666666665432 22333444444555555666666555    1111223344555555555555 5555


Q ss_pred             cc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           79 AR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        79 a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |.            +...|..+...+...|++++|.+.|++..+.. ..+...+..+...+...|++++|.+
T Consensus       110 A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~  180 (330)
T 3hym_B          110 ARRYLSKATTLEKTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLM-KGCHLPMLYIGLEYGLTNNSKLAER  180 (330)
T ss_dssp             HHHHHHHHHTTCTTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT-TTCSHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHhCCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhc-cccHHHHHHHHHHHHHHhhHHHHHH
Confidence            54            34445555555555555555555555554432 1123334445555555555555554

>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=98.71  E-value=8.4e-08  Score=68.91  Aligned_cols=135  Identities=16%  Similarity=-0.014  Sum_probs=111.0

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCC-ccHHHHHHHHHHhcCCCchHHHHHH-hh--hhhc-chhhHHHHHHHHHhcCCccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVH-TDEVTMVVVLTASSGPGAWILAKEL-QI--ELDL-SSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~-p~~~~~~~ll~~~~~~~~~~~a~~~-~~--~~~~-~~~~~~~ll~~~~~~g~~~~   78 (153)
                      .+.+.|++++|.+.|+++.+..-. ++..++..+-..+.+.|++++|.+. ..  ...| +...+..+...+.+.|++++
T Consensus       190 ~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~  269 (368)
T 1fch_A          190 SLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEE  269 (368)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHhhcccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHcCCHHH
Confidence            445789999999999999775322 2588899999999999999999998 22  2233 46788899999999999999


Q ss_pred             cc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC----------ChhhHHHHHHHhcCCCccccc
Q 039275           79 AR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT----------DEVTMVVVLAASSGPGALDFG  136 (153)
Q Consensus        79 a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p----------~~~t~~~li~~~~~~g~~~~a  136 (153)
                      |.            +...|..+...+.+.|++++|.+.|++........          ...+|..+..++.+.|+.++|
T Consensus       270 A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  349 (368)
T 1fch_A          270 AVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAY  349 (368)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGH
T ss_pred             HHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccchhhHHHHHHHHHHHHhCChHhH
Confidence            98            67789999999999999999999999987542111          267899999999999999998


Q ss_pred             hh
Q 039275          137 KS  138 (153)
Q Consensus       137 ~~  138 (153)
                      ..
T Consensus       350 ~~  351 (368)
T 1fch_A          350 GA  351 (368)
T ss_dssp             HH
T ss_pred             HH
Confidence            87

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=98.70  E-value=2.4e-07  Score=56.57  Aligned_cols=115  Identities=21%  Similarity=0.215  Sum_probs=81.1

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccch
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARD   81 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~   81 (153)
                      ..+.+.|++++|.++|+++.+.. +.+...+..+...+...|++++|.++ ......+..                   +
T Consensus         9 ~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-------------------~   68 (136)
T 2fo7_A            9 NAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPR-------------------S   68 (136)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-------------------C
T ss_pred             HHHHHcCcHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHCCC-------------------c
Confidence            46788999999999999997753 34677788888888889999999888 222211110                   2


Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           82 PVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        82 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ...|..+...+...|++++|.+.|+++.... ..+...+..+...+.+.|++++|.+
T Consensus        69 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~  124 (136)
T 2fo7_A           69 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIE  124 (136)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHH
T ss_pred             hHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHHccHHHHHH
Confidence            3455666677777788888888887776543 2345566777777778887777766

>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=98.68  E-value=9.8e-08  Score=67.23  Aligned_cols=133  Identities=11%  Similarity=-0.009  Sum_probs=110.8

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hh--hh-hcchhhHHHHHHHHHhcCCccccc
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QI--EL-DLSSYSLSSKTSRYAHSGRIRLAR   80 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~--~~-~~~~~~~~~ll~~~~~~g~~~~a~   80 (153)
                      +...|++++|.+.++++.+.. +.+...+..+...+.+.|++++|.+. ..  .. +.+...+..+...+.+.|++++|.
T Consensus       148 ~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~  226 (327)
T 3cv0_A          148 FAAPNEYRECRTLLHAALEMN-PNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEAL  226 (327)
T ss_dssp             TTSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHcccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHH
Confidence            677889999999999997753 34678888999999999999999998 22  12 334567888999999999999998


Q ss_pred             ------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-----------ChhhHHHHHHHhcCCCccccch
Q 039275           81 ------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-----------DEVTMVVVLAASSGPGALDFGK  137 (153)
Q Consensus        81 ------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-----------~~~t~~~li~~~~~~g~~~~a~  137 (153)
                                  +...|..+...+...|++++|.+.|++.......+           +...+..+..++.+.|+.++|.
T Consensus       227 ~~~~~a~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  306 (327)
T 3cv0_A          227 DAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVE  306 (327)
T ss_dssp             HHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHH
Confidence                        67889999999999999999999999987653221           4678889999999999999887


Q ss_pred             h
Q 039275          138 S  138 (153)
Q Consensus       138 ~  138 (153)
                      .
T Consensus       307 ~  307 (327)
T 3cv0_A          307 L  307 (327)
T ss_dssp             H
T ss_pred             H
Confidence            7

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=98.66  E-value=4.7e-07  Score=61.58  Aligned_cols=135  Identities=12%  Similarity=0.048  Sum_probs=109.3

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcC--CCcc----HHHHHHHHHHhcCCCchHHHHHH-hhh--------------------
Q 039275            3 SGYSQAGRFNEALEPFGKLESLG--VHTD----EVTMVVVLTASSGPGAWILAKEL-QIE--------------------   55 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g--~~p~----~~~~~~ll~~~~~~~~~~~a~~~-~~~--------------------   55 (153)
                      ..|...|++++|++.|++..+..  ..|+    ...+..+-..+.+.|++++|.+. ...                    
T Consensus        46 ~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~a~  125 (258)
T 3uq3_A           46 AAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFARIGNAYHKLGDLKKTIEYYQKSLTEHRTADILTKLRNAEKEL  125 (258)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhcCchhHHHHHHhHHHHHH
Confidence            46788999999999999986642  1122    57888888899999999999888 111                    


Q ss_pred             --------h-hcchhhHHHHHHHHHhcCCccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCC
Q 039275           56 --------L-DLSSYSLSSKTSRYAHSGRIRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVH  114 (153)
Q Consensus        56 --------~-~~~~~~~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~  114 (153)
                              . +.+...+..+...+.+.|++++|.            +...|..+...+...|++++|.+.|++..+.. .
T Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~  204 (258)
T 3uq3_A          126 KKAEAEAYVNPEKAEEARLEGKEYFTKSDWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-P  204 (258)
T ss_dssp             HHHHHHHHCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-T
T ss_pred             HHHHHHHHcCcchHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-H
Confidence                    1 223456777888999999999998            67889999999999999999999999998754 3


Q ss_pred             CChhhHHHHHHHhcCCCccccchh
Q 039275          115 TDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       115 p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .+...+..+...+.+.|++++|.+
T Consensus       205 ~~~~~~~~l~~~~~~~g~~~~A~~  228 (258)
T 3uq3_A          205 NFVRAYIRKATAQIAVKEYASALE  228 (258)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhHHHHHH
Confidence            357788889999999999999988

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=98.63  E-value=4e-07  Score=68.03  Aligned_cols=131  Identities=13%  Similarity=-0.016  Sum_probs=92.1

Q ss_pred             hcCChhHHHHHHHHhHH-----cCC--------CccHHHHHHHHHHhcCCCchHHHHHH---hhhhhcchhhHHHHHHHH
Q 039275            7 QAGRFNEALEPFGKLES-----LGV--------HTDEVTMVVVLTASSGPGAWILAKEL---QIELDLSSYSLSSKTSRY   70 (153)
Q Consensus         7 ~~g~~~~a~~~~~~m~~-----~g~--------~p~~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~~~~~~~~ll~~~   70 (153)
                      +.|++++|.+.|+++.+     ..-        +.+...+..+...+...|++++|.+.   -....|+...+..+...+
T Consensus       201 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~~~~~~~~~l~~~~  280 (514)
T 2gw1_A          201 SPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTGIFKFLKNDPLGAHEDIKKAIELFPRVNSYIYMALIM  280 (514)
T ss_dssp             CTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHCCCHHHHHHHHHHH
T ss_pred             hhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCccHHHHHHHHHHH
Confidence            37888888888888766     211        23456666777777888888888877   122234456677777888


Q ss_pred             HhcCCccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           71 AHSGRIRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        71 ~~~g~~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .+.|++++|.            +...|..+...+...|++++|.+.|++..+.. ..+...+..+...+.+.|++++|.+
T Consensus       281 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~  359 (514)
T 2gw1_A          281 ADRNDSTEYYNYFDKALKLDSNNSSVYYHRGQMNFILQNYDQAGKDFDKAKELD-PENIFPYIQLACLAYRENKFDDCET  359 (514)
T ss_dssp             HTSSCCTTGGGHHHHHHTTCTTCTHHHHHHHHHHHHTTCTTHHHHHHHHHHHTC-SSCSHHHHHHHHHTTTTTCHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHhhcCcCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-hhhHHHHHHHHHHHHHcCCHHHHHH
Confidence            8888888887            56677777777888888888888888777543 2245567777777888888877776

>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=98.63  E-value=3.7e-07  Score=64.23  Aligned_cols=55  Identities=9%  Similarity=-0.017  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ..|..+...+...|++++|.+.+++..+.. ..+...+..+...+...|++++|.+
T Consensus       173 ~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~  227 (327)
T 3cv0_A          173 QLHASLGVLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEALD  227 (327)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHH
Confidence            344444444555555555555555544332 1123444444445555555555444

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=98.60  E-value=4.9e-07  Score=64.00  Aligned_cols=126  Identities=13%  Similarity=0.019  Sum_probs=98.5

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-h--hhhhcchhhH---HHHHHHHHhcCCc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-Q--IELDLSSYSL---SSKTSRYAHSGRI   76 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~--~~~~~~~~~~---~~ll~~~~~~g~~   76 (153)
                      ..|.+.|++++|++.+++      +.+...+..+...+.+.|++++|.+. +  ....|+....   ...+..+...|++
T Consensus       109 ~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~l~~a~~~l~~~~~~~  182 (291)
T 3mkr_A          109 SIYFYDQNPDAALRTLHQ------GDSLECMAMTVQILLKLDRLDLARKELKKMQDQDEDATLTQLATAWVSLAAGGEKL  182 (291)
T ss_dssp             HHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCTTHH
T ss_pred             HHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcCcHHHHHHHHHHHHHhCchHH
Confidence            357889999999999987      57888999999999999999999998 2  2224554221   2233444455788


Q ss_pred             cccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccc
Q 039275           77 RLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFG  136 (153)
Q Consensus        77 ~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a  136 (153)
                      ++|.            +...|+.+-..+.+.|++++|.+.|++.....  | +..++..++..+...|+.+++
T Consensus       183 ~eA~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~--p~~~~~l~~l~~~~~~~g~~~ea  253 (291)
T 3mkr_A          183 QDAYYIFQEMADKCSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKD--SGHPETLINLVVLSQHLGKPPEV  253 (291)
T ss_dssp             HHHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCCHHH
Confidence            8887            77889999999999999999999999988653  5 666788888899899988753

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=98.58  E-value=1.1e-06  Score=59.32  Aligned_cols=132  Identities=20%  Similarity=0.070  Sum_probs=99.5

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCC-----------CchHHHHHH-hh--hhhc-chhhHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGP-----------GAWILAKEL-QI--ELDL-SSYSLSSKTS   68 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~-----------~~~~~a~~~-~~--~~~~-~~~~~~~ll~   68 (153)
                      .+.+.|++++|+..|++..+.. +.+...+..+-..+.+.           |++++|... +.  ...| +...+..+-.
T Consensus        48 ~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~lg~  126 (217)
T 2pl2_A           48 TQLKLGLVNPALENGKTLVART-PRYLGGYMVLSEAYVALYRQAEDRERGKGYLEQALSVLKDAERVNPRYAPLHLQRGL  126 (217)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhCcccHHHHHHHHH
Confidence            5778999999999999997752 33566777777788888           999999988 22  2334 3456777888


Q ss_pred             HHHhcCCccccc-----------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccc
Q 039275           69 RYAHSGRIRLAR-----------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFG  136 (153)
Q Consensus        69 ~~~~~g~~~~a~-----------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a  136 (153)
                      .|.+.|++++|.           +...|..+-..+...|++++|.+.|++..+..  | +...+..+...+.+.|++++|
T Consensus       127 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~--P~~~~~~~~la~~~~~~g~~~~A  204 (217)
T 2pl2_A          127 VYALLGERDKAEASLKQALALEDTPEIRSALAELYLSMGRLDEALAQYAKALEQA--PKDLDLRVRYASALLLKGKAEEA  204 (217)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHTC-------
T ss_pred             HHHHcCChHHHHHHHHHHHhcccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHccCHHHH
Confidence            999999999987           45778888899999999999999999998653  5 566788888999999999998


Q ss_pred             hh
Q 039275          137 KS  138 (153)
Q Consensus       137 ~~  138 (153)
                      .+
T Consensus       205 ~~  206 (217)
T 2pl2_A          205 AR  206 (217)
T ss_dssp             --
T ss_pred             HH
Confidence            76

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=98.57  E-value=5.1e-07  Score=67.43  Aligned_cols=133  Identities=7%  Similarity=-0.144  Sum_probs=112.1

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhh---hhcchhhHHHHHHHHHhcCCccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIE---LDLSSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~---~~~~~~~~~~ll~~~~~~g~~~~   78 (153)
                      ..+...|++++|.+.|++..+..  |+...+..+...+...|++++|.+. ...   .+.+...+..+...|.+.|++++
T Consensus       245 ~~~~~~~~~~~A~~~~~~~l~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  322 (514)
T 2gw1_A          245 IFKFLKNDPLGAHEDIKKAIELF--PRVNSYIYMALIMADRNDSTEYYNYFDKALKLDSNNSSVYYHRGQMNFILQNYDQ  322 (514)
T ss_dssp             HHHHHSSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTCTTCTHHHHHHHHHHHHTTCTTH
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhC--ccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcCcCCHHHHHHHHHHHHHhCCHHH
Confidence            35778999999999999998764  4488888889999999999999888 221   23356788889999999999999


Q ss_pred             cc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           79 AR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        79 a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |.            +...|..+...+...|++++|.+.|++..+.. ..+...+..+...+.+.|++++|.+
T Consensus       323 A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~  393 (514)
T 2gw1_A          323 AGKDFDKAKELDPENIFPYIQLACLAYRENKFDDCETLFSEAKRKF-PEAPEVPNFFAEILTDKNDFDKALK  393 (514)
T ss_dssp             HHHHHHHHHHTCSSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHhChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHc-ccCHHHHHHHHHHHHHCCCHHHHHH
Confidence            98            67788899999999999999999999998653 2356778888999999999999988

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=98.56  E-value=2.1e-06  Score=60.99  Aligned_cols=133  Identities=14%  Similarity=0.044  Sum_probs=75.7

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-h--hhhhc-chhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-Q--IELDL-SSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~--~~~~~-~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .+.+.|++++|++.|++..+. -+.+...+..+-..+...|++++|.+. .  ....| +...+..+...+.+.|++++|
T Consensus        12 ~~~~~g~~~~A~~~~~~~l~~-~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A   90 (359)
T 3ieg_A           12 KLLAAGQLADALSQFHAAVDG-DPDNYIAYYRRATVFLAMGKSKAALPDLTKVIALKMDFTAARLQRGHLLLKQGKLDEA   90 (359)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHhh-CcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHcCChHHH
Confidence            456667777777777776553 223455666666666667777776666 1  11122 334556666666666666666


Q ss_pred             c---------hH------HHHHHH------------HHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCc
Q 039275           80 R---------DP------VSCKAM------------ISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGA  132 (153)
Q Consensus        80 ~---------~~------~~~~~l------------i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~  132 (153)
                      .         ++      ..+..+            ...+...|++++|.+.|++..+.. ..+...+..+...+.+.|+
T Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  169 (359)
T 3ieg_A           91 EDDFKKVLKSNPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVC-VWDAELRELRAECFIKEGE  169 (359)
T ss_dssp             HHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHCCC
Confidence            5         11      112222            355566666666666666665443 2244555566666666666


Q ss_pred             cccchh
Q 039275          133 LDFGKS  138 (153)
Q Consensus       133 ~~~a~~  138 (153)
                      +++|.+
T Consensus       170 ~~~A~~  175 (359)
T 3ieg_A          170 PRKAIS  175 (359)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            666665

>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=98.56  E-value=1.2e-06  Score=65.93  Aligned_cols=132  Identities=11%  Similarity=-0.014  Sum_probs=112.2

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hh--hh-hcchhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QI--EL-DLSSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~--~~-~~~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .+...|++++|.+.|++..+.  .|+...+..+-..+...|++++|.+. ..  .. +.+..++..+...+.+.|++++|
T Consensus       252 ~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A  329 (537)
T 3fp2_A          252 FHFLKNNLLDAQVLLQESINL--HPTPNSYIFLALTLADKENSQEFFKFFQKAVDLNPEYPPTYYHRGQMYFILQDYKNA  329 (537)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--CCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHhcccHHHHHHHHHHHHhc--CCCchHHHHHHHHHHHhcCHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhcCCHHHH
Confidence            467789999999999999875  46688888899999999999999998 21  12 33567888899999999999999


Q ss_pred             c------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           80 R------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        80 ~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .            +...|..+...+...|++++|.+.|++..+.. ..+...+..+...+.+.|++++|.+
T Consensus       330 ~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~  399 (537)
T 3fp2_A          330 KEDFQKAQSLNPENVYPYIQLACLLYKQGKFTESEAFFNETKLKF-PTLPEVPTFFAEILTDRGDFDTAIK  399 (537)
T ss_dssp             HHHHHHHHHHCTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHH
Confidence            8            57789999999999999999999999998764 3346688888999999999999988

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=98.50  E-value=7.3e-07  Score=62.28  Aligned_cols=136  Identities=10%  Similarity=0.079  Sum_probs=107.7

Q ss_pred             hhHhhcCChhHHHHHHHHhHHc-------CCCccHHHHHHHHHHhcCCCchHHHHHH-hh-----------hhhcchhhH
Q 039275            3 SGYSQAGRFNEALEPFGKLESL-------GVHTDEVTMVVVLTASSGPGAWILAKEL-QI-----------ELDLSSYSL   63 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~-------g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~-----------~~~~~~~~~   63 (153)
                      ..|...|++++|...|++..+.       ..+.....+..+-..+...|++++|.+. ..           ..+.....+
T Consensus        35 ~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  114 (311)
T 3nf1_A           35 IQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGKDHPAVAATL  114 (311)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHH
Confidence            4678899999999999998763       3444567788888899999999999988 11           113345678


Q ss_pred             HHHHHHHHhcCCccccc--------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc------CCCC-C
Q 039275           64 SSKTSRYAHSGRIRLAR--------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESL------GVHT-D  116 (153)
Q Consensus        64 ~~ll~~~~~~g~~~~a~--------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~------g~~p-~  116 (153)
                      ..+...|...|++++|.                    ....|..+-..+...|++++|.++|++..+.      +-.| .
T Consensus       115 ~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~  194 (311)
T 3nf1_A          115 NNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTKLGPDDPNV  194 (311)
T ss_dssp             HHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTSCTTCHHH
T ss_pred             HHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCHHH
Confidence            88889999999999988                    3456778888999999999999999998754      2233 3


Q ss_pred             hhhHHHHHHHhcCCCccccchh
Q 039275          117 EVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       117 ~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ..++..+...+.+.|++++|.+
T Consensus       195 ~~~~~~la~~~~~~g~~~~A~~  216 (311)
T 3nf1_A          195 AKTKNNLASCYLKQGKFKQAET  216 (311)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHH
Confidence            4567888889999999999988

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=98.48  E-value=2.7e-06  Score=67.52  Aligned_cols=133  Identities=10%  Similarity=-0.042  Sum_probs=112.4

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hh--hhhcc-hhhHHHHHHHHHhcCCccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QI--ELDLS-SYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~--~~~~~-~~~~~~ll~~~~~~g~~~~   78 (153)
                      ..|.+.|++++|++.|++..+.. +-+...|..+-.++.+.|++++|.+. +.  .+.|+ ...|..+-..|.+.|++++
T Consensus        17 ~~~~~~G~~~eAi~~~~kAl~l~-P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~P~~~~a~~nLg~~l~~~g~~~~   95 (723)
T 4gyw_A           17 NIKREQGNIEEAVRLYRKALEVF-PEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQG   95 (723)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHH
Confidence            35788999999999999987742 23467888888999999999999998 22  23443 5678889999999999999


Q ss_pred             cc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           79 AR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        79 a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |.            +...|+.+-..+.+.|++++|.+.|++..+.  .| +...+..+...+...|++++|.+
T Consensus        96 A~~~~~kAl~l~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l--~P~~~~a~~~L~~~l~~~g~~~~A~~  166 (723)
T 4gyw_A           96 ALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKL--KPDFPDAYCNLAHCLQIVCDWTDYDE  166 (723)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCCTTHHH
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHHhhhhhHHHhcccHHHHHH
Confidence            98            7889999999999999999999999998865  46 46678889999999999999987

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=98.48  E-value=5.7e-07  Score=61.88  Aligned_cols=131  Identities=8%  Similarity=-0.087  Sum_probs=86.6

Q ss_pred             hhcCChhHHHHHHHHhHHcCC---CccHHHHHHHHHHhcCCCchHHHHHH-hhh--hhc-chhhHHHHHHHHHhcCCccc
Q 039275            6 SQAGRFNEALEPFGKLESLGV---HTDEVTMVVVLTASSGPGAWILAKEL-QIE--LDL-SSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         6 ~~~g~~~~a~~~~~~m~~~g~---~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~--~~~-~~~~~~~ll~~~~~~g~~~~   78 (153)
                      ...|++++|++.|+++.+...   +.+...+..+-..+...|++++|.+. ...  ..| +...+..+...|.+.|++++
T Consensus        16 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~   95 (275)
T 1xnf_A           16 QPTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDA   95 (275)
T ss_dssp             CCCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHH
T ss_pred             CccchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCHHH
Confidence            345677888888888776532   12456666777777788888888777 211  222 45667777778888888877


Q ss_pred             cc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           79 AR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        79 a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |.            +...|..+...+.+.|++++|.+.|++..+.  .|+.......+..+...|++++|..
T Consensus        96 A~~~~~~al~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~~~~~~~~~A~~  165 (275)
T 1xnf_A           96 AYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD--DPNDPFRSLWLYLAEQKLDEKQAKE  165 (275)
T ss_dssp             HHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHCHHHHHH
T ss_pred             HHHHHHHHHhcCccccHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHhcCHHHHHH
Confidence            77            5667777777888888888888888877754  3544444444444455566655554

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=98.47  E-value=5e-06  Score=58.96  Aligned_cols=76  Identities=11%  Similarity=-0.012  Sum_probs=44.8

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhh---hhcchhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIE---LDLSSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~---~~~~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .+...|++++|++.|+++.+. .+.+...+..+-..+...|++++|.+. ...   .+.+...+..+...+.+.|++++|
T Consensus       129 ~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A  207 (359)
T 3ieg_A          129 DAFDGADYTAAITFLDKILEV-CVWDAELRELRAECFIKEGEPRKAISDLKAASKLKSDNTEAFYKISTLYYQLGDHELS  207 (359)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCSCCHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHccCHHHHHHHHHHHHHh-CCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHH
Confidence            455667777777777776554 233455666666666667777776666 111   122344555566666666666665


Q ss_pred             c
Q 039275           80 R   80 (153)
Q Consensus        80 ~   80 (153)
                      .
T Consensus       208 ~  208 (359)
T 3ieg_A          208 L  208 (359)
T ss_dssp             H
T ss_pred             H
Confidence            5

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=98.46  E-value=9.1e-07  Score=60.78  Aligned_cols=108  Identities=12%  Similarity=0.136  Sum_probs=86.0

Q ss_pred             hhHhhcCChhHHHHHHHHhHHc------CC-CccHHHHHHHHHHhcCCCchHHHHHH-hhh-----------hhcchhhH
Q 039275            3 SGYSQAGRFNEALEPFGKLESL------GV-HTDEVTMVVVLTASSGPGAWILAKEL-QIE-----------LDLSSYSL   63 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~------g~-~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~-----------~~~~~~~~   63 (153)
                      ..|...|++++|.+.|++..+.      +- +....++..+-..+...|++++|.+. ...           .+.....+
T Consensus        51 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  130 (283)
T 3edt_B           51 LVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQL  130 (283)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             HHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHH
Confidence            3577899999999999998654      22 33467788888999999999999988 111           12345677


Q ss_pred             HHHHHHHHhcCCccccc--------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHH
Q 039275           64 SSKTSRYAHSGRIRLAR--------------------DPVSCKAMISGYSQAGRFNEALEPFGKLES  110 (153)
Q Consensus        64 ~~ll~~~~~~g~~~~a~--------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  110 (153)
                      ..+...|...|++++|.                    ...++..+-..+...|++++|.+.|++..+
T Consensus       131 ~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~  197 (283)
T 3edt_B          131 NNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKTKNNLASCYLKQGKYQDAETLYKEILT  197 (283)
T ss_dssp             HHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            88889999999999988                    356788888999999999999999998875

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=98.44  E-value=7.7e-06  Score=56.14  Aligned_cols=133  Identities=13%  Similarity=-0.028  Sum_probs=95.8

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhh--h-hcchhhHHHHHHHHHhcCCccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIE--L-DLSSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~--~-~~~~~~~~~ll~~~~~~g~~~~   78 (153)
                      ..|...|++++|.+.|++..+.. +.+...+..+-..+...|++++|.+. ..-  . +.+...+..+...|.+.|++++
T Consensus        51 ~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~g~~~~  129 (275)
T 1xnf_A           51 VLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKL  129 (275)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHcccHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCccccHHHHHHHHHHHHhccHHH
Confidence            46778999999999999997752 34678888999999999999999999 222  2 2356788889999999999999


Q ss_pred             cc-----------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           79 AR-----------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        79 a~-----------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |.           +...+...+..+...|++++|...+++..... .++...+ .+...+...++.++|.+
T Consensus       130 A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~-~~~~~~~~~~~~~~a~~  198 (275)
T 1xnf_A          130 AQDDLLAFYQDDPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKS-DKEQWGW-NIVEFYLGNISEQTLME  198 (275)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHS-CCCSTHH-HHHHHHTTSSCHHHHHH
T ss_pred             HHHHHHHHHHhCCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CcchHHH-HHHHHHHHhcCHHHHHH
Confidence            98           22233344455577799999999997776543 2333333 35555666666555554

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=98.44  E-value=1.2e-06  Score=61.15  Aligned_cols=108  Identities=12%  Similarity=0.141  Sum_probs=85.9

Q ss_pred             hhHhhcCChhHHHHHHHHhHHc------C-CCccHHHHHHHHHHhcCCCchHHHHHH-hhh-----------hhcchhhH
Q 039275            3 SGYSQAGRFNEALEPFGKLESL------G-VHTDEVTMVVVLTASSGPGAWILAKEL-QIE-----------LDLSSYSL   63 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~------g-~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~-----------~~~~~~~~   63 (153)
                      ..|...|++++|.+.|++..+.      + .+.....+..+-..+...|++++|.+. ...           .+.....+
T Consensus        77 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~  156 (311)
T 3nf1_A           77 LVYRDQNKYKDAANLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQL  156 (311)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHH
Confidence            3577899999999999988654      2 233467788888899999999999988 111           13344567


Q ss_pred             HHHHHHHHhcCCccccc--------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHH
Q 039275           64 SSKTSRYAHSGRIRLAR--------------------DPVSCKAMISGYSQAGRFNEALEPFGKLES  110 (153)
Q Consensus        64 ~~ll~~~~~~g~~~~a~--------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  110 (153)
                      ..+...+.+.|++++|.                    ...++..+...+...|++++|.+.|++..+
T Consensus       157 ~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  223 (311)
T 3nf1_A          157 NNLALLCQNQGKYEEVEYYYQRALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILT  223 (311)
T ss_dssp             HHHHHHHHTTTCHHHHHHHHHHHHHHHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            88889999999999888                    345688888999999999999999999875

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=98.40  E-value=1.3e-06  Score=65.90  Aligned_cols=134  Identities=10%  Similarity=-0.044  Sum_probs=96.9

Q ss_pred             hHhhcCCh-hHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH---hhhhhcchhhHHHHHHHHHhc------
Q 039275            4 GYSQAGRF-NEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL---QIELDLSSYSLSSKTSRYAHS------   73 (153)
Q Consensus         4 ~~~~~g~~-~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~~~~~~~~ll~~~~~~------   73 (153)
                      .|...|++ ++|++.|++..+.. +-+...|..+-..+.+.|++++|.+.   -....|+...+..+-..|.+.      
T Consensus       111 ~~~~~g~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~lg~~~~~~~~~~~~  189 (474)
T 4abn_A          111 ALNVTPDYSPEAEVLLSKAVKLE-PELVEAWNQLGEVYWKKGDVTSAHTCFSGALTHCKNKVSLQNLSMVLRQLQTDSGD  189 (474)
T ss_dssp             HHTSSSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTCCCHHHHHHHHHHHTTCCCSCHH
T ss_pred             HHHhccccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhccCChh
Confidence            45667788 88888888876642 23466777777788888888888877   223456666677777777777      


Q ss_pred             ---CCccccc------------hHHHHHHHHHHHHhc--------CChHHHHHHHHHHHHcCCC--CChhhHHHHHHHhc
Q 039275           74 ---GRIRLAR------------DPVSCKAMISGYSQA--------GRFNEALEPFGKLESLGVH--TDEVTMVVVLAASS  128 (153)
Q Consensus        74 ---g~~~~a~------------~~~~~~~li~~~~~~--------g~~~~a~~~~~~m~~~g~~--p~~~t~~~li~~~~  128 (153)
                         |++++|.            +...|..+-..|...        |++++|.+.|++..+....  -+...+..+-.++.
T Consensus       190 ~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~  269 (474)
T 4abn_A          190 EHSRHVMDSVRQAKLAVQMDVLDGRSWYILGNAYLSLYFNTGQNPKISQQALSAYAQAEKVDRKASSNPDLHLNRATLHK  269 (474)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCGGGGGCHHHHHHHHHHHH
T ss_pred             hhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHH
Confidence               7777777            667777777777777        8888888888887764310  26667777788888


Q ss_pred             CCCccccchh
Q 039275          129 GPGALDFGKS  138 (153)
Q Consensus       129 ~~g~~~~a~~  138 (153)
                      ..|++++|.+
T Consensus       270 ~~g~~~~A~~  279 (474)
T 4abn_A          270 YEESYGEALE  279 (474)
T ss_dssp             HTTCHHHHHH
T ss_pred             HcCCHHHHHH
Confidence            8888888877

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=98.40  E-value=3.6e-06  Score=57.87  Aligned_cols=132  Identities=16%  Similarity=0.015  Sum_probs=80.7

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhh--hcchhh----HHHHHHHHHhcCCc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIEL--DLSSYS----LSSKTSRYAHSGRI   76 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~--~~~~~~----~~~ll~~~~~~g~~   76 (153)
                      .+.+.|++++|++.|++..+.. +.+...+..+-..+...|++++|.+. ...+  .++...    |..+-..|.+.|++
T Consensus        12 ~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~~~~~~~   90 (272)
T 3u4t_A           12 FLFKNNNYAEAIEVFNKLEAKK-YNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKILMKKGQD   90 (272)
T ss_dssp             HHHTTTCHHHHHHHHHHHHHTT-CCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHcccH
Confidence            4567777888888887776542 22344666666677777777777777 1111  122222    56667777777777


Q ss_pred             cccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           77 RLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        77 ~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ++|.            +...|..+-..+...|++++|.+.|++..+.  .| +...+..+-..+...+++++|.+
T Consensus        91 ~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~~~~~~~~~~l~~~~~~~~~~~~A~~  163 (272)
T 3u4t_A           91 SLAIQQYQAAVDRDTTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRP--TTTDPKVFYELGQAYYYNKEYVKADS  163 (272)
T ss_dssp             HHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCS--SCCCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHhcCcccHHHHHHHHHHHHHccCHHHHHHHHHHHhhc--CCCcHHHHHHHHHHHHHHHHHHHHHH
Confidence            7776            5566777777777777777777777776644  33 33334444413333346666665

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=98.40  E-value=3.5e-06  Score=54.14  Aligned_cols=108  Identities=19%  Similarity=0.145  Sum_probs=90.2

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH----hhhhhcchhhHHHHHHHHHhcCCccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL----QIELDLSSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~----~~~~~~~~~~~~~ll~~~~~~g~~~~   78 (153)
                      ..+...|++++|.+.|++..+. .+.+...+..+...+...|++++|.+.    ....+.+...+..+...+.+.|++++
T Consensus        50 ~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~  128 (186)
T 3as5_A           50 IAYVKTGAVDRGTELLERSLAD-APDNVKVATVLGLTYVQVQKYDLAVPLLIKVAEANPINFNVRFRLGVALDNLGRFDE  128 (186)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCcHhHHHHHHHHHHHHHcCcHHH
Confidence            4578899999999999999775 344677888888899999999999998    12223456678888899999999999


Q ss_pred             cc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 039275           79 AR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESL  111 (153)
Q Consensus        79 a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  111 (153)
                      |.            +...|..+...+...|++++|.+.+++..+.
T Consensus       129 A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  173 (186)
T 3as5_A          129 AIDSFKIALGLRPNEGKVHRAIAFSYEQMGRHEEALPHFKKANEL  173 (186)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            98            6688899999999999999999999998754

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=98.36  E-value=4.3e-06  Score=50.76  Aligned_cols=99  Identities=18%  Similarity=0.104  Sum_probs=69.6

Q ss_pred             HHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 039275           33 MVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLESL  111 (153)
Q Consensus        33 ~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  111 (153)
                      +..+...+...|++++|.++ ...+..+..                   +...|..+...+...|++++|.++|+++...
T Consensus         4 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-------------------~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~   64 (136)
T 2fo7_A            4 WYNLGNAYYKQGDYDEAIEYYQKALELDPR-------------------SAEAWYNLGNAYYKQGDYDEAIEYYQKALEL   64 (136)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-------------------CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCcHHHHHHHHHHHHHcCCc-------------------chhHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence            44555566667777777776 222111110                   3456777888899999999999999999876


Q ss_pred             CCCCChhhHHHHHHHhcCCCccccchh-----------HHHHHHHHHHHhh
Q 039275          112 GVHTDEVTMVVVLAASSGPGALDFGKS-----------NIFLTTAIIEMYA  151 (153)
Q Consensus       112 g~~p~~~t~~~li~~~~~~g~~~~a~~-----------~~~~~~~li~~y~  151 (153)
                      . ..+...+..+...+.+.|++++|.+           +...+..+...|.
T Consensus        65 ~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~  114 (136)
T 2fo7_A           65 D-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYY  114 (136)
T ss_dssp             C-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             C-CCchHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHH
Confidence            4 3356678888999999999999987           4555656655554

>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=98.32  E-value=4.8e-06  Score=62.61  Aligned_cols=127  Identities=14%  Similarity=0.045  Sum_probs=103.7

Q ss_pred             CChhHHHHHHHHhHHcCCCcc--------HHHHHHHHHHhcCCCchHHHHHH---hhhhhcchhhHHHHHHHHHhcCCcc
Q 039275            9 GRFNEALEPFGKLESLGVHTD--------EVTMVVVLTASSGPGAWILAKEL---QIELDLSSYSLSSKTSRYAHSGRIR   77 (153)
Q Consensus         9 g~~~~a~~~~~~m~~~g~~p~--------~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~~~~~~~~ll~~~~~~g~~~   77 (153)
                      |++++|+++|+++.+.  .|+        ...+..+-..+...|++++|.+.   -....|+...+..+...+.+.|+++
T Consensus       216 ~~~~~A~~~~~~~l~~--~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  293 (537)
T 3fp2_A          216 DLLTKSTDMYHSLLSA--NTVDDPLRENAALALCYTGIFHFLKNNLLDAQVLLQESINLHPTPNSYIFLALTLADKENSQ  293 (537)
T ss_dssp             HHHHHHHHHHHHHHC----CCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHTCCSSCCH
T ss_pred             HHHHHHHHHHHHHHHH--CCCcchhhHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCCchHHHHHHHHHHHhcCHH
Confidence            5789999999998764  233        23466666778889999999998   3334666778888899999999999


Q ss_pred             ccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           78 LAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        78 ~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +|.            +..+|..+...+...|++++|.+.|++..+.. ..+...+..+...+.+.|++++|.+
T Consensus       294 ~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~  365 (537)
T 3fp2_A          294 EFFKFFQKAVDLNPEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLN-PENVYPYIQLACLLYKQGKFTESEA  365 (537)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCSHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHhccCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            998            67889999999999999999999999998754 2245778889999999999999988

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=98.30  E-value=1.2e-05  Score=54.12  Aligned_cols=128  Identities=14%  Similarity=0.112  Sum_probs=100.9

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-h--hhhhc-chhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-Q--IELDL-SSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~--~~~~~-~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .+.+.|++++|++.|++..+..-+++...+..+-.++.+.|++++|.+. .  ....| +...+..+-..|.+.|++++|
T Consensus        16 ~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A   95 (228)
T 4i17_A           16 DALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKNYNLANAYIGKSAAYRDMKNNQEY   95 (228)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCSHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCcchHHHHHHHHHHHHHcccHHHH
Confidence            5678999999999999998875447777777788889999999999998 2  22333 445778888999999999999


Q ss_pred             c------------hH-------HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC---hhhHHHHHHHhcCCCcc
Q 039275           80 R------------DP-------VSCKAMISGYSQAGRFNEALEPFGKLESLGVHTD---EVTMVVVLAASSGPGAL  133 (153)
Q Consensus        80 ~------------~~-------~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~---~~t~~~li~~~~~~g~~  133 (153)
                      .            +.       ..|..+-..+...|++++|.+.|++..+.  .|+   ...+..+-..+...|..
T Consensus        96 ~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~l~~~~~~~~~~  169 (228)
T 4i17_A           96 IATLTEGIKAVPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDV--TSKKWKTDALYSLGVLFYNNGAD  169 (228)
T ss_dssp             HHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--SCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhc--CCCcccHHHHHHHHHHHHHHHHH
Confidence            8            33       45777778889999999999999998754  565   45666666677766665

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=98.30  E-value=3.1e-06  Score=58.05  Aligned_cols=134  Identities=9%  Similarity=-0.014  Sum_probs=103.0

Q ss_pred             HhhcCChhHHHHHHHHhHHc-------CCCccHHHHHHHHHHhcCCCchHHHHHH-------h-----hhhhcchhhHHH
Q 039275            5 YSQAGRFNEALEPFGKLESL-------GVHTDEVTMVVVLTASSGPGAWILAKEL-------Q-----IELDLSSYSLSS   65 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~-------g~~p~~~~~~~ll~~~~~~~~~~~a~~~-------~-----~~~~~~~~~~~~   65 (153)
                      ....|++++|+++|++..+.       ..+....++..+-..+...|++++|.+.       .     ...+....++..
T Consensus        11 ~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~   90 (283)
T 3edt_B           11 SSGLVPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNN   90 (283)
T ss_dssp             --CCSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHH
Confidence            34567888888888777542       2334567788888899999999999988       1     111334567888


Q ss_pred             HHHHHHhcCCccccc--------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc------CCCC-Chh
Q 039275           66 KTSRYAHSGRIRLAR--------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESL------GVHT-DEV  118 (153)
Q Consensus        66 ll~~~~~~g~~~~a~--------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~------g~~p-~~~  118 (153)
                      +-..|...|++++|.                    ...+|..+-..+...|++++|.+.|++..+.      +-.| ...
T Consensus        91 l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~  170 (283)
T 3edt_B           91 LAVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAK  170 (283)
T ss_dssp             HHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHH
T ss_pred             HHHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHH
Confidence            999999999999998                    3556778888999999999999999998755      2233 356


Q ss_pred             hHHHHHHHhcCCCccccchh
Q 039275          119 TMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       119 t~~~li~~~~~~g~~~~a~~  138 (153)
                      ++..+-..+.+.|++++|.+
T Consensus       171 ~~~~la~~~~~~g~~~~A~~  190 (283)
T 3edt_B          171 TKNNLASCYLKQGKYQDAET  190 (283)
T ss_dssp             HHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHH
Confidence            78888899999999999988

>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=98.29  E-value=2.2e-05  Score=52.05  Aligned_cols=120  Identities=9%  Similarity=0.030  Sum_probs=91.4

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhh--h-hcchhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIE--L-DLSSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~--~-~~~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .+.+.|++++|++.|++.    +.|+...+..+-..+.+.|++++|.+. ...  . +.+...+..+-..|.+.|++++|
T Consensus        15 ~~~~~~~~~~A~~~~~~a----~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~lg~~~~~~~~~~~A   90 (213)
T 1hh8_A           15 LAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQTEKYDLA   90 (213)
T ss_dssp             HHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHhCCHHHHHHHHHHH----cCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcccHHHH
Confidence            567889999999999877    467889999999999999999999998 222  2 33456777888888999998888


Q ss_pred             c------------hH----------------HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHh
Q 039275           80 R------------DP----------------VSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAAS  127 (153)
Q Consensus        80 ~------------~~----------------~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~  127 (153)
                      .            +.                ..|..+-..+.+.|++++|.+.|++..+..-......+...+..+
T Consensus        91 ~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~a~~~~  166 (213)
T 1hh8_A           91 IKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEPRHSKIDKAMECV  166 (213)
T ss_dssp             HHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSGGGGHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHcCcccccchHHHHHHHH
Confidence            7            12                677788888999999999999999887654333333444444443

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=98.28  E-value=1e-05  Score=57.30  Aligned_cols=133  Identities=11%  Similarity=0.003  Sum_probs=96.6

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCcc-HH-HHHHHHHHhcCCCchHHHHHH-hhhh---hcchhhHHHHHHHH-HhcCCc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTD-EV-TMVVVLTASSGPGAWILAKEL-QIEL---DLSSYSLSSKTSRY-AHSGRI   76 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~-~~-~~~~ll~~~~~~~~~~~a~~~-~~~~---~~~~~~~~~ll~~~-~~~g~~   76 (153)
                      .+.+.|++++|.+.|++..+  +.|+ .. .|..+...+.+.|++++|.++ ...+   +++...|....... ...|+.
T Consensus       108 ~~~~~~~~~~A~~~~~~al~--~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~a~~~~~~~~~~  185 (308)
T 2ond_A          108 YEESRMKYEKVHSIYNRLLA--IEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYVTAALMEYYCSKDK  185 (308)
T ss_dssp             HHHHTTCHHHHHHHHHHHHT--SSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTTCCTHHHHHHHHHHHHTSCCH
T ss_pred             HHHhcCCHHHHHHHHHHHHh--ccccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCCH
Confidence            45678899999999999887  4454 33 788888888888899998888 2222   22333343322221 125787


Q ss_pred             cccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcC-CCCC--hhhHHHHHHHhcCCCccccchh
Q 039275           77 RLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLG-VHTD--EVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        77 ~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~--~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ++|.            +...|..++..+.+.|++++|..+|++..... +.|+  ...|..++....+.|+.+.+..
T Consensus       186 ~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~  262 (308)
T 2ond_A          186 SVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILK  262 (308)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            7777            67888888999999999999999999998763 5663  5677888888888888888776

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.27  E-value=1.1e-05  Score=56.91  Aligned_cols=135  Identities=13%  Similarity=-0.016  Sum_probs=102.7

Q ss_pred             hHhhcCChhHHHHHHHHhHHc----CCCcc-HHHHHHHHHHhcCCCchHHHHHH-hhh--hhc-------chhhHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESL----GVHTD-EVTMVVVLTASSGPGAWILAKEL-QIE--LDL-------SSYSLSSKTS   68 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~----g~~p~-~~~~~~ll~~~~~~~~~~~a~~~-~~~--~~~-------~~~~~~~ll~   68 (153)
                      .|...|++++|.+.|++....    |-+++ ..+|+.+-..+.+.|++++|... ..-  +.|       -..+++.+-.
T Consensus        46 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~  125 (292)
T 1qqe_A           46 IYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGE  125 (292)
T ss_dssp             HHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            567789999999999877542    33333 56888888999999999999887 111  111       1346778888


Q ss_pred             HHHhc-CCccccc------------h------HHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChh------hHHHH
Q 039275           69 RYAHS-GRIRLAR------------D------PVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEV------TMVVV  123 (153)
Q Consensus        69 ~~~~~-g~~~~a~------------~------~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~------t~~~l  123 (153)
                      .|... |++++|.            +      ..+|+.+-..+.+.|++++|.+.|++..+........      .+..+
T Consensus       126 ~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~l  205 (292)
T 1qqe_A          126 ILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKK  205 (292)
T ss_dssp             HHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHH
T ss_pred             HHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHH
Confidence            99996 9999998            1      3568888999999999999999999998764332221      56777


Q ss_pred             HHHhcCCCccccchh
Q 039275          124 LAASSGPGALDFGKS  138 (153)
Q Consensus       124 i~~~~~~g~~~~a~~  138 (153)
                      ..++...|+++.|..
T Consensus       206 g~~~~~~g~~~~A~~  220 (292)
T 1qqe_A          206 GLCQLAATDAVAAAR  220 (292)
T ss_dssp             HHHHHHTTCHHHHHH
T ss_pred             HHHHHHcCCHHHHHH
Confidence            788889999999988

>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=98.24  E-value=7.3e-05  Score=51.61  Aligned_cols=128  Identities=17%  Similarity=0.090  Sum_probs=65.2

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcC----CCchHHHHHH-hhhhh-cchhhHHHHHHHHHh----cC
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSG----PGAWILAKEL-QIELD-LSSYSLSSKTSRYAH----SG   74 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~----~~~~~~a~~~-~~~~~-~~~~~~~~ll~~~~~----~g   74 (153)
                      |.+.|++++|.+.|++..+.   -+...+..+-..+..    .+++++|.++ +.... .+...+..+-..|..    .+
T Consensus        16 ~~~~~~~~~A~~~~~~a~~~---~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~   92 (273)
T 1ouv_A           16 SYKEKDFTQAKKYFEKACDL---KENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNYSNGCHLLGNLYYSGQGVSQ   92 (273)
T ss_dssp             HHHTTCHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCC
T ss_pred             HHhCCCHHHHHHHHHHHHHC---CCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhCCCCccc
Confidence            44556666666666666552   233344444444455    6666666665 11111 133444445555555    55


Q ss_pred             Cccccc----------hHHHHHHHHHHHHh----cCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcC----CCccccc
Q 039275           75 RIRLAR----------DPVSCKAMISGYSQ----AGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSG----PGALDFG  136 (153)
Q Consensus        75 ~~~~a~----------~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~----~g~~~~a  136 (153)
                      ++++|.          +...+..+-..|..    .+++++|.+.|++..+.+   +...+..+-..+.+    .+++++|
T Consensus        93 ~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A  169 (273)
T 1ouv_A           93 NTNKALQYYSKACDLKYAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGCTILGSLYDAGRGTPKDLKKA  169 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHH
T ss_pred             CHHHHHHHHHHHHHcCCccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---cHHHHHHHHHHHHcCCCCCCCHHHH
Confidence            555555          44555555555555    566666666666655543   23333444444443    5555555


Q ss_pred             hh
Q 039275          137 KS  138 (153)
Q Consensus       137 ~~  138 (153)
                      ..
T Consensus       170 ~~  171 (273)
T 1ouv_A          170 LA  171 (273)
T ss_dssp             HH
T ss_pred             HH
Confidence            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=98.20  E-value=5.2e-05  Score=55.80  Aligned_cols=130  Identities=6%  Similarity=-0.134  Sum_probs=104.1

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCc-hHHHHHH-hhh--hhc-chhhHHHHHHHHHhcCCccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGA-WILAKEL-QIE--LDL-SSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~-~~~a~~~-~~~--~~~-~~~~~~~ll~~~~~~g~~~~   78 (153)
                      .+.+.|++++|++.|++..+.. +-+...|+.+-..+.+.|+ +++|.+. ..-  ..| +...|+.+-..+.+.|++++
T Consensus       106 ~~~~~g~~~~Al~~~~~al~l~-P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P~~~~a~~~~g~~~~~~g~~~e  184 (382)
T 2h6f_A          106 VLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLVEWLRDPSQ  184 (382)
T ss_dssp             HHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTT
T ss_pred             HHHHCCChHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHccCHHH
Confidence            4677899999999999998742 2356777888888889996 9999998 222  233 45678888899999999999


Q ss_pred             cc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcC-CCccccc
Q 039275           79 AR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSG-PGALDFG  136 (153)
Q Consensus        79 a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~-~g~~~~a  136 (153)
                      |.            +...|..+-..+.+.|++++|.+.|++..+..  | +...|..+-.++.+ .|..++|
T Consensus       185 Al~~~~kal~ldP~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~--P~~~~a~~~lg~~l~~l~~~~~eA  254 (382)
T 2h6f_A          185 ELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKED--VRNNSVWNQRYFVISNTTGYNDRA  254 (382)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCSCSHH
T ss_pred             HHHHHHHHHHhCccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhcCcchHH
Confidence            98            78889999999999999999999999998764  4 56677777788888 5554666

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=98.18  E-value=2.6e-05  Score=53.51  Aligned_cols=134  Identities=16%  Similarity=0.082  Sum_probs=100.7

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCcc--HHHHHHHHHHhcCCCchHHHHHH-hh--hh-hcchhhHHHHHHHHHhcCCc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTD--EVTMVVVLTASSGPGAWILAKEL-QI--EL-DLSSYSLSSKTSRYAHSGRI   76 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~--~~~~~~ll~~~~~~~~~~~a~~~-~~--~~-~~~~~~~~~ll~~~~~~g~~   76 (153)
                      ..|.+.|++++|++.|++..+..-.|+  ...|..+-..+...|++++|.+. ..  .. +.+...+..+...|.+.|++
T Consensus        45 ~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~  124 (272)
T 3u4t_A           45 VCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKILMKKGQDSLAIQQYQAAVDRDTTRLDMYGQIGSYFYNKGNF  124 (272)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHccCH
Confidence            467889999999999999988432222  33478888899999999999999 22  12 33556888899999999999


Q ss_pred             cccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC-hhhHHHHHHHhcCCCc---cccchh
Q 039275           77 RLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTD-EVTMVVVLAASSGPGA---LDFGKS  138 (153)
Q Consensus        77 ~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~---~~~a~~  138 (153)
                      ++|.            +...|..+-..+...+++++|.+.|++..+..  |+ ...+..+...+...|+   +++|..
T Consensus       125 ~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~--p~~~~~~~~~~~~~~~~~~~~~~~~A~~  200 (272)
T 3u4t_A          125 PLAIQYMEKQIRPTTTDPKVFYELGQAYYYNKEYVKADSSFVKVLELK--PNIYIGYLWRARANAAQDPDTKQGLAKP  200 (272)
T ss_dssp             HHHHHHHGGGCCSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHHSTTCSSCTTHH
T ss_pred             HHHHHHHHHHhhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC--ccchHHHHHHHHHHHHcCcchhhHHHHH
Confidence            9998            66777777634555669999999999998653  43 5566666667776676   666666

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=98.17  E-value=1.2e-05  Score=60.63  Aligned_cols=132  Identities=13%  Similarity=0.000  Sum_probs=106.3

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCC---------CchHHHHHH-hh--hhhc-chhhHHHHHHH
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGP---------GAWILAKEL-QI--ELDL-SSYSLSSKTSR   69 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~---------~~~~~a~~~-~~--~~~~-~~~~~~~ll~~   69 (153)
                      ..|.+.|++++|.+.|++..+.  .|+...+..+-..+...         |++++|.+. +.  ...| +...|..+-..
T Consensus       145 ~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~  222 (474)
T 4abn_A          145 EVYWKKGDVTSAHTCFSGALTH--CKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMDVLDGRSWYILGNA  222 (474)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHTT--CCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhh--CCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            3678899999999999999875  47788888888999999         999999998 22  2233 45677788888


Q ss_pred             HHhc--------CCccccc---------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHH
Q 039275           70 YAHS--------GRIRLAR---------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLA  125 (153)
Q Consensus        70 ~~~~--------g~~~~a~---------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~  125 (153)
                      |...        |++++|.               +...|..+-..|...|++++|.+.|++..+..  | +...+..+-.
T Consensus       223 ~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~--p~~~~a~~~l~~  300 (474)
T 4abn_A          223 YLSLYFNTGQNPKISQQALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALD--PAWPEPQQREQQ  300 (474)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHH
T ss_pred             HHHHHHhhccccchHHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHH
Confidence            8887        8888877               45678889999999999999999999988653  4 4456777778


Q ss_pred             HhcCCCccccchh
Q 039275          126 ASSGPGALDFGKS  138 (153)
Q Consensus       126 ~~~~~g~~~~a~~  138 (153)
                      .+...|++++|.+
T Consensus       301 ~~~~lg~~~eAi~  313 (474)
T 4abn_A          301 LLEFLSRLTSLLE  313 (474)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            8888888887776

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=98.15  E-value=3.7e-05  Score=55.84  Aligned_cols=135  Identities=8%  Similarity=-0.045  Sum_probs=104.0

Q ss_pred             hHhhcCChhHHHHHHHHhHHc----CCCc-cHHHHHHHHHHhcCCCchHHHHHH-hhh----------hhcchhhHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESL----GVHT-DEVTMVVVLTASSGPGAWILAKEL-QIE----------LDLSSYSLSSKT   67 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~~~~~ll~~~~~~~~~~~a~~~-~~~----------~~~~~~~~~~ll   67 (153)
                      .+...|++++|++.|++..+.    +-.+ ...++..+-..+...|++++|.+. ...          ......+++.+-
T Consensus       112 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg  191 (383)
T 3ulq_A          112 YELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHSLFA  191 (383)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHHHHH
T ss_pred             HHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHHHHH
Confidence            456789999999999998653    2222 346777777888999999998888 111          112235677788


Q ss_pred             HHHHhcCCccccc------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc----CC-CCChhhHHHHH
Q 039275           68 SRYAHSGRIRLAR------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESL----GV-HTDEVTMVVVL  124 (153)
Q Consensus        68 ~~~~~~g~~~~a~------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~-~p~~~t~~~li  124 (153)
                      ..|...|++++|.                  ...+|..+-..|...|++++|.+.|++..+.    +- .....++..+-
T Consensus       192 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~  271 (383)
T 3ulq_A          192 TNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLIT  271 (383)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHHH
Confidence            9999999999998                  2247888999999999999999999988752    33 23466788888


Q ss_pred             HHhcCCCccccchh
Q 039275          125 AASSGPGALDFGKS  138 (153)
Q Consensus       125 ~~~~~~g~~~~a~~  138 (153)
                      ..+.+.|++++|.+
T Consensus       272 ~~~~~~g~~~~A~~  285 (383)
T 3ulq_A          272 QIHYKLGKIDKAHE  285 (383)
T ss_dssp             HHHHHTTCHHHHHH
T ss_pred             HHHHHCCCHHHHHH
Confidence            99999999999988

>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=98.14  E-value=0.00017  Score=49.73  Aligned_cols=42  Identities=10%  Similarity=-0.082  Sum_probs=20.5

Q ss_pred             cCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcC----CCchHHHHHH
Q 039275            8 AGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSG----PGAWILAKEL   52 (153)
Q Consensus         8 ~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~----~~~~~~a~~~   52 (153)
                      .+++++|++.|++..+.+   ++..+..+-..+..    .+++++|.++
T Consensus        55 ~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~  100 (273)
T 1ouv_A           55 EKNLKKAASFYAKACDLN---YSNGCHLLGNLYYSGQGVSQNTNKALQY  100 (273)
T ss_dssp             CCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHhCCCCcccCHHHHHHH
Confidence            455555555555554443   33344444444444    5555555555

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=98.11  E-value=2.1e-05  Score=51.08  Aligned_cols=134  Identities=16%  Similarity=0.056  Sum_probs=94.3

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hh--hhhcchhhHHHHHHH-HHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QI--ELDLSSYSLSSKTSR-YAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~--~~~~~~~~~~~ll~~-~~~~g~~~~a   79 (153)
                      .+.+.|++++|...|++..+. -+-+...+..+-..+.+.|++++|... +.  ...|+......+... +.+.+...+|
T Consensus        15 ~~~~~g~~~~A~~~~~~al~~-~P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~a   93 (176)
T 2r5s_A           15 ELLQQGEHAQALNVIQTLSDE-LQSRGDVKLAKADCLLETKQFELAQELLATIPLEYQDNSYKSLIAKLELHQQAAESPE   93 (176)
T ss_dssp             HHHHTTCHHHHHHHHHTSCHH-HHTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGGCCHHHHHHHHHHHHHHHHTSCHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHH-CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhccCChHHHHHHHHHHHHhhcccchH
Confidence            577899999999999987653 123566777778888999999999998 11  123333222221111 1121122112


Q ss_pred             c------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           80 R------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        80 ~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .            +...+..+-..+...|++++|.+.|++..+....+ +...+..+...+...|+.++|..
T Consensus        94 ~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~  165 (176)
T 2r5s_A           94 LKRLEQELAANPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIAS  165 (176)
T ss_dssp             HHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHH
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHH
Confidence            2            67888889999999999999999999998765333 35678889999999999998876

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=98.07  E-value=8.5e-05  Score=48.13  Aligned_cols=112  Identities=19%  Similarity=0.118  Sum_probs=88.6

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH---hhhh-hcchhhHHHHHHHHHhcCCccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL---QIEL-DLSSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~---~~~~-~~~~~~~~~ll~~~~~~g~~~~   78 (153)
                      ..|.+.|++++|++.+.+..... +-+...+..+-..+...++++.+.+.   -... +.+...+..+-..|.+.|++++
T Consensus        47 ~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~lg~~~~~~g~~~~  125 (184)
T 3vtx_A           47 KTYMDIGLPNDAIESLKKFVVLD-TTSAEAYYILGSANFMIDEKQAAIDALQRAIALNTVYADAYYKLGLVYDSMGEHDK  125 (184)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHhcC-chhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHhCCchh
Confidence            36788999999999999987653 23455566666777888999998888   1222 3345677888899999999999


Q ss_pred             cc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCh
Q 039275           79 AR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDE  117 (153)
Q Consensus        79 a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  117 (153)
                      |.            +...|..+-..+.+.|++++|.+.|++..+.  .|+.
T Consensus       126 A~~~~~~~l~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~  174 (184)
T 3vtx_A          126 AIEAYEKTISIKPGFIRAYQSIGLAYEGKGLRDEAVKYFKKALEK--EEKK  174 (184)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--THHH
T ss_pred             HHHHHHHHHHhcchhhhHHHHHHHHHHHCCCHHHHHHHHHHHHhC--CccC
Confidence            98            7788999999999999999999999998753  4554

>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=98.04  E-value=6.6e-05  Score=63.22  Aligned_cols=120  Identities=13%  Similarity=0.141  Sum_probs=57.7

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH---hhhhhcchhhHHHHHHHHHhcCCccccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL---QIELDLSSYSLSSKTSRYAHSGRIRLAR   80 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~~~~~~~~ll~~~~~~g~~~~a~   80 (153)
                      ++.+.|++++|++-|.+-      -|...|.-+..++.+.|+++++.++   -....++....+.+..+|++.+++++..
T Consensus      1114 Aql~~G~~kEAIdsYiKA------dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~~e~~Idt~LafaYAKl~rleele 1187 (1630)
T 1xi4_A         1114 AQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYVETELIFALAKTNRLAELE 1187 (1630)
T ss_pred             HHHhCCCHHHHHHHHHhc------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhcccccccHHHHHHHHhhcCHHHHH
Confidence            444555666666655432      3455555566666666666666665   1122233333444555555555554333


Q ss_pred             ------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 ------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                            +...|..+-..|...|++++|..+|+..         ..|..+...+++.|+++.|.+
T Consensus      1188 ~fI~~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIE 1242 (1630)
T 1xi4_A         1188 EFINGPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVD 1242 (1630)
T ss_pred             HHHhCCCHHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHH
Confidence                  2233334444444444444444444442         244444444444444444444

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.02  E-value=9.1e-05  Score=52.05  Aligned_cols=134  Identities=14%  Similarity=0.004  Sum_probs=99.1

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHHhh---hhhcchhhHHHH-HHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQI---ELDLSSYSLSSK-TSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~---~~~~~~~~~~~l-l~~~~~~g~~~~a   79 (153)
                      .+.+.|++++|...|++..+.. +-+...+..+-..+.+.|++++|...-.   ...|+....... ...+.+.++.++|
T Consensus       126 ~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~~~~~~~l~~~~~~~~a  204 (287)
T 3qou_A          126 QLMQESNYTDALPLLXDAWQLS-NQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQDQDTRYQGLVAQIELLXQAADTPE  204 (287)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHT-TSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGGCSHHHHHHHHHHHHHHHHTSCHH
T ss_pred             HHHhCCCHHHHHHHHHHHHHhC-CcchhHHHHHHHHHHHCCCHHHHHHHHHhCchhhcchHHHHHHHHHHHHhhcccCcc
Confidence            4678899999999999987742 2356677778889999999999999911   223443322222 2234555665544


Q ss_pred             c------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCC-CChhhHHHHHHHhcCCCccccchh
Q 039275           80 R------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVH-TDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        80 ~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~-p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .            +...+..+-..+...|++++|.+.|.+..+..-. .+...+..+...+...|+.+++..
T Consensus       205 ~~~l~~al~~~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~a~~  276 (287)
T 3qou_A          205 IQQLQQQVAENPEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTGDALAS  276 (287)
T ss_dssp             HHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTTCHHHH
T ss_pred             HHHHHHHHhcCCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCCCcHHH
Confidence            4            6788889999999999999999999999876422 236678899999999999888766

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=98.01  E-value=2.7e-05  Score=59.71  Aligned_cols=129  Identities=15%  Similarity=0.024  Sum_probs=70.9

Q ss_pred             cCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhh--hhc-chhhHHHHHHHHHhcCCccccc---
Q 039275            8 AGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIE--LDL-SSYSLSSKTSRYAHSGRIRLAR---   80 (153)
Q Consensus         8 ~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~--~~~-~~~~~~~ll~~~~~~g~~~~a~---   80 (153)
                      .|++++|.+.|++..+. -+-+...+..+-..+.+.|++++|.+. +.-  ..| +...+..+-..|.+.|++++|.   
T Consensus         2 ~g~~~~A~~~~~~al~~-~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~   80 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRH-RPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRVRWTQQRHAEAAVLL   80 (568)
T ss_dssp             --------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTSTTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            35677777777766543 122355666666667777777777776 221  222 3445666667777777777776   


Q ss_pred             ---------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCC---Cccccchh
Q 039275           81 ---------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGP---GALDFGKS  138 (153)
Q Consensus        81 ---------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~---g~~~~a~~  138 (153)
                               +...|..+-..+.+.|++++|.+.|++..+.. .-+...+..+...+...   |+.++|.+
T Consensus        81 ~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~g~~~~A~~  149 (568)
T 2vsy_A           81 QQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLL-PEEPYITAQLLNWRRRLCDWRALDVLSA  149 (568)
T ss_dssp             HHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCTTHHHHHH
T ss_pred             HHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhhccccHHHHHH
Confidence                     55677777777777778888877777776543 12345566666677777   66666655

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=97.97  E-value=0.00013  Score=51.60  Aligned_cols=131  Identities=7%  Similarity=-0.094  Sum_probs=97.6

Q ss_pred             hcCCh-------hHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hh--hhhcch-h-hHHHHHHHHHhcC
Q 039275            7 QAGRF-------NEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QI--ELDLSS-Y-SLSSKTSRYAHSG   74 (153)
Q Consensus         7 ~~g~~-------~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~--~~~~~~-~-~~~~ll~~~~~~g   74 (153)
                      +.|++       ++|...|++..+.--+-+...|..+...+.+.|++++|.++ +.  ...|+. . .|..+...+.+.|
T Consensus        69 ~~g~~~~~~~~~~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~  148 (308)
T 2ond_A           69 EKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAE  148 (308)
T ss_dssp             HTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHH
T ss_pred             hccchhhcccchHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccccCccHHHHHHHHHHHHhc
Confidence            45776       89999999988742233566888888999999999999998 22  234543 3 7889999999999


Q ss_pred             Cccccc------------hHHHHHHHHHHH-HhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           75 RIRLAR------------DPVSCKAMISGY-SQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        75 ~~~~a~------------~~~~~~~li~~~-~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ++++|.            +...|....... ...|+.++|.++|++..+.. .-+...|..++..+.+.|++++|..
T Consensus       149 ~~~~A~~~~~~a~~~~p~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~A~~  224 (308)
T 2ond_A          149 GIKSGRMIFKKAREDARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRV  224 (308)
T ss_dssp             CHHHHHHHHHHHHTSTTCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHH
T ss_pred             CHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHH
Confidence            999987            223333222221 23699999999999987642 2266788889999999999999887

>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=97.96  E-value=0.00011  Score=61.88  Aligned_cols=133  Identities=9%  Similarity=0.069  Sum_probs=85.5

Q ss_pred             hhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHHhhhhhcchhhHHHHHHHHHhcCCccccc-
Q 039275            2 ISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIELDLSSYSLSSKTSRYAHSGRIRLAR-   80 (153)
Q Consensus         2 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~ll~~~~~~g~~~~a~-   80 (153)
                      +..|.+.|++++|++++..-++..  +++...+-+..+|++.+++++...+..  .++...|..+-..|...|++++|. 
T Consensus      1141 a~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~LafaYAKl~rleele~fI~--~~n~ad~~~iGd~le~eg~YeeA~~ 1216 (1630)
T 1xi4_A         1141 VQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKTNRLAELEEFIN--GPNNAHIQQVGDRCYDEKMYDAAKL 1216 (1630)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHHHHhhcCHHHHHHHHh--CCCHHHHHHHHHHHHhcCCHHHHHH
Confidence            567889999999999998766654  333333347888888888887666532  233344555667777777777777 


Q ss_pred             ---hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc------------------------CCCCChhhHHHHHHHhcCCCcc
Q 039275           81 ---DPVSCKAMISGYSQAGRFNEALEPFGKLESL------------------------GVHTDEVTMVVVLAASSGPGAL  133 (153)
Q Consensus        81 ---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~------------------------g~~p~~~t~~~li~~~~~~g~~  133 (153)
                         ....|..+...+++.|++++|.+.+++-...                        ++..+...+..++..|.+.|.+
T Consensus      1217 ~Y~kA~ny~rLA~tLvkLge~q~AIEaarKA~n~~aWkev~~acve~~Ef~LA~~cgl~Iiv~~deLeeli~yYe~~G~f 1296 (1630)
T 1xi4_A         1217 LYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYF 1296 (1630)
T ss_pred             HHHhhhHHHHHHHHHHHhCCHHHHHHHHHHhCCHHHHHHHHHHHhhhhHHHHHHHHHHhhhcCHHHHHHHHHHHHHcCCH
Confidence               5567777777777777777777766543211                        0112333455666666666666


Q ss_pred             ccchh
Q 039275          134 DFGKS  138 (153)
Q Consensus       134 ~~a~~  138 (153)
                      ++|..
T Consensus      1297 eEAI~ 1301 (1630)
T 1xi4_A         1297 EELIT 1301 (1630)
T ss_pred             HHHHH
Confidence            66665

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=97.96  E-value=0.00011  Score=51.62  Aligned_cols=136  Identities=10%  Similarity=-0.057  Sum_probs=98.4

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCC-ccH----HHHHHHHHHhcCCCchHHHHHH-hhhh-------hcc--hhhHHHHH
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVH-TDE----VTMVVVLTASSGPGAWILAKEL-QIEL-------DLS--SYSLSSKT   67 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~-p~~----~~~~~ll~~~~~~~~~~~a~~~-~~~~-------~~~--~~~~~~ll   67 (153)
                      ..+...|++++|.+.+++..+..-. ++.    ..+..+-..+...|++++|.+. ...+       .+.  ..+++.+-
T Consensus        83 ~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg  162 (293)
T 2qfc_A           83 IMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIA  162 (293)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHHHHHHHH
T ss_pred             HHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHH
Confidence            4577899999999999887664322 111    2233344566788899999887 2111       111  34778888


Q ss_pred             HHHHhcCCccccc-------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc----CCCC-ChhhHHHH
Q 039275           68 SRYAHSGRIRLAR-------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESL----GVHT-DEVTMVVV  123 (153)
Q Consensus        68 ~~~~~~g~~~~a~-------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~t~~~l  123 (153)
                      ..|...|++++|.                   ...+|+.+-..|.+.|++++|.+.+++..+.    +..+ -..+|..+
T Consensus       163 ~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~~~~~~l  242 (293)
T 2qfc_A          163 NIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQR  242 (293)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHH
Confidence            9999999999988                   1268888999999999999999999987633    2111 25678888


Q ss_pred             HHHhcCCCccccc-hh
Q 039275          124 LAASSGPGALDFG-KS  138 (153)
Q Consensus       124 i~~~~~~g~~~~a-~~  138 (153)
                      -..+.+.|++++| ..
T Consensus       243 g~~y~~~g~~~~Ai~~  258 (293)
T 2qfc_A          243 GECLRKLEYEEAEIED  258 (293)
T ss_dssp             HHHHHHTTCCHHHHHH
T ss_pred             HHHHHHcCCcHHHHHH
Confidence            8899999999998 44

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=97.94  E-value=5e-05  Score=53.05  Aligned_cols=134  Identities=12%  Similarity=0.027  Sum_probs=76.3

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCcc----HHHHHHHHHHhcCCCchHHHHHH-hh--------h-hhcchhhHHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTD----EVTMVVVLTASSGPGAWILAKEL-QI--------E-LDLSSYSLSSKTSR   69 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~----~~~~~~ll~~~~~~~~~~~a~~~-~~--------~-~~~~~~~~~~ll~~   69 (153)
                      .+.+.|++++|...|++..+..- .+    ...+..+-..+...|++++|.+. ..        + .+.....+..+...
T Consensus        14 ~~~~~g~~~~A~~~~~~al~~~~-~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~   92 (338)
T 3ro2_A           14 RLCKSGDCRAGVSFFEAAVQVGT-EDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNT   92 (338)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCC-SCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHhccHHHHHHHHHHHHhhCc-ccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHHH
Confidence            45667777777777777766421 12    35566666677777777777766 10        0 11123455556666


Q ss_pred             HHhcCCccccc------------------hHHHHHHHHHHHHhcCC--------------------hHHHHHHHHHHHHc
Q 039275           70 YAHSGRIRLAR------------------DPVSCKAMISGYSQAGR--------------------FNEALEPFGKLESL  111 (153)
Q Consensus        70 ~~~~g~~~~a~------------------~~~~~~~li~~~~~~g~--------------------~~~a~~~~~~m~~~  111 (153)
                      |...|++++|.                  ...++..+-..+...|+                    +++|.+.+++....
T Consensus        93 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a~~~  172 (338)
T 3ro2_A           93 LKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDLYEENLSL  172 (338)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHH
Confidence            66777776666                  12355566666666666                    66666666554321


Q ss_pred             ----CCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275          112 ----GVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       112 ----g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                          +-.| ....+..+...+...|++++|.+
T Consensus       173 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~  204 (338)
T 3ro2_A          173 VTALGDRAAQGRAFGNLGNTHYLLGNFRDAVI  204 (338)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHH
Confidence                1111 12345555556666666666655

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=97.93  E-value=3.1e-05  Score=56.36  Aligned_cols=49  Identities=14%  Similarity=0.026  Sum_probs=25.3

Q ss_pred             hHhhcCChhHHHHHHHHhHHc----C-CCccHHHHHHHHHHhcCCCchHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESL----G-VHTDEVTMVVVLTASSGPGAWILAKEL   52 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~----g-~~p~~~~~~~ll~~~~~~~~~~~a~~~   52 (153)
                      .|...|++++|.+.|++..+.    + .+.....+..+-..+...|++++|.+.
T Consensus        95 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  148 (411)
T 4a1s_A           95 AYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGNLGNTLKVMGRFDEAAIC  148 (411)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHCCCHHHHHHH
Confidence            345556666666666555332    1 112234444555555666666666555

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=97.92  E-value=7.8e-05  Score=51.23  Aligned_cols=134  Identities=12%  Similarity=0.087  Sum_probs=93.4

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCcc---HHHHHHHHHHhcCCCchHHHHHH-hh--hhhcc----hhhHHHHHHHHHh-
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTD---EVTMVVVLTASSGPGAWILAKEL-QI--ELDLS----SYSLSSKTSRYAH-   72 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~---~~~~~~ll~~~~~~~~~~~a~~~-~~--~~~~~----~~~~~~ll~~~~~-   72 (153)
                      .+.+.|++++|++.|+++.+.. +-+   ...+..+-.++.+.|++++|... ..  ...|+    ...+..+-..+.+ 
T Consensus        24 ~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~  102 (261)
T 3qky_A           24 EFYNQGKYDRAIEYFKAVFTYG-RTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAEYERAMCYYKL  102 (261)
T ss_dssp             HHHHTTCHHHHHHHHHHHGGGC-SCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHH
T ss_pred             HHHHhCCHHHHHHHHHHHHHhC-CCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHHh
Confidence            5678999999999999997753 112   56677777888999999999998 21  22232    2345556667777 


Q ss_pred             -------cCCccccc------------hHHHH-----------------HHHHHHHHhcCChHHHHHHHHHHHHcCCC-C
Q 039275           73 -------SGRIRLAR------------DPVSC-----------------KAMISGYSQAGRFNEALEPFGKLESLGVH-T  115 (153)
Q Consensus        73 -------~g~~~~a~------------~~~~~-----------------~~li~~~~~~g~~~~a~~~~~~m~~~g~~-p  115 (153)
                             .|++++|.            +...+                 -.+-..|.+.|++++|...|++..+.... |
T Consensus       103 ~~~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~  182 (261)
T 3qky_A          103 SPPYELDQTDTRKAIEAFQLFIDRYPNHELVDDATQKIRELRAKLARKQYEAARLYERRELYEAAAVTYEAVFDAYPDTP  182 (261)
T ss_dssp             CCCTTSCCHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTST
T ss_pred             cccccccchhHHHHHHHHHHHHHHCcCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCCc
Confidence                   88888887            22233                 34567788999999999999999865421 1


Q ss_pred             -ChhhHHHHHHHhcCC----------Cccccchh
Q 039275          116 -DEVTMVVVLAASSGP----------GALDFGKS  138 (153)
Q Consensus       116 -~~~t~~~li~~~~~~----------g~~~~a~~  138 (153)
                       ....+..+..++.+.          |++++|..
T Consensus       183 ~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~  216 (261)
T 3qky_A          183 WADDALVGAMRAYIAYAEQSVRARQPERYRRAVE  216 (261)
T ss_dssp             THHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhcccchhhcccchHHHHHH
Confidence             234566677777766          66666666

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=97.91  E-value=0.00029  Score=41.90  Aligned_cols=90  Identities=23%  Similarity=0.314  Sum_probs=63.7

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccch
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARD   81 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~   81 (153)
                      ..+.+.|++++|.+.|+++.+.. +.+...+..+...+.+.|++++|..+ ...+..+..                   +
T Consensus        17 ~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~-------------------~   76 (125)
T 1na0_A           17 NAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPN-------------------N   76 (125)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------C
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCc-------------------c
Confidence            35677888888888888886652 34566777777788888888888777 222211110                   3


Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 039275           82 PVSCKAMISGYSQAGRFNEALEPFGKLESLG  112 (153)
Q Consensus        82 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  112 (153)
                      ...|..+...+...|++++|.+.|++..+..
T Consensus        77 ~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  107 (125)
T 1na0_A           77 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD  107 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC
Confidence            3567778888899999999999999887653

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=97.90  E-value=5.4e-05  Score=54.96  Aligned_cols=134  Identities=13%  Similarity=-0.022  Sum_probs=101.6

Q ss_pred             HhhcCChhHHHHHHHHhHHcC-CCc----cHHHHHHHHHHhcCCCchHHHHHH-------hhh---hh-cchhhHHHHHH
Q 039275            5 YSQAGRFNEALEPFGKLESLG-VHT----DEVTMVVVLTASSGPGAWILAKEL-------QIE---LD-LSSYSLSSKTS   68 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g-~~p----~~~~~~~ll~~~~~~~~~~~a~~~-------~~~---~~-~~~~~~~~ll~   68 (153)
                      +...|++++|++.|++..+.- -.+    ...++..+-..+...|++++|...       ...   .. ....+++.+-.
T Consensus       111 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~  190 (378)
T 3q15_A          111 EFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIAG  190 (378)
T ss_dssp             HHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHH
T ss_pred             HHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHH
Confidence            567899999999999886531 112    245677777788999999988887       111   01 12456777888


Q ss_pred             HHHhcCCccccc------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc----CCCCChhhHHHHHHH
Q 039275           69 RYAHSGRIRLAR------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESL----GVHTDEVTMVVVLAA  126 (153)
Q Consensus        69 ~~~~~g~~~~a~------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~~~t~~~li~~  126 (153)
                      .|...|++++|.                  ...+++.+-..+...|++++|.+.|++....    +-.....++..+-..
T Consensus       191 ~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~  270 (378)
T 3q15_A          191 NYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWT  270 (378)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHH
T ss_pred             HHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHHHH
Confidence            999999999998                  2457788888999999999999999988751    222336778888889


Q ss_pred             hcCCCccccchh
Q 039275          127 SSGPGALDFGKS  138 (153)
Q Consensus       127 ~~~~g~~~~a~~  138 (153)
                      +.+.|++++|.+
T Consensus       271 ~~~~g~~~~A~~  282 (378)
T 3q15_A          271 LCKAGQTQKAFQ  282 (378)
T ss_dssp             HHHTTCHHHHHH
T ss_pred             HHHCCCHHHHHH
Confidence            999999999988

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=97.90  E-value=6.3e-05  Score=49.22  Aligned_cols=133  Identities=11%  Similarity=-0.066  Sum_probs=92.1

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hh---------hhhcchhhHHHHHHHHHhcC
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QI---------ELDLSSYSLSSKTSRYAHSG   74 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~---------~~~~~~~~~~~ll~~~~~~g   74 (153)
                      ....|++++|.+.++.+... .......+..+-..+...|++++|... ..         ........+..+-..|...|
T Consensus         2 ~~~~g~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g   80 (203)
T 3gw4_A            2 AFEAHDYALAERQAQALLAH-PATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAG   80 (203)
T ss_dssp             -----CHHHHHHHHHHHHTS-TTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTT
T ss_pred             ccccccHHHHHHHHHHhcCC-hHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcC
Confidence            35678999999965555432 223567777888888889999998888 11         11223456777778888999


Q ss_pred             Cccccc-------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcC---CCC--ChhhHHHHHHHhcCC
Q 039275           75 RIRLAR-------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLG---VHT--DEVTMVVVLAASSGP  130 (153)
Q Consensus        75 ~~~~a~-------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g---~~p--~~~t~~~li~~~~~~  130 (153)
                      ++++|.                   ....+..+-..+...|++++|.+.+++.....   -.|  -..++..+-..+...
T Consensus        81 ~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~  160 (203)
T 3gw4_A           81 NWDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQE  160 (203)
T ss_dssp             CHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHC
Confidence            988888                   13457777888899999999999998876331   111  233457778889999


Q ss_pred             Cccccchh
Q 039275          131 GALDFGKS  138 (153)
Q Consensus       131 g~~~~a~~  138 (153)
                      |++++|.+
T Consensus       161 g~~~~A~~  168 (203)
T 3gw4_A          161 KNLLEAQQ  168 (203)
T ss_dssp             TCHHHHHH
T ss_pred             cCHHHHHH
Confidence            99999987

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=97.90  E-value=6.7e-05  Score=54.55  Aligned_cols=134  Identities=14%  Similarity=0.037  Sum_probs=90.7

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccH----HHHHHHHHHhcCCCchHHHHHH-hhh---------hhcchhhHHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDE----VTMVVVLTASSGPGAWILAKEL-QIE---------LDLSSYSLSSKTSR   69 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~----~~~~~ll~~~~~~~~~~~a~~~-~~~---------~~~~~~~~~~ll~~   69 (153)
                      .+...|++++|++.|++..+.+- .+.    ..+..+-..+...|++++|.+. +..         .+.....+..+-..
T Consensus        57 ~~~~~g~~~~A~~~~~~al~~~~-~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~  135 (411)
T 4a1s_A           57 RLCNAGDCRAGVAFFQAAIQAGT-EDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGNLGNT  135 (411)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCC-SCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHhCcHHHHHHHHHHHHHhcc-cChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHHHHHHH
Confidence            56788999999999999987632 222    4677778888899999999888 111         12334566777788


Q ss_pred             HHhcCCccccc------------------hHHHHHHHHHHHHhcCC-----------------hHHHHHHHHHHHHc---
Q 039275           70 YAHSGRIRLAR------------------DPVSCKAMISGYSQAGR-----------------FNEALEPFGKLESL---  111 (153)
Q Consensus        70 ~~~~g~~~~a~------------------~~~~~~~li~~~~~~g~-----------------~~~a~~~~~~m~~~---  111 (153)
                      |...|++++|.                  ...+|..+-..+...|+                 +++|.+.+++..+.   
T Consensus       136 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~  215 (411)
T 4a1s_A          136 LKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQENLKLMRD  215 (411)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence            88888888877                  23466666677777777                 77777777665421   


Q ss_pred             -CCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275          112 -GVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       112 -g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                       +-.| ....+..+-..+...|++++|.+
T Consensus       216 ~~~~~~~~~~~~~la~~~~~~g~~~~A~~  244 (411)
T 4a1s_A          216 LGDRGAQGRACGNLGNTYYLLGDFQAAIE  244 (411)
T ss_dssp             HTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHHHcCChHHHHH
Confidence             1111 22355666666777777777666

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=97.88  E-value=6.6e-05  Score=52.43  Aligned_cols=135  Identities=13%  Similarity=0.064  Sum_probs=88.0

Q ss_pred             hHhhcCChhHHHHHHHHhHHc----CCCc-cHHHHHHHHHHhcCCCc--------------------hHHHHHH-hh---
Q 039275            4 GYSQAGRFNEALEPFGKLESL----GVHT-DEVTMVVVLTASSGPGA--------------------WILAKEL-QI---   54 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~~~~~ll~~~~~~~~--------------------~~~a~~~-~~---   54 (153)
                      .|...|++++|.+.|++..+.    +-.+ ...++..+-..+...|+                    +++|.+. ..   
T Consensus        92 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a~~  171 (338)
T 3ro2_A           92 TLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDLYEENLS  171 (338)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHHHHHHHH
Confidence            466778888888888776442    1111 13366666667777777                    7777666 11   


Q ss_pred             -----h-hhcchhhHHHHHHHHHhcCCccccc------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHH
Q 039275           55 -----E-LDLSSYSLSSKTSRYAHSGRIRLAR------------------DPVSCKAMISGYSQAGRFNEALEPFGKLES  110 (153)
Q Consensus        55 -----~-~~~~~~~~~~ll~~~~~~g~~~~a~------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  110 (153)
                           + .......+..+...+...|++++|.                  ...+|..+...+...|++++|.+.+++...
T Consensus       172 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  251 (338)
T 3ro2_A          172 LVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLL  251 (338)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                 0 1112345666777788888888877                  233777777888888888888888887653


Q ss_pred             cC----CCC-ChhhHHHHHHHhcCCCccccchh
Q 039275          111 LG----VHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       111 ~g----~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ..    -.+ ...++..+-..+...|++++|..
T Consensus       252 ~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  284 (338)
T 3ro2_A          252 LARQLKDRAVEAQSCYSLGNTYTLLQDYEKAID  284 (338)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHH
Confidence            21    111 14566777778888888888877

>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=97.88  E-value=0.00047  Score=50.70  Aligned_cols=145  Identities=8%  Similarity=-0.065  Sum_probs=104.1

Q ss_pred             hHhhcCC-hhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhh--hc-chhhHHHHHHHHHhcCCccc
Q 039275            4 GYSQAGR-FNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIEL--DL-SSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         4 ~~~~~g~-~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~--~~-~~~~~~~ll~~~~~~g~~~~   78 (153)
                      .+.+.|+ +++|+..|++..+.. +-+...|..+-.++.+.|++++|... ..-+  .| +...|..+-..+.+.|++++
T Consensus       140 ~l~~~g~d~~eAl~~~~~al~l~-P~~~~a~~~~g~~~~~~g~~~eAl~~~~kal~ldP~~~~a~~~lg~~~~~~g~~~e  218 (382)
T 2h6f_A          140 LLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRRVLVEWLRDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDN  218 (382)
T ss_dssp             HHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTT
T ss_pred             HHHHcccCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCccCHHHHHHHHHHHHHcCChHH
Confidence            4667786 999999999997752 23567777778888888999998888 2222  33 45677888888999999999


Q ss_pred             cc------------hHHHHHHHHHHHHh-cCChHHH-----HHHHHHHHHcCCCC-ChhhHHHHHHHhcCCC--ccccch
Q 039275           79 AR------------DPVSCKAMISGYSQ-AGRFNEA-----LEPFGKLESLGVHT-DEVTMVVVLAASSGPG--ALDFGK  137 (153)
Q Consensus        79 a~------------~~~~~~~li~~~~~-~g~~~~a-----~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g--~~~~a~  137 (153)
                      |.            +...|+.+-..+.+ .|..++|     .+.|++....  .| +...|..+-..+.+.|  +++++.
T Consensus       219 Al~~~~~al~l~P~~~~a~~~lg~~l~~l~~~~~eA~~~~el~~~~~Al~l--~P~~~~a~~~l~~ll~~~g~~~~~~a~  296 (382)
T 2h6f_A          219 ELQYVDQLLKEDVRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKL--VPHNESAWNYLKGILQDRGLSKYPNLL  296 (382)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHH--STTCHHHHHHHHHHHTTTCGGGCHHHH
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHccCccchHHHH
Confidence            88            77888888888888 6665777     4777776653  45 4556777777788877  455555


Q ss_pred             h----------HHHHHHHHHHHhh
Q 039275          138 S----------NIFLTTAIIEMYA  151 (153)
Q Consensus       138 ~----------~~~~~~~li~~y~  151 (153)
                      +          +...+..|.+.|.
T Consensus       297 ~~~~~~~~~p~~~~al~~La~~~~  320 (382)
T 2h6f_A          297 NQLLDLQPSHSSPYLIAFLVDIYE  320 (382)
T ss_dssp             HHHHHHTTTCCCHHHHHHHHHHHH
T ss_pred             HHHHHhccCCCCHHHHHHHHHHHH
Confidence            4          3445555555543

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=97.88  E-value=0.00014  Score=45.84  Aligned_cols=114  Identities=11%  Similarity=0.060  Sum_probs=71.8

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDP   82 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~   82 (153)
                      .+...|++++|.+.|++..+.. +.+...+..+-..+...|++++|.+. ...+..+..                   +.
T Consensus        22 ~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~-------------------~~   81 (166)
T 1a17_A           22 DYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKK-------------------YI   81 (166)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CH
T ss_pred             HHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcc-------------------cH
Confidence            4678899999999999887642 33577777778888889999998888 222221110                   22


Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhH--HHHHHHhcCCCccccchh
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTM--VVVLAASSGPGALDFGKS  138 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~--~~li~~~~~~g~~~~a~~  138 (153)
                      ..|..+-..+...|++++|.+.|++...... .+...+  ......+.+.|++++|.+
T Consensus        82 ~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~p-~~~~~~~~~~~~~~~~~~~~~~~A~~  138 (166)
T 1a17_A           82 KGYYRRAASNMALGKFRAALRDYETVVKVKP-HDKDAKMKYQECNKIVKQKAFERAIA  138 (166)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555666667777777777777777665421 122222  333333556666666665

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=97.87  E-value=0.0006  Score=41.84  Aligned_cols=95  Identities=7%  Similarity=0.015  Sum_probs=68.6

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDP   82 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~   82 (153)
                      .|.+.|++++|++.|++..+. -+.+...|..+-.++.+.|++++|.+. ..-+..+..                   +.
T Consensus        22 ~~~~~g~~~~A~~~~~~al~~-~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~-------------------~~   81 (126)
T 4gco_A           22 EYFKKGDYPTAMRHYNEAVKR-DPENAILYSNRAACLTKLMEFQRALDDCDTCIRLDSK-------------------FI   81 (126)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CH
T ss_pred             HHHHcCCHHHHHHHHHHHHHh-CCCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhh-------------------hh
Confidence            467888888888888887664 234567777777888888888888877 333322221                   34


Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhH
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTM  120 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~  120 (153)
                      ..|..+-..+...|++++|.+.|++..+.  .|+....
T Consensus        82 ~a~~~lg~~~~~~~~~~~A~~~~~~al~l--~P~~~~a  117 (126)
T 4gco_A           82 KGYIRKAACLVAMREWSKAQRAYEDALQV--DPSNEEA  117 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHH--CcCCHHH
Confidence            66778888899999999999999988764  5654433

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=97.86  E-value=0.00029  Score=53.45  Aligned_cols=133  Identities=12%  Similarity=0.040  Sum_probs=95.7

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCcc-H-HHHHHHHHHhcCCCchHHHHHH-hhhh--hcc-hhhHHHHHH-HHHhcCCc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTD-E-VTMVVVLTASSGPGAWILAKEL-QIEL--DLS-SYSLSSKTS-RYAHSGRI   76 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~-~-~~~~~ll~~~~~~~~~~~a~~~-~~~~--~~~-~~~~~~ll~-~~~~~g~~   76 (153)
                      .+.+.|++++|.++|++..+.  .|+ . ..|......+.+.|++++|.++ ...+  .|+ ...+..... .+...|+.
T Consensus       330 ~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~~~~~~~~~~~a~~~~~~~~~~  407 (530)
T 2ooe_A          330 YEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYVTAALMEYYCSKDK  407 (530)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHS--SSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCCTHHHHHHHHHHHHHTCCH
T ss_pred             HHHhcCCHHHHHHHHHHHhCc--cccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhccCCchHHHHHHHHHHHHHcCCh
Confidence            456789999999999999874  454 2 4788888888888899999888 2222  222 222222111 13357888


Q ss_pred             cccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcC-CCCC--hhhHHHHHHHhcCCCccccchh
Q 039275           77 RLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLG-VHTD--EVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        77 ~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~--~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ++|.            +...|..++..+.+.|+.++|..+|++....+ ..|+  ...|...+....+.|+.+.+..
T Consensus       408 ~~A~~~~e~al~~~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~~~~~~~lw~~~~~~e~~~G~~~~~~~  484 (530)
T 2ooe_A          408 SVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILK  484 (530)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSCGGGCHHHHHHHHHHHHHSSCHHHHHH
T ss_pred             hHHHHHHHHHHHHCCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            8887            67889999999999999999999999988764 3343  4467777888888888887766

>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=97.86  E-value=0.00014  Score=57.78  Aligned_cols=121  Identities=10%  Similarity=-0.006  Sum_probs=100.1

Q ss_pred             cHHHHHHHHHHhcCCCchHHHHHH-hh--hhhcc-hhhHHHHHHHHHhcCCccccc------------hHHHHHHHHHHH
Q 039275           29 DEVTMVVVLTASSGPGAWILAKEL-QI--ELDLS-SYSLSSKTSRYAHSGRIRLAR------------DPVSCKAMISGY   92 (153)
Q Consensus        29 ~~~~~~~ll~~~~~~~~~~~a~~~-~~--~~~~~-~~~~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~~   92 (153)
                      +...|+.+=..+.+.|++++|.+. +.  .+.|+ ...++.|-..|.+.|++++|.            +...|..+-..+
T Consensus         8 ~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~P~~~~a~~nLg~~l   87 (723)
T 4gyw_A            8 HADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTL   87 (723)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            457788888899999999999999 32  23443 567888999999999999998            688999999999


Q ss_pred             HhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh-----------HHHHHHHHHHHhh
Q 039275           93 SQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS-----------NIFLTTAIIEMYA  151 (153)
Q Consensus        93 ~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~-----------~~~~~~~li~~y~  151 (153)
                      .+.|++++|.+.|++..+.  .| +...+..+-..+.++|++++|.+           +...+..|...|.
T Consensus        88 ~~~g~~~~A~~~~~kAl~l--~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~~~~a~~~L~~~l~  156 (723)
T 4gyw_A           88 KEMQDVQGALQCYTRAIQI--NPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQ  156 (723)
T ss_dssp             HHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHhhhhhHHH
Confidence            9999999999999998864  45 56788999999999999999998           5566666655553

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=97.85  E-value=7.1e-05  Score=58.95  Aligned_cols=129  Identities=12%  Similarity=-0.054  Sum_probs=60.6

Q ss_pred             hcCChhHHHHHHHHhHH-------cCCCccHHHHHHHHHHhcCCCchHHHHHH-hh--hhhc-chhhHHHHHHHHHhcCC
Q 039275            7 QAGRFNEALEPFGKLES-------LGVHTDEVTMVVVLTASSGPGAWILAKEL-QI--ELDL-SSYSLSSKTSRYAHSGR   75 (153)
Q Consensus         7 ~~g~~~~a~~~~~~m~~-------~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~--~~~~-~~~~~~~ll~~~~~~g~   75 (153)
                      ..|++++|++.|++..+       ..-+.+...+..+-.++.+.|++++|.+. ..  ...| +...+..+-..|.+.|+
T Consensus       403 ~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~  482 (681)
T 2pzi_A          403 VLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAERVGWRWRLVWYRAVAELLTGD  482 (681)
T ss_dssp             TTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHTC
T ss_pred             cccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccCcchHHHHHHHHHHHHHcCC
Confidence            34555555555555541       11122334444444455555555555555 11  1122 22344444455555555


Q ss_pred             ccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           76 IRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        76 ~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +++|.            +...|..+-..+.+.|++++ .+.|++..+..  | +...+..+-.++.+.|++++|.+
T Consensus       483 ~~~A~~~~~~al~l~P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~--P~~~~a~~~lg~~~~~~g~~~~A~~  555 (681)
T 2pzi_A          483 YDSATKHFTEVLDTFPGELAPKLALAATAELAGNTDE-HKFYQTVWSTN--DGVISAAFGLARARSAEGDRVGAVR  555 (681)
T ss_dssp             HHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhC--CchHHHHHHHHHHHHHcCCHHHHHH
Confidence            55554            34445555555555555555 55555544332  2 23344445555555555555544

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=97.83  E-value=9.2e-05  Score=53.41  Aligned_cols=76  Identities=12%  Similarity=-0.009  Sum_probs=38.4

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCcc----HHHHHHHHHHhcCCCchHHHHHH-hh--------h-hhcchhhHHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTD----EVTMVVVLTASSGPGAWILAKEL-QI--------E-LDLSSYSLSSKTSR   69 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~----~~~~~~ll~~~~~~~~~~~a~~~-~~--------~-~~~~~~~~~~ll~~   69 (153)
                      .+.+.|++++|+..|++..+.+- .+    ...+..+-..+...|++++|... ..        + .+.....+..+-..
T Consensus        18 ~~~~~g~~~~A~~~~~~al~~~~-~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~   96 (406)
T 3sf4_A           18 RLCKSGDCRAGVSFFEAAVQVGT-EDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNT   96 (406)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCC-SCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHhccHHHHHHHHHHHHhcCc-ccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHH
Confidence            34556666666666666655421 12    23455555566666666666655 00        0 01112344445555


Q ss_pred             HHhcCCccccc
Q 039275           70 YAHSGRIRLAR   80 (153)
Q Consensus        70 ~~~~g~~~~a~   80 (153)
                      |...|++++|.
T Consensus        97 ~~~~g~~~~A~  107 (406)
T 3sf4_A           97 LKVLGNFDEAI  107 (406)
T ss_dssp             HHHTTCHHHHH
T ss_pred             HHHcCCHHHHH
Confidence            55555555555

>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=97.83  E-value=0.00022  Score=49.95  Aligned_cols=137  Identities=10%  Similarity=-0.051  Sum_probs=99.2

Q ss_pred             hhhHhhcCChhHHHHHHHHhHHcC-CCccHH----HHHHHHHHhcCCCchHHHHHH-hhhh-----hcc----hhhHHHH
Q 039275            2 ISGYSQAGRFNEALEPFGKLESLG-VHTDEV----TMVVVLTASSGPGAWILAKEL-QIEL-----DLS----SYSLSSK   66 (153)
Q Consensus         2 i~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~----~~~~ll~~~~~~~~~~~a~~~-~~~~-----~~~----~~~~~~l   66 (153)
                      +..+.+.|++++|.+.+++..... ..|+..    .+..+...+...+++++|.+. ..-+     .++    ..+++.+
T Consensus        82 i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~l  161 (293)
T 3u3w_A           82 VIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAI  161 (293)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHHH
T ss_pred             HHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHHH
Confidence            345778899999999999987642 334422    333456667778899999887 2211     122    2257888


Q ss_pred             HHHHHhcCCccccc-------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc----CCCCC-hhhHHH
Q 039275           67 TSRYAHSGRIRLAR-------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESL----GVHTD-EVTMVV  122 (153)
Q Consensus        67 l~~~~~~g~~~~a~-------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~-~~t~~~  122 (153)
                      -..|...|++++|.                   ...+|..+-..|.+.|++++|.+.+++..+.    +-.+. ..+|..
T Consensus       162 g~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~~  241 (293)
T 3u3w_A          162 ANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQ  241 (293)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHH
Confidence            88999999999888                   3347888899999999999999999877532    32332 567888


Q ss_pred             HHHHhcCCCc-cccchh
Q 039275          123 VLAASSGPGA-LDFGKS  138 (153)
Q Consensus       123 li~~~~~~g~-~~~a~~  138 (153)
                      +-.++.+.|+ +++|.+
T Consensus       242 lg~~~~~~g~~~~~A~~  258 (293)
T 3u3w_A          242 RGECLRKLEYEEAEIED  258 (293)
T ss_dssp             HHHHHHHTTCCHHHHHH
T ss_pred             HHHHHHHhCCcHHHHHH
Confidence            8888889995 588877

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=97.82  E-value=0.00012  Score=43.98  Aligned_cols=109  Identities=17%  Similarity=0.076  Sum_probs=74.7

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDP   82 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~   82 (153)
                      .+...|++++|.+.|++..+.. +.+...+..+-..+...|++++|.+. ...+..+..                   +.
T Consensus        21 ~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-------------------~~   80 (131)
T 2vyi_A           21 EQMKVENFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICIDPA-------------------YS   80 (131)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CH
T ss_pred             HHHHccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcCcc-------------------CH
Confidence            4667888888888888876642 33566777777777888888888777 222221110                   33


Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCcc
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGAL  133 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~  133 (153)
                      ..|..+-..+...|++++|.+.|++..+.. ..+...+..+..++.+.|++
T Consensus        81 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~~  130 (131)
T 2vyi_A           81 KAYGRMGLALSSLNKHVEAVAYYKKALELD-PDNETYKSNLKIAELKLREA  130 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHHhcC
Confidence            567777888999999999999999988653 12455666666666665554

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=97.82  E-value=0.00018  Score=46.40  Aligned_cols=108  Identities=8%  Similarity=0.042  Sum_probs=78.9

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hh--hhhc-chhhHHHHHHH-HHhcCCc--
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QI--ELDL-SSYSLSSKTSR-YAHSGRI--   76 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~--~~~~-~~~~~~~ll~~-~~~~g~~--   76 (153)
                      .+...|++++|++.|++..+.. +.+...+..+-..+...|++++|... ..  ...| +...+..+... +.+.|++  
T Consensus        19 ~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~l~~~~~~~~~   97 (177)
T 2e2e_A           19 QFASQQNPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLRGENAELYAALATVLYYQASQHMT   97 (177)
T ss_dssp             CCC-----CCCCHHHHHHHHHC-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHTTTCCC
T ss_pred             hhhhccCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCcch
Confidence            3567889999999999887652 34677888888899999999999998 22  2233 44566666677 6788887  


Q ss_pred             cccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 039275           77 RLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLG  112 (153)
Q Consensus        77 ~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  112 (153)
                      ++|.            +...|..+-..+...|++++|.+.|++..+..
T Consensus        98 ~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~  145 (177)
T 2e2e_A           98 AQTRAMIDKALALDSNEITALMLLASDAFMQANYAQAIELWQKVMDLN  145 (177)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhhC
Confidence            7777            56778888888999999999999999887653

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=97.82  E-value=4.8e-05  Score=54.88  Aligned_cols=128  Identities=15%  Similarity=0.110  Sum_probs=89.4

Q ss_pred             hhHHHHHHHHhHHc----CCCc-cHHHHHHHHHHhcCCCchHHHHHH-hhhh---------hcchhhHHHHHHHHHhcCC
Q 039275           11 FNEALEPFGKLESL----GVHT-DEVTMVVVLTASSGPGAWILAKEL-QIEL---------DLSSYSLSSKTSRYAHSGR   75 (153)
Q Consensus        11 ~~~a~~~~~~m~~~----g~~p-~~~~~~~ll~~~~~~~~~~~a~~~-~~~~---------~~~~~~~~~ll~~~~~~g~   75 (153)
                      +++|.+.+++..+.    +-.| ...++..+-..+...|++++|.+. ...+         ......+..+...|.+.|+
T Consensus       163 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~  242 (406)
T 3sf4_A          163 LQAAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGE  242 (406)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCC
Confidence            78888888766432    2222 234666777788888898888887 1111         1112367777888889999


Q ss_pred             ccccc------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcC----CCC-ChhhHHHHHHHhcCCCc
Q 039275           76 IRLAR------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLG----VHT-DEVTMVVVLAASSGPGA  132 (153)
Q Consensus        76 ~~~a~------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g----~~p-~~~t~~~li~~~~~~g~  132 (153)
                      +++|.                  ...++..+-..+...|++++|.+.|++.....    -.+ ...++..+-..+.+.|+
T Consensus       243 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~  322 (406)
T 3sf4_A          243 FETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGN  322 (406)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTC
T ss_pred             hHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCC
Confidence            88887                  25677888888899999999999998876431    111 25567778888888899


Q ss_pred             cccchh
Q 039275          133 LDFGKS  138 (153)
Q Consensus       133 ~~~a~~  138 (153)
                      +++|.+
T Consensus       323 ~~~A~~  328 (406)
T 3sf4_A          323 HDQAMH  328 (406)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            988887

>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=97.80  E-value=8e-05  Score=52.73  Aligned_cols=134  Identities=8%  Similarity=-0.033  Sum_probs=81.6

Q ss_pred             hHhhcCChhHHHHHHHHhHHc----CCCc-cHHHHHHHHHHhcCCCchHHHHHH-hhhh---------hcchhhHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESL----GVHT-DEVTMVVVLTASSGPGAWILAKEL-QIEL---------DLSSYSLSSKTS   68 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~~~~~ll~~~~~~~~~~~a~~~-~~~~---------~~~~~~~~~ll~   68 (153)
                      .|...|++++|.+.|.+....    |-.+ -..+|+.+-..+.+.|++++|... ..-+         ..-..+++.+-.
T Consensus        45 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~  124 (307)
T 2ifu_A           45 AFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGK  124 (307)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            455667777777777766432    1111 134666666777777877777776 1110         111345666667


Q ss_pred             HHHhcCCccccc------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc----CCCCC-hhhHHHHHH
Q 039275           69 RYAHSGRIRLAR------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESL----GVHTD-EVTMVVVLA  125 (153)
Q Consensus        69 ~~~~~g~~~~a~------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~-~~t~~~li~  125 (153)
                      .|.+ |++++|.                  ...+|+.+-..+.+.|++++|.+.|++....    +..+. ...+..+..
T Consensus       125 ~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~  203 (307)
T 2ifu_A          125 LMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVL  203 (307)
T ss_dssp             HHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Confidence            7766 7777776                  1456777777788888888888888777642    21121 225555666


Q ss_pred             HhcCCCccccchh
Q 039275          126 ASSGPGALDFGKS  138 (153)
Q Consensus       126 ~~~~~g~~~~a~~  138 (153)
                      ++...|++++|..
T Consensus       204 ~~~~~g~~~~A~~  216 (307)
T 2ifu_A          204 VQLHRADYVAAQK  216 (307)
T ss_dssp             HHHHTTCHHHHHH
T ss_pred             HHHHcCCHHHHHH
Confidence            6666677777765

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=97.78  E-value=0.0007  Score=40.83  Aligned_cols=89  Identities=11%  Similarity=0.067  Sum_probs=65.7

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccch
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARD   81 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~   81 (153)
                      ..+.+.|++++|.+.|++..+.. +.+...+..+-..+...|++++|.+. ...+..+..                   +
T Consensus        24 ~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~-------------------~   83 (133)
T 2lni_A           24 NECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQLEPT-------------------F   83 (133)
T ss_dssp             HHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHCTT-------------------C
T ss_pred             HHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCC-------------------c
Confidence            35678899999999998887642 33677777888888889999988887 222221111                   3


Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 039275           82 PVSCKAMISGYSQAGRFNEALEPFGKLESL  111 (153)
Q Consensus        82 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  111 (153)
                      ...|..+-..+.+.|++++|.+.|++..+.
T Consensus        84 ~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  113 (133)
T 2lni_A           84 IKGYTRKAAALEAMKDYTKAMDVYQKALDL  113 (133)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhhHHHHHHHHHHHHHh
Confidence            356777788889999999999999988764

>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=97.73  E-value=0.00025  Score=46.87  Aligned_cols=105  Identities=10%  Similarity=-0.081  Sum_probs=86.2

Q ss_pred             HHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccc------------hHHHHHHHHHHHHhcCChHH
Q 039275           34 VVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLAR------------DPVSCKAMISGYSQAGRFNE  100 (153)
Q Consensus        34 ~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~~~~~g~~~~  100 (153)
                      ..+-..+...|++++|.+. ..-+.|+...+..+-..|.+.|++++|.            +...|..+-..+...|++++
T Consensus        10 ~~~g~~~~~~~~~~~A~~~~~~a~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~lg~~~~~~~~~~~   89 (213)
T 1hh8_A           10 WNEGVLAADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQTEKYDL   89 (213)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHcCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcccHHH
Confidence            3444566788999999998 5556778889999999999999999998            67788899999999999999


Q ss_pred             HHHHHHHHHHcCC--------------CC-ChhhHHHHHHHhcCCCccccchh
Q 039275          101 ALEPFGKLESLGV--------------HT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       101 a~~~~~~m~~~g~--------------~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |.+.|++..+..-              .| +...+..+-.++.+.|++++|.+
T Consensus        90 A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  142 (213)
T 1hh8_A           90 AIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEE  142 (213)
T ss_dssp             HHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHH
Confidence            9999999886431              12 22677888889999999999987

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=97.67  E-value=0.00012  Score=52.33  Aligned_cols=122  Identities=10%  Similarity=-0.031  Sum_probs=88.0

Q ss_pred             HHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhc-----chhhHHHHHHHHHhcCCccccc-------
Q 039275           14 ALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDL-----SSYSLSSKTSRYAHSGRIRLAR-------   80 (153)
Q Consensus        14 a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~-----~~~~~~~ll~~~~~~g~~~~a~-------   80 (153)
                      |+..|++....+ +++..++..+-.++...|++++|.++ ..++.+     +...+..++..+.+.|+++.|.       
T Consensus        85 a~~~l~~l~~~~-~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~  163 (310)
T 3mv2_B           85 NIEELENLLKDK-QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYT  163 (310)
T ss_dssp             CCHHHHHTTTTS-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            556666665554 45666666777888889999999999 444443     3455667789999999999988       


Q ss_pred             --h-------HHHHHHHHHH--HHhcC--ChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 --D-------PVSCKAMISG--YSQAG--RFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 --~-------~~~~~~li~~--~~~~g--~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                        +       ..+...|..+  ....|  +..+|+.+|+++.+.  -|+..+-..++.++.++|++++|++
T Consensus       164 ~~~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~--~p~~~~~~lLln~~~~~g~~~eAe~  232 (310)
T 3mv2_B          164 NAIEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT--FPTWKTQLGLLNLHLQQRNIAEAQG  232 (310)
T ss_dssp             HHSCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             hcCccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHHHHHHHHHHcCCHHHHHH
Confidence              2       3455555555  34334  999999999998754  3654455566668999999999998

>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=97.67  E-value=0.00053  Score=45.90  Aligned_cols=109  Identities=8%  Similarity=-0.031  Sum_probs=88.2

Q ss_pred             ccHHHHHHHHHHhcCCCchHHHHHH-----hhhhhcchhhHHHHHHHHHhcCCccccc------------hHHHHHHHHH
Q 039275           28 TDEVTMVVVLTASSGPGAWILAKEL-----QIELDLSSYSLSSKTSRYAHSGRIRLAR------------DPVSCKAMIS   90 (153)
Q Consensus        28 p~~~~~~~ll~~~~~~~~~~~a~~~-----~~~~~~~~~~~~~ll~~~~~~g~~~~a~------------~~~~~~~li~   90 (153)
                      .|+..+...-..+.+.|++++|.+.     ....+++...+..+-..+.+.|++++|.            +...|..+-.
T Consensus         5 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~   84 (228)
T 4i17_A            5 TDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKNYNLANAYIGKSA   84 (228)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCSHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCcchHHHHHHHHH
Confidence            4567777777888999999999998     2222256667777889999999999998            6778999999


Q ss_pred             HHHhcCChHHHHHHHHHHHHcCCCCC-h-------hhHHHHHHHhcCCCccccchh
Q 039275           91 GYSQAGRFNEALEPFGKLESLGVHTD-E-------VTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        91 ~~~~~g~~~~a~~~~~~m~~~g~~p~-~-------~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .+...|++++|.+.|++..+..  |+ .       ..|..+-..+.+.|++++|.+
T Consensus        85 ~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~  138 (228)
T 4i17_A           85 AYRDMKNNQEYIATLTEGIKAV--PGNATIEKLYAIYYLKEGQKFQQAGNIEKAEE  138 (228)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHcccHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHHHHhHHHHHhccHHHHHH
Confidence            9999999999999999988653  43 2       457777788889999999988

>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=97.64  E-value=0.00061  Score=52.18  Aligned_cols=108  Identities=8%  Similarity=-0.071  Sum_probs=89.8

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhh--hhc-chhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIE--LDL-SSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~--~~~-~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .|.+.|++++|.+.|++..+.. +.+...+..+-..+.+.|++++|.+. +.-  ..| +...+..+-..|.+.|++++|
T Consensus        32 ~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A  110 (568)
T 2vsy_A           32 AELGMGDTTAGEMAVQRGLALH-PGHPEAVARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAA  110 (568)
T ss_dssp             HHHHHTCHHHHHHHHHHHHTTS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHH
Confidence            5678899999999999987752 34577888888899999999999998 222  233 456788888999999999999


Q ss_pred             c------------hHHHHHHHHHHHHhc---CChHHHHHHHHHHHHcC
Q 039275           80 R------------DPVSCKAMISGYSQA---GRFNEALEPFGKLESLG  112 (153)
Q Consensus        80 ~------------~~~~~~~li~~~~~~---g~~~~a~~~~~~m~~~g  112 (153)
                      .            +...+..+...+...   |+.++|.+.+++..+.+
T Consensus       111 ~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~~~  158 (568)
T 2vsy_A          111 AAAYTRAHQLLPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQG  158 (568)
T ss_dssp             HHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhcC
Confidence            8            677888899999999   99999999999998664

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.64  E-value=0.00013  Score=55.41  Aligned_cols=77  Identities=10%  Similarity=-0.012  Sum_probs=50.2

Q ss_pred             hHhhcCChhHHHHHHHHhHHc---CC---Cc-cHHHHHHHHHHhcCCCchHHHHHH-hhh-----------hhcchhhHH
Q 039275            4 GYSQAGRFNEALEPFGKLESL---GV---HT-DEVTMVVVLTASSGPGAWILAKEL-QIE-----------LDLSSYSLS   64 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~---g~---~p-~~~~~~~ll~~~~~~~~~~~a~~~-~~~-----------~~~~~~~~~   64 (153)
                      .+...|++++|..++++....   -+   .| ...+++.+...|...|++++|..+ +.-           .+....+++
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            355789999999999887542   12   22 357788888899999999999888 111           112233455


Q ss_pred             HHHHHHHhcCCccccc
Q 039275           65 SKTSRYAHSGRIRLAR   80 (153)
Q Consensus        65 ~ll~~~~~~g~~~~a~   80 (153)
                      .|-..|...|++++|.
T Consensus       398 nLa~~~~~~G~~~eA~  413 (490)
T 3n71_A          398 RAGLTNWHAGHIEVGH  413 (490)
T ss_dssp             HHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHCCCHHHHH
Confidence            5555555555555555

>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=97.62  E-value=0.00036  Score=49.33  Aligned_cols=130  Identities=12%  Similarity=-0.025  Sum_probs=94.9

Q ss_pred             cCChhHHHHHHHHhHHc------CCCccH----HHHHHHHHHhcCCCchHHHHHH-hhh--h-------hcchhhHHHHH
Q 039275            8 AGRFNEALEPFGKLESL------GVHTDE----VTMVVVLTASSGPGAWILAKEL-QIE--L-------DLSSYSLSSKT   67 (153)
Q Consensus         8 ~g~~~~a~~~~~~m~~~------g~~p~~----~~~~~ll~~~~~~~~~~~a~~~-~~~--~-------~~~~~~~~~ll   67 (153)
                      .|++++|.+++++..+.      ++.++.    ..|......+...|++++|.+. ..-  +       ..-...++.+.
T Consensus         4 ~~~~~eA~~~~~~a~k~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg   83 (307)
T 2ifu_A            4 AQKISEAHEHIAKAEKYLKTSFMKWKPDYDSAASEYAKAAVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAG   83 (307)
T ss_dssp             HHHHHHHHHHHHHHHHHHCCCSSSCSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHccccccCCCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            56788888888876542      223443    4677777888889999998887 111  1       11235788888


Q ss_pred             HHHHhcCCccccc------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCC---CC--ChhhHHHHH
Q 039275           68 SRYAHSGRIRLAR------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGV---HT--DEVTMVVVL  124 (153)
Q Consensus        68 ~~~~~~g~~~~a~------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~---~p--~~~t~~~li  124 (153)
                      ..|.+.|++++|.                  ...+|+.+-..|.. |++++|.+.|++-....-   .+  ...++..+-
T Consensus        84 ~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg  162 (307)
T 2ifu_A           84 MMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKAS  162 (307)
T ss_dssp             HHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHH
Confidence            9999999999998                  23567777788888 999999999988764311   11  146788888


Q ss_pred             HHhcCCCccccchh
Q 039275          125 AASSGPGALDFGKS  138 (153)
Q Consensus       125 ~~~~~~g~~~~a~~  138 (153)
                      ..+.+.|++++|.+
T Consensus       163 ~~~~~~g~~~~A~~  176 (307)
T 2ifu_A          163 RLLVRQQKFDEAAA  176 (307)
T ss_dssp             HHHHHTTCHHHHHH
T ss_pred             HHHHHcCCHHHHHH
Confidence            99999999999988

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=97.61  E-value=0.00048  Score=40.90  Aligned_cols=89  Identities=19%  Similarity=0.151  Sum_probs=67.1

Q ss_pred             HHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHH
Q 039275           30 EVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKL  108 (153)
Q Consensus        30 ~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m  108 (153)
                      ...+..+...+...|++++|.++ ...+..+..                   +...|..+...+.+.|++++|..+|+++
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~-------------------~~~~~~~la~~~~~~~~~~~A~~~~~~~   69 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELDPN-------------------NAEAWYNLGNAYYKQGDYDEAIEYYQKA   69 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC-------------------cHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            45666777777888888888777 222211110                   3467778888999999999999999999


Q ss_pred             HHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275          109 ESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       109 ~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .+.. ..+..++..+...+.+.|++++|.+
T Consensus        70 ~~~~-~~~~~~~~~la~~~~~~~~~~~A~~   98 (125)
T 1na0_A           70 LELD-PNNAEAWYNLGNAYYKQGDYDEAIE   98 (125)
T ss_dssp             HHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHhC-CccHHHHHHHHHHHHHhcCHHHHHH
Confidence            8654 3466788889999999999999988

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=97.60  E-value=0.0003  Score=44.48  Aligned_cols=74  Identities=7%  Similarity=-0.082  Sum_probs=43.5

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCcc-HHHHHHHHHHhcCCCchHHHHHH-hhh--hhc-chhhHHHHHHHHHhcCCcccc
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTD-EVTMVVVLTASSGPGAWILAKEL-QIE--LDL-SSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~-~~~~~~ll~~~~~~~~~~~a~~~-~~~--~~~-~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      +...|++++|+..+.+....  .|+ ...+-.+=..|.+.|++++|.+. ..-  +.| +...|..+-..|.+.|++++|
T Consensus         7 ~~~~~~~e~ai~~~~~a~~~--~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~~~~A   84 (150)
T 4ga2_A            7 RRSKADVERYIASVQGSTPS--PRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQERDPKAHRFLGLLYELEENTDKA   84 (150)
T ss_dssp             CCCHHHHHHHHHHHHHHSCS--HHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHcChHHHHHHHHHHhccc--CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCchHHH
Confidence            45667888888888776542  333 33444556678888999999888 222  333 233444444444444444444


Q ss_pred             c
Q 039275           80 R   80 (153)
Q Consensus        80 ~   80 (153)
                      .
T Consensus        85 ~   85 (150)
T 4ga2_A           85 V   85 (150)
T ss_dssp             H
T ss_pred             H
Confidence            4

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=97.60  E-value=0.00025  Score=44.09  Aligned_cols=122  Identities=15%  Similarity=0.095  Sum_probs=70.8

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCC-Ccc----HHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCcc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGV-HTD----EVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIR   77 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~-~p~----~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~   77 (153)
                      .|...|++++|.+.+++..+..- .++    ...+..+-..+...|++++|.+. ...+...           -..++..
T Consensus        18 ~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~-----------~~~~~~~   86 (164)
T 3ro3_A           18 THYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLA-----------RQLKDRA   86 (164)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-----------HHTTCHH
T ss_pred             HHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH-----------HHhCCcH
Confidence            56778999999999988754311 111    24666777788888999988887 1111100           0000000


Q ss_pred             ccchHHHHHHHHHHHHhcCChHHHHHHHHHHHHc----CCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           78 LARDPVSCKAMISGYSQAGRFNEALEPFGKLESL----GVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        78 ~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .  ....+..+-..+...|++++|.+.+++..+.    +-.+ ....+..+-..+...|++++|.+
T Consensus        87 ~--~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  150 (164)
T 3ro3_A           87 V--EAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMH  150 (164)
T ss_dssp             H--HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             H--HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHH
Confidence            0  2245556666667777777777777665432    1111 23455666666777777777665

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=97.59  E-value=0.00059  Score=53.73  Aligned_cols=129  Identities=8%  Similarity=-0.070  Sum_probs=97.2

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-h--hhhhc-chhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-Q--IELDL-SSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~--~~~~~-~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .|.+.|++++|++.|++..+.. +-+...|..+-.++.+.|++++|.+. +  ....| +...+..+-..|.+.|++++ 
T Consensus       442 ~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~~~~~lg~~~~~~g~~~~-  519 (681)
T 2pzi_A          442 ALLDLGDVAKATRKLDDLAERV-GWRWRLVWYRAVAELLTGDYDSATKHFTEVLDTFPGELAPKLALAATAELAGNTDE-  519 (681)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHHTCCCT-
T ss_pred             HHHhcCCHHHHHHHHHHHhccC-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCChHH-
Confidence            5778999999999999997642 23566777777888999999999988 2  22334 45678888899999999999 


Q ss_pred             c------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC-hhhHHHHHHHhcCCCccccc
Q 039275           80 R------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTD-EVTMVVVLAASSGPGALDFG  136 (153)
Q Consensus        80 ~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~g~~~~a  136 (153)
                      .            +...|..+-..+.+.|++++|.+.|++..+.  .|+ ...+..+..++...+..+++
T Consensus       520 ~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~~~~~~~~~~~~~~~  587 (681)
T 2pzi_A          520 HKFYQTVWSTNDGVISAAFGLARARSAEGDRVGAVRTLDEVPPT--SRHFTTARLTSAVTLLSGRSTSEV  587 (681)
T ss_dssp             TCHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHTSCTT--STTHHHHHHHHHHHTC-------C
T ss_pred             HHHHHHHHHhCCchHHHHHHHHHHHHHcCCHHHHHHHHHhhccc--CcccHHHHHHHHHHHHccCCCCCC
Confidence            7            6778999999999999999999999987643  565 45666777777776663333

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=97.58  E-value=0.0014  Score=46.83  Aligned_cols=134  Identities=8%  Similarity=-0.068  Sum_probs=94.1

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCC-CccHHHHHHHHHHhcCCCchHHHHHH---hhhhhc-----chhhHHHHHHHH--H
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGV-HTDEVTMVVVLTASSGPGAWILAKEL---QIELDL-----SSYSLSSKTSRY--A   71 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~-~p~~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~-----~~~~~~~ll~~~--~   71 (153)
                      ..+...|++++|++++.+-...|- .-+...+..++..+.+.|+++.|.+.   -....|     +..+...|..++  .
T Consensus       108 ~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~~~~~d~~~~~d~~l~~Laea~v~l  187 (310)
T 3mv2_B          108 TAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYTNAIEDTVSGDNEMILNLAESYIKF  187 (310)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCccccccchHHHHHHHHHHHHH
Confidence            357788999999999998755443 23677888889999999999999999   234566     356666677663  3


Q ss_pred             hcC--Cccccc-----------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc-----C---CCC-ChhhHHHHHHHhcC
Q 039275           72 HSG--RIRLAR-----------DPVSCKAMISGYSQAGRFNEALEPFGKLESL-----G---VHT-DEVTMVVVLAASSG  129 (153)
Q Consensus        72 ~~g--~~~~a~-----------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-----g---~~p-~~~t~~~li~~~~~  129 (153)
                      ..|  +..+|.           +..+-..++.++.+.|++++|.+.++.+.+.     .   ..| +..+...+|.....
T Consensus       188 ~~g~~~~q~A~~~f~El~~~~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~~~~p~~~~k~~~~p~~~~~LaN~i~l~~~  267 (310)
T 3mv2_B          188 ATNKETATSNFYYYEELSQTFPTWKTQLGLLNLHLQQRNIAEAQGIVELLLSDYYSVEQKENAVLYKPTFLANQITLALM  267 (310)
T ss_dssp             HHTCSTTTHHHHHHHHHHTTSCSHHHHHHHHHHHHHHTCHHHHHHHHHHHHSHHHHTTTCHHHHSSHHHHHHHHHHHHHH
T ss_pred             HhCCccHHHHHHHHHHHHHhCCCcccHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHH
Confidence            334  777776           2234455666899999999999999977643     1   124 55555577666666


Q ss_pred             CCccccchh
Q 039275          130 PGALDFGKS  138 (153)
Q Consensus       130 ~g~~~~a~~  138 (153)
                      .|+  .+.+
T Consensus       268 lgk--~a~~  274 (310)
T 3mv2_B          268 QGL--DTED  274 (310)
T ss_dssp             TTC--TTHH
T ss_pred             hCh--HHHH
Confidence            675  4444

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=97.58  E-value=0.00066  Score=40.68  Aligned_cols=105  Identities=11%  Similarity=0.128  Sum_probs=73.9

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhh--hcch-hhHHHHHHHHHhcCCccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIEL--DLSS-YSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~--~~~~-~~~~~ll~~~~~~g~~~~   78 (153)
                      ..+.+.|++++|...|++..+.. +.+...+..+-..+...|++++|... ...+  .|+. ..+..             
T Consensus        12 ~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~-------------   77 (131)
T 1elr_A           12 NDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQ-------------   77 (131)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHH-------------
T ss_pred             HHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHH-------------
Confidence            35678899999999999987753 44677777888888889999999888 2211  1211 11100             


Q ss_pred             cchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHH
Q 039275           79 ARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLA  125 (153)
Q Consensus        79 a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~  125 (153)
                        ...+|..+-..+...|++++|.+.|++..+..  |+......+-.
T Consensus        78 --~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~l~~  120 (131)
T 1elr_A           78 --IAKAYARIGNSYFKEEKYKDAIHFYNKSLAEH--RTPDVLKKCQQ  120 (131)
T ss_dssp             --HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHH
T ss_pred             --HHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CCHHHHHHHHH
Confidence              14677788888999999999999999988754  55554444433

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=97.58  E-value=0.0012  Score=44.45  Aligned_cols=133  Identities=11%  Similarity=0.046  Sum_probs=89.8

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCC-Cc-cHHHHHHHHHHhcCCCchHHHHHH---hhhhhcchh----hHHHHHHHHHh--
Q 039275            4 GYSQAGRFNEALEPFGKLESLGV-HT-DEVTMVVVLTASSGPGAWILAKEL---QIELDLSSY----SLSSKTSRYAH--   72 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~-~p-~~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~~~~----~~~~ll~~~~~--   72 (153)
                      .+.+.|++++|++.|+++.+..- .| ....+..+-.++.+.|++++|.+.   .....|+..    .+-.+-..+.+  
T Consensus        13 ~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~~~g~~~~~~~   92 (225)
T 2yhc_A           13 QKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALD   92 (225)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHHHHHHHHHhhh
Confidence            57789999999999999977421 12 235666677889999999999988   222234332    12222222322  


Q ss_pred             ----------------cCCccccc------------hHHHH-----------------HHHHHHHHhcCChHHHHHHHHH
Q 039275           73 ----------------SGRIRLAR------------DPVSC-----------------KAMISGYSQAGRFNEALEPFGK  107 (153)
Q Consensus        73 ----------------~g~~~~a~------------~~~~~-----------------~~li~~~~~~g~~~~a~~~~~~  107 (153)
                                      .|+.++|.            +...+                 -.+-..+.+.|++++|...|++
T Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~P~~~~a~~a~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~  172 (225)
T 2yhc_A           93 DSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEG  172 (225)
T ss_dssp             C--------------CCHHHHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             hhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHCcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHH
Confidence                            45566665            22222                 2344567889999999999999


Q ss_pred             HHHcCCCCCh----hhHHHHHHHhcCCCccccchh
Q 039275          108 LESLGVHTDE----VTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       108 m~~~g~~p~~----~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +.+.-  |+.    ..+..+..++.+.|+.++|.+
T Consensus       173 ~l~~~--p~~~~~~~a~~~l~~~~~~~g~~~~A~~  205 (225)
T 2yhc_A          173 MLRDY--PDTQATRDALPLMENAYRQMQMNAQAEK  205 (225)
T ss_dssp             HHHHS--TTSHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHC--cCCCccHHHHHHHHHHHHHcCCcHHHHH
Confidence            98653  432    467788899999999999887

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=97.57  E-value=0.00016  Score=45.83  Aligned_cols=72  Identities=14%  Similarity=0.081  Sum_probs=39.9

Q ss_pred             HHHHHHHHHhcCCccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcC
Q 039275           63 LSSKTSRYAHSGRIRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSG  129 (153)
Q Consensus        63 ~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~  129 (153)
                      +-.+-..|.+.|++++|.            +..+|..+-..+.+.|++++|...|++..+.  .| +...+..+-..+.+
T Consensus        34 ~~~la~~y~~~~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~  111 (150)
T 4ga2_A           34 GFYFAKLYYEAKEYDLAKKYICTYINVQERDPKAHRFLGLLYELEENTDKAVECYRRSVEL--NPTQKDLVLKIAELLCK  111 (150)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCchHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHH
Confidence            334455566666666665            5555666666666666666666666655543  23 23445555555555


Q ss_pred             CCccccc
Q 039275          130 PGALDFG  136 (153)
Q Consensus       130 ~g~~~~a  136 (153)
                      .|+.+++
T Consensus       112 ~~~~~~a  118 (150)
T 4ga2_A          112 NDVTDGR  118 (150)
T ss_dssp             HCSSSSH
T ss_pred             cCChHHH
Confidence            5555443

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=97.53  E-value=0.0019  Score=37.48  Aligned_cols=91  Identities=13%  Similarity=0.032  Sum_probs=63.4

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDP   82 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~   82 (153)
                      .+.+.|++++|...|++..+.. +.+...+..+-..+.+.|++++|.+. ...+..+....                 +.
T Consensus        15 ~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~-----------------~~   76 (112)
T 2kck_A           15 LQYDAGNYTESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYVINVIEDEY-----------------NK   76 (112)
T ss_dssp             HHHSSCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSCCTT-----------------CH
T ss_pred             HHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccc-----------------hH
Confidence            4667888899999888887652 33566677777778888888888877 32222221100                 23


Q ss_pred             HHHHHHHHHHHhc-CChHHHHHHHHHHHHcC
Q 039275           83 VSCKAMISGYSQA-GRFNEALEPFGKLESLG  112 (153)
Q Consensus        83 ~~~~~li~~~~~~-g~~~~a~~~~~~m~~~g  112 (153)
                      ..|..+-..+.+. |++++|.+.|++.....
T Consensus        77 ~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~  107 (112)
T 2kck_A           77 DVWAAKADALRYIEGKEVEAEIAEARAKLEH  107 (112)
T ss_dssp             HHHHHHHHHHTTCSSCSHHHHHHHHHHGGGC
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHhhcc
Confidence            5677777888888 88898888888887654

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=97.52  E-value=0.00062  Score=48.94  Aligned_cols=110  Identities=15%  Similarity=0.054  Sum_probs=65.0

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCcc--------------HHHHHHHHHHhcCCCchHHHHHH-hhh--hhcchhhHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTD--------------EVTMVVVLTASSGPGAWILAKEL-QIE--LDLSSYSLSSK   66 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~--------------~~~~~~ll~~~~~~~~~~~a~~~-~~~--~~~~~~~~~~l   66 (153)
                      .|.+.|++++|+..|++..+..-...              ...|..+-.++.+.|++++|.+. ..-  +.|+       
T Consensus       156 ~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~-------  228 (336)
T 1p5q_A          156 VYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELDSN-------  228 (336)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------
T ss_pred             HHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-------
Confidence            57788999999999999877532211              47777778888888898888888 222  2232       


Q ss_pred             HHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccc
Q 039275           67 TSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFG  136 (153)
Q Consensus        67 l~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a  136 (153)
                                    +...|..+-..+...|++++|.+.|++..+..  | +...+..+-..+.+.|+.+++
T Consensus       229 --------------~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~--P~~~~a~~~l~~~~~~~~~~~~a  283 (336)
T 1p5q_A          229 --------------NEKGLSRRGEAHLAVNDFELARADFQKVLQLY--PNNKAAKTQLAVCQQRIRRQLAR  283 (336)
T ss_dssp             --------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--SSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             --------------cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHH
Confidence                          22334444455555555555555555544332  2 233444444444445555444

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=97.52  E-value=0.0007  Score=40.50  Aligned_cols=73  Identities=15%  Similarity=0.042  Sum_probs=51.9

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hh--hhhc-chhhHHHHHHHHHhcCCc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QI--ELDL-SSYSLSSKTSRYAHSGRI   76 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~--~~~~-~~~~~~~ll~~~~~~g~~   76 (153)
                      ..+...|++++|.+.+++..+. .+.+...+..+-..+.+.|++++|.+. ..  ...| +...+..+...+.+.|+.
T Consensus        54 ~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~  130 (131)
T 2vyi_A           54 AAYSKLGNYAGAVQDCERAICI-DPAYSKAYGRMGLALSSLNKHVEAVAYYKKALELDPDNETYKSNLKIAELKLREA  130 (131)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHhhchHHHHHHHHHHHhc-CccCHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHhcC
Confidence            3567889999999999998775 234577788888889999999999988 22  2233 344555566666666554

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=97.51  E-value=0.0012  Score=42.06  Aligned_cols=90  Identities=17%  Similarity=0.038  Sum_probs=56.7

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhh--hhcchhhHHHHHHHHHhcCCccccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIE--LDLSSYSLSSKTSRYAHSGRIRLAR   80 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~--~~~~~~~~~~ll~~~~~~g~~~~a~   80 (153)
                      .+.+.|++++|++.|++..+.. +-+...|..+-.++.+.|++++|.+. +.-  +.|+                     
T Consensus        45 ~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P~---------------------  102 (151)
T 3gyz_A           45 DFYNKGRIEEAEVFFRFLCIYD-FYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKN---------------------  102 (151)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSS---------------------
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCCC---------------------
Confidence            3455666666666666665431 22345555555566666666666665 222  2222                     


Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDE  117 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  117 (153)
                      +...|..+-..|.+.|++++|.+.|++..+..  ||.
T Consensus       103 ~~~~~~~lg~~~~~lg~~~eA~~~~~~al~l~--~~~  137 (151)
T 3gyz_A          103 DYTPVFHTGQCQLRLKAPLKAKECFELVIQHS--NDE  137 (151)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCH
T ss_pred             CcHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCH
Confidence            45677888889999999999999999988653  544

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=97.47  E-value=0.00025  Score=47.29  Aligned_cols=91  Identities=13%  Similarity=-0.007  Sum_probs=59.4

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCcc-HHHHHH----------------HHHHhcCCCchHHHHHH-hhh--hhc-chhh
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTD-EVTMVV----------------VLTASSGPGAWILAKEL-QIE--LDL-SSYS   62 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~-~~~~~~----------------ll~~~~~~~~~~~a~~~-~~~--~~~-~~~~   62 (153)
                      .+.+.|++++|+..|++..+.  .|+ ...+..                +-..+.+.|++++|... ..-  ..| +...
T Consensus        13 ~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~   90 (208)
T 3urz_A           13 AAIEAGQNGQAVSYFRQTIAL--NIDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQKAPNNVDC   90 (208)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--CHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHh--CCCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHH
Confidence            467889999999999988764  343 334444                66677888888888887 222  233 3456


Q ss_pred             HHHHHHHHHhcCCccccc------------hHHHHHHHHHHHHhcC
Q 039275           63 LSSKTSRYAHSGRIRLAR------------DPVSCKAMISGYSQAG   96 (153)
Q Consensus        63 ~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~~~~~g   96 (153)
                      +..+-..|...|++++|.            +...|..+-..|...|
T Consensus        91 ~~~lg~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~  136 (208)
T 3urz_A           91 LEACAEMQVCRGQEKDALRMYEKILQLEADNLAANIFLGNYYYLTA  136 (208)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHh
Confidence            666677777777777776            4455555555544433

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=97.47  E-value=0.0015  Score=49.55  Aligned_cols=129  Identities=9%  Similarity=-0.041  Sum_probs=97.1

Q ss_pred             cCChh-------HHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-h--hhhhcch--hhHHHHHHHHHhcCC
Q 039275            8 AGRFN-------EALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-Q--IELDLSS--YSLSSKTSRYAHSGR   75 (153)
Q Consensus         8 ~g~~~-------~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~--~~~~~~~--~~~~~ll~~~~~~g~   75 (153)
                      .|+++       +|.++|++..+.-.+-+...+..+...+.+.|++++|.++ +  ....|+.  ..|..+...+.+.|+
T Consensus       292 ~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~  371 (530)
T 2ooe_A          292 KGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEG  371 (530)
T ss_dssp             TTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSSSSCHHHHHHHHHHHHHHHHH
T ss_pred             ccchhhhhhhhHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCccccCchHHHHHHHHHHHHhcC
Confidence            68887       8999999887633444688888888999999999999999 2  2234542  478888888888999


Q ss_pred             ccccc------------hHHHHHHHH-HHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           76 IRLAR------------DPVSCKAMI-SGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        76 ~~~a~------------~~~~~~~li-~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +++|.            +...|-... ..+...|+.++|..+|+...+..  | +...|..++....+.|+.++|..
T Consensus       372 ~~~A~~~~~~Al~~~~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~~--p~~~~~~~~~~~~~~~~g~~~~Ar~  446 (530)
T 2ooe_A          372 IKSGRMIFKKAREDARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY--GDIPEYVLAYIDYLSHLNEDNNTRV  446 (530)
T ss_dssp             HHHHHHHHHHHHTCTTCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHH--TTCHHHHHHHHHHHTTTTCHHHHHH
T ss_pred             HHHHHHHHHHHHhccCCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHHC--CCCHHHHHHHHHHHHhCCCHhhHHH
Confidence            88887            111222211 12346899999999999887643  5 56788999999999999999888

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=97.47  E-value=0.0023  Score=38.65  Aligned_cols=88  Identities=9%  Similarity=0.015  Sum_probs=65.2

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDP   82 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~   82 (153)
                      .+.+.|++++|++.|++..+.. +.+...|..+-.++.+.|++++|.+. ..-+..+..                   +.
T Consensus        13 ~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~-------------------~~   72 (126)
T 3upv_A           13 EYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPN-------------------FV   72 (126)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CH
T ss_pred             HHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-------------------cH
Confidence            4678899999999999887652 34577788888888889999988887 322222211                   23


Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESL  111 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~  111 (153)
                      ..|..+-..+...|++++|.+.|++..+.
T Consensus        73 ~~~~~lg~~~~~~~~~~~A~~~~~~al~~  101 (126)
T 3upv_A           73 RAYIRKATAQIAVKEYASALETLDAARTK  101 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCHHHHHHHHHHHHHh
Confidence            56777778888999999999999887754

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.46  E-value=0.00034  Score=42.10  Aligned_cols=104  Identities=10%  Similarity=-0.027  Sum_probs=70.2

Q ss_pred             hcCChhHHHHHHHHhHHcC--CCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHH
Q 039275            7 QAGRFNEALEPFGKLESLG--VHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPV   83 (153)
Q Consensus         7 ~~g~~~~a~~~~~~m~~~g--~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~   83 (153)
                      ..|++++|+..|++..+.+  -+-+...+..+-..+.+.|++++|.+. ..-+..+..                   +..
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-------------------~~~   62 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPN-------------------HQA   62 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-------------------chH
Confidence            4688999999999998864  233456777777888999999999988 332222111                   235


Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHHcC-CCCChhhHHHHHHHhcC
Q 039275           84 SCKAMISGYSQAGRFNEALEPFGKLESLG-VHTDEVTMVVVLAASSG  129 (153)
Q Consensus        84 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~t~~~li~~~~~  129 (153)
                      .|..+-..+...|++++|.+.|++..... -.|+...|...+..+.+
T Consensus        63 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~ai~~~~~  109 (117)
T 3k9i_A           63 LRVFYAMVLYNLGRYEQGVELLLKIIAETSDDETIQSYKQAILFYAD  109 (117)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHCCCHHHHHTHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHH
Confidence            66778888999999999999999887542 34455556666665554

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=97.46  E-value=0.0017  Score=39.73  Aligned_cols=100  Identities=8%  Similarity=-0.013  Sum_probs=71.4

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhh--hcch-hhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIEL--DLSS-YSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~--~~~~-~~~~~ll~~~~~~g~~~~a   79 (153)
                      .+.+.|++++|++.|++..+. -+-+...|..+-.++.+.|++++|.+. ...+  .|+. ..+..+             
T Consensus        17 ~~~~~~~~~~A~~~y~~Al~~-~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~-------------   82 (127)
T 4gcn_A           17 AAYKQKDFEKAHVHYDKAIEL-DPSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLI-------------   82 (127)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHH-------------
T ss_pred             HHHHcCCHHHHHHHHHHHHHh-CCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHH-------------
Confidence            577899999999999998764 234577788888899999999999888 2222  2322 122221             


Q ss_pred             chHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHH
Q 039275           80 RDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMV  121 (153)
Q Consensus        80 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~  121 (153)
                        ..+|..+-..+...|++++|.+.|++-...  .||..+..
T Consensus        83 --a~~~~~lg~~~~~~~~~~~A~~~~~kal~~--~~~~~~~~  120 (127)
T 4gcn_A           83 --AKAMSRAGNAFQKQNDLSLAVQWFHRSLSE--FRDPELVK  120 (127)
T ss_dssp             --HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCCHHHHH
T ss_pred             --HHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CcCHHHHH
Confidence              246667777889999999999999987754  35544433

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=97.46  E-value=0.0009  Score=40.31  Aligned_cols=92  Identities=12%  Similarity=-0.057  Sum_probs=67.6

Q ss_pred             CccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHH
Q 039275           27 HTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPF  105 (153)
Q Consensus        27 ~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~  105 (153)
                      +.+...+..+-..+.+.|++++|.+. ...+..+..                   +...|..+-..+...|++++|.+.|
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~-------------------~~~~~~~la~~~~~~~~~~~A~~~~   73 (133)
T 2lni_A           13 PDLALMVKNKGNECFQKGDYPQAMKHYTEAIKRNPK-------------------DAKLYSNRAACYTKLLEFQLALKDC   73 (133)
T ss_dssp             SCHHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTCTT-------------------CHHHHHHHHHHHTTTTCHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-------------------cHHHHHHHHHHHHHhccHHHHHHHH
Confidence            34556666666777777777777776 222221111                   3467778888899999999999999


Q ss_pred             HHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275          106 GKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       106 ~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ++..+.. ..+...+..+-..+.+.|++++|.+
T Consensus        74 ~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~  105 (133)
T 2lni_A           74 EECIQLE-PTFIKGYTRKAAALEAMKDYTKAMD  105 (133)
T ss_dssp             HHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHhC-CCchHHHHHHHHHHHHHhhHHHHHH
Confidence            9988653 2356778888889999999999988

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=97.45  E-value=0.0012  Score=43.00  Aligned_cols=107  Identities=21%  Similarity=0.202  Sum_probs=79.6

Q ss_pred             hHhhcCChhHHHHHHHHhHH----cCCCc-cHHHHHHHHHHhcCCCchHHHHHH-hh------hhh----cchhhHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLES----LGVHT-DEVTMVVVLTASSGPGAWILAKEL-QI------ELD----LSSYSLSSKT   67 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~----~g~~p-~~~~~~~ll~~~~~~~~~~~a~~~-~~------~~~----~~~~~~~~ll   67 (153)
                      .|...|++++|...|++...    .+..| ....+..+-..+...|++++|.+. ..      ...    .....+..+-
T Consensus        35 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg  114 (203)
T 3gw4_A           35 VYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNWDAARRCFLEERELLASLPEDPLAASANAYEVA  114 (203)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHH
T ss_pred             HHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHH
Confidence            56788999999999998865    22222 345666777788899999999888 11      111    1234567778


Q ss_pred             HHHHhcCCccccc------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHH
Q 039275           68 SRYAHSGRIRLAR------------------DPVSCKAMISGYSQAGRFNEALEPFGKLES  110 (153)
Q Consensus        68 ~~~~~~g~~~~a~------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  110 (153)
                      ..+...|++++|.                  ...++..+-..+...|++++|.+.+++..+
T Consensus       115 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  175 (203)
T 3gw4_A          115 TVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEKNLLEAQQHWLRARD  175 (203)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            8899999999998                  233467778889999999999999988764

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=97.39  E-value=0.0024  Score=45.87  Aligned_cols=135  Identities=14%  Similarity=-0.042  Sum_probs=92.6

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHH----HHHHHHHHhcCCCchHHHHHH-hhhh--h---cc----hhhHHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEV----TMVVVLTASSGPGAWILAKEL-QIEL--D---LS----SYSLSSKTSR   69 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~----~~~~ll~~~~~~~~~~~a~~~-~~~~--~---~~----~~~~~~ll~~   69 (153)
                      .+...|++++|...+++.....-..+..    .++.+-..+...|++++|.+. ...+  .   ++    ......+-..
T Consensus        23 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~  102 (373)
T 1hz4_A           23 VAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEI  102 (373)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHH
Confidence            3567899999999999987653222222    444555667778999998887 1111  1   11    1234566777


Q ss_pred             HHhcCCccccc--------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCC--C--ChhhHHHHHH
Q 039275           70 YAHSGRIRLAR--------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVH--T--DEVTMVVVLA  125 (153)
Q Consensus        70 ~~~~g~~~~a~--------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~--p--~~~t~~~li~  125 (153)
                      +...|++++|.                    ....+..+-..+...|++++|.+.+++.....-.  |  ...++..+-.
T Consensus       103 ~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~  182 (373)
T 1hz4_A          103 LFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQ  182 (373)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHHHH
Confidence            88899998887                    1234555667888999999999999988754321  2  2345777778


Q ss_pred             HhcCCCccccchh
Q 039275          126 ASSGPGALDFGKS  138 (153)
Q Consensus       126 ~~~~~g~~~~a~~  138 (153)
                      .+...|++++|..
T Consensus       183 ~~~~~g~~~~A~~  195 (373)
T 1hz4_A          183 CSLARGDLDNARS  195 (373)
T ss_dssp             HHHHHTCHHHHHH
T ss_pred             HHHHcCCHHHHHH
Confidence            8888999999887

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=97.39  E-value=0.00071  Score=42.54  Aligned_cols=88  Identities=9%  Similarity=-0.003  Sum_probs=63.5

Q ss_pred             HHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 039275           31 VTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLE  109 (153)
Q Consensus        31 ~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  109 (153)
                      ..+..+-..+...|++++|... ...+..+..                   +...|..+-..+...|++++|.+.|++..
T Consensus        14 ~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~-------------------~~~~~~~~a~~~~~~~~~~~A~~~~~~a~   74 (166)
T 1a17_A           14 EELKTQANDYFKAKDYENAIKFYSQAIELNPS-------------------NAIYYGNRSLAYLRTECYGYALGDATRAI   74 (166)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-------------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-------------------ChHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            3444555566677777777776 222221110                   34667788888999999999999999988


Q ss_pred             HcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275          110 SLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       110 ~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ... ..+...+..+-..+.+.|++++|.+
T Consensus        75 ~~~-~~~~~~~~~~a~~~~~~~~~~~A~~  102 (166)
T 1a17_A           75 ELD-KKYIKGYYRRAASNMALGKFRAALR  102 (166)
T ss_dssp             HHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HhC-cccHHHHHHHHHHHHHhccHHHHHH
Confidence            654 2356778888899999999999988

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=97.38  E-value=0.0017  Score=46.97  Aligned_cols=133  Identities=10%  Similarity=-0.021  Sum_probs=90.0

Q ss_pred             hhHhhcCChhHHHHHHHHhH-----HcCCCccHHHHHHHHHHhcCCCchHHHHHH-hh--------hh-hcchhhHHHHH
Q 039275            3 SGYSQAGRFNEALEPFGKLE-----SLGVHTDEVTMVVVLTASSGPGAWILAKEL-QI--------EL-DLSSYSLSSKT   67 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~-----~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~--------~~-~~~~~~~~~ll   67 (153)
                      ..|...|++++|.+.|++..     .........++..+-..+...|++++|.+. ..        +. +....++..+-
T Consensus       192 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~  271 (383)
T 3ulq_A          192 TNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLIT  271 (383)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHHH
Confidence            45777888888888887664     144455677778888888888888888777 11        12 22344567777


Q ss_pred             HHHHhcCCccccc-----------------hHHHHHHHHHHHHhcCC---hHHHHHHHHHHHHcCCCC-ChhhHHHHHHH
Q 039275           68 SRYAHSGRIRLAR-----------------DPVSCKAMISGYSQAGR---FNEALEPFGKLESLGVHT-DEVTMVVVLAA  126 (153)
Q Consensus        68 ~~~~~~g~~~~a~-----------------~~~~~~~li~~~~~~g~---~~~a~~~~~~m~~~g~~p-~~~t~~~li~~  126 (153)
                      ..|.+.|++++|.                 ....++.+-..+...|+   +++|..++++.   +..| ....+..+-..
T Consensus       272 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~---~~~~~~~~~~~~la~~  348 (383)
T 3ulq_A          272 QIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESK---MLYADLEDFAIDVAKY  348 (383)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHC---cCHHHHHHHHHHHHHH
Confidence            8888888888887                 12235566677777788   66666666654   3333 33456677778


Q ss_pred             hcCCCccccchh
Q 039275          127 SSGPGALDFGKS  138 (153)
Q Consensus       127 ~~~~g~~~~a~~  138 (153)
                      +.+.|++++|.+
T Consensus       349 y~~~g~~~~A~~  360 (383)
T 3ulq_A          349 YHERKNFQKASA  360 (383)
T ss_dssp             HHHTTCHHHHHH
T ss_pred             HHHCCCHHHHHH
Confidence            888888888876

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=97.38  E-value=0.0026  Score=39.44  Aligned_cols=88  Identities=19%  Similarity=0.139  Sum_probs=55.9

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDP   82 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~   82 (153)
                      .+.+.|++++|.+.|++..... +.+...|..+-.++.+.|++++|... ..-+..+..                   +.
T Consensus        27 ~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-------------------~~   86 (142)
T 2xcb_A           27 NQYQAGKWDDAQKIFQALCMLD-HYDARYFLGLGACRQSLGLYEQALQSYSYGALMDIN-------------------EP   86 (142)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CT
T ss_pred             HHHHHccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC-------------------Cc
Confidence            3556677777777777665531 23455555555666667777777666 222211110                   34


Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESL  111 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~  111 (153)
                      ..|..+-..+...|++++|.+.|+...+.
T Consensus        87 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~  115 (142)
T 2xcb_A           87 RFPFHAAECHLQLGDLDGAESGFYSARAL  115 (142)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            56667778888999999999999887754

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=97.36  E-value=0.0015  Score=37.95  Aligned_cols=89  Identities=9%  Similarity=-0.009  Sum_probs=62.8

Q ss_pred             HHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 039275           31 VTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLE  109 (153)
Q Consensus        31 ~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  109 (153)
                      ..+..+-..+.+.|++++|... ...+..+..                   +...|..+-..+...|++++|.+.|++..
T Consensus         7 ~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~-------------------~~~~~~~~a~~~~~~~~~~~A~~~~~~a~   67 (112)
T 2kck_A            7 EEYYLEGVLQYDAGNYTESIDLFEKAIQLDPE-------------------ESKYWLMKGKALYNLERYEEAVDCYNYVI   67 (112)
T ss_dssp             TGGGGHHHHHHSSCCHHHHHHHHHHHHHHCCC-------------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHhCcC-------------------CHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            4444555566667777777666 222211110                   34567788888999999999999999988


Q ss_pred             HcCCC-CChhhHHHHHHHhcCC-Cccccchh
Q 039275          110 SLGVH-TDEVTMVVVLAASSGP-GALDFGKS  138 (153)
Q Consensus       110 ~~g~~-p~~~t~~~li~~~~~~-g~~~~a~~  138 (153)
                      +.... .+...+..+...+.+. |++++|.+
T Consensus        68 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~   98 (112)
T 2kck_A           68 NVIEDEYNKDVWAAKADALRYIEGKEVEAEI   98 (112)
T ss_dssp             HTSCCTTCHHHHHHHHHHHTTCSSCSHHHHH
T ss_pred             HhCcccchHHHHHHHHHHHHHHhCCHHHHHH
Confidence            65311 1477888899999999 99999887

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=97.34  E-value=0.0034  Score=39.82  Aligned_cols=88  Identities=11%  Similarity=0.071  Sum_probs=60.5

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDP   82 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~   82 (153)
                      .+.+.|++++|++.|++..+.. +-+...|..+-.++.+.|++++|.+. ..-+..+..                   +.
T Consensus        20 ~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~-------------------~~   79 (164)
T 3sz7_A           20 AAMARKEYSKAIDLYTQALSIA-PANPIYLSNRAAAYSASGQHEKAAEDAELATVVDPK-------------------YS   79 (164)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-------------------CH
Confidence            5677888888888888887642 23567777777788888888888887 222222111                   23


Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESL  111 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~  111 (153)
                      ..|..+-..+...|++++|.+.|++..+.
T Consensus        80 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~  108 (164)
T 3sz7_A           80 KAWSRLGLARFDMADYKGAKEAYEKGIEA  108 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            55666777777778888888887777643

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=97.33  E-value=0.00063  Score=49.27  Aligned_cols=132  Identities=15%  Similarity=0.110  Sum_probs=84.0

Q ss_pred             hHhhcCChhHHHHHHHHhHHc----CCCc-cHHHHHHHHHHhcCCCchHHHHHH-hh--------hhhcchhhHHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESL----GVHT-DEVTMVVVLTASSGPGAWILAKEL-QI--------ELDLSSYSLSSKTSR   69 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~~~~~ll~~~~~~~~~~~a~~~-~~--------~~~~~~~~~~~ll~~   69 (153)
                      .|...|++++|.+.|++..+.    +-++ ...++..+-..+...|++++|.+. ..        +.+....++..+-..
T Consensus       191 ~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~  270 (378)
T 3q15_A          191 NYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWT  270 (378)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHH
T ss_pred             HHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHHHH
Confidence            567788899999888877542    2211 234566666777888888888887 11        222234556667778


Q ss_pred             HHhcCCccccc-----------------hHHHHHHHHHHHHhcCC---hHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhc
Q 039275           70 YAHSGRIRLAR-----------------DPVSCKAMISGYSQAGR---FNEALEPFGKLESLGVHT-DEVTMVVVLAASS  128 (153)
Q Consensus        70 ~~~~g~~~~a~-----------------~~~~~~~li~~~~~~g~---~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~  128 (153)
                      |.+.|++++|.                 ....++.+-..+...|+   +.+|...+++   .+..| ....+..+-..+.
T Consensus       271 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~---~~~~~~~~~~~~~la~~y~  347 (378)
T 3q15_A          271 LCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEK---KNLHAYIEACARSAAAVFE  347 (378)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHh---CCChhHHHHHHHHHHHHHH
Confidence            88888888777                 22345555556666677   6666666655   22222 2334556777888


Q ss_pred             CCCccccchh
Q 039275          129 GPGALDFGKS  138 (153)
Q Consensus       129 ~~g~~~~a~~  138 (153)
                      +.|++++|.+
T Consensus       348 ~~g~~~~A~~  357 (378)
T 3q15_A          348 SSCHFEQAAA  357 (378)
T ss_dssp             HTTCHHHHHH
T ss_pred             HCCCHHHHHH
Confidence            8888888776

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=97.33  E-value=0.0042  Score=43.45  Aligned_cols=133  Identities=9%  Similarity=-0.048  Sum_probs=91.1

Q ss_pred             hHhhcCChhHHHHHHHHhHHc----CCCc-cHHHHHHHHHHhcCC-CchHHHHHH-hhh--hhcc-------hhhHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESL----GVHT-DEVTMVVVLTASSGP-GAWILAKEL-QIE--LDLS-------SYSLSSKT   67 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~~~~~ll~~~~~~-~~~~~a~~~-~~~--~~~~-------~~~~~~ll   67 (153)
                      .|.+.|++++|+..|++..+.    |-.+ -..+++.+-..+... |++++|.+. ..-  +.|+       ..+++.+.
T Consensus        86 ~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg  165 (292)
T 1qqe_A           86 CFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCA  165 (292)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHH
Confidence            567889999999999887542    2111 145777778888885 999999888 111  1121       34678888


Q ss_pred             HHHHhcCCccccc------------hH-------HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCh------hhHHH
Q 039275           68 SRYAHSGRIRLAR------------DP-------VSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDE------VTMVV  122 (153)
Q Consensus        68 ~~~~~~g~~~~a~------------~~-------~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~------~t~~~  122 (153)
                      ..+.+.|++++|.            +.       ..|..+...+...|++++|.+.|++..+.  .|+.      ..+..
T Consensus       166 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~~~~~~~~~l~~  243 (292)
T 1qqe_A          166 DLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSE--DPNFADSRESNFLKS  243 (292)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC-----------HHHHHH
T ss_pred             HHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCCCCcHHHHHHHH
Confidence            9999999999998            11       15677778899999999999999987642  3332      23455


Q ss_pred             HHHHhc--CCCccccchh
Q 039275          123 VLAASS--GPGALDFGKS  138 (153)
Q Consensus       123 li~~~~--~~g~~~~a~~  138 (153)
                      ++.++.  ..+++++|..
T Consensus       244 l~~~~~~~~~~~~~~A~~  261 (292)
T 1qqe_A          244 LIDAVNEGDSEQLSEHCK  261 (292)
T ss_dssp             HHHHHHTTCTTTHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHH
Confidence            666664  4455655554

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=97.32  E-value=0.0033  Score=39.56  Aligned_cols=87  Identities=20%  Similarity=0.140  Sum_probs=51.5

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHH
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPV   83 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~   83 (153)
                      +.+.|++++|+..|++..... +.+...+..+-.++.+.|++++|.+. +.-+..+..                   +..
T Consensus        31 ~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~-------------------~~~   90 (148)
T 2vgx_A           31 QYQSGXYEDAHXVFQALCVLD-HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDIX-------------------EPR   90 (148)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-------------------CTH
T ss_pred             HHHcCChHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC-------------------Cch
Confidence            455566666666666554431 22444444555555566666666555 221111110                   446


Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 039275           84 SCKAMISGYSQAGRFNEALEPFGKLESL  111 (153)
Q Consensus        84 ~~~~li~~~~~~g~~~~a~~~~~~m~~~  111 (153)
                      .|..+-..+...|++++|.+.|+...+.
T Consensus        91 ~~~~lg~~~~~~g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A           91 FPFHAAECLLQXGELAEAESGLFLAQEL  118 (148)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            6777788888999999999999887754

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.31  E-value=0.00097  Score=48.77  Aligned_cols=135  Identities=10%  Similarity=-0.060  Sum_probs=92.7

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCcc----------------HHHHHHHHHHhcCCCchHHHHHH-h-----hhhhcch-
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTD----------------EVTMVVVLTASSGPGAWILAKEL-Q-----IELDLSS-   60 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~----------------~~~~~~ll~~~~~~~~~~~a~~~-~-----~~~~~~~-   60 (153)
                      .+.+.|++++|++.|.+..+..-...                ...+..+...|.+.|++++|.+. .     .+-.++. 
T Consensus        13 ~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~~~   92 (434)
T 4b4t_Q           13 RLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFAKSK   92 (434)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccchH
Confidence            46788999999999999876432111                12367788899999999999988 1     1111111 


Q ss_pred             ---hhHHHHHHHHHhcCCccccc------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCC----CC
Q 039275           61 ---YSLSSKTSRYAHSGRIRLAR------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGV----HT  115 (153)
Q Consensus        61 ---~~~~~ll~~~~~~g~~~~a~------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~----~p  115 (153)
                         .+.+.+-..+...|+.++|.                  ...++..+...+...|++++|..++++....-.    +|
T Consensus        93 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~  172 (434)
T 4b4t_Q           93 TVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDDKP  172 (434)
T ss_dssp             HHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCST
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcccch
Confidence               12222223333445555554                  356788899999999999999999999864421    22


Q ss_pred             -ChhhHHHHHHHhcCCCccccchh
Q 039275          116 -DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       116 -~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                       ...++..+...|...|++++|..
T Consensus       173 ~~~~~~~~~~~~~~~~~~~~~A~~  196 (434)
T 4b4t_Q          173 SLVDVHLLESKVYHKLRNLAKSKA  196 (434)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhCcHHHHHH
Confidence             34578888899999999999988

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=97.31  E-value=0.0013  Score=49.69  Aligned_cols=115  Identities=11%  Similarity=0.051  Sum_probs=78.6

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDP   82 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~   82 (153)
                      .+.+.|++++|++.|++..+. -+-+...+..+-.++.+.|++++|.+. ..-+..+..                   +.
T Consensus        15 ~~~~~g~~~~A~~~~~~Al~~-~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~-------------------~~   74 (477)
T 1wao_1           15 DYFKAKDYENAIKFYSQAIEL-NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKK-------------------YI   74 (477)
T ss_dssp             STTTTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTT-------------------CH
T ss_pred             HHHHhCCHHHHHHHHHHHHHh-CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-------------------CH
Confidence            467889999999999998775 233578888888899999999999988 333332221                   33


Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHcCC-CCChhhHHHHHHHhcCCCccccchh
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESLGV-HTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~-~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ..|..+-..|...|++++|.+.|++..+..- .++.......+..+.+.|++++|.+
T Consensus        75 ~~~~~lg~~~~~~g~~~eA~~~~~~al~~~p~~~~~~~~l~~~~~~~~~g~~~~A~~  131 (477)
T 1wao_1           75 KGYYRRAASNMALGKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIA  131 (477)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCTTHHHHHHHHHHHHHHHHHCCC--
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            5677778888889999999999988876531 2222222222323666677777765

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=97.29  E-value=0.0018  Score=46.58  Aligned_cols=135  Identities=11%  Similarity=-0.065  Sum_probs=92.3

Q ss_pred             hHhhcCChhHHHHHHHHhHHc----CCC--cc-HHHHHHHHHHhcCCCchHHHHHH-hhhh--------hcchhhHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESL----GVH--TD-EVTMVVVLTASSGPGAWILAKEL-QIEL--------DLSSYSLSSKT   67 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~----g~~--p~-~~~~~~ll~~~~~~~~~~~a~~~-~~~~--------~~~~~~~~~ll   67 (153)
                      .+...|++++|.+.+++..+.    +..  |. ...+..+-..+...|++++|... ...+        ......+..+.
T Consensus       102 ~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la  181 (373)
T 1hz4_A          102 ILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLI  181 (373)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHHH
Confidence            467789999999999887542    322  33 34555666788889999999988 1111        11234566777


Q ss_pred             HHHHhcCCccccc--------------hHHHHHH-----HHHHHHhcCChHHHHHHHHHHHHcCCCC---ChhhHHHHHH
Q 039275           68 SRYAHSGRIRLAR--------------DPVSCKA-----MISGYSQAGRFNEALEPFGKLESLGVHT---DEVTMVVVLA  125 (153)
Q Consensus        68 ~~~~~~g~~~~a~--------------~~~~~~~-----li~~~~~~g~~~~a~~~~~~m~~~g~~p---~~~t~~~li~  125 (153)
                      ..+...|++++|.              ....|..     ....+...|++++|.+.+++.......+   ....+..+..
T Consensus       182 ~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~la~  261 (373)
T 1hz4_A          182 QCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIAR  261 (373)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHHHHHHH
Confidence            8889999999888              1112322     2234779999999999998876533221   1234567778


Q ss_pred             HhcCCCccccchh
Q 039275          126 ASSGPGALDFGKS  138 (153)
Q Consensus       126 ~~~~~g~~~~a~~  138 (153)
                      .+...|++++|..
T Consensus       262 ~~~~~g~~~~A~~  274 (373)
T 1hz4_A          262 AQILLGEFEPAEI  274 (373)
T ss_dssp             HHHHTTCHHHHHH
T ss_pred             HHHHcCCHHHHHH
Confidence            8889999998887

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.26  E-value=0.0087  Score=36.57  Aligned_cols=92  Identities=13%  Similarity=0.105  Sum_probs=55.3

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCcc----HHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTD----EVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~----~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~   78 (153)
                      .+.+.|++++|++.|++..+.  .|+    ...+..+-..+.+.|++++|.+. ...+..+..                 
T Consensus        37 ~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-----------------   97 (148)
T 2dba_A           37 ELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKDGG-----------------   97 (148)
T ss_dssp             HHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSC-----------------
T ss_pred             HHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCcc-----------------
Confidence            345666777777777666553  344    45555555566666666666665 211111100                 


Q ss_pred             cchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChh
Q 039275           79 ARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEV  118 (153)
Q Consensus        79 a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  118 (153)
                        +...|..+-..+...|++++|.+.|++....  .|+..
T Consensus        98 --~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~--~p~~~  133 (148)
T 2dba_A           98 --DVKALYRRSQALEKLGRLDQAVLDLQRCVSL--EPKNK  133 (148)
T ss_dssp             --CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CSSCH
T ss_pred             --CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCcH
Confidence              3355667777788888888888888888754  35433

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=97.25  E-value=0.0054  Score=35.74  Aligned_cols=89  Identities=17%  Similarity=0.105  Sum_probs=64.2

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccch
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARD   81 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~   81 (153)
                      ..+...|++++|.+.|++..+.. +.+...+..+-..+.+.|++++|... ...+..+..                   +
T Consensus        12 ~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-------------------~   71 (118)
T 1elw_A           12 NKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPD-------------------W   71 (118)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-------------------C
T ss_pred             HHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCcc-------------------c
Confidence            35677889999999998887642 33566777777778888888888877 222221110                   3


Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 039275           82 PVSCKAMISGYSQAGRFNEALEPFGKLESL  111 (153)
Q Consensus        82 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  111 (153)
                      ...|..+...+...|++++|.+.|++..+.
T Consensus        72 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~  101 (118)
T 1elw_A           72 GKGYSRKAAALEFLNRFEEAKRTYEEGLKH  101 (118)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHc
Confidence            356777788889999999999999988754

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=97.23  E-value=0.0028  Score=38.55  Aligned_cols=88  Identities=13%  Similarity=-0.016  Sum_probs=57.9

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDP   82 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~   82 (153)
                      .+.+.|++++|+..|++..+.. +.+...+..+-..+...|++++|... ...+..+..                   +.
T Consensus        18 ~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~-------------------~~   77 (137)
T 3q49_B           18 RLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQ-------------------SV   77 (137)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CH
T ss_pred             HHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCch-------------------hH
Confidence            4567777777777777766542 23456666666677777777777766 222221111                   34


Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESL  111 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~  111 (153)
                      ..|..+-..+...|++++|.+.|++....
T Consensus        78 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~  106 (137)
T 3q49_B           78 KAHFFLGQCQLEMESYDEAIANLQRAYSL  106 (137)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            56777778888888888888888887643

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=97.22  E-value=0.0021  Score=43.99  Aligned_cols=113  Identities=12%  Similarity=0.030  Sum_probs=79.0

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcC--CCccHHHHHHHHHHhcC--------CCchHHHHHH-hh--hhhcch-hhH-----
Q 039275            3 SGYSQAGRFNEALEPFGKLESLG--VHTDEVTMVVVLTASSG--------PGAWILAKEL-QI--ELDLSS-YSL-----   63 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g--~~p~~~~~~~ll~~~~~--------~~~~~~a~~~-~~--~~~~~~-~~~-----   63 (153)
                      ..|.+.|++++|++.|++..+..  -+.....+..+-.++.+        .|++++|... ..  ...|+. ...     
T Consensus        60 ~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~  139 (261)
T 3qky_A           60 RAYYQNKEYLLAASEYERFIQIYQIDPRVPQAEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRYPNHELVDDATQK  139 (261)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHCTTCTTHHHHHHH
T ss_pred             HHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHCcCchhHHHHHHH
Confidence            35788999999999999998752  11224455555666666        8999999998 21  123432 233     


Q ss_pred             ------------HHHHHHHHhcCCccccc---------------hHHHHHHHHHHHHhc----------CChHHHHHHHH
Q 039275           64 ------------SSKTSRYAHSGRIRLAR---------------DPVSCKAMISGYSQA----------GRFNEALEPFG  106 (153)
Q Consensus        64 ------------~~ll~~~~~~g~~~~a~---------------~~~~~~~li~~~~~~----------g~~~~a~~~~~  106 (153)
                                  -.+-..|.+.|++++|.               ....+..+...|...          |++++|.+.|+
T Consensus       140 ~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~  219 (261)
T 3qky_A          140 IRELRAKLARKQYEAARLYERRELYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYE  219 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHH
Confidence                        34467889999999998               234566666677655          89999999999


Q ss_pred             HHHHcCCCCCh
Q 039275          107 KLESLGVHTDE  117 (153)
Q Consensus       107 ~m~~~g~~p~~  117 (153)
                      +..+.-  |+.
T Consensus       220 ~~~~~~--p~~  228 (261)
T 3qky_A          220 RLLQIF--PDS  228 (261)
T ss_dssp             HHHHHC--TTC
T ss_pred             HHHHHC--CCC
Confidence            998653  544

>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=97.22  E-value=0.0023  Score=44.72  Aligned_cols=106  Identities=8%  Similarity=-0.088  Sum_probs=81.3

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCC-cc----HHHHHHHHHHhcCCCchHHHHHH-hh---------hhhc-chhhHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVH-TD----EVTMVVVLTASSGPGAWILAKEL-QI---------ELDL-SSYSLSSKT   67 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~-p~----~~~~~~ll~~~~~~~~~~~a~~~-~~---------~~~~-~~~~~~~ll   67 (153)
                      .+...|++++|++.|++....... ++    ..+++.+-..+...|++++|... ..         +..+ ...++..+.
T Consensus       124 ~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg  203 (293)
T 3u3w_A          124 YVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHA  203 (293)
T ss_dssp             HHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHH
T ss_pred             HHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHH
Confidence            345678999999999999874322 22    34688888899999999999988 11         1111 224778888


Q ss_pred             HHHHhcCCccccc------------------hHHHHHHHHHHHHhcCC-hHHHHHHHHHHH
Q 039275           68 SRYAHSGRIRLAR------------------DPVSCKAMISGYSQAGR-FNEALEPFGKLE  109 (153)
Q Consensus        68 ~~~~~~g~~~~a~------------------~~~~~~~li~~~~~~g~-~~~a~~~~~~m~  109 (153)
                      ..|.+.|++++|.                  -..+|..+-..+.+.|+ .++|.+.|++..
T Consensus       204 ~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~~A~~~~~~Al  264 (293)
T 3u3w_A          204 KALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHH
Confidence            9999999999998                  26678888899999995 699999888765

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=97.22  E-value=0.0027  Score=37.12  Aligned_cols=90  Identities=14%  Similarity=-0.011  Sum_probs=65.3

Q ss_pred             cHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHH
Q 039275           29 DEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGK  107 (153)
Q Consensus        29 ~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~  107 (153)
                      ....+..+-..+...|++++|... ...+..+..                   +...|..+-..+...|++++|.+.+++
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~-------------------~~~~~~~~a~~~~~~~~~~~A~~~~~~   63 (118)
T 1elw_A            3 QVNELKEKGNKALSVGNIDDALQCYSEAIKLDPH-------------------NHVLYSNRSAAYAKKGDYQKAYEDGCK   63 (118)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCC-------------------cHHHHHHHHHHHHhhccHHHHHHHHHH
Confidence            345566666677778888888777 222211110                   345677778888999999999999999


Q ss_pred             HHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275          108 LESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       108 m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ..+.. ..+...+..+..++.+.|++++|.+
T Consensus        64 ~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~   93 (118)
T 1elw_A           64 TVDLK-PDWGKGYSRKAAALEFLNRFEEAKR   93 (118)
T ss_dssp             HHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHhC-cccHHHHHHHHHHHHHHhhHHHHHH
Confidence            88654 2256778888889999999999988

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=97.16  E-value=0.0027  Score=38.84  Aligned_cols=88  Identities=8%  Similarity=-0.074  Sum_probs=65.5

Q ss_pred             HHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 039275           31 VTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLE  109 (153)
Q Consensus        31 ~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  109 (153)
                      ..+.-.=..+.+.|++++|.+. ..-+..+..                   +...|..+-..+.+.|++++|.+.|++..
T Consensus        14 ~~~~~~G~~~~~~g~~~~A~~~~~~al~~~p~-------------------~~~~~~~~~~~~~~~~~~~~A~~~~~~al   74 (126)
T 4gco_A           14 QEEKNKGNEYFKKGDYPTAMRHYNEAVKRDPE-------------------NAILYSNRAACLTKLMEFQRALDDCDTCI   74 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-------------------CHHHHHHHhhHHHhhccHHHHHHHHHHHH
Confidence            3445555677777888887777 222222211                   45678888899999999999999999988


Q ss_pred             HcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275          110 SLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       110 ~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +.. ..+...|..+-.++...|++++|.+
T Consensus        75 ~~~-p~~~~a~~~lg~~~~~~~~~~~A~~  102 (126)
T 4gco_A           75 RLD-SKFIKGYIRKAACLVAMREWSKAQR  102 (126)
T ss_dssp             HHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             Hhh-hhhhHHHHHHHHHHHHCCCHHHHHH
Confidence            653 2356778889999999999999998

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=97.15  E-value=0.0016  Score=42.70  Aligned_cols=113  Identities=12%  Similarity=-0.005  Sum_probs=74.9

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCC-Ccc--------------HHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGV-HTD--------------EVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKT   67 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~-~p~--------------~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll   67 (153)
                      .+.+.|++++|++.|++..+..- .|+              ...+..+-.++.+.|++++|... ...+..+..      
T Consensus        47 ~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~------  120 (198)
T 2fbn_A           47 EFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKIDKN------  120 (198)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT------
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcc------
Confidence            56788999999999999876421 111              25666677777888888888877 222221111      


Q ss_pred             HHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccch
Q 039275           68 SRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGK  137 (153)
Q Consensus        68 ~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~  137 (153)
                                   +...|..+-..+...|++++|.+.|++..+.  .| +...+..+-..+...++.+++.
T Consensus       121 -------------~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~~~  176 (198)
T 2fbn_A          121 -------------NVKALYKLGVANMYFGFLEEAKENLYKAASL--NPNNLDIRNSYELCVNKLKEARKKD  176 (198)
T ss_dssp             -------------CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHHHC--
T ss_pred             -------------cHHHHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHHHHHHHH
Confidence                         3356667777888889999999998887754  34 4455566666666666666655

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=97.14  E-value=0.0014  Score=47.14  Aligned_cols=56  Identities=14%  Similarity=0.098  Sum_probs=49.2

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           82 PVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        82 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ...|..+-..+.+.|++++|.+.|++..+.. ..+...+..+-.++.+.|++++|..
T Consensus       196 ~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~  251 (336)
T 1p5q_A          196 LASHLNLAMCHLKLQAFSAAIESCNKALELD-SNNEKGLSRRGEAHLAVNDFELARA  251 (336)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHH
Confidence            5788999999999999999999999998754 2367788889999999999999988

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=97.14  E-value=0.0013  Score=41.96  Aligned_cols=56  Identities=14%  Similarity=0.052  Sum_probs=48.7

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +...|..+-..+...|++++|.+.|++.....  | +...+..+-.++.+.|++++|..
T Consensus        69 ~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~--P~~~~~~~~lg~~~~~lg~~~eA~~  125 (151)
T 3gyz_A           69 NVDYIMGLAAIYQIKEQFQQAADLYAVAFALG--KNDYTPVFHTGQCQLRLKAPLKAKE  125 (151)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--SSCCHHHHHHHHHHHHTTCHHHHHH
T ss_pred             CHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC--CCCcHHHHHHHHHHHHcCCHHHHHH
Confidence            55788889999999999999999999998654  4 46678888899999999999988

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=97.09  E-value=0.0063  Score=42.46  Aligned_cols=124  Identities=7%  Similarity=-0.081  Sum_probs=88.4

Q ss_pred             hHhhcCChhHHHHHHHHhHHcC---CCcc--HHHHHHHHHHhcCCCchHHHHHH-hhh-----hhcc-----hhhHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESLG---VHTD--EVTMVVVLTASSGPGAWILAKEL-QIE-----LDLS-----SYSLSSKT   67 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g---~~p~--~~~~~~ll~~~~~~~~~~~a~~~-~~~-----~~~~-----~~~~~~ll   67 (153)
                      .+...|++++|++.|++.....   ..+.  ..+|+.+-..+...|++++|... ...     ..|+     ..++..+-
T Consensus       124 ~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg  203 (293)
T 2qfc_A          124 YVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHA  203 (293)
T ss_dssp             HHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHH
T ss_pred             HHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHH
Confidence            4567789999999999886532   1222  45888888899999999999988 111     1222     25788888


Q ss_pred             HHHHhcCCccccc-----------h-------HHHHHHHHHHHHhcCChHHH-HHHHHHHH----HcCCCCChhhHHHHH
Q 039275           68 SRYAHSGRIRLAR-----------D-------PVSCKAMISGYSQAGRFNEA-LEPFGKLE----SLGVHTDEVTMVVVL  124 (153)
Q Consensus        68 ~~~~~~g~~~~a~-----------~-------~~~~~~li~~~~~~g~~~~a-~~~~~~m~----~~g~~p~~~t~~~li  124 (153)
                      ..|.+.|++++|.           +       ..+|..+-..+.+.|+.++| ...+++-.    ..+-++-...+..+|
T Consensus       204 ~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~Ai~~~~~~Al~~~~~~~~~~~~~~~~~~~  283 (293)
T 2qfc_A          204 KALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKASFFFDILEMHAYKEALVNKI  283 (293)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHhCcHhhHHHHHHHH
Confidence            9999999999999           2       66788888899999999999 77676643    223333344455555


Q ss_pred             HHh
Q 039275          125 AAS  127 (153)
Q Consensus       125 ~~~  127 (153)
                      +-+
T Consensus       284 ~~~  286 (293)
T 2qfc_A          284 SRL  286 (293)
T ss_dssp             HHC
T ss_pred             HHH
Confidence            443

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=97.03  E-value=0.004  Score=37.38  Aligned_cols=94  Identities=10%  Similarity=0.003  Sum_probs=65.6

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccH---HHHHHHHHHhcCCCchHHHHHH-hhhh--hcchhhHHHHHHHHHhcCCcc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDE---VTMVVVLTASSGPGAWILAKEL-QIEL--DLSSYSLSSKTSRYAHSGRIR   77 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~---~~~~~ll~~~~~~~~~~~a~~~-~~~~--~~~~~~~~~ll~~~~~~g~~~   77 (153)
                      .+.+.|++++|.+.|++..+..- .+.   ..+..+-..+.+.|++++|... ..-+  .|+...               
T Consensus        11 ~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~~~~---------------   74 (129)
T 2xev_A           11 DALKNGKYDDASQLFLSFLELYP-NGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPTHDK---------------   74 (129)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCS-SSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTT---------------
T ss_pred             HHHHhCCHHHHHHHHHHHHHHCC-CCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCCCcc---------------
Confidence            56789999999999999877421 122   4566667788899999999988 2222  232210               


Q ss_pred             ccchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChh
Q 039275           78 LARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEV  118 (153)
Q Consensus        78 ~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  118 (153)
                         ....+..+-..+...|++++|.+.|++.....  |+..
T Consensus        75 ---~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~--p~~~  110 (129)
T 2xev_A           75 ---AAGGLLKLGLSQYGEGKNTEAQQTLQQVATQY--PGSD  110 (129)
T ss_dssp             ---HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTSH
T ss_pred             ---cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCCh
Confidence               12455667778888999999999999988653  5443

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=97.02  E-value=0.007  Score=42.71  Aligned_cols=108  Identities=9%  Similarity=0.028  Sum_probs=72.8

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHHhhh-h-hcc----hhhHHHHHHHHHhcCCc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIE-L-DLS----SYSLSSKTSRYAHSGRI   76 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~-~-~~~----~~~~~~ll~~~~~~g~~   76 (153)
                      ..+.+.|++++|.++|+.+...+  |+....-.+-..+.+.+++++|+..... . .|+    ...+..+=.++.+.|++
T Consensus       110 ~~L~~~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~d~~~~~~a~~~LG~al~~LG~~  187 (282)
T 4f3v_A          110 ACEAAQGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWPDKFLAGAAGVAHGVAAANLALF  187 (282)
T ss_dssp             HHHHHHTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCSCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHCCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccCCcccHHHHHHHHHHHHHHCCCH
Confidence            35788999999999999887654  5443333334477899999999999221 1 121    22455556777788888


Q ss_pred             cccc---------h--H----HHHHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 039275           77 RLAR---------D--P----VSCKAMISGYSQAGRFNEALEPFGKLESLG  112 (153)
Q Consensus        77 ~~a~---------~--~----~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  112 (153)
                      ++|.         .  +    ..+...-..+.+.|+.++|..+|+++....
T Consensus       188 ~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~  238 (282)
T 4f3v_A          188 TEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTH  238 (282)
T ss_dssp             HHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            7776         1  1    133445566777888888888888887653

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=97.01  E-value=0.0047  Score=37.40  Aligned_cols=88  Identities=14%  Similarity=-0.046  Sum_probs=62.1

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDP   82 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~   82 (153)
                      .+.+.|++++|+..|++..+.. +-+...+..+-.++.+.|++++|... +.-+..+..                   +.
T Consensus        26 ~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~-------------------~~   85 (121)
T 1hxi_A           26 SMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPK-------------------DI   85 (121)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-------------------CH
Confidence            5677888888888888887641 23556666666677888888888877 332222221                   33


Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESL  111 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~  111 (153)
                      ..|..+-..+...|++++|.+.|++..+.
T Consensus        86 ~~~~~la~~~~~~g~~~~A~~~~~~al~~  114 (121)
T 1hxi_A           86 AVHAALAVSHTNEHNANAALASLRAWLLS  114 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            56777888889999999999999988743

>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=96.98  E-value=0.0024  Score=40.21  Aligned_cols=88  Identities=13%  Similarity=0.072  Sum_probs=64.0

Q ss_pred             HHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHH
Q 039275           30 EVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKL  108 (153)
Q Consensus        30 ~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m  108 (153)
                      ...+..+-..+.+.|++++|... ..-+..+..                   +...|..+-..+...|++++|.+.|++.
T Consensus        21 ~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~-------------------~~~~~~~lg~~~~~~g~~~~A~~~~~~a   81 (148)
T 2vgx_A           21 LEQLYSLAFNQYQSGXYEDAHXVFQALCVLDHY-------------------DSRFFLGLGACRQAMGQYDLAIHSYSYG   81 (148)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHHcCcc-------------------cHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            34445555666777888887777 221111110                   4466778888899999999999999998


Q ss_pred             HHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275          109 ESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       109 ~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ....  | +...+..+-.++...|++++|.+
T Consensus        82 l~l~--p~~~~~~~~lg~~~~~~g~~~~A~~  110 (148)
T 2vgx_A           82 AVMD--IXEPRFPFHAAECLLQXGELAEAES  110 (148)
T ss_dssp             HHHS--TTCTHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HhcC--CCCchHHHHHHHHHHHcCCHHHHHH
Confidence            8653  4 55677888889999999999988

>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=96.94  E-value=0.039  Score=36.57  Aligned_cols=129  Identities=12%  Similarity=-0.007  Sum_probs=88.9

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCC----chHHHHHH-hhhhhc-chhhHHHHHHHHHh----c
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPG----AWILAKEL-QIELDL-SSYSLSSKTSRYAH----S   73 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~----~~~~a~~~-~~~~~~-~~~~~~~ll~~~~~----~   73 (153)
                      .|...+++++|++.|++..+.|   ++..+..+=..+.. +    ++++|.++ +....+ +...+..|-..|..    .
T Consensus        27 ~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~~g~~~a~~~Lg~~y~~g~g~~  102 (212)
T 3rjv_A           27 TWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQLAEKAVEAGSKSGEIVLARVLVNRQAGA  102 (212)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTCGGGSS
T ss_pred             HHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCc
Confidence            4567899999999999998876   44555555555666 6    89999998 333333 34455556566655    6


Q ss_pred             CCccccc----------h----HHHHHHHHHHHHh----cCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCC-C---
Q 039275           74 GRIRLAR----------D----PVSCKAMISGYSQ----AGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGP-G---  131 (153)
Q Consensus        74 g~~~~a~----------~----~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~-g---  131 (153)
                      +++++|.          +    ...+..|-..|..    .+++++|.+.|++-.+.+  ++...+..+-..|.+. |   
T Consensus       103 ~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~--~~~~a~~~Lg~~y~~g~gg~~  180 (212)
T 3rjv_A          103 TDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSLS--RTGYAEYWAGMMFQQGEKGFI  180 (212)
T ss_dssp             CCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHTS--CTTHHHHHHHHHHHHCBTTTB
T ss_pred             cCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHcCCCCCC
Confidence            6777776          3    6888888888888    889999999999987762  2333455555555432 2   


Q ss_pred             --ccccchh
Q 039275          132 --ALDFGKS  138 (153)
Q Consensus       132 --~~~~a~~  138 (153)
                        +.++|.+
T Consensus       181 ~~d~~~A~~  189 (212)
T 3rjv_A          181 EPNKQKALH  189 (212)
T ss_dssp             CCCHHHHHH
T ss_pred             CCCHHHHHH
Confidence              6676666

>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=96.92  E-value=0.0039  Score=37.89  Aligned_cols=91  Identities=8%  Similarity=-0.103  Sum_probs=68.4

Q ss_pred             ccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHH
Q 039275           28 TDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFG  106 (153)
Q Consensus        28 p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~  106 (153)
                      .+...+..+-..+.+.|++++|... ..-+..+..                   +...|..+-..+...|++++|...|+
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~-------------------~~~~~~~l~~~~~~~~~~~~A~~~~~   67 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPL-------------------VAVYYTNRALCYLKMQQPEQALADCR   67 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhCcC-------------------cHHHHHHHHHHHHHhcCHHHHHHHHH
Confidence            4566677777777888888888777 222222111                   34678888889999999999999999


Q ss_pred             HHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275          107 KLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       107 ~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +..+.. .-+...+..+-.++...|++++|..
T Consensus        68 ~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~   98 (137)
T 3q49_B           68 RALELD-GQSVKAHFFLGQCQLEMESYDEAIA   98 (137)
T ss_dssp             HHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHhC-chhHHHHHHHHHHHHHHhhHHHHHH
Confidence            988754 2256778888899999999999988

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=96.92  E-value=0.011  Score=41.28  Aligned_cols=123  Identities=8%  Similarity=-0.108  Sum_probs=88.7

Q ss_pred             CccHHHHHHHHHHhcCCCchHHHHHH-h--hhhhc-chhhHHHHHHHHHhcCCccccc-----------h-HHHHHHHHH
Q 039275           27 HTDEVTMVVVLTASSGPGAWILAKEL-Q--IELDL-SSYSLSSKTSRYAHSGRIRLAR-----------D-PVSCKAMIS   90 (153)
Q Consensus        27 ~p~~~~~~~ll~~~~~~~~~~~a~~~-~--~~~~~-~~~~~~~ll~~~~~~g~~~~a~-----------~-~~~~~~li~   90 (153)
                      +.+...+..+-..+.+.|++++|... +  ....| +...+..+...+.+.|++++|.           + .........
T Consensus       114 p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~~~~~~  193 (287)
T 3qou_A          114 PREEELXAQQAMQLMQESNYTDALPLLXDAWQLSNQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQDQDTRYQGLVAQI  193 (287)
T ss_dssp             CCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGGCSHHHHHHHHHH
T ss_pred             CCchhhHHHHHHHHHhCCCHHHHHHHHHHHHHhCCcchhHHHHHHHHHHHCCCHHHHHHHHHhCchhhcchHHHHHHHHH
Confidence            44556666667778889999999998 2  22344 4457778889999999999998           2 222222333


Q ss_pred             HHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh-------------HHHHHHHHHHHh
Q 039275           91 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS-------------NIFLTTAIIEMY  150 (153)
Q Consensus        91 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~-------------~~~~~~~li~~y  150 (153)
                      .+...++.++|.+.|++..... ..+...+..+-..+.+.|++++|.+             +...+..|...|
T Consensus       194 ~l~~~~~~~~a~~~l~~al~~~-P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~  265 (287)
T 3qou_A          194 ELLXQAADTPEIQQLQQQVAEN-PEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEIL  265 (287)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHH
T ss_pred             HHHhhcccCccHHHHHHHHhcC-CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHH
Confidence            4677888899999998887653 2356778888899999999999998             255666666555

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=96.89  E-value=0.054  Score=40.53  Aligned_cols=125  Identities=11%  Similarity=-0.012  Sum_probs=63.0

Q ss_pred             cCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcC----CCchHHHHHH-hhhhh-cchhhHHHHHHHHHh----cCCcc
Q 039275            8 AGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSG----PGAWILAKEL-QIELD-LSSYSLSSKTSRYAH----SGRIR   77 (153)
Q Consensus         8 ~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~----~~~~~~a~~~-~~~~~-~~~~~~~~ll~~~~~----~g~~~   77 (153)
                      .+++++|++.|++..+.|.   +..+..+=..+..    .+++++|.++ +.-.. .+...+..|-..|..    .++++
T Consensus        56 ~~~~~~A~~~~~~a~~~~~---~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~  132 (490)
T 2xm6_A           56 TKDLTQAMDWFRRAAEQGY---TPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKGLPQAQQNLGVMYHEGNGVKVDKA  132 (490)
T ss_dssp             CCCHHHHHHHHHHHHHTTC---HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHH
T ss_pred             CcCHHHHHHHHHHHHHCCC---HHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHH
Confidence            5667777777776665542   3333333334443    5666666666 11111 123334444444544    45555


Q ss_pred             ccc----------hHHHHHHHHHHHHh----cCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcC----CCccccchh
Q 039275           78 LAR----------DPVSCKAMISGYSQ----AGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSG----PGALDFGKS  138 (153)
Q Consensus        78 ~a~----------~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~----~g~~~~a~~  138 (153)
                      +|.          +...+..|-..|..    .++.++|.+.|++..+.|   +...+..+-..+.+    .++.++|.+
T Consensus       133 ~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~  208 (490)
T 2xm6_A          133 ESVKWFRLAAEQGRDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQG---NVWSCNQLGYMYSRGLGVERNDAISAQ  208 (490)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCCCcCHHHHHH
Confidence            555          44445455555554    556666666666655543   33344444444443    455555444

>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=96.86  E-value=0.0039  Score=37.54  Aligned_cols=89  Identities=9%  Similarity=-0.057  Sum_probs=64.6

Q ss_pred             HHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHH
Q 039275           30 EVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKL  108 (153)
Q Consensus        30 ~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m  108 (153)
                      ...+...-..+.+.|++++|.+. ...+..+..                   +...|..+-..+.+.|++++|.+.|++.
T Consensus         4 a~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~-------------------~~~~~~~~a~~~~~~~~~~~A~~~~~~a   64 (126)
T 3upv_A            4 AEEARLEGKEYFTKSDWPNAVKAYTEMIKRAPE-------------------DARGYSNRAAALAKLMSFPEAIADCNKA   64 (126)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-------------------ChHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            34455555666777777777776 222221111                   3467888889999999999999999998


Q ss_pred             HHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275          109 ESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       109 ~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .+.. .-+...+..+-.++...|++++|.+
T Consensus        65 l~~~-p~~~~~~~~lg~~~~~~~~~~~A~~   93 (126)
T 3upv_A           65 IEKD-PNFVRAYIRKATAQIAVKEYASALE   93 (126)
T ss_dssp             HHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHhC-CCcHHHHHHHHHHHHHHhCHHHHHH
Confidence            8654 2246678888889999999999988

>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=96.86  E-value=0.0023  Score=41.04  Aligned_cols=97  Identities=9%  Similarity=-0.019  Sum_probs=71.3

Q ss_pred             hcCCCchHHHHHH-hh--hh-hcchhhHHHHHHHHHhcCCccccc------------hHHHHHHHHHH-HHhcCCh--HH
Q 039275           40 SSGPGAWILAKEL-QI--EL-DLSSYSLSSKTSRYAHSGRIRLAR------------DPVSCKAMISG-YSQAGRF--NE  100 (153)
Q Consensus        40 ~~~~~~~~~a~~~-~~--~~-~~~~~~~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~-~~~~g~~--~~  100 (153)
                      +...|++++|.+. ..  .. +.+...+..+-..|...|++++|.            +...|..+-.. +...|++  ++
T Consensus        20 ~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~l~~~~~~~~~~~   99 (177)
T 2e2e_A           20 FASQQNPEAQLQALQDKIRANPQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLRGENAELYAALATVLYYQASQHMTAQ   99 (177)
T ss_dssp             CC-----CCCCHHHHHHHHHCCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHTTTCCCHH
T ss_pred             hhhccCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCcchHH
Confidence            3455667766665 11  12 335567888889999999999998            56677777777 7789998  99


Q ss_pred             HHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275          101 ALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       101 a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |.+.|++.....  | +...+..+...+...|++++|..
T Consensus       100 A~~~~~~al~~~--p~~~~~~~~la~~~~~~g~~~~A~~  136 (177)
T 2e2e_A          100 TRAMIDKALALD--SNEITALMLLASDAFMQANYAQAIE  136 (177)
T ss_dssp             HHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHhC--CCcHHHHHHHHHHHHHcccHHHHHH
Confidence            999999998654  4 45677788889999999999988

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=96.83  E-value=0.026  Score=37.71  Aligned_cols=110  Identities=14%  Similarity=0.012  Sum_probs=72.8

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcC-CCccH-HHHHHHHHHh------------------cCCCchHHHHHH-hh--hhhcc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLG-VHTDE-VTMVVVLTAS------------------SGPGAWILAKEL-QI--ELDLS   59 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g-~~p~~-~~~~~ll~~~------------------~~~~~~~~a~~~-~~--~~~~~   59 (153)
                      ..|.+.|++++|++.|++..+.. -.|.. ..+-.+-.++                  ...|++++|... +.  ...|+
T Consensus        49 ~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~P~  128 (225)
T 2yhc_A           49 YAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGYPN  128 (225)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTTCTT
T ss_pred             HHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHHHHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHCcC
Confidence            46788999999999999997642 11221 1222222222                  246788888887 11  12233


Q ss_pred             hh-hH-----------------HHHHHHHHhcCCccccc---------------hHHHHHHHHHHHHhcCChHHHHHHHH
Q 039275           60 SY-SL-----------------SSKTSRYAHSGRIRLAR---------------DPVSCKAMISGYSQAGRFNEALEPFG  106 (153)
Q Consensus        60 ~~-~~-----------------~~ll~~~~~~g~~~~a~---------------~~~~~~~li~~~~~~g~~~~a~~~~~  106 (153)
                      .. .+                 -.+-..|.+.|++++|.               ....+..+...+.+.|+.++|.+.++
T Consensus       129 ~~~a~~a~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~  208 (225)
T 2yhc_A          129 SQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAK  208 (225)
T ss_dssp             CTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             ChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHH
Confidence            22 22                 13445678889998888               13567888899999999999999999


Q ss_pred             HHHHcC
Q 039275          107 KLESLG  112 (153)
Q Consensus       107 ~m~~~g  112 (153)
                      .+...+
T Consensus       209 ~l~~~~  214 (225)
T 2yhc_A          209 IIAANS  214 (225)
T ss_dssp             HHHHCC
T ss_pred             HHHhhC
Confidence            988765

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=96.82  E-value=0.013  Score=38.70  Aligned_cols=116  Identities=9%  Similarity=-0.001  Sum_probs=78.7

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-h--hhhhc-chhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-Q--IELDL-SSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~--~~~~~-~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .|.+.|++++|+..|++..+.. +-+...+..+-..+...|++++|.+. +  ....| +...+..+-..|...|+.+.+
T Consensus        63 ~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~~  141 (208)
T 3urz_A           63 AYKKNRNYDKAYLFYKELLQKA-PNNVDCLEACAEMQVCRGQEKDALRMYEKILQLEADNLAANIFLGNYYYLTAEQEKK  141 (208)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhHHHHH
Confidence            5778999999999999997752 34677888888899999999999999 2  22334 344566666665544432221


Q ss_pred             c-----------hH--HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHH
Q 039275           80 R-----------DP--VSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVV  122 (153)
Q Consensus        80 ~-----------~~--~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~  122 (153)
                      .           +.  ..|-.+-.++...|++++|...|++..+  +.|+......
T Consensus       142 ~~~~~~~~~~~~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~--l~P~~~~~~~  195 (208)
T 3urz_A          142 KLETDYKKLSSPTKMQYARYRDGLSKLFTTRYEKARNSLQKVIL--RFPSTEAQKT  195 (208)
T ss_dssp             HHHHHHC---CCCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTT--TSCCHHHHHH
T ss_pred             HHHHHHHHHhCCCchhHHHHHHHHHHHHccCHHHHHHHHHHHHH--hCCCHHHHHH
Confidence            1           11  2233344456678999999999999875  4577654443

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=96.82  E-value=0.0039  Score=39.51  Aligned_cols=90  Identities=13%  Similarity=0.072  Sum_probs=67.2

Q ss_pred             cHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHH
Q 039275           29 DEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGK  107 (153)
Q Consensus        29 ~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~  107 (153)
                      +...+..+-..+.+.|++++|.+. ..-+..+..                   +...|..+-..+.+.|++++|.+.|++
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~-------------------~~~~~~~l~~~~~~~g~~~~A~~~~~~   70 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSKAIDLYTQALSIAPA-------------------NPIYLSNRAAAYSASGQHEKAAEDAEL   70 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-------------------CHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCc-------------------CHHHHHHHHHHHHHccCHHHHHHHHHH
Confidence            455666666677777888887777 222221111                   346788888999999999999999999


Q ss_pred             HHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275          108 LESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       108 m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ..+.. .-+...|..+-.++.+.|++++|.+
T Consensus        71 al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~  100 (164)
T 3sz7_A           71 ATVVD-PKYSKAWSRLGLARFDMADYKGAKE  100 (164)
T ss_dssp             HHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHhC-CCCHHHHHHHHHHHHHccCHHHHHH
Confidence            88654 2257778888999999999999988

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=96.82  E-value=0.004  Score=38.57  Aligned_cols=87  Identities=16%  Similarity=0.136  Sum_probs=62.4

Q ss_pred             HHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHHH
Q 039275           32 TMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLES  110 (153)
Q Consensus        32 ~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  110 (153)
                      .+..+-..+.+.|++++|... ..-+..+..                   +...|..+-..+.+.|++++|...|+....
T Consensus        20 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~-------------------~~~~~~~lg~~~~~~g~~~~A~~~~~~al~   80 (142)
T 2xcb_A           20 QLYALGFNQYQAGKWDDAQKIFQALCMLDHY-------------------DARYFLGLGACRQSLGLYEQALQSYSYGAL   80 (142)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccHHHHHHHHHHHHHhCCc-------------------cHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            344444566777888888777 221211111                   446677888889999999999999999986


Q ss_pred             cCCCCChhhHHHHHHHhcCCCccccchh
Q 039275          111 LGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       111 ~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .. .-+...+..+-.++...|++++|.+
T Consensus        81 ~~-p~~~~~~~~lg~~~~~~g~~~~A~~  107 (142)
T 2xcb_A           81 MD-INEPRFPFHAAECHLQLGDLDGAES  107 (142)
T ss_dssp             HC-TTCTHHHHHHHHHHHHTTCHHHHHH
T ss_pred             cC-CCCcHHHHHHHHHHHHcCCHHHHHH
Confidence            54 2245567788889999999999988

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.81  E-value=0.016  Score=42.20  Aligned_cols=136  Identities=4%  Similarity=-0.124  Sum_probs=96.1

Q ss_pred             hhHhhcCChhHHHHHHHHhHHc-CCCccH---HHHHHHHHH-hcCCCchHHHHHH---------hhhhhc-chhhHHHHH
Q 039275            3 SGYSQAGRFNEALEPFGKLESL-GVHTDE---VTMVVVLTA-SSGPGAWILAKEL---------QIELDL-SSYSLSSKT   67 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~-g~~p~~---~~~~~ll~~-~~~~~~~~~a~~~---------~~~~~~-~~~~~~~ll   67 (153)
                      ..|.+.|++++|.+.+.+.... +-.++.   ......+.. +...|.++.+.++         ..+-.+ -..++..+.
T Consensus        63 ~~y~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la  142 (434)
T 4b4t_Q           63 QLYVTMGAKDKLREFIPHSTEYMMQFAKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLA  142 (434)
T ss_dssp             HHHHHHTCHHHHHHHHHHTHHHHHTSCHHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHccchHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHH
Confidence            5688999999999999888542 111222   233344443 4456788888877         111111 134667788


Q ss_pred             HHHHhcCCccccc------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc--CC-CC---ChhhHHHH
Q 039275           68 SRYAHSGRIRLAR------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESL--GV-HT---DEVTMVVV  123 (153)
Q Consensus        68 ~~~~~~g~~~~a~------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~--g~-~p---~~~t~~~l  123 (153)
                      ..|...|++++|.                  ....|..++..|...|++++|..++++....  .+ .|   -...+..+
T Consensus       143 ~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~  222 (434)
T 4b4t_Q          143 TLHYQKKQYKDSLALINDLLREFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMS  222 (434)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHH
T ss_pred             HHHHHccChHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHH
Confidence            9999999999988                  4568999999999999999999999887632  12 22   24567777


Q ss_pred             HHHhcCCCccccchh
Q 039275          124 LAASSGPGALDFGKS  138 (153)
Q Consensus       124 i~~~~~~g~~~~a~~  138 (153)
                      ...+...|+++.|..
T Consensus       223 g~~~~~~~~y~~A~~  237 (434)
T 4b4t_Q          223 GILHCEDKDYKTAFS  237 (434)
T ss_dssp             HHHTTSSSCHHHHHH
T ss_pred             HHHHHHHHhHHHHHH
Confidence            788889999998877

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=96.80  E-value=0.0038  Score=38.49  Aligned_cols=95  Identities=12%  Similarity=0.012  Sum_probs=62.5

Q ss_pred             HHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 039275           31 VTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLE  109 (153)
Q Consensus        31 ~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  109 (153)
                      .++..+-..+...|++++|.+. ...+....           +.++...  ...++..+-..+...|++++|.+.+++..
T Consensus        10 ~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~-----------~~~~~~~--~~~~~~~l~~~~~~~g~~~~A~~~~~~a~   76 (164)
T 3ro3_A           10 RAFGNLGNTHYLLGNFRDAVIAHEQRLLIAK-----------EFGDKAA--ERIAYSNLGNAYIFLGEFETASEYYKKTL   76 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH-----------HHTCHHH--HHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHH-----------HhCCchH--HHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4556666677778888888877 22111100           0000000  23577788888999999999999999876


Q ss_pred             HcC----CCC-ChhhHHHHHHHhcCCCccccchh
Q 039275          110 SLG----VHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       110 ~~g----~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +..    -.+ ....+..+-..+...|++++|.+
T Consensus        77 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~  110 (164)
T 3ro3_A           77 LLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAID  110 (164)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHhCCcHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence            431    111 24567778889999999999988

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=96.74  E-value=0.075  Score=39.74  Aligned_cols=15  Identities=33%  Similarity=0.142  Sum_probs=7.3

Q ss_pred             cCChHHHHHHHHHHH
Q 039275           95 AGRFNEALEPFGKLE  109 (153)
Q Consensus        95 ~g~~~~a~~~~~~m~  109 (153)
                      .+++++|.+.|++..
T Consensus       272 ~~d~~~A~~~~~~a~  286 (490)
T 2xm6_A          272 AKEPLKALEWYRKSA  286 (490)
T ss_dssp             SCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH
Confidence            444555555554444

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.70  E-value=0.03  Score=34.06  Aligned_cols=60  Identities=10%  Similarity=-0.051  Sum_probs=34.1

Q ss_pred             ccHHHHHHHHHHhcCCCchHHHHHH-h--hhhhcc----hhhHHHHHHHHHhcCCccccchHHHHHHHH
Q 039275           28 TDEVTMVVVLTASSGPGAWILAKEL-Q--IELDLS----SYSLSSKTSRYAHSGRIRLARDPVSCKAMI   89 (153)
Q Consensus        28 p~~~~~~~ll~~~~~~~~~~~a~~~-~--~~~~~~----~~~~~~ll~~~~~~g~~~~a~~~~~~~~li   89 (153)
                      .+...+..+-..+.+.|++++|.+. .  ....|+    ...+..+...|.+.|++++|.  ..|...+
T Consensus        26 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~--~~~~~~~   92 (148)
T 2dba_A           26 SSVEQLRKEGNELFKCGDYGGALAAYTQALGLDATPQDQAVLHRNRAACHLKLEDYDKAE--TEASKAI   92 (148)
T ss_dssp             CCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHTTCHHHHH--HHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHccHHHHH--HHHHHHH
Confidence            3455556666666677777777666 1  122333    345556666667777776655  4444433

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=96.66  E-value=0.039  Score=40.62  Aligned_cols=42  Identities=5%  Similarity=-0.208  Sum_probs=24.2

Q ss_pred             CChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           96 GRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        96 g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |+.++|.+++++..... ..+...+..+-..+.+.|++++|.+
T Consensus       227 ~~~~~a~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~~~A~~  268 (472)
T 4g1t_A          227 EEEGEGEKLVEEALEKA-PGVTDVLRSAAKFYRRKDEPDKAIE  268 (472)
T ss_dssp             ---CHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhC-ccHHHHHHHHHHHHHHcCchHHHHH
Confidence            45566666666655432 2244456666667777777777766

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=96.65  E-value=0.0097  Score=44.55  Aligned_cols=114  Identities=13%  Similarity=0.093  Sum_probs=69.2

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCC-cc-------------HHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVH-TD-------------EVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTS   68 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~-p~-------------~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~   68 (153)
                      .|.+.|++++|+..|++..+..-. ++             ...|..+-.++.+.|++++|.+. ..-+..+..       
T Consensus       277 ~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~-------  349 (457)
T 1kt0_A          277 VYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLDSA-------  349 (457)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-------
T ss_pred             HHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCc-------
Confidence            577899999999999988763211 11             46666677777778888887777 222221111       


Q ss_pred             HHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           69 RYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        69 ~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                                  +...|..+-.+|...|++++|...|++..+.  .| +...+..+-.++.+.++.+++.+
T Consensus       350 ------------~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~l~~~~~~~~~~~~a~~  406 (457)
T 1kt0_A          350 ------------NEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQNKAARLQISMCQKKAKEHNERDR  406 (457)
T ss_dssp             ------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--C----CHHHHHHHHHHHHHHHHHHHH
T ss_pred             ------------cHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence                        2345556666777777777777777776643  34 33445555555555555555443

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=96.61  E-value=0.011  Score=43.18  Aligned_cols=113  Identities=11%  Similarity=0.120  Sum_probs=71.3

Q ss_pred             hHhhcCChhHHHHHHHHhHHc---------------CCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESL---------------GVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKT   67 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~---------------g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll   67 (153)
                      .+.+.|++++|++.|++..+.               --+.+...|..+-.++.+.|++++|.+. ..-+..+..      
T Consensus       232 ~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~------  305 (370)
T 1ihg_A          232 TFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEIDPS------  305 (370)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTT------
T ss_pred             HHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhCch------
Confidence            567889999999999888651               1112335555555666666777776666 222221110      


Q ss_pred             HHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccch
Q 039275           68 SRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGK  137 (153)
Q Consensus        68 ~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~  137 (153)
                                   +...|..+-..|...|++++|.+.|++..+.  .| +...+..+-..+.+.++.+++.
T Consensus       306 -------------~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l--~P~~~~~~~~l~~~~~~~~~~~~a~  361 (370)
T 1ihg_A          306 -------------NTKALYRRAQGWQGLKEYDQALADLKKAQEI--APEDKAIQAELLKVKQKIKAQKDKE  361 (370)
T ss_dssp             -------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -------------hHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHHH
Confidence                         3466777788889999999999999988764  35 4444555555555555555443

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=96.58  E-value=0.02  Score=35.99  Aligned_cols=94  Identities=13%  Similarity=0.012  Sum_probs=59.5

Q ss_pred             hHhhcCChhHHHHHHHHhHHc-------C----------CCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESL-------G----------VHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSS   65 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~-------g----------~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~   65 (153)
                      .+.+.|++++|++.|.+..+.       .          -+.+...|..+-.++.+.|++++|... ..-+..+..    
T Consensus        20 ~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al~~~p~----   95 (162)
T 3rkv_A           20 ELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVLKREET----   95 (162)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTT----
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhcCCc----
Confidence            567889999999999887653       0          011224455555566666666666665 222211111    


Q ss_pred             HHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChh
Q 039275           66 KTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEV  118 (153)
Q Consensus        66 ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  118 (153)
                                     +...|..+-..+...|++++|.+.|++....  .|+..
T Consensus        96 ---------------~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l--~p~~~  131 (162)
T 3rkv_A           96 ---------------NEKALFRRAKARIAAWKLDEAEEDLKLLLRN--HPAAA  131 (162)
T ss_dssp             ---------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CGGGH
T ss_pred             ---------------chHHHHHHHHHHHHHhcHHHHHHHHHHHHhc--CCCCH
Confidence                           3456677778888888888888888887754  46544

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=96.58  E-value=0.014  Score=43.63  Aligned_cols=96  Identities=9%  Similarity=-0.041  Sum_probs=63.8

Q ss_pred             hhHhhcCChhHHHHHHHHhHHc---CCCc----cHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcC
Q 039275            3 SGYSQAGRFNEALEPFGKLESL---GVHT----DEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSG   74 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~---g~~p----~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g   74 (153)
                      ..+.+.|++++|.+++++....   -+.|    ...+++.+..+|...|++++|..+ +.-+..-..++.          
T Consensus       295 e~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg----------  364 (429)
T 3qwp_A          295 EELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFP----------  364 (429)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSC----------
T ss_pred             HHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcC----------
Confidence            3456788999999999888643   1222    346788888888889999999888 111111000000          


Q ss_pred             CccccchHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 039275           75 RIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLE  109 (153)
Q Consensus        75 ~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  109 (153)
                       .+.-....+++.|-..|...|++++|..++++-.
T Consensus       365 -~~Hp~~a~~l~nLa~~~~~~g~~~eA~~~~~~Al  398 (429)
T 3qwp_A          365 -GSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAF  398 (429)
T ss_dssp             -SSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             -CCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence             0000034778888899999999999999888765

>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=96.54  E-value=0.006  Score=36.27  Aligned_cols=90  Identities=10%  Similarity=-0.005  Sum_probs=64.6

Q ss_pred             HHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHH
Q 039275           30 EVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKL  108 (153)
Q Consensus        30 ~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m  108 (153)
                      ...+..+-..+...|++++|... ...+..+..                   +...|..+-..+...|++++|...|++.
T Consensus         4 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~-------------------~~~~~~~la~~~~~~~~~~~A~~~~~~~   64 (131)
T 1elr_A            4 ALKEKELGNDAYKKKDFDTALKHYDKAKELDPT-------------------NMTYITNQAAVYFEKGDYNKCRELCEKA   64 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCc-------------------cHHHHHHHHHHHHHhccHHHHHHHHHHH
Confidence            34556666677778888888777 222221111                   3356777888889999999999999998


Q ss_pred             HHcCC--CCC----hhhHHHHHHHhcCCCccccchh
Q 039275          109 ESLGV--HTD----EVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       109 ~~~g~--~p~----~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .....  .++    ...+..+...+.+.|++++|.+
T Consensus        65 ~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~  100 (131)
T 1elr_A           65 IEVGRENREDYRQIAKAYARIGNSYFKEEKYKDAIH  100 (131)
T ss_dssp             HHHHHHSTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HhhccccchhHHHHHHHHHHHHHHHHHhccHHHHHH
Confidence            75531  223    6778888899999999999988

>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=96.47  E-value=0.016  Score=37.84  Aligned_cols=123  Identities=7%  Similarity=-0.063  Sum_probs=71.0

Q ss_pred             cCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhh--hcchhhHHHH-HHHHHhcCCccccchHH
Q 039275            8 AGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIEL--DLSSYSLSSK-TSRYAHSGRIRLARDPV   83 (153)
Q Consensus         8 ~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~--~~~~~~~~~l-l~~~~~~g~~~~a~~~~   83 (153)
                      .|.++++.+.|+.-... .......+..+-..+.+.|++++|.+. ..-+  .|+...+... +..      ........
T Consensus        17 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~------~~~~~~~~   89 (198)
T 2fbn_A           17 LYFQGAKKSIYDYTDEE-KVQSAFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLD------KKKNIEIS   89 (198)
T ss_dssp             -----CCCSGGGCCHHH-HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHH------HHHHHHHH
T ss_pred             hhhccccCchhhCCHHH-HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHH------HHHHHHHH
Confidence            44455555555322111 111234455555666777888887777 2111  1211100000 000      00000236


Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           84 SCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        84 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .|..+-..+.+.|++++|.+.+++..+.. ..+...+..+-.++...|++++|.+
T Consensus        90 ~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~  143 (198)
T 2fbn_A           90 CNLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKE  143 (198)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcccHHHHHH
Confidence            78888899999999999999999988653 2356778888889999999999988

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=96.45  E-value=0.018  Score=40.05  Aligned_cols=77  Identities=12%  Similarity=-0.163  Sum_probs=54.4

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhh--hc-chhhHHHHHHHHHhcCCccc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIEL--DL-SSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~--~~-~~~~~~~ll~~~~~~g~~~~   78 (153)
                      ..+.+.|++++|++.|++..+. -+.+...|..+-..+.+.|++++|.+. ..-+  .| +...+..+-..|.+.|++++
T Consensus        12 ~~~~~~g~~~~A~~~~~~al~~-~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~   90 (281)
T 2c2l_A           12 NRLFVGRKYPEAAACYGRAITR-NPLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDE   90 (281)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH-CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHh-CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHH
Confidence            3567899999999999988775 223677778888888999999999988 2222  23 33445555566666666666


Q ss_pred             cc
Q 039275           79 AR   80 (153)
Q Consensus        79 a~   80 (153)
                      |.
T Consensus        91 A~   92 (281)
T 2c2l_A           91 AI   92 (281)
T ss_dssp             HH
T ss_pred             HH
Confidence            55

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=96.45  E-value=0.019  Score=42.97  Aligned_cols=92  Identities=11%  Similarity=-0.114  Sum_probs=60.3

Q ss_pred             hcCChhHHHHHHHHhHHc---CCCc----cHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccc
Q 039275            7 QAGRFNEALEPFGKLESL---GVHT----DEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRL   78 (153)
Q Consensus         7 ~~g~~~~a~~~~~~m~~~---g~~p----~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~   78 (153)
                      +.|++++|..++++....   -+.|    ...+++.+..+|...|++++|..+ +.-+..-..++.           .+.
T Consensus       310 ~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG-----------~~H  378 (433)
T 3qww_A          310 HYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYP-----------VYS  378 (433)
T ss_dssp             TTSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSC-----------SSC
T ss_pred             hccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcC-----------CCC
Confidence            356788999998877542   1222    247788888899999999999888 211111000000           000


Q ss_pred             cchHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 039275           79 ARDPVSCKAMISGYSQAGRFNEALEPFGKLE  109 (153)
Q Consensus        79 a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  109 (153)
                      -....+|+.|-..|...|++++|..++++-.
T Consensus       379 p~~a~~l~nLa~~~~~qg~~~eA~~~~~~Al  409 (433)
T 3qww_A          379 LNVASMWLKLGRLYMGLENKAAGEKALKKAI  409 (433)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhccCHHHHHHHHHHHH
Confidence            0034778889999999999999999988765

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=96.35  E-value=0.0097  Score=34.55  Aligned_cols=89  Identities=9%  Similarity=0.016  Sum_probs=59.0

Q ss_pred             ccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHH
Q 039275           28 TDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFG  106 (153)
Q Consensus        28 p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~  106 (153)
                      ++...+..+-..+.+.|++++|.+. ..-+..+..                   +...|..+-..+.+.|++++|.+.|+
T Consensus         2 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~-------------------~~~~~~~lg~~~~~~g~~~~A~~~~~   62 (111)
T 2l6j_A            2 SQFEKQKEQGNSLFKQGLYREAVHCYDQLITAQPQ-------------------NPVGYSNKAMALIKLGEYTQAIQMCQ   62 (111)
T ss_dssp             THHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTT-------------------CHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-------------------CHHHHHHHHHHHHHhcCHHHHHHHHH
Confidence            3456666777777888888888877 222221111                   33667788888999999999999999


Q ss_pred             HHHHcCCCCC-------hhhHHHHHHHhcCCCccccch
Q 039275          107 KLESLGVHTD-------EVTMVVVLAASSGPGALDFGK  137 (153)
Q Consensus       107 ~m~~~g~~p~-------~~t~~~li~~~~~~g~~~~a~  137 (153)
                      +..+.  .|+       ...+..+-.++...|+.+.+.
T Consensus        63 ~al~~--~p~~~~~~~~~~~~~~~~~~~~~~~~~~~a~   98 (111)
T 2l6j_A           63 QGLRY--TSTAEHVAIRSKLQYRLELAQGAVGSVQIPV   98 (111)
T ss_dssp             HHHTS--CSSTTSHHHHHHHHHHHHHHHHHHHCCCCCS
T ss_pred             HHHHh--CCCccHHHHHHHHHHHHHHHHHHHHhHhhhH
Confidence            98754  454       344555555565566655554

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=96.29  E-value=0.021  Score=32.99  Aligned_cols=48  Identities=17%  Similarity=0.176  Sum_probs=40.6

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL   52 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~   52 (153)
                      .+.+.|++++|++.|++..+. -+.+...+..+-.++.+.|++++|.+.
T Consensus        13 ~~~~~~~~~~A~~~~~~al~~-~p~~~~~~~~lg~~~~~~g~~~~A~~~   60 (111)
T 2l6j_A           13 SLFKQGLYREAVHCYDQLITA-QPQNPVGYSNKAMALIKLGEYTQAIQM   60 (111)
T ss_dssp             HHHTTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHhcCHHHHHHH
Confidence            567899999999999998775 234677788888899999999999988

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=96.27  E-value=0.02  Score=34.03  Aligned_cols=57  Identities=11%  Similarity=0.008  Sum_probs=48.1

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +...|..+-..+...|++++|.+.|++..+... -+...+..+-.++.+.|++++|.+
T Consensus        26 ~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~g~~~~A~~   82 (117)
T 3k9i_A           26 LAECYLGLGSTFRTLGEYRKAEAVLANGVKQFP-NHQALRVFYAMVLYNLGRYEQGVE   82 (117)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CchHHHHHHHHHHHHcCCHHHHHH
Confidence            456788888999999999999999999987642 246677888889999999999988

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=96.21  E-value=0.0081  Score=43.12  Aligned_cols=86  Identities=13%  Similarity=0.120  Sum_probs=54.7

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHH------------------HHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEV------------------TMVVVLTASSGPGAWILAKEL-QIELDLSSYSLS   64 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~------------------~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~   64 (153)
                      .+.+.|++++|+..|++..+.  .|+..                  .|..+-.++.+.|++++|... ..-+..+..   
T Consensus       188 ~~~~~g~~~~A~~~y~~Al~~--~p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~---  262 (338)
T 2if4_A          188 SLFKEEKLEEAMQQYEMAIAY--MGDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNIVLTEEEK---  262 (338)
T ss_dssp             HTCSSSCCHHHHHHHHHHHHH--SCHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHHHHHHHHHCTT---
T ss_pred             HHHhcCCHHHHHHHHHHHHHH--hccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC---
Confidence            466789999999999987653  34433                  444444555555555555555 111111110   


Q ss_pred             HHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHHH
Q 039275           65 SKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLES  110 (153)
Q Consensus        65 ~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  110 (153)
                                      +...|..+-.+|...|++++|.+.|++..+
T Consensus       263 ----------------~~~a~~~lg~a~~~~g~~~~A~~~l~~al~  292 (338)
T 2if4_A          263 ----------------NPKALFRRGKAKAELGQMDSARDDFRKAQK  292 (338)
T ss_dssp             ----------------CHHHHHHHHHHHHTTTCHHHHHHHHHHTTC
T ss_pred             ----------------CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                            446677777888888888888888887763

>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=96.20  E-value=0.015  Score=35.35  Aligned_cols=88  Identities=14%  Similarity=0.078  Sum_probs=60.7

Q ss_pred             HHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHHH
Q 039275           32 TMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLES  110 (153)
Q Consensus        32 ~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  110 (153)
                      .+.-+=..+.+.|++++|.+. ..-+..+..                   +...|+.+-..|.+.|++++|.+.|++..+
T Consensus        10 a~~~lG~~~~~~~~~~~A~~~y~~Al~~~p~-------------------~~~~~~nlg~~~~~~~~~~~A~~~~~~al~   70 (127)
T 4gcn_A           10 AEKDLGNAAYKQKDFEKAHVHYDKAIELDPS-------------------NITFYNNKAAVYFEEKKFAECVQFCEKAVE   70 (127)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-------------------CHHHHHhHHHHHHHhhhHHHHHHHHHHHHH
Confidence            444555667777777777777 222222111                   446788888999999999999999998864


Q ss_pred             cC--CCCC----hhhHHHHHHHhcCCCccccchh
Q 039275          111 LG--VHTD----EVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       111 ~g--~~p~----~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ..  ..++    ..+|..+-.++...|++++|.+
T Consensus        71 ~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~  104 (127)
T 4gcn_A           71 VGRETRADYKLIAKAMSRAGNAFQKQNDLSLAVQ  104 (127)
T ss_dssp             HHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             hCcccchhhHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            32  1222    2356777788889999999887

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=96.11  E-value=0.033  Score=41.04  Aligned_cols=130  Identities=14%  Similarity=-0.102  Sum_probs=72.5

Q ss_pred             cCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH---hhhhhcc-hhhHHHHHHHHHhcCC--------
Q 039275            8 AGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL---QIELDLS-SYSLSSKTSRYAHSGR--------   75 (153)
Q Consensus         8 ~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~~-~~~~~~ll~~~~~~g~--------   75 (153)
                      .|++++|.+.+++.... -+.+...+..+-..+.+.|++++|.+.   -....|+ ..++..+-..|...+.        
T Consensus       226 ~~~~~~a~~~~~~al~~-~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~y~~~~~~~~~~~~~  304 (472)
T 4g1t_A          226 GEEEGEGEKLVEEALEK-APGVTDVLRSAAKFYRRKDEPDKAIELLKKALEYIPNNAYLHCQIGCCYRAKVFQVMNLREN  304 (472)
T ss_dssp             ----CHHHHHHHHHHHH-CSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHC---
T ss_pred             hhHHHHHHHHHHHHHHh-CccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHhhhHHHH
Confidence            45667777777766554 234556666677777778888877777   1122332 2233333322221110        


Q ss_pred             -----------ccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChh--hHHHHHH-HhcC
Q 039275           76 -----------IRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEV--TMVVVLA-ASSG  129 (153)
Q Consensus        76 -----------~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~--t~~~li~-~~~~  129 (153)
                                 .++|.            +..+|..+-..+...|++++|.+.|++..+....|...  .+..+.. ...+
T Consensus       305 ~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~~~~~~~~~~~~~~~~~~~~~~  384 (472)
T 4g1t_A          305 GMYGKRKLLELIGHAVAHLKKADEANDNLFRVCSILASLHALADQYEEAEYYFQKEFSKELTPVAKQLLHLRYGNFQLYQ  384 (472)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHHHHCTTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHhhcCCchhhhhhhHHHHHHHhccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHH
Confidence                       11111            34567778888999999999999999987665444321  1222221 2346


Q ss_pred             CCccccchh
Q 039275          130 PGALDFGKS  138 (153)
Q Consensus       130 ~g~~~~a~~  138 (153)
                      .|+.++|.+
T Consensus       385 ~~~~~~Ai~  393 (472)
T 4g1t_A          385 MKCEDKAIH  393 (472)
T ss_dssp             SSCHHHHHH
T ss_pred             CCCHHHHHH
Confidence            788877766

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=96.09  E-value=0.049  Score=32.41  Aligned_cols=54  Identities=15%  Similarity=0.045  Sum_probs=44.4

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC----hhhHHHHHHHhcCCCccccchh
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESLGVHTD----EVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~----~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ..+..+-..+.+.|++++|.+.|++..+..  |+    ...+..+-.++.+.|++++|..
T Consensus        40 ~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~la~~~~~~g~~~~A~~   97 (129)
T 2xev_A           40 NALYWLGESYYATRNFQLAEAQFRDLVSRY--PTHDKAAGGLLKLGLSQYGEGKNTEAQQ   97 (129)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTSTTHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHHC--CCCcccHHHHHHHHHHHHHcCCHHHHHH
Confidence            456677788899999999999999998754  43    4557778889999999999988

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=96.07  E-value=0.016  Score=43.98  Aligned_cols=99  Identities=8%  Similarity=-0.111  Sum_probs=67.5

Q ss_pred             hcCCCchHHHHHH------------hhhhhcchhhHHHHHHHHHhcCCccccc--------------------hHHHHHH
Q 039275           40 SSGPGAWILAKEL------------QIELDLSSYSLSSKTSRYAHSGRIRLAR--------------------DPVSCKA   87 (153)
Q Consensus        40 ~~~~~~~~~a~~~------------~~~~~~~~~~~~~ll~~~~~~g~~~~a~--------------------~~~~~~~   87 (153)
                      +...|++++|..+            ....+....+++.|...|...|++++|.                    ...+++.
T Consensus       319 ~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~n  398 (490)
T 3n71_A          319 ARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMR  398 (490)
T ss_dssp             HHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            4578899998887            1112234567888889999999999988                    6778888


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHc---CCCCChhh----HHHHHHHhcCCCccccchh
Q 039275           88 MISGYSQAGRFNEALEPFGKLESL---GVHTDEVT----MVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        88 li~~~~~~g~~~~a~~~~~~m~~~---g~~p~~~t----~~~li~~~~~~g~~~~a~~  138 (153)
                      |-..|...|++++|..++++-..-   -+-||...    ...+-.+...++.+++|+.
T Consensus       399 La~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~  456 (490)
T 3n71_A          399 AGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEF  456 (490)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            889999999999999888876522   12343322    2333345555566666555

>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=96.02  E-value=0.021  Score=36.53  Aligned_cols=104  Identities=13%  Similarity=0.031  Sum_probs=69.6

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHh--cCCCchHHHHHH-hh--hhhc-chhhHHHHHHHHHhcCCc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTAS--SGPGAWILAKEL-QI--ELDL-SSYSLSSKTSRYAHSGRI   76 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~--~~~~~~~~a~~~-~~--~~~~-~~~~~~~ll~~~~~~g~~   76 (153)
                      ..+.+.|++++|+..|++..+.  .|++..+. +...+  ...+...++.+. +.  ...| +...+..+-..+.+.|++
T Consensus        48 ~~~~~~g~~~~A~~~~~~a~~~--~p~~~~~~-~~~~~~~~~~~~~~~a~~~~~~al~~~P~~~~~~~~la~~~~~~g~~  124 (176)
T 2r5s_A           48 DCLLETKQFELAQELLATIPLE--YQDNSYKS-LIAKLELHQQAAESPELKRLEQELAANPDNFELACELAVQYNQVGRD  124 (176)
T ss_dssp             HHHHHTTCHHHHHHHHTTCCGG--GCCHHHHH-HHHHHHHHHHHTSCHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHCCCHHHHHHHHHHhhhc--cCChHHHH-HHHHHHHHhhcccchHHHHHHHHHHhCCCCHHHHHHHHHHHHHcccH
Confidence            3577899999999999988654  23443332 22111  111111112222 22  2334 456788888999999999


Q ss_pred             cccc--------------hHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 039275           77 RLAR--------------DPVSCKAMISGYSQAGRFNEALEPFGKLE  109 (153)
Q Consensus        77 ~~a~--------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~  109 (153)
                      ++|.              +...+..+...+...|+.++|...|.+..
T Consensus       125 ~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y~~al  171 (176)
T 2r5s_A          125 EEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYRRQL  171 (176)
T ss_dssp             HHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHHHHHH
Confidence            9998              24578899999999999999999998764

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=96.01  E-value=0.1  Score=33.58  Aligned_cols=107  Identities=17%  Similarity=0.148  Sum_probs=71.9

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCC-c-----c-----HHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVH-T-----D-----EVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYA   71 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~-p-----~-----~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~   71 (153)
                      .+.+.|++++|++.|++..+..-. |     +     ...|.-+-.++.+.|++++|... ..-+           ..|-
T Consensus        20 ~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL-----------~l~n   88 (159)
T 2hr2_A           20 RQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKAL-----------HYFN   88 (159)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH-----------HHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHH-----------Hhhh
Confidence            467889999999999998764211 0     2     23777778888999999998887 2222           2233


Q ss_pred             hcCCccccchHHHH----HHHHHHHHhcCChHHHHHHHHHHHH-----cCCCCChhhHHH
Q 039275           72 HSGRIRLARDPVSC----KAMISGYSQAGRFNEALEPFGKLES-----LGVHTDEVTMVV  122 (153)
Q Consensus        72 ~~g~~~~a~~~~~~----~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~~~t~~~  122 (153)
                      +.+.++.. +...|    ...=.++...|++++|...|++-.+     .|+.+.......
T Consensus        89 ~~~e~~pd-~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel~p~d~~~~~~~~~~~~  147 (159)
T 2hr2_A           89 RRGELNQD-EGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGKERMME  147 (159)
T ss_dssp             HHCCTTST-HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCCSCCTTHHHHHH
T ss_pred             ccccCCCc-hHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHH
Confidence            33333221 34566    7888899999999999999988753     355555444433

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=95.80  E-value=0.07  Score=29.48  Aligned_cols=53  Identities=19%  Similarity=0.191  Sum_probs=23.2

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           85 CKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        85 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |..+-..+...|++++|.+.|++..+.. ..+...+..+-..+.+.|++++|.+
T Consensus        12 ~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~   64 (91)
T 1na3_A           12 WYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIE   64 (91)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHH
Confidence            3334444444455555555554444322 1123334444444444555444444

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=95.72  E-value=0.09  Score=30.80  Aligned_cols=79  Identities=11%  Similarity=0.029  Sum_probs=49.9

Q ss_pred             hHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHH
Q 039275           12 NEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMIS   90 (153)
Q Consensus        12 ~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~   90 (153)
                      ++|++.|++..+.. +.+...+..+-..+...|++++|.+. +.-+..+..                   +...|..+-.
T Consensus         2 ~~a~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-------------------~~~~~~~la~   61 (115)
T 2kat_A            2 QAITERLEAMLAQG-TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFDPT-------------------YSVAWKWLGK   61 (115)
T ss_dssp             CCHHHHHHHHHTTT-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCC-------------------cHHHHHHHHH
Confidence            45777787776642 34567777788888999999999888 222221110                   2244555566


Q ss_pred             HHHhcCChHHHHHHHHHHHH
Q 039275           91 GYSQAGRFNEALEPFGKLES  110 (153)
Q Consensus        91 ~~~~~g~~~~a~~~~~~m~~  110 (153)
                      .+...|++++|.+.|++...
T Consensus        62 ~~~~~g~~~~A~~~~~~al~   81 (115)
T 2kat_A           62 TLQGQGDRAGARQAWESGLA   81 (115)
T ss_dssp             HHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHH
Confidence            66666677777766666553

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=95.72  E-value=0.065  Score=30.90  Aligned_cols=55  Identities=13%  Similarity=-0.076  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ..|..+-..+...|++++|.+.|++..+... -+...|..+-.++.+.|++++|.+
T Consensus         8 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~g~~~~A~~   62 (100)
T 3ma5_A            8 FTRYALAQEHLKHDNASRALALFEELVETDP-DYVGTYYHLGKLYERLDRTDDAID   62 (100)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCTHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHcCCHHHHHH
Confidence            3445555555666666666666665554321 123345555555666666665555

>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=95.71  E-value=0.14  Score=31.52  Aligned_cols=104  Identities=15%  Similarity=0.055  Sum_probs=62.4

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhh-cchhhHHHHHHHHHh----cCCcc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELD-LSSYSLSSKTSRYAH----SGRIR   77 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~-~~~~~~~~ll~~~~~----~g~~~   77 (153)
                      +..-.+++++|++.|++.-+.|. |+..    +=..+..-+.+++|.++ +.... -+......|-..|..    .++++
T Consensus         4 G~g~~~d~~~A~~~~~~aa~~g~-~~a~----lg~~y~~g~~~~~A~~~~~~Aa~~g~~~a~~~Lg~~y~~G~g~~~d~~   78 (138)
T 1klx_A            4 GGTVKKDLKKAIQYYVKACELNE-MFGC----LSLVSNSQINKQKLFQYLSKACELNSGNGCRFLGDFYENGKYVKKDLR   78 (138)
T ss_dssp             CSSHHHHHHHHHHHHHHHHHTTC-TTHH----HHHHTCTTSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHH
T ss_pred             CcCCccCHHHHHHHHHHHHcCCC-Hhhh----HHHHHHcCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCccHH
Confidence            34445678999999999988873 3333    44555666677778777 22222 233444444444444    45555


Q ss_pred             ccc----------hHHHHHHHHHHHHh----cCChHHHHHHHHHHHHcC
Q 039275           78 LAR----------DPVSCKAMISGYSQ----AGRFNEALEPFGKLESLG  112 (153)
Q Consensus        78 ~a~----------~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g  112 (153)
                      +|.          +...+..|-..|..    .+++++|.+.|++-.+.|
T Consensus        79 ~A~~~~~~Aa~~g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g  127 (138)
T 1klx_A           79 KAAQYYSKACGLNDQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  127 (138)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCC
Confidence            555          45555555556655    667777777776665554

>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=95.66  E-value=0.034  Score=38.69  Aligned_cols=82  Identities=7%  Similarity=-0.092  Sum_probs=58.1

Q ss_pred             cHHHHHHHHHHhcCCCchHHHHHH-hhh--hhc-chhhHHHHHHHHHhcCCccccc------------hHHHHHHHHHHH
Q 039275           29 DEVTMVVVLTASSGPGAWILAKEL-QIE--LDL-SSYSLSSKTSRYAHSGRIRLAR------------DPVSCKAMISGY   92 (153)
Q Consensus        29 ~~~~~~~ll~~~~~~~~~~~a~~~-~~~--~~~-~~~~~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~~   92 (153)
                      +...+..+-..+.+.|++++|.+. ...  ..| +...+..+-..|.+.|++++|.            +...|..+-..+
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~   82 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQCQ   82 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            456667777788889999999988 222  234 4556666777777777777776            566677777777


Q ss_pred             HhcCChHHHHHHHHHHHH
Q 039275           93 SQAGRFNEALEPFGKLES  110 (153)
Q Consensus        93 ~~~g~~~~a~~~~~~m~~  110 (153)
                      ...|++++|.+.|++..+
T Consensus        83 ~~~g~~~~A~~~~~~al~  100 (281)
T 2c2l_A           83 LEMESYDEAIANLQRAYS  100 (281)
T ss_dssp             HHTTCHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHH
Confidence            777777777777777654

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=95.61  E-value=0.025  Score=34.08  Aligned_cols=56  Identities=5%  Similarity=0.005  Sum_probs=45.9

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +...|..+-..+...|++++|...|++..+..  | +...+..+-.++.+.|++++|..
T Consensus        50 ~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~--P~~~~~~~~la~~~~~~g~~~~A~~  106 (121)
T 1hxi_A           50 REEAWRSLGLTQAENEKDGLAIIALNHARMLD--PKDIAVHAALAVSHTNEHNANAALA  106 (121)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            44667778888999999999999999988653  5 45677788889999999998877

>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=95.55  E-value=0.13  Score=34.01  Aligned_cols=123  Identities=10%  Similarity=-0.014  Sum_probs=83.0

Q ss_pred             hHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhc-chhhHHHHHHHHHhcC----Cccccc-----
Q 039275           12 NEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDL-SSYSLSSKTSRYAHSG----RIRLAR-----   80 (153)
Q Consensus        12 ~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~-~~~~~~~ll~~~~~~g----~~~~a~-----   80 (153)
                      .+|++.|++.-+.|   ++..+..+=..+...+++++|.++ +.-..+ +...+..|-..|.. +    ++++|.     
T Consensus         3 ~eA~~~~~~aa~~g---~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~   78 (212)
T 3rjv_A            3 TEPGSQYQQQAEAG---DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQGDGDALALLAQLKIR-NPQQADYPQARQLAEK   78 (212)
T ss_dssp             -CTTHHHHHHHHTT---CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCHHHHHHHHHHTTS-STTSCCHHHHHHHHHH
T ss_pred             chHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHc-CCCCCCHHHHHHHHHH
Confidence            35677888877764   455565666666668999999999 333322 34455566666666 6    666666     


Q ss_pred             -----hHHHHHHHHHHHHh----cCChHHHHHHHHHHHHcCCC-CChhhHHHHHHHhcC----CCccccchh
Q 039275           81 -----DPVSCKAMISGYSQ----AGRFNEALEPFGKLESLGVH-TDEVTMVVVLAASSG----PGALDFGKS  138 (153)
Q Consensus        81 -----~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~-p~~~t~~~li~~~~~----~g~~~~a~~  138 (153)
                           +...+..|-..|..    .+++++|.+.|++-.+.|.. .....+..+-..|..    .+++++|.+
T Consensus        79 A~~~g~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~  150 (212)
T 3rjv_A           79 AVEAGSKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASE  150 (212)
T ss_dssp             HHHTTCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHH
Confidence                 66777777777776    88999999999998876632 014555666666655    667777766

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=95.35  E-value=0.058  Score=29.82  Aligned_cols=63  Identities=22%  Similarity=0.233  Sum_probs=43.7

Q ss_pred             HHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHH
Q 039275           30 EVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKL  108 (153)
Q Consensus        30 ~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m  108 (153)
                      ...+..+-..+.+.|++++|.+. ..-+..+..                   +...|..+-..+.+.|++++|.+.|++.
T Consensus         9 ~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~-------------------~~~~~~~l~~~~~~~~~~~~A~~~~~~a   69 (91)
T 1na3_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELDPN-------------------NAEAWYNLGNAYYKQGDYDEAIEYYQKA   69 (91)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCC-------------------CHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            45555666677777888888777 222221110                   3356777888899999999999999998


Q ss_pred             HHc
Q 039275          109 ESL  111 (153)
Q Consensus       109 ~~~  111 (153)
                      .+.
T Consensus        70 ~~~   72 (91)
T 1na3_A           70 LEL   72 (91)
T ss_dssp             HHH
T ss_pred             Hhc
Confidence            765

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=95.04  E-value=0.18  Score=28.96  Aligned_cols=24  Identities=17%  Similarity=-0.043  Sum_probs=13.8

Q ss_pred             cHHHHHHHHHHhcCCCchHHHHHH
Q 039275           29 DEVTMVVVLTASSGPGAWILAKEL   52 (153)
Q Consensus        29 ~~~~~~~ll~~~~~~~~~~~a~~~   52 (153)
                      +...+..+-..+.+.|++++|.+.
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~   29 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALAL   29 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHH
Confidence            344455555556666666666665

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=94.81  E-value=0.19  Score=35.92  Aligned_cols=101  Identities=8%  Similarity=-0.007  Sum_probs=70.5

Q ss_pred             HHHHHHHHHHhcCCCchHHHHHH-hhh--hhcchhhHHHHHHHHHhcCCccccc---hHHHHHHHHHHHHhcCChHHHHH
Q 039275           30 EVTMVVVLTASSGPGAWILAKEL-QIE--LDLSSYSLSSKTSRYAHSGRIRLAR---DPVSCKAMISGYSQAGRFNEALE  103 (153)
Q Consensus        30 ~~~~~~ll~~~~~~~~~~~a~~~-~~~--~~~~~~~~~~ll~~~~~~g~~~~a~---~~~~~~~li~~~~~~g~~~~a~~  103 (153)
                      ...+..+-..+.+.|++++|... ..-  ..|+...+       ...++.+++.   ....|..+-..+.+.|++++|.+
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~-------~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~  251 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAYMGDDFMF-------QLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIG  251 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHHSCHHHHH-------TCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhccchhh-------hhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            34455666788889999998887 222  23332211       1111111111   22478889999999999999999


Q ss_pred             HHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275          104 PFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       104 ~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .+++..+.. .-+...+..+-.++...|++++|..
T Consensus       252 ~~~~al~~~-p~~~~a~~~lg~a~~~~g~~~~A~~  285 (338)
T 2if4_A          252 HCNIVLTEE-EKNPKALFRRGKAKAELGQMDSARD  285 (338)
T ss_dssp             HHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHH
T ss_pred             HHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            999988653 2356788889999999999999988

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=94.74  E-value=0.22  Score=31.01  Aligned_cols=99  Identities=13%  Similarity=-0.015  Sum_probs=66.8

Q ss_pred             HHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccc-------cchHHHHHHHHHHHHhcCChHHHH
Q 039275           31 VTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRL-------ARDPVSCKAMISGYSQAGRFNEAL  102 (153)
Q Consensus        31 ~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~-------a~~~~~~~~li~~~~~~g~~~~a~  102 (153)
                      ..+...-..+.+.|++++|.+. ...+.....        ....++...       -.+...|..+-..+.+.|++++|.
T Consensus        12 ~~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~   83 (162)
T 3rkv_A           12 EALRQKGNELFVQKDYKEAIDAYRDALTRLDT--------LILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAE   83 (162)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH--------HHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH--------hcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHH
Confidence            3445555677788888888887 111111000        000000000       004578888999999999999999


Q ss_pred             HHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275          103 EPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       103 ~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ..+++..... ..+...|..+-.++...|++++|..
T Consensus        84 ~~~~~al~~~-p~~~~a~~~~g~~~~~~g~~~~A~~  118 (162)
T 3rkv_A           84 ETSSEVLKRE-ETNEKALFRRAKARIAAWKLDEAEE  118 (162)
T ss_dssp             HHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHhcC-CcchHHHHHHHHHHHHHhcHHHHHH
Confidence            9999988653 2356778888999999999999998

>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=94.34  E-value=0.16  Score=37.93  Aligned_cols=56  Identities=14%  Similarity=0.068  Sum_probs=48.6

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           82 PVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        82 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ...|..+-..+.+.|++++|.+.|++..+.. .-+...+..+-.++.+.|++++|..
T Consensus       317 ~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~~g~a~~~~g~~~~A~~  372 (457)
T 1kt0_A          317 LAAFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKG  372 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHccCHHHHHH
Confidence            5788899999999999999999999998654 2356778888899999999999988

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=94.21  E-value=0.1  Score=30.51  Aligned_cols=57  Identities=14%  Similarity=0.103  Sum_probs=48.0

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +...|..+-..+...|++++|.+.|++..+.. ..+...+..+-.++.+.|++++|..
T Consensus        18 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~   74 (115)
T 2kat_A           18 NMLLRFTLGKTYAEHEQFDAALPHLRAALDFD-PTYSVAWKWLGKTLQGQGDRAGARQ   74 (115)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHcCCHHHHHH
Confidence            45678888899999999999999999988654 2346678888889999999999988

>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=94.19  E-value=0.6  Score=33.85  Aligned_cols=98  Identities=7%  Similarity=-0.056  Sum_probs=67.4

Q ss_pred             HHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCcccc-----chHHHHHHHHHHHHhcCChHHHHHH
Q 039275           31 VTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLA-----RDPVSCKAMISGYSQAGRFNEALEP  104 (153)
Q Consensus        31 ~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a-----~~~~~~~~li~~~~~~g~~~~a~~~  104 (153)
                      ..+..+-..+.+.|++++|.+. ..-+.......        .....+++     .+...|..+-..+.+.|++++|.+.
T Consensus       224 ~~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~--------~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~  295 (370)
T 1ihg_A          224 EDLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSR--------AAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDS  295 (370)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHH--------HHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCc--------cccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHH
Confidence            3455566677888888888887 22221000000        00000000     0567888999999999999999999


Q ss_pred             HHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275          105 FGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       105 ~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +++..+.  .| +...+..+-.++.+.|++++|.+
T Consensus       296 ~~~al~~--~p~~~~a~~~lg~~~~~~g~~~eA~~  328 (370)
T 1ihg_A          296 CLEALEI--DPSNTKALYRRAQGWQGLKEYDQALA  328 (370)
T ss_dssp             HHHHHTT--CTTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHh--CchhHHHHHHHHHHHHHccCHHHHHH
Confidence            9998864  35 56778888889999999999988

>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=94.17  E-value=0.67  Score=36.69  Aligned_cols=134  Identities=8%  Similarity=-0.078  Sum_probs=87.0

Q ss_pred             HhhcCChhHHHHHHHHhHHcC---------CCc------------cHHHHHHHHHHhcCCCchHHHHHH-hhhh----hc
Q 039275            5 YSQAGRFNEALEPFGKLESLG---------VHT------------DEVTMVVVLTASSGPGAWILAKEL-QIEL----DL   58 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g---------~~p------------~~~~~~~ll~~~~~~~~~~~a~~~-~~~~----~~   58 (153)
                      .-+.|++++|.++|+++....         -.|            ....|...+....+.+..+.|.++ ....    .+
T Consensus       388 ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A~~~~~~~  467 (679)
T 4e6h_A          388 YELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCRRLKKLV  467 (679)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTGGGS
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCCC
Confidence            456789999999999987641         013            123566667776777888888888 2211    11


Q ss_pred             chhhHHHHHHHHHhc-CCccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC--ChhhHHHH
Q 039275           59 SSYSLSSKTSRYAHS-GRIRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT--DEVTMVVV  123 (153)
Q Consensus        59 ~~~~~~~ll~~~~~~-g~~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p--~~~t~~~l  123 (153)
                      ...+|......--+. ++.+.|.            +...|...+......|+.+.|..+|+........|  ....|...
T Consensus       468 ~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~~p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~~~~~~~~~~lw~~~  547 (679)
T 4e6h_A          468 TPDIYLENAYIEYHISKDTKTACKVLELGLKYFATDGEYINKYLDFLIYVNEESQVKSLFESSIDKISDSHLLKMIFQKV  547 (679)
T ss_dssp             CTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence            223333222222233 3466666            66777788888888899999999999887654322  34567777


Q ss_pred             HHHhcCCCccccchh
Q 039275          124 LAASSGPGALDFGKS  138 (153)
Q Consensus       124 i~~~~~~g~~~~a~~  138 (153)
                      +..=.+.|+.+.+..
T Consensus       548 ~~fE~~~G~~~~~~~  562 (679)
T 4e6h_A          548 IFFESKVGSLNSVRT  562 (679)
T ss_dssp             HHHHHHTCCSHHHHH
T ss_pred             HHHHHHcCCHHHHHH
Confidence            777777788777665

>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=94.06  E-value=1.1  Score=35.40  Aligned_cols=120  Identities=10%  Similarity=-0.033  Sum_probs=85.9

Q ss_pred             hhcCChhHHHHHHHHhHHc-C-CCccHHHHHHHHHHhcCCCchHHHHHH-hhhh---hcchhhHHHHHHHHHhcCCcccc
Q 039275            6 SQAGRFNEALEPFGKLESL-G-VHTDEVTMVVVLTASSGPGAWILAKEL-QIEL---DLSSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         6 ~~~g~~~~a~~~~~~m~~~-g-~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~---~~~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .+.|..+.|.++|.+..+. + ..+........|.-.. .++.+.|.++ ..++   +.+...+...+......|+.+.|
T Consensus       445 rR~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE~~~-~~d~e~Ar~ife~~Lk~~p~~~~~w~~y~~fe~~~~~~~~A  523 (679)
T 4e6h_A          445 KRIQGLAASRKIFGKCRRLKKLVTPDIYLENAYIEYHI-SKDTKTACKVLELGLKYFATDGEYINKYLDFLIYVNEESQV  523 (679)
T ss_dssp             HHHHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHHHTT-TSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHh-CCCHHHHHHHHHHHHHHCCCchHHHHHHHHHHHhCCCHHHH
Confidence            4568899999999999876 2 3344455445555332 3558888888 3333   34555667788877888888877


Q ss_pred             c---------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhc
Q 039275           80 R---------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASS  128 (153)
Q Consensus        80 ~---------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~  128 (153)
                      +               ....|...+..-.+.|+.+.+..+.+.+.+.-  |+......+++-|.
T Consensus       524 R~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~~--P~~~~~~~f~~ry~  585 (679)
T 4e6h_A          524 KSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEKF--PEVNKLEEFTNKYK  585 (679)
T ss_dssp             HHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHS--TTCCHHHHHHHHTC
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCcHHHHHHHHhc
Confidence            7               23679999999999999999999999998764  66556666666554

>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=93.77  E-value=0.18  Score=37.53  Aligned_cols=58  Identities=14%  Similarity=0.012  Sum_probs=48.4

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc-----C-CCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESL-----G-VHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-----g-~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ...+++.+...|...|++++|..++++...-     | -.| ...+++.+-..|..+|++++|..
T Consensus       328 ~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~l~nLa~~~~~~g~~~eA~~  392 (429)
T 3qwp_A          328 QLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMK  392 (429)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHHHHHHHHHHHhcCCHHHHHH
Confidence            4578999999999999999999999987632     2 233 45668889999999999999998

>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=93.76  E-value=0.33  Score=36.28  Aligned_cols=58  Identities=9%  Similarity=-0.153  Sum_probs=48.6

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc-----C-CCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESL-----G-VHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-----g-~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ...+++.|...|...|++++|..++++...-     | -.| ...+++.+-..|..+|++++|..
T Consensus       339 ~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~qg~~~eA~~  403 (433)
T 3qww_A          339 MLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRLYMGLENKAAGEK  403 (433)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHhccCHHHHHH
Confidence            4578999999999999999999999988632     3 234 45668899999999999999998

>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=93.39  E-value=0.76  Score=34.52  Aligned_cols=77  Identities=9%  Similarity=-0.056  Sum_probs=54.5

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhh--hhcc-hhhHHHHHHH--HHhcCCc
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIE--LDLS-SYSLSSKTSR--YAHSGRI   76 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~--~~~~-~~~~~~ll~~--~~~~g~~   76 (153)
                      ..|.+.|++++|++.|++..+.. +-+...+..+-.++.+.|++++|.+. +.-  ..|+ ...+..+-.+  +.+.|++
T Consensus        48 ~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~p~~~~~~~~l~~~~~~~~~g~~  126 (477)
T 1wao_1           48 LAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAF  126 (477)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCTTHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHH
Confidence            36788999999999999998752 34567788888899999999999998 222  2333 3344444444  6666777


Q ss_pred             cccc
Q 039275           77 RLAR   80 (153)
Q Consensus        77 ~~a~   80 (153)
                      ++|.
T Consensus       127 ~~A~  130 (477)
T 1wao_1          127 ERAI  130 (477)
T ss_dssp             CCC-
T ss_pred             HHHh
Confidence            7666

>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2ybb_P* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* ...

Probab=93.13  E-value=0.51  Score=27.95  Aligned_cols=59  Identities=8%  Similarity=-0.039  Sum_probs=45.0

Q ss_pred             ChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH----hhhhhcchhhHHHHHH
Q 039275           10 RFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL----QIELDLSSYSLSSKTS   68 (153)
Q Consensus        10 ~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~----~~~~~~~~~~~~~ll~   68 (153)
                      +.=++.+-++.+-...+.|++.+....|.+|-+.+++..|..+    +........+|..++.
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~~~~~~iY~~~lq   87 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVIQ   87 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCchhhHHHHHH
Confidence            3445666677777888999999999999999999999999998    4444444555666553

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=93.04  E-value=0.13  Score=40.56  Aligned_cols=90  Identities=21%  Similarity=0.252  Sum_probs=42.3

Q ss_pred             hhcCChhHHHH-HHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHHhhhhhcchhhHHHHHHHHHhcCCccccc----
Q 039275            6 SQAGRFNEALE-PFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIELDLSSYSLSSKTSRYAHSGRIRLAR----   80 (153)
Q Consensus         6 ~~~g~~~~a~~-~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~ll~~~~~~g~~~~a~----   80 (153)
                      ...+++++|.+ ++..+.      +......++..+-+.|.+++|.++-....       .-.....+.|++++|.    
T Consensus       610 ~~~~~~~~a~~~~l~~i~------~~~~~~~~~~~l~~~~~~~~a~~~~~~~~-------~~f~~~l~~~~~~~A~~~~~  676 (814)
T 3mkq_A          610 TLRGEIEEAIENVLPNVE------GKDSLTKIARFLEGQEYYEEALNISPDQD-------QKFELALKVGQLTLARDLLT  676 (814)
T ss_dssp             HHTTCHHHHHHHTGGGCC------CHHHHHHHHHHHHHTTCHHHHHHHCCCHH-------HHHHHHHHHTCHHHHHHHHT
T ss_pred             HHhCCHHHHHHHHHhcCC------chHHHHHHHHHHHhCCChHHheecCCCcc-------hheehhhhcCCHHHHHHHHH
Confidence            34567777766 442211      01122555555566666666665511100       0012223444444443    


Q ss_pred             ---hHHHHHHHHHHHHhcCChHHHHHHHHHH
Q 039275           81 ---DPVSCKAMISGYSQAGRFNEALEPFGKL  108 (153)
Q Consensus        81 ---~~~~~~~li~~~~~~g~~~~a~~~~~~m  108 (153)
                         +...|..+-..+.+.|+++.|.+.|..+
T Consensus       677 ~~~~~~~W~~la~~al~~~~~~~A~~~y~~~  707 (814)
T 3mkq_A          677 DESAEMKWRALGDASLQRFNFKLAIEAFTNA  707 (814)
T ss_dssp             TCCCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             hhCcHhHHHHHHHHHHHcCCHHHHHHHHHHc
Confidence               4455555555555555555555555544

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=92.82  E-value=0.25  Score=34.81  Aligned_cols=103  Identities=13%  Similarity=-0.005  Sum_probs=72.3

Q ss_pred             HHHHhcCCCchHHHHHHhhh---hhcchhhHHHHHHHHHhcCCccccc----------h----HHHHHHHHHHHHhcCCh
Q 039275           36 VLTASSGPGAWILAKELQIE---LDLSSYSLSSKTSRYAHSGRIRLAR----------D----PVSCKAMISGYSQAGRF   98 (153)
Q Consensus        36 ll~~~~~~~~~~~a~~~~~~---~~~~~~~~~~ll~~~~~~g~~~~a~----------~----~~~~~~li~~~~~~g~~   98 (153)
                      .-..+...|++++|.++...   ..|+....-.+-..+.+.+++++|.          +    ...+-.+=..+...|++
T Consensus       108 yA~~L~~~g~y~eA~~~l~~~~~~~p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~d~~~~~~a~~~LG~al~~LG~~  187 (282)
T 4f3v_A          108 FAACEAAQGNYADAMEALEAAPVAGSEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWPDKFLAGAAGVAHGVAAANLALF  187 (282)
T ss_dssp             HHHHHHHHTCHHHHHHHHTSSCCTTCHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCSCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhcCCchHHHHHHHHHHHHcCCHHHHHHHHHHhhccCCcccHHHHHHHHHHHHHHCCCH
Confidence            34566778899999999221   1233324444555788888888887          1    23566677889999999


Q ss_pred             HHHHHHHHHHHHcCCCCCh--hhHHHHHHHhcCCCccccchh
Q 039275           99 NEALEPFGKLESLGVHTDE--VTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        99 ~~a~~~~~~m~~~g~~p~~--~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ++|++.|++.......|..  ......-.++.++|+.++|..
T Consensus       188 ~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~  229 (282)
T 4f3v_A          188 TEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVA  229 (282)
T ss_dssp             HHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHH
Confidence            9999999998744333652  245566678888999999887

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=92.60  E-value=1.4  Score=28.80  Aligned_cols=93  Identities=17%  Similarity=0.168  Sum_probs=55.8

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHHhhhhhcchhhHHHHHHHHHhcCCccccc----
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIELDLSSYSLSSKTSRYAHSGRIRLAR----   80 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~ll~~~~~~g~~~~a~----   80 (153)
                      ..+.|+++.|.++-+.+      -+...|..+-....+.|+++-|++......    .+..+.-.|...|+.++-.    
T Consensus        15 AL~lg~l~~A~e~a~~l------~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~----D~~~L~~Ly~~tg~~e~L~kla~   84 (177)
T 3mkq_B           15 ALEYGNLDAALDEAKKL------NDSITWERLIQEALAQGNASLAEMIYQTQH----SFDKLSFLYLVTGDVNKLSKMQN   84 (177)
T ss_dssp             HHHTTCHHHHHHHHHHH------CCHHHHHHHHHHHHHTTCHHHHHHHHHHTT----CHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHhcCCHHHHHHHHHHh------CCHHHHHHHHHHHHHcCChHHHHHHHHHhC----CHHHHHHHHHHhCCHHHHHHHHH
Confidence            46789999999998766      367889999999899999888888722111    1223333333333332221    


Q ss_pred             ---hHHHHHHHHHHHHhcCChHHHHHHHHH
Q 039275           81 ---DPVSCKAMISGYSQAGRFNEALEPFGK  107 (153)
Q Consensus        81 ---~~~~~~~li~~~~~~g~~~~a~~~~~~  107 (153)
                         ..--+|.-...+...|+++++.++|.+
T Consensus        85 iA~~~g~~n~af~~~l~lGdv~~~i~lL~~  114 (177)
T 3mkq_B           85 IAQTREDFGSMLLNTFYNNSTKERSSIFAE  114 (177)
T ss_dssp             HHHHTTCHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHCccHHHHHHHHHHcCCHHHHHHHHHH
Confidence               112234444555556666666666644

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=92.17  E-value=2.7  Score=31.13  Aligned_cols=103  Identities=18%  Similarity=0.074  Sum_probs=54.6

Q ss_pred             HhhcC---ChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcC----CCchHHHHHH-hhhhhcchhhHHHHHHH-H--Hhc
Q 039275            5 YSQAG---RFNEALEPFGKLESLGVHTDEVTMVVVLTASSG----PGAWILAKEL-QIELDLSSYSLSSKTSR-Y--AHS   73 (153)
Q Consensus         5 ~~~~g---~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~----~~~~~~a~~~-~~~~~~~~~~~~~ll~~-~--~~~   73 (153)
                      |.+.|   +.++|++.|++..+.|..... .+..+-..|..    .+++++|.++ +.-.+-+...+..|-.. |  ...
T Consensus       186 ~~~~g~~~~~~~A~~~~~~aa~~g~~~a~-~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa~g~~~a~~~Lg~~~~~~~~~  264 (452)
T 3e4b_A          186 YQKKQQPEQQAELLKQMEAGVSRGTVTAQ-RVDSVARVLGDATLGTPDEKTAQALLEKIAPGYPASWVSLAQLLYDFPEL  264 (452)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHTTCSCHH-HHHHHHHHHTCGGGSSCCHHHHHHHHHHHGGGSTHHHHHHHHHHHHSGGG
T ss_pred             HHHcCCcccHHHHHHHHHHHHHCCCHHHH-HHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCC
Confidence            44456   777777777777766643332 22222333322    2567777777 22223334444444444 2  345


Q ss_pred             CCccccc----------hHHHHHHHHHHHHhcC-----ChHHHHHHHHHHH
Q 039275           74 GRIRLAR----------DPVSCKAMISGYSQAG-----RFNEALEPFGKLE  109 (153)
Q Consensus        74 g~~~~a~----------~~~~~~~li~~~~~~g-----~~~~a~~~~~~m~  109 (153)
                      +++++|.          +...+..|-..|. .|     ++++|.+.|++-.
T Consensus       265 ~d~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~-~G~g~~~d~~~A~~~~~~Aa  314 (452)
T 3e4b_A          265 GDVEQMMKYLDNGRAADQPRAELLLGKLYY-EGKWVPADAKAAEAHFEKAV  314 (452)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HCSSSCCCHHHHHHHHHTTT
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHHHHH-cCCCCCCCHHHHHHHHHHHh
Confidence            6666665          4455555555444 44     7777777766554

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=92.14  E-value=1.3  Score=34.81  Aligned_cols=24  Identities=25%  Similarity=0.041  Sum_probs=14.9

Q ss_pred             cHHHHHHHHHHhcCCCchHHHHHH
Q 039275           29 DEVTMVVVLTASSGPGAWILAKEL   52 (153)
Q Consensus        29 ~~~~~~~ll~~~~~~~~~~~a~~~   52 (153)
                      +...|..+-..+.+.++++.|.+.
T Consensus       680 ~~~~W~~la~~al~~~~~~~A~~~  703 (814)
T 3mkq_A          680 AEMKWRALGDASLQRFNFKLAIEA  703 (814)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cHhHHHHHHHHHHHcCCHHHHHHH
Confidence            455666666666666666666665

>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=91.97  E-value=0.4  Score=30.75  Aligned_cols=93  Identities=16%  Similarity=0.072  Sum_probs=65.1

Q ss_pred             HHHHHHHHhcCCCchHHHHHH-h--hhhhcchhhHHHHHHHHHhcCCccccc-----hHHHHHHHHHHHHhcCChHHHHH
Q 039275           32 TMVVVLTASSGPGAWILAKEL-Q--IELDLSSYSLSSKTSRYAHSGRIRLAR-----DPVSCKAMISGYSQAGRFNEALE  103 (153)
Q Consensus        32 ~~~~ll~~~~~~~~~~~a~~~-~--~~~~~~~~~~~~ll~~~~~~g~~~~a~-----~~~~~~~li~~~~~~g~~~~a~~  103 (153)
                      .+...-..+.+.|++++|.+. .  -.+.|+.  ...            ++.     +...|+.+-.++.+.|++++|..
T Consensus        13 ~~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~--~~~------------~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~   78 (159)
T 2hr2_A           13 LALSDAQRQLVAGEYDEAAANCRRAMEISHTM--PPE------------EAFDHAGFDAFCHAGLAEALAGLRSFDEALH   78 (159)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTS--CTT------------SCCCHHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCC--cch------------hhhhhccchHHHHHHHHHHHHHCCCHHHHHH
Confidence            344445566778888888887 2  2223331  000            011     34589999999999999999999


Q ss_pred             HHHHHHHc-----CCCCCh-hhH----HHHHHHhcCCCccccchh
Q 039275          104 PFGKLESL-----GVHTDE-VTM----VVVLAASSGPGALDFGKS  138 (153)
Q Consensus       104 ~~~~m~~~-----g~~p~~-~t~----~~li~~~~~~g~~~~a~~  138 (153)
                      .++.-.+.     .+.|+. ..|    ...-.++..+|++++|..
T Consensus        79 ~~~kAL~l~n~~~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~  123 (159)
T 2hr2_A           79 SADKALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMP  123 (159)
T ss_dssp             HHHHHHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHhhhccccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHH
Confidence            99988764     236754 455    677889999999999988

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=91.86  E-value=2.6  Score=31.18  Aligned_cols=48  Identities=13%  Similarity=0.079  Sum_probs=28.0

Q ss_pred             hHHHHHHHHHHHHhcC---ChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcC
Q 039275           81 DPVSCKAMISGYSQAG---RFNEALEPFGKLESLGVHTDEVTMVVVLAASSG  129 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g---~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~  129 (153)
                      ++..+..|-..|...|   +.++|.+.|+.-.+.| .++...+..+-..|..
T Consensus       175 ~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g-~~~a~~~~~Lg~~y~~  225 (452)
T 3e4b_A          175 TDICYVELATVYQKKQQPEQQAELLKQMEAGVSRG-TVTAQRVDSVARVLGD  225 (452)
T ss_dssp             CTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT-CSCHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhC
Confidence            3445666666667777   7777777777776665 3334333344444433

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=91.62  E-value=0.53  Score=27.30  Aligned_cols=49  Identities=8%  Similarity=-0.165  Sum_probs=40.0

Q ss_pred             hHhhcCChhHHHHHHHHhHHc------CCCccHHHHHHHHHHhcCCCchHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESL------GVHTDEVTMVVVLTASSGPGAWILAKEL   52 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~------g~~p~~~~~~~ll~~~~~~~~~~~a~~~   52 (153)
                      .+.+.|++++|..+|+...+.      .-.+...++..+-.++.+.|+++.|...
T Consensus        14 ~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~   68 (104)
T 2v5f_A           14 VAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLL   68 (104)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHH
Confidence            567889999999999887653      1235677888888999999999999988

>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=90.85  E-value=1.2  Score=27.94  Aligned_cols=56  Identities=9%  Similarity=-0.026  Sum_probs=39.6

Q ss_pred             hHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH----hhhhhcchhhHHHHH
Q 039275           12 NEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL----QIELDLSSYSLSSKT   67 (153)
Q Consensus        12 ~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~----~~~~~~~~~~~~~ll   67 (153)
                      =+..+-++.+....+.|++.+....|.+|-+.+++..|..+    +....+...+|..++
T Consensus        70 wElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K~~~~~~iY~y~l  129 (152)
T 2y69_E           70 WELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVI  129 (152)
T ss_dssp             HHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHH
T ss_pred             HHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhcCCchhhHHHHH
Confidence            34455555556677888888888889998888888888888    444445555565554

>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=90.64  E-value=0.67  Score=33.96  Aligned_cols=58  Identities=17%  Similarity=0.296  Sum_probs=46.6

Q ss_pred             HHHHHHHhcCCccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHH-----cCCCCChhhHHH
Q 039275           65 SKTSRYAHSGRIRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLES-----LGVHTDEVTMVV  122 (153)
Q Consensus        65 ~ll~~~~~~g~~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~~~t~~~  122 (153)
                      .++..+.+.|+.+++.            +...|..+|.++.+.|+..+|.+.|+...+     -|+.|+..+-..
T Consensus       176 ~~~~~~l~~g~~~~a~~~l~~~~~~~P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~l  250 (388)
T 2ff4_A          176 AKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRAL  250 (388)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence            4556677788877776            777899999999999999999999998753     399998875433

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=90.07  E-value=0.018  Score=43.97  Aligned_cols=130  Identities=12%  Similarity=0.072  Sum_probs=84.6

Q ss_pred             hhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHHh-----------------hh-------hh
Q 039275            2 ISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQ-----------------IE-------LD   57 (153)
Q Consensus         2 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~-----------------~~-------~~   57 (153)
                      |.+..+.|.+++-++.+.-.++..-  ++.+=+.|+-+|++.+++.+.+++-                 .+       +-
T Consensus        90 i~~A~~~~~~edLv~yL~MaRk~~k--e~~IDteLi~ayAk~~rL~elEefl~~~N~A~iq~VGDrcf~e~lYeAAKily  167 (624)
T 3lvg_A           90 VQAANTSGNWEELVKYLQMARKKAR--ESYVETELIFALAKTNRLAELEEFINGPNNAHIQQVGDRCYDEKMYDAAKLLY  167 (624)
T ss_dssp             HHHTTTSSCCTTHHHHHHTTSTTCC--STTTTHHHHHHHHTSCSSSTTTSTTSCCSSSCTHHHHHHHHHSCCSTTSSTTG
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHHhc--ccccHHHHHHHHHhhCcHHHHHHHHcCCCcccHHHHHHHHHHccCHHHHHHHH
Confidence            5566777888887777744444433  3344457888888888877766661                 11       11


Q ss_pred             cchhhHHHHHHHHHhcCCccccc-------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCC
Q 039275           58 LSSYSLSSKTSRYAHSGRIRLAR-------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGP  130 (153)
Q Consensus        58 ~~~~~~~~ll~~~~~~g~~~~a~-------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  130 (153)
                      -+...|..|...+.+.|++..|.       ++.||--+-.+|...+++.-|.-.--.+.   +.||  ....++..|-..
T Consensus       168 s~isN~akLAstLV~L~~yq~AVdaArKAns~ktWKeV~~ACvd~~EfrLAqicGLniI---vhad--eL~elv~~YE~~  242 (624)
T 3lvg_A          168 NNVSNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIV---VHAD--ELEELINYYQDR  242 (624)
T ss_dssp             GGSCCCTTTSSSSSSCSGGGSSTTTTTTCCSSCSHHHHTHHHHHSCTTTTTTHHHHHHH---CCSS--CCSGGGSSSSTT
T ss_pred             HhCccHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHhCchHHHHHHHhcchhc---ccHH--HHHHHHHHHHhC
Confidence            13344555666777777777766       88899999999999999888776555554   1232  234556667777


Q ss_pred             Cccccchh
Q 039275          131 GALDFGKS  138 (153)
Q Consensus       131 g~~~~a~~  138 (153)
                      |.+++-..
T Consensus       243 G~f~ELIs  250 (624)
T 3lvg_A          243 GYFEELIT  250 (624)
T ss_dssp             CCCTTSTT
T ss_pred             CCHHHHHH
Confidence            77776555

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=89.92  E-value=0.53  Score=26.37  Aligned_cols=48  Identities=15%  Similarity=0.160  Sum_probs=38.6

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHH-HHHHHHHHhcCCCchHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEV-TMVVVLTASSGPGAWILAKEL   52 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~-~~~~ll~~~~~~~~~~~a~~~   52 (153)
                      .+.+.|++++|++.|++..+.. +.+.. .+..+-.++.+.|++++|.+.
T Consensus         9 ~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~lg~~~~~~~~~~~A~~~   57 (99)
T 2kc7_A            9 ELINQGDIENALQALEEFLQTE-PVGKDEAYYLMGNAYRKLGDWQKALNN   57 (99)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHC-SSTHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            5678999999999999987752 23455 677777788889999999888

>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=89.62  E-value=0.98  Score=28.87  Aligned_cols=102  Identities=10%  Similarity=-0.008  Sum_probs=62.9

Q ss_pred             hhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCch----------HHHHHH-hhhhhcchhhHHHHHHHHHhcC
Q 039275            6 SQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAW----------ILAKEL-QIELDLSSYSLSSKTSRYAHSG   74 (153)
Q Consensus         6 ~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~----------~~a~~~-~~~~~~~~~~~~~ll~~~~~~g   74 (153)
                      .+.+.+++|++.+++..+.. +-+...|..+=.++.+.+++          ++|... +.-+..|..             
T Consensus        13 ~r~~~feeA~~~~~~Ai~l~-P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~-------------   78 (158)
T 1zu2_A           13 DRILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPK-------------   78 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTT-------------
T ss_pred             HHHhHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcC-------------
Confidence            45667888888888886642 33566666666666666554          355555 333322221             


Q ss_pred             CccccchHHHHHHHHHHHHhc-----------CChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcC
Q 039275           75 RIRLARDPVSCKAMISGYSQA-----------GRFNEALEPFGKLESLGVHTDEVTMVVVLAASSG  129 (153)
Q Consensus        75 ~~~~a~~~~~~~~li~~~~~~-----------g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~  129 (153)
                            ....|..+=.+|...           |++++|.+.|++-.+.  .|+...|...+...-+
T Consensus        79 ------~~~A~~~LG~ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl~l--~P~~~~y~~al~~~~k  136 (158)
T 1zu2_A           79 ------KDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVDE--QPDNTHYLKSLEMTAK  136 (158)
T ss_dssp             ------CHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHT
T ss_pred             ------cHHHHHHHHHHHHHhcccCcchhhhhccHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHh
Confidence                  223444455555444           5899999999988864  6888777776665433

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=89.38  E-value=1.7  Score=24.10  Aligned_cols=29  Identities=21%  Similarity=0.340  Sum_probs=22.8

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 039275           84 SCKAMISGYSQAGRFNEALEPFGKLESLG  112 (153)
Q Consensus        84 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g  112 (153)
                      .|..+-..+...|++++|.+.|++..+..
T Consensus        37 ~~~~lg~~~~~~~~~~~A~~~~~~al~~~   65 (99)
T 2kc7_A           37 AYYLMGNAYRKLGDWQKALNNYQSAIELN   65 (99)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            66677777888888888888888887653

>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=87.59  E-value=5.5  Score=29.15  Aligned_cols=56  Identities=9%  Similarity=-0.018  Sum_probs=49.0

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +..+|.++-..+...|++++|...+++....+  |+...|..+-..+.-.|+.++|.+
T Consensus       276 ~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e  331 (372)
T 3ly7_A          276 LSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAAD  331 (372)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             CHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHH
Confidence            77888888777788899999999999999876  888888777888889999999988

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=86.16  E-value=4.9  Score=30.34  Aligned_cols=122  Identities=11%  Similarity=-0.049  Sum_probs=77.2

Q ss_pred             hhcCChhHHHHHHHHhHHcCCCccHHHHH--HHHHHhcCCCchHHHHHH-hhhhh--c-chhhHHHHHHHHHhcCCcccc
Q 039275            6 SQAGRFNEALEPFGKLESLGVHTDEVTMV--VVLTASSGPGAWILAKEL-QIELD--L-SSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         6 ~~~g~~~~a~~~~~~m~~~g~~p~~~~~~--~ll~~~~~~~~~~~a~~~-~~~~~--~-~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .+.+.++.|.++|++....+  ++..+|.  ..+.... .++.+.|.++ +.++.  | +...+...+....+.|+.+.|
T Consensus       297 ~r~~~~~~AR~i~~~A~~~~--~~~~v~i~~A~lE~~~-~~d~~~ar~ife~al~~~~~~~~~~~~yid~e~~~~~~~~a  373 (493)
T 2uy1_A          297 LKKRGLELFRKLFIELGNEG--VGPHVFIYCAFIEYYA-TGSRATPYNIFSSGLLKHPDSTLLKEEFFLFLLRIGDEENA  373 (493)
T ss_dssp             HHHHCHHHHHHHHHHHTTSC--CCHHHHHHHHHHHHHH-HCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHcCCHHHHHHHHHHhhCCC--CChHHHHHHHHHHHHH-CCChHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHH
Confidence            35677999999999882222  2333333  3333322 2257778887 33322  2 234456667777788888877


Q ss_pred             c--------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc--C---CCCC------------hhhHHHHHHHhcCC
Q 039275           80 R--------DPVSCKAMISGYSQAGRFNEALEPFGKLESL--G---VHTD------------EVTMVVVLAASSGP  130 (153)
Q Consensus        80 ~--------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~--g---~~p~------------~~t~~~li~~~~~~  130 (153)
                      +        ....|...+..-...|+.+.+..++++....  +   -.|-            .-++..+++.|.-.
T Consensus       374 R~l~er~~k~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~~~~~~~~~~~~~~~~~~~~fe~~~g~l~~~~~~~~~~  449 (493)
T 2uy1_A          374 RALFKRLEKTSRMWDSMIEYEFMVGSMELFRELVDQKMDAIKADAILPPLPPREHNVQMEGILGRYHCFLDSFNFL  449 (493)
T ss_dssp             HHHHHHSCCBHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHTTCCBCCCCCC--CCCCCHHHHHHHHHHHHHCBT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhcccccCCcccccccHHHHHHHhhhHHHHHHHhhhh
Confidence            6        3677888888888889999999988888631  1   1121            25677788887443

>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=85.69  E-value=1.8  Score=31.71  Aligned_cols=59  Identities=14%  Similarity=-0.017  Sum_probs=42.9

Q ss_pred             hhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH----------hhhhhcchhh
Q 039275            3 SGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL----------QIELDLSSYS   62 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~----------~~~~~~~~~~   62 (153)
                      ..+...|++++|+.....+... .+.+...+..+|.++.+.|+..+|.+.          +-|++|+..+
T Consensus       179 ~~~l~~g~~~~a~~~l~~~~~~-~P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l  247 (388)
T 2ff4_A          179 EAEIACGRASAVIAELEALTFE-HPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  247 (388)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH-STTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHH
Confidence            4566778888888877777543 445677888888888888888888776          4566776644

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=85.04  E-value=5.4  Score=25.24  Aligned_cols=90  Identities=10%  Similarity=-0.024  Sum_probs=53.8

Q ss_pred             hcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCC---chHHHHHH-hhhhhcc-hhhHHHHHHHHHhcCCccccch
Q 039275            7 QAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPG---AWILAKEL-QIELDLS-SYSLSSKTSRYAHSGRIRLARD   81 (153)
Q Consensus         7 ~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~---~~~~a~~~-~~~~~~~-~~~~~~ll~~~~~~g~~~~a~~   81 (153)
                      ..+....+.+-|.+..+.|. ++..+--.+-.++++.+   +++++..+ +.-++.+ ...-                 .
T Consensus        10 ~~~~l~~~~~~y~~e~~~~~-~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~~p~~~-----------------r   71 (152)
T 1pc2_A           10 SVEDLLKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKGSKEEQ-----------------R   71 (152)
T ss_dssp             CHHHHHHHHHHHHHHHHTTC-CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHH-----------------H
T ss_pred             CHHHHHHHHHHHHHHHccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccch-----------------H
Confidence            33456677777777766665 66666666667778877   56677766 1111111 0000                 1


Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCCh
Q 039275           82 PVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDE  117 (153)
Q Consensus        82 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  117 (153)
                      ...| .|--++.+.|++++|.+.++.+.+.  .|+.
T Consensus        72 d~lY-~LAv~~~kl~~Y~~A~~y~~~lL~i--eP~n  104 (152)
T 1pc2_A           72 DYVF-YLAVGNYRLKEYEKALKYVRGLLQT--EPQN  104 (152)
T ss_dssp             HHHH-HHHHHHHHTSCHHHHHHHHHHHHHH--CTTC
T ss_pred             HHHH-HHHHHHHHccCHHHHHHHHHHHHhc--CCCC
Confidence            1223 3445668888888888888888764  4644

>3lpz_A GET4 (YOR164C homolog); protein targeting, tail-anchored protein biogenesis, GET PAT GET5 binding, protein transport; 1.98A {Chaetomium thermophilum}

Probab=84.56  E-value=9.3  Score=27.55  Aligned_cols=42  Identities=14%  Similarity=0.177  Sum_probs=22.9

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCC
Q 039275           86 KAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPG  131 (153)
Q Consensus        86 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g  131 (153)
                      ..+-..|.+.+++.+|..-|  +  .|-.++...|..++--+.+.+
T Consensus       140 ~~ig~~~~~e~~~~~Ae~H~--i--lg~~~s~~~~a~mL~ew~~~~  181 (336)
T 3lpz_A          140 HVVGTLYVEEGEFEAAEKHL--V--LGTKESPEVLARMEYEWYKQD  181 (336)
T ss_dssp             HHHHHHHHHTTCHHHHHHHH--T--TSCTTHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHccCCHHHHHHHH--H--hcCCchHHHHHHHHHHHHHhc
Confidence            34446667777777777665  2  244455456655544444333

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=83.42  E-value=9.7  Score=26.86  Aligned_cols=129  Identities=7%  Similarity=-0.097  Sum_probs=72.4

Q ss_pred             CChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchH--HHHHH-hhhhh---cchhhHHHHHHHHHhcCC------c
Q 039275            9 GRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWI--LAKEL-QIELD---LSSYSLSSKTSRYAHSGR------I   76 (153)
Q Consensus         9 g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~--~a~~~-~~~~~---~~~~~~~~ll~~~~~~g~------~   76 (153)
                      +++++++++++++.+. -+-|...|+.---.+.+.+.++  ++.++ ..-+.   .|-..|+..-..+.+.+.      +
T Consensus       124 ~~~~~EL~~~~~~l~~-~pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~~N~sAW~~R~~ll~~l~~~~~~~~~  202 (306)
T 3dra_A          124 FDPYREFDILEAMLSS-DPKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDLKNNSAWSHRFFLLFSKKHLATDNTI  202 (306)
T ss_dssp             CCTHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHSSGGGCCHHHH
T ss_pred             CCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhccccchhhhH
Confidence            6778888888888664 2345556655545555555555  55555 22222   233344443333333333      3


Q ss_pred             cccc------------hHHHHHHHHHHHHhcCChHH-HHHHHHHHHHcC--CCCChhhHHHHHHHhcCCCccccchh
Q 039275           77 RLAR------------DPVSCKAMISGYSQAGRFNE-ALEPFGKLESLG--VHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        77 ~~a~------------~~~~~~~li~~~~~~g~~~~-a~~~~~~m~~~g--~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +++.            |...|+-+-..+.+.|+... +.++..++...+  -..+...+..+.+.+.+.|+.++|.+
T Consensus       203 ~eEl~~~~~aI~~~p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A~~  279 (306)
T 3dra_A          203 DEELNYVKDKIVKCPQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNESRT  279 (306)
T ss_dssp             HHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHHHH
Confidence            3333            77777777777777777444 444555544322  12355666777777777777777766

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=83.23  E-value=4  Score=23.40  Aligned_cols=75  Identities=12%  Similarity=0.025  Sum_probs=48.8

Q ss_pred             ccHHHHHHHHHHhcCCCchHHHHHH-hhh---hhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHH
Q 039275           28 TDEVTMVVVLTASSGPGAWILAKEL-QIE---LDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALE  103 (153)
Q Consensus        28 p~~~~~~~ll~~~~~~~~~~~a~~~-~~~---~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~  103 (153)
                      .+..-+-.+-..+.+.++++.|..+ +.-   ..++..               ........+..|-.++.+.|++++|..
T Consensus         3 Lsa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~---------------~~~~~~~i~~~L~~~~~~~g~~~~A~~   67 (104)
T 2v5f_A            3 LTAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEI---------------STIDKVSVLDYLSYAVYQQGDLDKALL   67 (104)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCC---------------CSSCHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             CCHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCC---------------CcccHHHHHHHHHHHHHHccCHHHHHH
Confidence            3445555666777888899998888 111   111100               001144677888889999999999999


Q ss_pred             HHHHHHHcCCCCChhh
Q 039275          104 PFGKLESLGVHTDEVT  119 (153)
Q Consensus       104 ~~~~m~~~g~~p~~~t  119 (153)
                      .+++..+.  .|+...
T Consensus        68 ~~~~al~l--~P~~~~   81 (104)
T 2v5f_A           68 LTKKLLEL--DPEHQR   81 (104)
T ss_dssp             HHHHHHHH--CTTCHH
T ss_pred             HHHHHHhc--CCCCHH
Confidence            99888753  565543

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=82.54  E-value=10  Score=30.59  Aligned_cols=104  Identities=12%  Similarity=0.010  Sum_probs=62.5

Q ss_pred             hhcCC-hhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCc--hHHHHHHhhhh----------hcchh----hH---HH
Q 039275            6 SQAGR-FNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGA--WILAKELQIEL----------DLSSY----SL---SS   65 (153)
Q Consensus         6 ~~~g~-~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~--~~~a~~~~~~~----------~~~~~----~~---~~   65 (153)
                      ...|+ .+.|+++|+++....-.-+......++..+.+.++  ++...-+...+          .+...    ..   ..
T Consensus       259 ~~t~~~~~~a~~~le~L~~~~p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~  338 (754)
T 4gns_B          259 AITPSLVDFTIDYLKGLTKKDPIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPRDADSARLMNCMSD  338 (754)
T ss_dssp             HTCGGGHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSCCHHHHHHHHHHHH
T ss_pred             cccccHHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhcccccccccccCcchH
Confidence            34445 47799999999775322222223344444444442  22221121111          11110    01   12


Q ss_pred             HH----HHHHhcCCccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 039275           66 KT----SRYAHSGRIRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLE  109 (153)
Q Consensus        66 ll----~~~~~~g~~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~  109 (153)
                      ||    +.+...|+++.|.            +-.+|-.|...|...|+++.|+-.+..+.
T Consensus       339 LL~~Qa~FLl~K~~~elAL~~Ak~AV~~aPseF~tW~~La~vYi~l~d~e~ALLtLNScP  398 (754)
T 4gns_B          339 LLNIQTNFLLNRGDYELALGVSNTSTELALDSFESWYNLARCHIKKEEYEKALFAINSMP  398 (754)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHSC
T ss_pred             HHHHHHHHHhccCcHHHHHHHHHHHHhcCchhhHHHHHHHHHHHHhccHHHHHHHHhcCC
Confidence            33    4456688888888            78999999999999999999999998884

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=81.71  E-value=3.4  Score=26.09  Aligned_cols=48  Identities=15%  Similarity=-0.001  Sum_probs=27.9

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL   52 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~   52 (153)
                      .....|+-++..++...+.. +.+|++...-.+-+||.+.|+..++.++
T Consensus       100 ~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Klg~~r~a~eL  147 (172)
T 1wy6_A          100 ILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTL  147 (172)
T ss_dssp             HHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHhcchhhHHHH
Confidence            34455555555555555422 3456666666666677777776666666

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=81.27  E-value=8.1  Score=24.44  Aligned_cols=124  Identities=8%  Similarity=-0.027  Sum_probs=83.7

Q ss_pred             hhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH--hhhhhcchh---hHHHHHHHHHhcCCccccc
Q 039275            6 SQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL--QIELDLSSY---SLSSKTSRYAHSGRIRLAR   80 (153)
Q Consensus         6 ~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~--~~~~~~~~~---~~~~ll~~~~~~g~~~~a~   80 (153)
                      .-.|.+++..++..+..+.   -+...||.+|--....-+.+-..+.  .-|---|..   ..-.+++.|.+.+...   
T Consensus        18 ildG~v~qGveii~k~~~s---sni~E~NW~ICNiiD~a~C~y~v~vLd~IGkiFDis~C~NlKrVi~C~~~~n~~s---   91 (172)
T 1wy6_A           18 LLDGYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDKCQNLKSVVECGVINNTLN---   91 (172)
T ss_dssp             HHTTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGGCSCTHHHHHHHHHTTCCC---
T ss_pred             HHhhhHHHHHHHHHHHcCC---CCccccceeeeecchhhchhHHHHHHHHHhhhcCcHhhhcHHHHHHHHHHhcchH---
Confidence            3467788888888877553   3455566555544444444444444  222122222   1235677777777653   


Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                        ...+.-+..+..+|+-|+-.++..++.. +.+|+......+-+||.+.|+..++.+
T Consensus        92 --e~vd~ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Klg~~r~a~e  146 (172)
T 1wy6_A           92 --EHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATT  146 (172)
T ss_dssp             --HHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             --HHHHHHHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHhcchhhHHH
Confidence              4667788899999999999999999643 447788888899999999999988877

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=80.41  E-value=6  Score=22.39  Aligned_cols=31  Identities=16%  Similarity=0.131  Sum_probs=24.6

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 039275           82 PVSCKAMISGYSQAGRFNEALEPFGKLESLG  112 (153)
Q Consensus        82 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  112 (153)
                      ......+-..+.+.|++++|.+.|+.+.+..
T Consensus        43 ~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~   73 (93)
T 3bee_A           43 EAALSLIANDHFISFRFQEAIDTWVLLLDSN   73 (93)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            3444556677899999999999999998654

---

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	153
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	98.68
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.56
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	98.49
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.08
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.07
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	97.76
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	97.69
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.66
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	97.65
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	97.63
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	97.54
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	97.51
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	97.46
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.34
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	97.28
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.16
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.16
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.11
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.07
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	96.82
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	96.76
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	96.76
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	96.74
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	96.74
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	96.72
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	96.68
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	96.45
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	96.44
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	96.38
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	96.19
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	96.07
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	95.92
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	95.91
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	95.72
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	95.7
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	95.68
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	95.29
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	95.29
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	95.19
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	94.98
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	94.66
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	93.88
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	93.54
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	93.03
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	92.26
d1peqa1	162	R1 subunit of ribonucleotide reductase, N-terminal	91.95
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	91.78
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	91.25
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	90.71
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	89.3
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	87.67
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	87.54
d1u9pa1	36	Arc repressor {Salmonella bacteriophage P22 [TaxId	86.89
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	85.02
d1sxjd1	91	Replication factor C2 {Baker's yeast (Saccharomyce	81.92

>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=98.68  E-value=4e-07  Score=63.40  Aligned_cols=145  Identities=14%  Similarity=0.057  Sum_probs=108.7

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hh--hhhc-chhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QI--ELDL-SSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~--~~~~-~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .+...|++++|++.|++....+ +.+...+..+-..+.+.|++++|.+. +.  ...| +...+..+...+.+.|++++|
T Consensus       212 ~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A  290 (388)
T d1w3ba_         212 VLKEARIFDRAVAAYLRALSLS-PNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEA  290 (388)
T ss_dssp             HHHTTTCTTHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHSCHHHH
T ss_pred             hhhccccHHHHHHHHHHhHHHh-hhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHH
Confidence            4667788888888888876653 24456666677777888888888887 22  2233 345677788888888888888


Q ss_pred             c------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh--------
Q 039275           80 R------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS--------  138 (153)
Q Consensus        80 ~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~--------  138 (153)
                      .            +...+..+...+.+.|++++|.+.|++..+.  .| +...+..+-..+.+.|++++|..        
T Consensus       291 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l  368 (388)
T d1w3ba_         291 EDCYNTALRLCPTHADSLNNLANIKREQGNIEEAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI  368 (388)
T ss_dssp             HHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTS--CTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTT
T ss_pred             HHHHHhhhccCCccchhhhHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            7            6677888888999999999999999987653  46 45567778889999999999988        


Q ss_pred             ---HHHHHHHHHHHhh
Q 039275          139 ---NIFLTTAIIEMYA  151 (153)
Q Consensus       139 ---~~~~~~~li~~y~  151 (153)
                         +...|..|-..|-
T Consensus       369 ~P~~~~a~~~lg~~~~  384 (388)
T d1w3ba_         369 SPTFADAYSNMGNTLK  384 (388)
T ss_dssp             CTTCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHH
Confidence               5666776666654

>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=98.56  E-value=1.6e-06  Score=59.76  Aligned_cols=132  Identities=15%  Similarity=0.095  Sum_probs=88.3

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-h--hhhhc-chhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-Q--IELDL-SSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~--~~~~~-~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .+.+.|++++|++.|++..+.. +-+...|..+-..+...|++++|... .  -.+.| +...+..+...|...|++++|
T Consensus        28 ~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A  106 (323)
T d1fcha_          28 RRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQA  106 (323)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHhhhcccccccccccccccccccccccccc
Confidence            4677888888888888887642 23466777777788888888888777 1  12223 334555566667777776665


Q ss_pred             c---------------------------------------------------------------hHHHHHHHHHHHHhcC
Q 039275           80 R---------------------------------------------------------------DPVSCKAMISGYSQAG   96 (153)
Q Consensus        80 ~---------------------------------------------------------------~~~~~~~li~~~~~~g   96 (153)
                      .                                                               +...|..+-..+...|
T Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~~~~~  186 (323)
T d1fcha_         107 CEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSG  186 (323)
T ss_dssp             HHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTT
T ss_pred             ccchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHHH
Confidence            4                                                               2345556666777778


Q ss_pred             ChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           97 RFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        97 ~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ++++|...|++.....  | +...|..+-..+.+.|++++|.+
T Consensus       187 ~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~  227 (323)
T d1fcha_         187 EYDKAVDCFTAALSVR--PNDYLLWNKLGATLANGNQSEEAVA  227 (323)
T ss_dssp             CHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHhhhhcccccccccc--cccccchhhhhhcccccccchhHHH
Confidence            8888888877766443  3 35556667777777788777776

>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=98.49  E-value=3.7e-06  Score=58.32  Aligned_cols=146  Identities=12%  Similarity=0.050  Sum_probs=114.5

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hh--h-hhcchhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QI--E-LDLSSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~--~-~~~~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .+...|++++|...+++..+.. +-+...+..+-..+...|++++|.+. ..  . -+.+...+..+...+.+.|++++|
T Consensus       178 ~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A  256 (388)
T d1w3ba_         178 VFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLA  256 (388)
T ss_dssp             HHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             cccccCcHHHHHHHHHHHHHhC-cccHHHHHHHhhhhhccccHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHCCCHHHH
Confidence            4567889999999999887642 23566788888899999999999888 11  1 233445677788889999999998


Q ss_pred             c------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh---------
Q 039275           80 R------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS---------  138 (153)
Q Consensus        80 ~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~---------  138 (153)
                      .            +...|..+-..+...|++++|.+.++...... ..+...+..+...+.+.|++++|.+         
T Consensus       257 ~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~  335 (388)
T d1w3ba_         257 IDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLANIKREQGNIEEAVRLYRKALEVF  335 (388)
T ss_dssp             HHHHHHHHHTCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSC
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccC-CccchhhhHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            7            67788899999999999999999999887653 4577788888999999999999988         


Q ss_pred             --HHHHHHHHHHHhh
Q 039275          139 --NIFLTTAIIEMYA  151 (153)
Q Consensus       139 --~~~~~~~li~~y~  151 (153)
                        +...+..+-..|.
T Consensus       336 p~~~~~~~~la~~~~  350 (388)
T d1w3ba_         336 PEFAAAHSNLASVLQ  350 (388)
T ss_dssp             TTCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH
Confidence              4555665555553

>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=98.08  E-value=6.7e-05  Score=48.26  Aligned_cols=123  Identities=10%  Similarity=0.014  Sum_probs=90.9

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhh--hhc-chhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIE--LDL-SSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~--~~~-~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .+...|++++|++.|+++    .+|++.++..+=.++.+.|++++|.+. ..-  +.| +...|..+-.+|.+.|++++|
T Consensus        14 ~~~~~~d~~~Al~~~~~i----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp~~~~a~~~~g~~~~~~g~~~~A   89 (192)
T d1hh8a_          14 LAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQTEKYDLA   89 (192)
T ss_dssp             HHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHCCCHHHHHHHHHhc----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhhhhhHHHHHHHHHhhccHHHH
Confidence            457889999999999875    457888888888899999999999999 222  233 344667777888888888887


Q ss_pred             c----------------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCC
Q 039275           80 R----------------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGP  130 (153)
Q Consensus        80 ~----------------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  130 (153)
                      .                            ...++..+-..+.+.|++++|.+.|.........|+.......+....+.
T Consensus        90 ~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~~~~~~~~~~Al~~~~~~  168 (192)
T d1hh8a_          90 IKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEPRHSKIDKAMECVWKQ  168 (192)
T ss_dssp             HHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSGGGGHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHhh
Confidence            6                            12445566677889999999999988877666666565566556555443

>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=98.07  E-value=3.2e-05  Score=52.89  Aligned_cols=132  Identities=11%  Similarity=0.032  Sum_probs=97.5

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-------------------------------
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-------------------------------   52 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-------------------------------   52 (153)
                      .|...|++++|+..|.+..+.. +-+...+..+...+...|++++|.+.                               
T Consensus        62 ~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  140 (323)
T d1fcha_          62 TQAENEQELLAISALRRCLELK-PDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSK  140 (323)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC---------------
T ss_pred             HHHHcCChHHHHHHHHhhhccc-cccccccccccccccccccccccccchhhHHHhccchHHHHHhhhhhhhhcccccch
Confidence            5677788888888887776532 22455566666667777777766554                               


Q ss_pred             -------------------hh--hhhc---chhhHHHHHHHHHhcCCccccc------------hHHHHHHHHHHHHhcC
Q 039275           53 -------------------QI--ELDL---SSYSLSSKTSRYAHSGRIRLAR------------DPVSCKAMISGYSQAG   96 (153)
Q Consensus        53 -------------------~~--~~~~---~~~~~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~~~~~g   96 (153)
                                         ..  ...|   +..++..+-..+...|++++|.            +...|..+-..+.+.|
T Consensus       141 ~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g  220 (323)
T d1fcha_         141 RILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGN  220 (323)
T ss_dssp             CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT
T ss_pred             hhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHHHHHhhhhcccccccccccccccchhhhhhcccccc
Confidence                               00  0111   2344556667888999999987            6888999999999999


Q ss_pred             ChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           97 RFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        97 ~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ++++|.+.|++..+.  .| +...+..+-.+|.+.|++++|.+
T Consensus       221 ~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~~~~A~~  261 (323)
T d1fcha_         221 QSEEAVAAYRRALEL--QPGYIRSRYNLGISCINLGAHREAVE  261 (323)
T ss_dssp             CHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             cchhHHHHHHHHHHH--hhccHHHHHHHHHHHHHCCCHHHHHH
Confidence            999999999998764  45 45668889999999999999988

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.76  E-value=0.00024  Score=48.18  Aligned_cols=135  Identities=12%  Similarity=-0.039  Sum_probs=91.0

Q ss_pred             hHhhcCChhHHHHHHHHhHHc----CCCc-cHHHHHHHHHHhcCCCchHHHHHH-hhh---------hhcchhhHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESL----GVHT-DEVTMVVVLTASSGPGAWILAKEL-QIE---------LDLSSYSLSSKTS   68 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~----g~~p-~~~~~~~ll~~~~~~~~~~~a~~~-~~~---------~~~~~~~~~~ll~   68 (153)
                      .|...|++++|.+.|.+...-    +-+| -..+|..+-.+|.+.|++++|.+. ..-         ......++..+..
T Consensus        46 ~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~  125 (290)
T d1qqea_          46 IYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGE  125 (290)
T ss_dssp             HHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHHHHHH
Confidence            567788999999999887542    2222 246778888889999999998888 111         1112334555555


Q ss_pred             HHH-hcCCccccc------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-----Ch-hhHHHH
Q 039275           69 RYA-HSGRIRLAR------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-----DE-VTMVVV  123 (153)
Q Consensus        69 ~~~-~~g~~~~a~------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-----~~-~t~~~l  123 (153)
                      .|- ..|++++|.                  ...+|..+...+...|++++|.+.|++........     .. ..+...
T Consensus       126 ~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~  205 (290)
T d1qqea_         126 ILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKK  205 (290)
T ss_dssp             HHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHH
T ss_pred             hHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHHHHHH
Confidence            563 468888888                  24568888999999999999999999987543221     11 112334


Q ss_pred             HHHhcCCCccccchh
Q 039275          124 LAASSGPGALDFGKS  138 (153)
Q Consensus       124 i~~~~~~g~~~~a~~  138 (153)
                      +..+...|+++.|.+
T Consensus       206 ~~~~l~~~d~~~A~~  220 (290)
T d1qqea_         206 GLCQLAATDAVAAAR  220 (290)
T ss_dssp             HHHHHHTTCHHHHHH
T ss_pred             HHHHHHhccHHHHHH
Confidence            445566788887766

>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=97.69  E-value=0.00087  Score=46.08  Aligned_cols=125  Identities=6%  Similarity=-0.139  Sum_probs=85.0

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCcc-HHHHHHHHHHhcCCC-chHHHHHH-hh--hh-hcchhhHHHHHHHHHhcCCcc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTD-EVTMVVVLTASSGPG-AWILAKEL-QI--EL-DLSSYSLSSKTSRYAHSGRIR   77 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~-~~~~~~ll~~~~~~~-~~~~a~~~-~~--~~-~~~~~~~~~ll~~~~~~g~~~   77 (153)
                      .+.+.+..++|++.+++..+.  -|+ ...|+..-..+.+.+ ++++|.+. ..  .. +-+..+|+.+-..+.+.|+++
T Consensus        52 ~~~~~e~~~~Al~~~~~ai~l--nP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p~~~~a~~~~~~~~~~l~~~~  129 (315)
T d2h6fa1          52 VLQRDERSERAFKLTRDAIEL--NAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLVEWLRDPS  129 (315)
T ss_dssp             HHHHTCCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCT
T ss_pred             HHHhCCchHHHHHHHHHHHHH--CCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHhhhhHHHHHhHHHHhhccHH
Confidence            355778889999999988774  343 445565555666655 58888887 22  22 234567777788888888888


Q ss_pred             ccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCc
Q 039275           78 LAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGA  132 (153)
Q Consensus        78 ~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~  132 (153)
                      +|.            +...|..+...+.+.|++++|.+.|+...+..  | +...|+..-..+.+.+.
T Consensus       130 eAl~~~~kal~~dp~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~--p~n~~a~~~r~~~l~~~~~  195 (315)
T d2h6fa1         130 QELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKED--VRNNSVWNQRYFVISNTTG  195 (315)
T ss_dssp             THHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHhhhhhhhhcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHC--CccHHHHHHHHHHHHHccc
Confidence            888            67788888888888888888888888887643  4 33345444333333333

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.66  E-value=0.00073  Score=39.53  Aligned_cols=98  Identities=15%  Similarity=0.076  Sum_probs=73.8

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDP   82 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~   82 (153)
                      .+.+.|++++|+..|++..+. -+-+...|..+-.++.+.|++++|... ...+..+..                   +.
T Consensus        12 ~~~~~g~~~eAi~~~~~al~~-~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~-------------------~~   71 (117)
T d1elwa_          12 KALSVGNIDDALQCYSEAIKL-DPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPD-------------------WG   71 (117)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-------------------CH
T ss_pred             HHHHcCCHHHHHHHHHHHHhc-CCcchhhhhcccccccccccccccchhhhhHHHhccc-------------------hh
Confidence            467889999999999998765 345667788888888889999998888 333332221                   44


Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHH
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVV  123 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l  123 (153)
                      ..|..+-..+...|++++|...|++..+  ..|+...+...
T Consensus        72 ~~~~~~g~~~~~~~~~~~A~~~~~~a~~--~~p~~~~~~~~  110 (117)
T d1elwa_          72 KGYSRKAAALEFLNRFEEAKRTYEEGLK--HEANNPQLKEG  110 (117)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHT--TCTTCHHHHHH
T ss_pred             hHHHHHHHHHHHccCHHHHHHHHHHHHH--hCCCCHHHHHH
Confidence            6788888999999999999999999885  35765544433

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.65  E-value=0.00035  Score=44.22  Aligned_cols=76  Identities=11%  Similarity=-0.167  Sum_probs=51.9

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhh--hcc-hhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIEL--DLS-SYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~--~~~-~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .|.+.|++++|++.|++..... +-++..|.-+-.++.+.|++++|... ..-+  .|+ ...|..+-.+|.+.|++++|
T Consensus        13 ~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~p~~~~a~~~lg~~~~~l~~~~~A   91 (201)
T d2c2la1          13 RLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEA   91 (201)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHH
Confidence            5788999999999999886652 45677788888899999999999998 3333  342 22334444444444444444


Q ss_pred             c
Q 039275           80 R   80 (153)
Q Consensus        80 ~   80 (153)
                      .
T Consensus        92 ~   92 (201)
T d2c2la1          92 I   92 (201)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=97.63  E-value=0.00063  Score=46.42  Aligned_cols=134  Identities=12%  Similarity=0.036  Sum_probs=76.7

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhh---hcchhhHHHHHHH-HHhcCCcccc
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIEL---DLSSYSLSSKTSR-YAHSGRIRLA   79 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~---~~~~~~~~~ll~~-~~~~g~~~~a   79 (153)
                      ..+.|++++|..+|+++.+..-......|...+..+.+.++++.|.++ ...+   +.+...|...... +...|+.+.|
T Consensus       109 ~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al~~~~~~~~~~~~~a~~e~~~~~~~~~a  188 (308)
T d2onda1         109 EESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYVTAALMEYYCSKDKSVA  188 (308)
T ss_dssp             HHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTTCCTHHHHHHHHHHHHTSCCHHHH
T ss_pred             HHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhccCHHHH
Confidence            345677777777777776543333344566666666667777777766 2211   1222223222221 2233555555


Q ss_pred             c------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcC-CCCC--hhhHHHHHHHhcCCCccccchh
Q 039275           80 R------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLG-VHTD--EVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        80 ~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~--~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .            +...|...+..+.+.|++++|..+|++-.... ..|+  ...|...+..=...|+.+.+..
T Consensus       189 ~~i~e~~l~~~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~~~~~~iw~~~~~fE~~~G~~~~~~~  262 (308)
T d2onda1         189 FKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILK  262 (308)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHH
T ss_pred             HHHHHHHHHhhhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            5            56677777777777788888877777765543 4443  3356666665555566665544

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.54  E-value=0.0012  Score=40.49  Aligned_cols=94  Identities=12%  Similarity=0.107  Sum_probs=69.5

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDP   82 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~   82 (153)
                      .|.+.|++++|+..|.+..+.. +-+...|..+-..+...|++++|... ..-+..+..                   +.
T Consensus        19 ~~~~~~~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p~-------------------~~   78 (159)
T d1a17a_          19 DYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKK-------------------YI   78 (159)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CH
T ss_pred             HHHHcCCHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHHHHHHccc-------------------ch
Confidence            4778999999999999988753 44667777777788889999998888 333333222                   33


Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhh
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVT  119 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t  119 (153)
                      ..|..+...+...|++++|.+.|++.....  |+...
T Consensus        79 ~a~~~~g~~~~~~g~~~eA~~~~~~a~~~~--p~~~~  113 (159)
T d1a17a_          79 KGYYRRAASNMALGKFRAALRDYETVVKVK--PHDKD  113 (159)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCCHH
Confidence            567788888899999999999988887653  54333

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=97.51  E-value=0.001  Score=43.61  Aligned_cols=76  Identities=20%  Similarity=0.135  Sum_probs=45.5

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH---hhhhhc-chhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL---QIELDL-SSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~-~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .|.+.|++++|++.|++..+. -+-++.+|..+-.++.+.|++++|.+.   -....| +...+..+-..|...|++++|
T Consensus        46 ~y~~~g~~~~A~~~~~~al~l-~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A  124 (259)
T d1xnfa_          46 LYDSLGLRALARNDFSQALAI-RPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLA  124 (259)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHCCCHHHHHHHHHHhhcc-CCCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHHHhhhhhhHHHHHHHHHHHhhHHHH
Confidence            456677777777777777653 123456666666677777777777766   111222 233455555666666666666


Q ss_pred             c
Q 039275           80 R   80 (153)
Q Consensus        80 ~   80 (153)
                      .
T Consensus       125 ~  125 (259)
T d1xnfa_         125 Q  125 (259)
T ss_dssp             H
T ss_pred             H
Confidence            5

>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=97.46  E-value=0.0016  Score=44.36  Aligned_cols=129  Identities=7%  Similarity=-0.104  Sum_probs=96.2

Q ss_pred             CChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hh--hhhcc--hhhHHHHHHHHHhcCCccccc---
Q 039275            9 GRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QI--ELDLS--SYSLSSKTSRYAHSGRIRLAR---   80 (153)
Q Consensus         9 g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~--~~~~~--~~~~~~ll~~~~~~g~~~~a~---   80 (153)
                      +..++|.++|++..+...+.+...+.......-+.|+++.|..+ ..  ...|.  ..+|...+....+.|+++.|.   
T Consensus        78 ~~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~  157 (308)
T d2onda1          78 LFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIF  157 (308)
T ss_dssp             HHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHH
Confidence            34578888998887765566677777778888889999999998 22  23343  346888999999999998887   


Q ss_pred             ---------hHHHHHHHHHH-HHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 ---------DPVSCKAMISG-YSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ---------~~~~~~~li~~-~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                               +...|-..... +...|+.+.|..+|+..... ..-+...|...++...+.|++++|+.
T Consensus       158 ~~al~~~~~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~-~p~~~~~w~~y~~~~~~~g~~~~aR~  224 (308)
T d2onda1         158 KKAREDARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKK-YGDIPEYVLAYIDYLSHLNEDNNTRV  224 (308)
T ss_dssp             HHHHTSTTCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHTTCCHHHHHH
T ss_pred             HHHHHhCCCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHh-hhhhHHHHHHHHHHHHHcCChHHHHH
Confidence                     33333333322 34468999999999999875 23456789999999999999999987

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=97.34  E-value=0.00073  Score=39.25  Aligned_cols=86  Identities=14%  Similarity=-0.031  Sum_probs=65.1

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDP   82 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~   82 (153)
                      .+.+.|++++|+..|++..+.. +-++..|..+-.++.+.+++++|... +.-+..+..                   +.
T Consensus        25 ~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-------------------~~   84 (112)
T d1hxia_          25 SMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPK-------------------DI   84 (112)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CH
T ss_pred             HHHHHhhhHHHHHHHhhhcccc-cccchhhhhhhhhhhhhhhHHHhhcccccccccccc-------------------cc
Confidence            4678899999999999987652 23578888888888999999999888 333333221                   34


Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHH
Q 039275           83 VSCKAMISGYSQAGRFNEALEPFGKLE  109 (153)
Q Consensus        83 ~~~~~li~~~~~~g~~~~a~~~~~~m~  109 (153)
                      ..|..+-..|...|++++|.+.|++..
T Consensus        85 ~a~~~la~~y~~~g~~~~A~~~l~~~l  111 (112)
T d1hxia_          85 AVHAALAVSHTNEHNANAALASLRAWL  111 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHCCCHHHHHHHHHHHh
Confidence            667788888899999999999888753

>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=97.28  E-value=0.0069  Score=41.36  Aligned_cols=130  Identities=7%  Similarity=-0.129  Sum_probs=91.8

Q ss_pred             HhhcC-ChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhh--h-cchhhHHHHHHHHHhcCCcccc
Q 039275            5 YSQAG-RFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIEL--D-LSSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         5 ~~~~g-~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~--~-~~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      +...| ++++|++.+++..+.. +-+...|...-..+.+.|++++|.+. ...+  . .+...|+.+...+.+.|++++|
T Consensus        87 l~~l~~~~~eal~~~~~al~~~-p~~~~a~~~~~~~~~~l~~~~eAl~~~~kal~~dp~n~~a~~~~~~~~~~~~~~~~A  165 (315)
T d2h6fa1          87 LKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRRVLVEWLRDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNE  165 (315)
T ss_dssp             HHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTH
T ss_pred             HHHhCcCHHHHHHHHHHHHHHH-HhhhhHHHHHhHHHHhhccHHHHHHHHhhhhhhhhcchHHHHHHHHHHHHHHhhHHH
Confidence            34445 5899999999986642 34577888888888889999999999 3333  2 3466788888999999999999


Q ss_pred             c------------hHHHHHHHHHHHHhcCC------hHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           80 R------------DPVSCKAMISGYSQAGR------FNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        80 ~------------~~~~~~~li~~~~~~g~------~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .            +...|+.+-..+.+.+.      +++|.+.+.+..+.  .| +...|..+...+...+ .+++.+
T Consensus       166 l~~~~~al~~~p~n~~a~~~r~~~l~~~~~~~~~~~~~~ai~~~~~al~~--~P~~~~~~~~l~~ll~~~~-~~~~~~  240 (315)
T d2h6fa1         166 LQYVDQLLKEDVRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKL--VPHNESAWNYLKGILQDRG-LSKYPN  240 (315)
T ss_dssp             HHHHHHHHHHCTTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHH--STTCHHHHHHHHHHHTTTC-GGGCHH
T ss_pred             HHHHHHHHHHCCccHHHHHHHHHHHHHccccchhhhhHHhHHHHHHHHHh--CCCchHHHHHHHHHHHhcC-hHHHHH
Confidence            8            67778877666666655      56788877776654  35 4555655555555444 455554

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.16  E-value=0.0055  Score=36.05  Aligned_cols=103  Identities=10%  Similarity=-0.052  Sum_probs=70.1

Q ss_pred             hhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCc---hHHHHHH-hhhhhcchhhHHHHHHHHHhcCCcc
Q 039275            2 ISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGA---WILAKEL-QIELDLSSYSLSSKTSRYAHSGRIR   77 (153)
Q Consensus         2 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~---~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~   77 (153)
                      ++.+...+++++|.+.|++....+ +.++.++.-+-.++.+.++   +++|.++ ..-+..+....              
T Consensus         6 ~n~~~~~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~--------------   70 (122)
T d1nzna_           6 LNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEE--------------   70 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHH--------------
T ss_pred             HHHhcCHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCch--------------
Confidence            567788899999999999998753 3466777777777777654   4457666 32222111100              


Q ss_pred             ccchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHH
Q 039275           78 LARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVL  124 (153)
Q Consensus        78 ~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li  124 (153)
                         ...+|..+-.+|.+.|++++|.+.|++..+.  .|+..-...+.
T Consensus        71 ---~~~~~~~Lg~~y~~~g~~~~A~~~~~~aL~~--~P~~~~A~~l~  112 (122)
T d1nzna_          71 ---QRDYVFYLAVGNYRLKEYEKALKYVRGLLQT--EPQNNQAKELE  112 (122)
T ss_dssp             ---HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHH
T ss_pred             ---HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHh--CcCCHHHHHHH
Confidence               1245667788889999999999999999874  57655444433

>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=97.16  E-value=0.0031  Score=38.54  Aligned_cols=40  Identities=18%  Similarity=0.089  Sum_probs=25.9

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHH
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVV  122 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~  122 (153)
                      +..+|-.+-.++...|++++|...|++..+.  .|+......
T Consensus       100 ~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l--~P~n~~~~~  139 (153)
T d2fbna1         100 NVKALYKLGVANMYFGFLEEAKENLYKAASL--NPNNLDIRN  139 (153)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTCHHHHH
T ss_pred             hhhhhHHhHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHH
Confidence            4566777777777777777777777776654  354443333

>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=97.11  E-value=0.0028  Score=39.97  Aligned_cols=103  Identities=18%  Similarity=0.244  Sum_probs=68.2

Q ss_pred             hHhhcCChhHHHHHHHHhHHc--C-CCccHHHHHHHHHHhcCCCchHHHHHHhhhhhc-chhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESL--G-VHTDEVTMVVVLTASSGPGAWILAKELQIELDL-SSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~--g-~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~-~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .....|++++|.+.|.+-..-  | ..++.           ..+.+-  ......+.+ ....+..+...+.+.|++++|
T Consensus        20 ~~~~~g~~e~A~~~~~~AL~l~rG~~l~~~-----------~~~~w~--~~~r~~l~~~~~~a~~~la~~~~~~g~~~~A   86 (179)
T d2ff4a2          20 HAAAAGRFEQASRHLSAALREWRGPVLDDL-----------RDFQFV--EPFATALVEDKVLAHTAKAEAEIACGRASAV   86 (179)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTTCCSSTTGGG-----------TTSTTH--HHHHHHHHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHhhCcccccccC-----------cchHHH--HHHHHHHHHHHHHHHHHHHHHHHHCCCchHH
Confidence            356778888888888877552  1 11110           001111  111111111 223456677777788887777


Q ss_pred             c------------hHHHHHHHHHHHHhcCChHHHHHHHHHHH-----HcCCCCChhh
Q 039275           80 R------------DPVSCKAMISGYSQAGRFNEALEPFGKLE-----SLGVHTDEVT  119 (153)
Q Consensus        80 ~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~-----~~g~~p~~~t  119 (153)
                      .            +...|..++.++.+.|+..+|.+.|++..     +-|+.|+..+
T Consensus        87 l~~~~~al~~~P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          87 IAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            7            88999999999999999999999999984     3599998765

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.07  E-value=0.0047  Score=36.44  Aligned_cols=92  Identities=13%  Similarity=0.180  Sum_probs=68.4

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhhh--cc-hhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIELD--LS-SYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~--~~-~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .|.+.|++++|++.|.+..+.+ +.+...+..+-.++.+.|++++|... ...+.  |+ ...+..+             
T Consensus        13 ~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~-------------   78 (128)
T d1elra_          13 DAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQI-------------   78 (128)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHH-------------
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHH-------------
Confidence            5788999999999999998763 34678888888999999999999998 33232  22 2222222             


Q ss_pred             chHHHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 039275           80 RDPVSCKAMISGYSQAGRFNEALEPFGKLESL  111 (153)
Q Consensus        80 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  111 (153)
                        ..+|..+-..+...+++++|.+.|+.-...
T Consensus        79 --a~~~~~lg~~~~~~~~~~~A~~~~~kal~~  108 (128)
T d1elra_          79 --AKAYARIGNSYFKEEKYKDAIHFYNKSLAE  108 (128)
T ss_dssp             --HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             --HHHHHHHHHHHHHhCCHHHHHHHHHHHHhc
Confidence              246667777888889999999999876644

>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=96.82  E-value=0.0031  Score=36.70  Aligned_cols=81  Identities=16%  Similarity=0.029  Sum_probs=62.6

Q ss_pred             HHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCC
Q 039275           38 TASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTD  116 (153)
Q Consensus        38 ~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  116 (153)
                      +.+.+.|++++|... ...+..++.                   +...|..+-..+...|++++|.+.+....+.. ..+
T Consensus        11 ~~~~~~g~~~eAi~~~~~al~~~p~-------------------~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~   70 (117)
T d1elwa_          11 NKALSVGNIDDALQCYSEAIKLDPH-------------------NHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDW   70 (117)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTT-------------------CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTC
T ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCc-------------------chhhhhcccccccccccccccchhhhhHHHhc-cch
Confidence            445667777777777 333322221                   45778888899999999999999999998765 347


Q ss_pred             hhhHHHHHHHhcCCCccccchh
Q 039275          117 EVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       117 ~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ...|..+-.++...|++++|..
T Consensus        71 ~~~~~~~g~~~~~~~~~~~A~~   92 (117)
T d1elwa_          71 GKGYSRKAAALEFLNRFEEAKR   92 (117)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHH
T ss_pred             hhHHHHHHHHHHHccCHHHHHH
Confidence            7788999999999999999988

>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=96.76  E-value=0.0021  Score=40.38  Aligned_cols=83  Identities=7%  Similarity=-0.090  Sum_probs=60.3

Q ss_pred             ccHHHHHHHHHHhcCCCchHHHHHH-hhh--hhc-chhhHHHHHHHHHhcCCccccc------------hHHHHHHHHHH
Q 039275           28 TDEVTMVVVLTASSGPGAWILAKEL-QIE--LDL-SSYSLSSKTSRYAHSGRIRLAR------------DPVSCKAMISG   91 (153)
Q Consensus        28 p~~~~~~~ll~~~~~~~~~~~a~~~-~~~--~~~-~~~~~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~   91 (153)
                      |+...+.-.=+.+.+.|++++|... ...  ..| +...|+.+-.+|.+.|++++|.            +..+|..+-..
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~p~~~~a~~~lg~~   81 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQC   81 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhCCCcHHHHHHHHHH
Confidence            6666777777888999999999999 222  233 4456667777777777777777            56667777777


Q ss_pred             HHhcCChHHHHHHHHHHHH
Q 039275           92 YSQAGRFNEALEPFGKLES  110 (153)
Q Consensus        92 ~~~~g~~~~a~~~~~~m~~  110 (153)
                      |.+.|++++|...|++...
T Consensus        82 ~~~l~~~~~A~~~~~~al~  100 (201)
T d2c2la1          82 QLEMESYDEAIANLQRAYS  100 (201)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHH
Confidence            7777888888777776553

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.76  E-value=0.016  Score=35.81  Aligned_cols=100  Identities=18%  Similarity=0.148  Sum_probs=59.5

Q ss_pred             hHhhcCChhHHHHHHHHhHHcC-----CCcc---------HHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESLG-----VHTD---------EVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTS   68 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g-----~~p~---------~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~   68 (153)
                      .+.+.|++++|++.|.+..+.-     ....         ..+|+-+-.++.+.|++++|... ..-+..+..       
T Consensus        22 ~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~p~-------   94 (170)
T d1p5qa1          22 VYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELDSN-------   94 (170)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------
T ss_pred             HHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhcccc-------
Confidence            5778899999999998876531     0000         12233333344445555555544 221211111       


Q ss_pred             HHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHH
Q 039275           69 RYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVL  124 (153)
Q Consensus        69 ~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li  124 (153)
                                  ++.+|..+-.++...|++++|...|++..+.  .|+.......+
T Consensus        95 ------------~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l--~P~n~~~~~~l  136 (170)
T d1p5qa1          95 ------------NEKGLSRRGEAHLAVNDFELARADFQKVLQL--YPNNKAAKTQL  136 (170)
T ss_dssp             ------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSSCHHHHHHH
T ss_pred             ------------chhhhHHHHHHHHHhhhHHHHHHHHHHHHHh--CCCCHHHHHHH
Confidence                        4567778888899999999999999988764  46444443333

>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=96.74  E-value=0.0081  Score=40.17  Aligned_cols=135  Identities=15%  Similarity=-0.008  Sum_probs=86.9

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCcc----HHHHHHHHHHhcCCCchHHHHHH-hhhh---------hcchhhHHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTD----EVTMVVVLTASSGPGAWILAKEL-QIEL---------DLSSYSLSSKTSR   69 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~----~~~~~~ll~~~~~~~~~~~a~~~-~~~~---------~~~~~~~~~ll~~   69 (153)
                      .+...|++++|++++++.....-..+    ...+..+-..+...|++++|... +.-+         ......+..+...
T Consensus        21 ~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  100 (366)
T d1hz4a_          21 VAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEI  100 (366)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHH
Confidence            46789999999999998876421111    23555666788889999999888 1111         1112344556677


Q ss_pred             HHhcCCccccc--------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCC----CCChhhHHHHHH
Q 039275           70 YAHSGRIRLAR--------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGV----HTDEVTMVVVLA  125 (153)
Q Consensus        70 ~~~~g~~~~a~--------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~----~p~~~t~~~li~  125 (153)
                      +...|++..+.                    ....+..+-..+...|+++.+...+.......-    ......+.....
T Consensus       101 ~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~  180 (366)
T d1hz4a_         101 LFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQ  180 (366)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHHHH
Confidence            77888877776                    223455566778899999999999988875432    223334444445


Q ss_pred             HhcCCCccccchh
Q 039275          126 ASSGPGALDFGKS  138 (153)
Q Consensus       126 ~~~~~g~~~~a~~  138 (153)
                      .+...++...+..
T Consensus       181 ~~~~~~~~~~a~~  193 (366)
T d1hz4a_         181 CSLARGDLDNARS  193 (366)
T ss_dssp             HHHHHTCHHHHHH
T ss_pred             HHHhhhhHHHHHH
Confidence            5555666665554

>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=96.74  E-value=0.0037  Score=39.70  Aligned_cols=99  Identities=11%  Similarity=-0.014  Sum_probs=77.2

Q ss_pred             hcCCCchHHHHHHhhh-hhcchhhHHHHHHHHHhcCCccccc------------hHHHHHHHHHHHHhcCChHHHHHHHH
Q 039275           40 SSGPGAWILAKELQIE-LDLSSYSLSSKTSRYAHSGRIRLAR------------DPVSCKAMISGYSQAGRFNEALEPFG  106 (153)
Q Consensus        40 ~~~~~~~~~a~~~~~~-~~~~~~~~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~  106 (153)
                      +...|+++.|.+.... .+|+..+|..+-..|.+.|++++|.            ....|..+-..+.+.|++++|.+.|+
T Consensus        15 ~~~~~d~~~Al~~~~~i~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp~~~~a~~~~g~~~~~~g~~~~A~~~~~   94 (192)
T d1hh8a_          15 AADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQTEKYDLAIKDLK   94 (192)
T ss_dssp             HHHTTCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhhhhhHHHHHHHHHhhccHHHHHHHHH
Confidence            3677889988888333 4567778888999999999999999            78899999999999999999999998


Q ss_pred             HHHHc------------CCC--CC-hhhHHHHHHHhcCCCccccchh
Q 039275          107 KLESL------------GVH--TD-EVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       107 ~m~~~------------g~~--p~-~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +-...            |..  ++ ..++..+-.++.+.|++++|.+
T Consensus        95 kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~  141 (192)
T d1hh8a_          95 EALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEE  141 (192)
T ss_dssp             HHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHH
Confidence            87532            111  11 2345566677888999999887

>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=96.72  E-value=0.0038  Score=38.14  Aligned_cols=56  Identities=11%  Similarity=-0.002  Sum_probs=49.6

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +...|..+-..+...|++++|.+.|+...+..  | +...|..+..++...|++++|..
T Consensus        43 ~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~--p~~~~a~~~~g~~~~~~g~~~eA~~   99 (159)
T d1a17a_          43 NAIYYGNRSLAYLRTECYGYALGDATRAIELD--KKYIKGYYRRAASNMALGKFRAALR   99 (159)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             hhhhhhhhHHHHHhccccchHHHHHHHHHHHc--ccchHHHHHHHHHHHHcCCHHHHHH
Confidence            55788889999999999999999999998654  5 55789999999999999999988

>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=96.68  E-value=0.016  Score=38.74  Aligned_cols=127  Identities=9%  Similarity=-0.055  Sum_probs=82.5

Q ss_pred             hhHhhcCChhHHHHHHHHhHHc----C-CCccHHHHHHHHHHh-cCCCchHHHHHH-h--------hhhhc-chhhHHHH
Q 039275            3 SGYSQAGRFNEALEPFGKLESL----G-VHTDEVTMVVVLTAS-SGPGAWILAKEL-Q--------IELDL-SSYSLSSK   66 (153)
Q Consensus         3 ~~~~~~g~~~~a~~~~~~m~~~----g-~~p~~~~~~~ll~~~-~~~~~~~~a~~~-~--------~~~~~-~~~~~~~l   66 (153)
                      ..|.+.|++++|++.+++....    | ......++..+...+ ...|++++|.+. .        .+-++ -..++..+
T Consensus        85 ~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~l  164 (290)
T d1qqea_          85 KCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKC  164 (290)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHH
Confidence            3577899999999999876432    2 222245555555566 456999998888 1        11111 23457778


Q ss_pred             HHHHHhcCCccccc-------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCC-C---ChhhHHHH
Q 039275           67 TSRYAHSGRIRLAR-------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVH-T---DEVTMVVV  123 (153)
Q Consensus        67 l~~~~~~g~~~~a~-------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~-p---~~~t~~~l  123 (153)
                      ...|.+.|++++|.                   ....|...+..+...|+++.|.+.|++..+.... +   .......+
T Consensus       165 a~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l  244 (290)
T d1qqea_         165 ADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSL  244 (290)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHH
T ss_pred             HHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHH
Confidence            89999999999998                   1123444555667889999999999988754311 1   23355667


Q ss_pred             HHHhcC
Q 039275          124 LAASSG  129 (153)
Q Consensus       124 i~~~~~  129 (153)
                      +.++-.
T Consensus       245 ~~a~~~  250 (290)
T d1qqea_         245 IDAVNE  250 (290)
T ss_dssp             HHHHHT
T ss_pred             HHHHHh
Confidence            777665

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=96.45  E-value=0.011  Score=39.48  Aligned_cols=106  Identities=13%  Similarity=0.007  Sum_probs=71.4

Q ss_pred             HhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH---hhhhhcchh-hHHHHHHHHHhcCCccccc
Q 039275            5 YSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL---QIELDLSSY-SLSSKTSRYAHSGRIRLAR   80 (153)
Q Consensus         5 ~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~---~~~~~~~~~-~~~~ll~~~~~~g~~~~a~   80 (153)
                      ..+.|++++|+..+++..+. -+-|...+..+...++..|++++|.+.   -....|+.. .+..+-..+...+..+++.
T Consensus         6 aL~~G~l~eAl~~l~~al~~-~P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l~P~~~~~~~~l~~ll~a~~~~~~a~   84 (264)
T d1zbpa1           6 ALSEGQLQQALELLIEAIKA-SPKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPEYLPGASQLRHLVKAAQARKDFA   84 (264)
T ss_dssp             HTTTTCHHHHHHHHHHHHHT-CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhccccHHHH
Confidence            45789999999999999775 355778889999999999999999988   223344432 2222222222222222211


Q ss_pred             -------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 039275           81 -------------DPVSCKAMISGYSQAGRFNEALEPFGKLESL  111 (153)
Q Consensus        81 -------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  111 (153)
                                   +...+......+...|+.++|.+.+++..+.
T Consensus        85 ~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~  128 (264)
T d1zbpa1          85 QGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEEL  128 (264)
T ss_dssp             TSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhc
Confidence                         3333444456678889999999999998755

>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=96.44  E-value=0.0068  Score=40.56  Aligned_cols=135  Identities=13%  Similarity=0.041  Sum_probs=91.5

Q ss_pred             hHhhcCChhHHHHHHHHhHHc----CCCccHHHHHHHHHHhcCCCchHHHHHH-------hh--h--hhcchhhHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESL----GVHTDEVTMVVVLTASSGPGAWILAKEL-------QI--E--LDLSSYSLSSKTS   68 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~----g~~p~~~~~~~ll~~~~~~~~~~~a~~~-------~~--~--~~~~~~~~~~ll~   68 (153)
                      .+...|+++.+...+.+....    +.......+......+...+.+..+...       ..  +  .......+..+..
T Consensus       142 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  221 (366)
T d1hz4a_         142 LLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVI  221 (366)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHH
T ss_pred             HHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHH
Confidence            466789999999999887653    2333344555555556666666665555       11  1  1112234555667


Q ss_pred             HHHhcCCccccc----------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHH----cCCCCC-hhhHHHHHHHh
Q 039275           69 RYAHSGRIRLAR----------------DPVSCKAMISGYSQAGRFNEALEPFGKLES----LGVHTD-EVTMVVVLAAS  127 (153)
Q Consensus        69 ~~~~~g~~~~a~----------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~----~g~~p~-~~t~~~li~~~  127 (153)
                      .+...|++++|.                ....+..+-..+...|++++|.+.+++...    .+..|+ ...+..+-..+
T Consensus       222 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~  301 (366)
T d1hz4a_         222 YWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLY  301 (366)
T ss_dssp             HHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHH
Confidence            777888877776                345666778889999999999999998763    255554 34566777889


Q ss_pred             cCCCccccchh
Q 039275          128 SGPGALDFGKS  138 (153)
Q Consensus       128 ~~~g~~~~a~~  138 (153)
                      .+.|++++|.+
T Consensus       302 ~~~g~~~~A~~  312 (366)
T d1hz4a_         302 WQAGRKSDAQR  312 (366)
T ss_dssp             HHHTCHHHHHH
T ss_pred             HHCCCHHHHHH
Confidence            99999999988

>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=96.38  E-value=0.017  Score=37.42  Aligned_cols=105  Identities=9%  Similarity=-0.087  Sum_probs=75.5

Q ss_pred             cCChhHHHHHHHHhHHcCC-Cc--cHHHHHHHHHHhcCCCchHHHHHH-hhh--hhc-chhhHHHHHHHHHhcCCccccc
Q 039275            8 AGRFNEALEPFGKLESLGV-HT--DEVTMVVVLTASSGPGAWILAKEL-QIE--LDL-SSYSLSSKTSRYAHSGRIRLAR   80 (153)
Q Consensus         8 ~g~~~~a~~~~~~m~~~g~-~p--~~~~~~~ll~~~~~~~~~~~a~~~-~~~--~~~-~~~~~~~ll~~~~~~g~~~~a~   80 (153)
                      ..+.+.++.-+++.....- .+  ...+|..+=..+.+.|++++|.+. ...  +.| +..+|+.+-..|.+.|++++|.
T Consensus        12 ~~~~e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~p~~~~a~~~lg~~~~~~g~~~~A~   91 (259)
T d1xnfa_          12 TLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAY   91 (259)
T ss_dssp             CHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             cHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccCCCCHHHHhhhchHHHHHHHHHHhh
Confidence            3445667777777765422 22  124555555788889999999998 222  334 4467888888999999999988


Q ss_pred             ------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 039275           81 ------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLG  112 (153)
Q Consensus        81 ------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  112 (153)
                                  +..+|..+-..+...|++++|.+.|++..+..
T Consensus        92 ~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~  135 (259)
T d1xnfa_          92 EAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD  135 (259)
T ss_dssp             HHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             hhhhHHHHHHhhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhc
Confidence                        56678888888899999999999998887553

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=96.19  E-value=0.039  Score=33.29  Aligned_cols=95  Identities=17%  Similarity=0.141  Sum_probs=61.9

Q ss_pred             hHhhcCChhHHHHHHHHhHHc--CCCc---------cHHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESL--GVHT---------DEVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYA   71 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~--g~~p---------~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~   71 (153)
                      .+.+.|++++|++.|++..+.  ..+.         ....|+.+-.++.+.|++++|.+. ...+.           .+-
T Consensus        18 ~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~-----------~~~   86 (156)
T d2hr2a1          18 RQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALH-----------YFN   86 (156)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-----------HHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhh-----------ccc
Confidence            456789999999999998652  2211         246777888889999999988877 11111           111


Q ss_pred             hcCCccccc---hHHHHHHHHHHHHhcCChHHHHHHHHHHH
Q 039275           72 HSGRIRLAR---DPVSCKAMISGYSQAGRFNEALEPFGKLE  109 (153)
Q Consensus        72 ~~g~~~~a~---~~~~~~~li~~~~~~g~~~~a~~~~~~m~  109 (153)
                      +.+....-.   ....|+.+-..|...|++++|.+.|++..
T Consensus        87 ~~~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al  127 (156)
T d2hr2a1          87 RRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVV  127 (156)
T ss_dssp             HHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             ccccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHH
Confidence            111110000   22456777888999999999999998865

>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=96.07  E-value=0.0093  Score=40.62  Aligned_cols=127  Identities=9%  Similarity=-0.068  Sum_probs=75.1

Q ss_pred             CChhHHHHHHHHhHHcCCCccHHHHHHHH-HHhcCCCchHHHHHH-hhhh---hcchhhHHHHHHHHHhcCCccccc---
Q 039275            9 GRFNEALEPFGKLESLGVHTDEVTMVVVL-TASSGPGAWILAKEL-QIEL---DLSSYSLSSKTSRYAHSGRIRLAR---   80 (153)
Q Consensus         9 g~~~~a~~~~~~m~~~g~~p~~~~~~~ll-~~~~~~~~~~~a~~~-~~~~---~~~~~~~~~ll~~~~~~g~~~~a~---   80 (153)
                      +++++|+..+.+..+.. +++...+...+ ..+...+.+++|.+. ..-+   +-+...|+.+-..+.+.|++++|.   
T Consensus       123 ~~~~~a~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p~~~~a~~~l~~~~~~~~~~~~A~~~~  201 (334)
T d1dcea1         123 PNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDSGPQG  201 (334)
T ss_dssp             CCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHHHHSCCCCSSSCC
T ss_pred             ccHHHHHHHHHHHHhhC-chhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCHHHHHHHH
Confidence            45677888887776642 23344443333 555667778887777 2222   234456777778888888888887   


Q ss_pred             ---------------------------------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhH
Q 039275           81 ---------------------------------------DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTM  120 (153)
Q Consensus        81 ---------------------------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~  120 (153)
                                                             ....+..+...+...|+.++|.+.+.+....  .| +...+
T Consensus       202 ~~~~~~~~~~~~~~~~~~~l~~~~~a~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~p~~~~~~  279 (334)
T d1dcea1         202 RLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGRAEPLFRCELSVEKSTVLQSELESCKELQELEPE--NKWCLLTI  279 (334)
T ss_dssp             SSCHHHHHHHHHHHHHHHHHCSSCSHHHHHHHHHHSCCCCSSSCCCCHHHHHHHHHHHHHHHHHHHHCTT--CHHHHHHH
T ss_pred             HHhHHhHHHHHHHHHHHHHhcchhHHHHHHHHHHHhCcchhhHHHHHHHHHHHHhhHHHHHHHHHHHHhh--CchHHHHH
Confidence                                                   0111112223334445555555555544422  23 44566


Q ss_pred             HHHHHHhcCCCccccchh
Q 039275          121 VVVLAASSGPGALDFGKS  138 (153)
Q Consensus       121 ~~li~~~~~~g~~~~a~~  138 (153)
                      ..+...+.+.|++++|.+
T Consensus       280 ~~l~~~~~~~~~~~eA~~  297 (334)
T d1dcea1         280 ILLMRALDPLLYEKETLQ  297 (334)
T ss_dssp             HHHHHHHCTGGGHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHH
Confidence            667778888888888877

>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=95.92  E-value=0.0053  Score=35.34  Aligned_cols=56  Identities=5%  Similarity=0.005  Sum_probs=47.0

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      +...|..+-..+.+.|++++|...|++..+..  | +...+..+-..+...|++++|.+
T Consensus        49 ~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~--p~~~~a~~~la~~y~~~g~~~~A~~  105 (112)
T d1hxia_          49 REEAWRSLGLTQAENEKDGLAIIALNHARMLD--PKDIAVHAALAVSHTNEHNANAALA  105 (112)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchhhhhhhhhhhhhhhHHHhhcccccccccc--cccccchHHHHHHHHHCCCHHHHHH
Confidence            45778888899999999999999999987653  5 57778888889999999998876

>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=95.91  E-value=0.0044  Score=36.51  Aligned_cols=86  Identities=8%  Similarity=-0.032  Sum_probs=56.2

Q ss_pred             HHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCC---hHHHHHHHHHHH
Q 039275           34 VVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGR---FNEALEPFGKLE  109 (153)
Q Consensus        34 ~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~---~~~a~~~~~~m~  109 (153)
                      ..+++.+...+++++|++. +.-+..+..                   +..++..+-.++.+.++   +++|.++|++..
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~p~-------------------~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l   63 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAGSV-------------------SKSTQFEYAWCLVRTRYNDDIRKGIVLLEELL   63 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSCC-------------------CHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHT
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhCCC-------------------CHHHHHHHHHHHHHhcchHHHHHHHHHHHHHH
Confidence            3455666666677777666 222221111                   33455566666776554   457999999987


Q ss_pred             HcCCCCCh-hhHHHHHHHhcCCCccccchh
Q 039275          110 SLGVHTDE-VTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       110 ~~g~~p~~-~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .....|+. .++..+-.+|.+.|++++|.+
T Consensus        64 ~~~~~~~~~~~~~~Lg~~y~~~g~~~~A~~   93 (122)
T d1nzna_          64 PKGSKEEQRDYVFYLAVGNYRLKEYEKALK   93 (122)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             hccCCchHHHHHHHHHHHHHHHhhhHHHHH
Confidence            65544543 467788889999999999998

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=95.72  E-value=0.075  Score=32.34  Aligned_cols=50  Identities=10%  Similarity=0.093  Sum_probs=33.7

Q ss_pred             hHHHHHHHHHhcCCccccc------------hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 039275           62 SLSSKTSRYAHSGRIRLAR------------DPVSCKAMISGYSQAGRFNEALEPFGKLESL  111 (153)
Q Consensus        62 ~~~~ll~~~~~~g~~~~a~------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  111 (153)
                      .+..+-.+|.+.|++++|.            +...|..+-.++.+.|++++|.+.|+...+.
T Consensus        79 ~~~nla~~~~~~~~~~~Ai~~~~~al~~~p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l  140 (169)
T d1ihga1          79 CVLNIGACKLKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEI  140 (169)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcccchhhhhhhhhhhhhhhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHh
Confidence            3444445555555555555            5567777778888888888888888877754

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=95.70  E-value=0.065  Score=32.72  Aligned_cols=101  Identities=15%  Similarity=0.127  Sum_probs=59.2

Q ss_pred             hHhhcCChhHHHHHHHHhHHc---CCCcc-----------HHHHHHHHHHhcCCCchHHHHHH-hhhhhcchhhHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESL---GVHTD-----------EVTMVVVLTASSGPGAWILAKEL-QIELDLSSYSLSSKTS   68 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~---g~~p~-----------~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~   68 (153)
                      .+.+.|++++|++.|.+....   ...++           ...|.-+-.++.+.|++++|... ..-+..+..       
T Consensus        24 ~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~p~-------   96 (168)
T d1kt1a1          24 VYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLDSA-------   96 (168)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-------
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcccc-------
Confidence            467899999999999776431   11111           11122222334445555555544 111111111       


Q ss_pred             HHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHH
Q 039275           69 RYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLA  125 (153)
Q Consensus        69 ~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~  125 (153)
                                  +..+|..+-.++...|++++|.+.|++....  .|+.......+.
T Consensus        97 ------------~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l--~P~n~~~~~~l~  139 (168)
T d1kt1a1          97 ------------NEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQNKAARLQIF  139 (168)
T ss_dssp             ------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--CTTCHHHHHHHH
T ss_pred             ------------hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHH
Confidence                        4567778888899999999999999998753  565554444443

>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=95.68  E-value=0.036  Score=34.64  Aligned_cols=57  Identities=11%  Similarity=-0.031  Sum_probs=50.9

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ....+..+...+.+.|++++|...++...... .-+...|..++.++.+.|+..+|.+
T Consensus        66 ~~~a~~~la~~~~~~g~~~~Al~~~~~al~~~-P~~e~~~~~l~~al~~~Gr~~eAl~  122 (179)
T d2ff4a2          66 KVLAHTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALG  122 (179)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCchHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHH
Confidence            45678889999999999999999999998653 3488999999999999999999988

>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=95.29  E-value=0.16  Score=34.91  Aligned_cols=117  Identities=12%  Similarity=0.083  Sum_probs=63.4

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHHhhhhhcchhhHHHHHHHHHhcCCccccc---
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQIELDLSSYSLSSKTSRYAHSGRIRLAR---   80 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~ll~~~~~~g~~~~a~---   80 (153)
                      -|.+.|.++.|..+|..+..         |..++..+.+.++++.|.+.-.... +..+|..+...+.+.....-+.   
T Consensus        23 ~c~~~~lye~A~~lY~~~~d---------~~rl~~~~v~l~~~~~avd~~~k~~-~~~~~k~~~~~l~~~~e~~la~i~~   92 (336)
T d1b89a_          23 RCYDEKMYDAAKLLYNNVSN---------FGRLASTLVHLGEYQAAVDGARKAN-STRTWKEVCFACVDGKEFRLAQMCG   92 (336)
T ss_dssp             ------CTTTHHHHHHHTTC---------HHHHHHHHHTTTCHHHHHHHHHHHT-CHHHHHHHHHHHHHTTCHHHHHHTT
T ss_pred             HHHHCCCHHHHHHHHHhCCC---------HHHHHHHHHhhccHHHHHHHHHHcC-CHHHHHHHHHHHHhCcHHHHHHHHH
Confidence            45577888888888875543         5556666667777777766622211 2334555555555444333221   


Q ss_pred             -----hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCC
Q 039275           81 -----DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPG  131 (153)
Q Consensus        81 -----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g  131 (153)
                           ++.....++..|-..|.+++...+++..... -+++...++-++..+++.+
T Consensus        93 ~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~-~~~~~~~~~~L~~lyak~~  147 (336)
T d1b89a_          93 LHIVVHADELEELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSKFK  147 (336)
T ss_dssp             TTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS-TTCCHHHHHHHHHHHHTTC
T ss_pred             HHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcC-CccchHHHHHHHHHHHHhC
Confidence                 3344456666777777777777766665421 2445556666666666643

>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=95.29  E-value=0.041  Score=33.80  Aligned_cols=56  Identities=14%  Similarity=0.103  Sum_probs=49.2

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ...+|+.+-..|.+.|++++|.+.+++.....  | +...+..+-.++...|++++|..
T Consensus        61 ~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~--p~~~~a~~~~g~~~~~~g~~~~A~~  117 (170)
T d1p5qa1          61 RLASHLNLAMCHLKLQAFSAAIESCNKALELD--SNNEKGLSRRGEAHLAVNDFELARA  117 (170)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhhcccccchhhhhhhcc--ccchhhhHHHHHHHHHhhhHHHHHH
Confidence            34678888899999999999999999998764  5 77788889999999999999998

>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=95.19  E-value=0.037  Score=33.39  Aligned_cols=57  Identities=12%  Similarity=0.139  Sum_probs=50.0

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ...+|+.+-..|.+.|++++|.+.+++..+.. ..+...|..+..++...|+++.|..
T Consensus        66 ~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~-p~~~ka~~~~g~~~~~lg~~~~A~~  122 (153)
T d2fbna1          66 EISCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKE  122 (153)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHhhHHHHHHHhcccchhhhhhhcccccc-chhhhhhHHhHHHHHHcCCHHHHHH
Confidence            34678889999999999999999999988654 3377899999999999999999998

>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=94.98  E-value=0.096  Score=31.84  Aligned_cols=57  Identities=5%  Similarity=-0.034  Sum_probs=48.9

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ....|..+-..+.+.|++++|...+++..+.. .-+...|..+-.++.+.|++++|.+
T Consensus        76 ~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p~~~~a~~~~g~~~~~l~~~~~A~~  132 (169)
T d1ihga1          76 ALSCVLNIGACKLKMSDWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLKEYDQALA  132 (169)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             hHHHHHHHHHHHHhhcccchhhhhhhhhhhhh-hhhhhHHHhHHHHHHHccCHHHHHH
Confidence            55678888899999999999999999988643 2366778889999999999999988

>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=94.66  E-value=0.39  Score=32.94  Aligned_cols=108  Identities=10%  Similarity=0.007  Sum_probs=68.0

Q ss_pred             hhhHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHHhh--h-hh--------cchhhHHHHHHHH
Q 039275            2 ISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKELQI--E-LD--------LSSYSLSSKTSRY   70 (153)
Q Consensus         2 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~~~--~-~~--------~~~~~~~~ll~~~   70 (153)
                      +..|-+.|.+++.+.+++..... -.++...++.++..+++-+.-....-++.  + ..        .....|.-++..|
T Consensus       106 v~~ye~~~~~e~Li~~Le~~~~~-~~~~~~~~~~L~~lyak~~~~kl~e~l~~~s~~y~~~k~~~~c~~~~l~~elv~Ly  184 (336)
T d1b89a_         106 INYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSKFKPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLY  184 (336)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHTTS-TTCCHHHHHHHHHHHHTTCHHHHHHHHHHHSTTSCHHHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHcCChHHHHHHHHHHHcC-CccchHHHHHHHHHHHHhChHHHHHHHHhccccCCHHHHHHHHHHcCChHHHHHHH
Confidence            45677888999989888876432 35677788999999998876444444411  1 11        1223456677888


Q ss_pred             HhcCCccccc--------hHHHHHHHHHHHHhcCChHHHHHHHHHHHH
Q 039275           71 AHSGRIRLAR--------DPVSCKAMISGYSQAGRFNEALEPFGKLES  110 (153)
Q Consensus        71 ~~~g~~~~a~--------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  110 (153)
                      .+.|+++.|.        +..--...+..+.+.++++...++.....+
T Consensus       185 ~~~~~~~~A~~~~i~~~~~~~~~~~f~e~~~k~~N~e~~~~~i~~yL~  232 (336)
T d1b89a_         185 DKYEEYDNAIITMMNHPTDAWKEGQFKDIITKVANVELYYRAIQFYLE  232 (336)
T ss_dssp             HHTTCHHHHHHHHHHSTTTTCCHHHHHHHHHHCSSTHHHHHHHHHHHH
T ss_pred             HhcCCHHHHHHHHHHcchhhhhHHHHHHHHHccCChHHHHHHHHHHHH
Confidence            8888888776        111123345556666666666666665544

>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=93.88  E-value=0.027  Score=32.96  Aligned_cols=83  Identities=10%  Similarity=-0.004  Sum_probs=55.0

Q ss_pred             HHHhcCCCchHHHHHH-hhhhhcchhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCC-C
Q 039275           37 LTASSGPGAWILAKEL-QIELDLSSYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGV-H  114 (153)
Q Consensus        37 l~~~~~~~~~~~a~~~-~~~~~~~~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~-~  114 (153)
                      =+.+.+.|++++|.+. ..-+..+..                   +...|..+-..|.+.|++++|.+.+++..+..- .
T Consensus        11 G~~~~~~~~y~~Ai~~y~~al~~~p~-------------------~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~   71 (128)
T d1elra_          11 GNDAYKKKDFDTALKHYDKAKELDPT-------------------NMTYITNQAAVYFEKGDYNKCRELCEKAIEVGREN   71 (128)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCTT-------------------CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCcc-------------------cHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCccc
Confidence            3456666777777776 222211111                   456788889999999999999999999764311 1


Q ss_pred             CC-----hhhHHHHHHHhcCCCccccchh
Q 039275          115 TD-----EVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       115 p~-----~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      |.     ..+|..+-..+...+++++|.+
T Consensus        72 ~~~~~~~a~~~~~lg~~~~~~~~~~~A~~  100 (128)
T d1elra_          72 REDYRQIAKAYARIGNSYFKEEKYKDAIH  100 (128)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCHHHHHH
Confidence            11     2456667777788888888877

>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=93.54  E-value=0.098  Score=31.85  Aligned_cols=97  Identities=12%  Similarity=-0.022  Sum_probs=66.5

Q ss_pred             HHHHHHHHHhcCCCchHHHHHHhhhhhcchhhHHHHHHHHHhcCCccccc-------hHHHHHHHHHHHHhcCChHHHHH
Q 039275           31 VTMVVVLTASSGPGAWILAKELQIELDLSSYSLSSKTSRYAHSGRIRLAR-------DPVSCKAMISGYSQAGRFNEALE  103 (153)
Q Consensus        31 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~ll~~~~~~g~~~~a~-------~~~~~~~li~~~~~~g~~~~a~~  103 (153)
                      ..+.-.-..+.+.|++++|....          ...|..+-....+....       ....|+.+-..|.+.|++++|.+
T Consensus        16 ~~~~e~G~~~~~~~~~~~A~~~Y----------~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~   85 (168)
T d1kt1a1          16 AIVKEKGTVYFKGGKYVQAVIQY----------GKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVE   85 (168)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHH----------HHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHH----------HHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchh
Confidence            33444556778888888888771          11111111111100000       44667778888999999999999


Q ss_pred             HHHHHHHcCCCCChhhHHHHHHHhcCCCccccchh
Q 039275          104 PFGKLESLGVHTDEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus       104 ~~~~m~~~g~~p~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      .+++..... ..+...|...-.++...|++++|..
T Consensus        86 ~~~~al~l~-p~~~~a~~~~~~~~~~l~~~~~A~~  119 (168)
T d1kt1a1          86 CCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKG  119 (168)
T ss_dssp             HHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             hhhhhhhcc-cchHHHHHHHHHHHHHcCCHHHHHH
Confidence            999988653 3477888899999999999999998

>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=93.03  E-value=0.18  Score=30.18  Aligned_cols=58  Identities=17%  Similarity=0.129  Sum_probs=44.9

Q ss_pred             hHHHHHHHHHHHHhcCChHHHHHHHHHHHHc-----CCCCC-----hhhHHHHHHHhcCCCccccchh
Q 039275           81 DPVSCKAMISGYSQAGRFNEALEPFGKLESL-----GVHTD-----EVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        81 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-----g~~p~-----~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ...+|+.+-.+|...|++++|.+.+++..+.     ...|+     ...+..+-.++.+.|++++|.+
T Consensus        54 ~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~  121 (156)
T d2hr2a1          54 DAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMP  121 (156)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCccchhhHhhhhhhhcccccccccccccchhHHHHhhhHHHHHHHHHHHHHHH
Confidence            3478889999999999999999999887632     12222     2246667789999999999988

>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=92.26  E-value=0.38  Score=26.88  Aligned_cols=58  Identities=9%  Similarity=-0.040  Sum_probs=44.2

Q ss_pred             ChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH----hhhhhcchhhHHHHH
Q 039275           10 RFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL----QIELDLSSYSLSSKT   67 (153)
Q Consensus        10 ~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~----~~~~~~~~~~~~~ll   67 (153)
                      +.=++.+-++.+....+.|++.+....|.||-+.+++..|..+    +....++...|.-++
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~~~~k~~y~yil   82 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVI   82 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCcHHHHHHHH
Confidence            4446666677777888999999999999999999999999999    333444444565544

>d1peqa1 a.98.1.1 (A:13-174) R1 subunit of ribonucleotide reductase, N-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: R1 subunit of ribonucleotide reductase, N-terminal domain
superfamily: R1 subunit of ribonucleotide reductase, N-terminal domain
family: R1 subunit of ribonucleotide reductase, N-terminal domain
domain: R1 subunit of ribonucleotide reductase, N-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=91.95  E-value=0.23  Score=30.44  Aligned_cols=60  Identities=10%  Similarity=-0.123  Sum_probs=39.2

Q ss_pred             HHHHHHHHHhcCCccc--cchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHH
Q 039275           63 LSSKTSRYAHSGRIRL--ARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVV  122 (153)
Q Consensus        63 ~~~ll~~~~~~g~~~~--a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~  122 (153)
                      +..+.+.|+-..+-.+  .+++--.-.++..+...|+.+.|.++++.|....+.|-+.|+..
T Consensus        93 ~~~l~~~YllK~~d~~~~~E~pq~~~m~vAl~l~~~~~~~a~~~y~~~~~~~~~~aTPT~~N  154 (162)
T d1peqa1          93 AWKFYTSYTLKTFDGKRYLEHFEDRVTMVALTLAQGDETLATQLTDEMLSGRFQPATPTFLN  154 (162)
T ss_dssp             HHHHHHHTSCBCTTSSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSEEECHHHHHH
T ss_pred             HHHHHHHHhhccCCCCchhhCHHHHHHHHHHHHccCcHHHHHHHHHHHHhCCeeCCCcHhhh
Confidence            3445556655433211  11333333455556668999999999999998889998888765

>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=91.78  E-value=0.25  Score=26.95  Aligned_cols=49  Identities=10%  Similarity=-0.168  Sum_probs=38.9

Q ss_pred             hHhhcCChhHHHHHHHHhHHc-----CCCcc-HHHHHHHHHHhcCCCchHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESL-----GVHTD-EVTMVVVLTASSGPGAWILAKEL   52 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~-----g~~p~-~~~~~~ll~~~~~~~~~~~a~~~   52 (153)
                      .+.+.|++++|++.|++..+.     ...++ ..+++.+-.++.+.|++++|.+.
T Consensus        14 ~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~   68 (95)
T d1tjca_          14 VAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLL   68 (95)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHH
Confidence            567899999999999887543     11222 56788888999999999999998

>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=91.25  E-value=0.84  Score=32.63  Aligned_cols=53  Identities=8%  Similarity=-0.120  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           84 SCKAMISGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        84 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                      ++..+-..+...|++++|.+.|++-.+.  .| +...|+.+-..+...|+..+|..
T Consensus       154 ~~~~LG~l~~~~~~~~~A~~~y~~A~~l--~P~~~~~~~~Lg~~~~~~~~~~~A~~  207 (497)
T d1ya0a1         154 CLVHLGDIARYRNQTSQAESYYRHAAQL--VPSNGQPYNQLAILASSKGDHLTTIF  207 (497)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTBSHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCchHHHHHHHHHHHHcCCHHHHHH
Confidence            3444455556666666666666665543  34 33456666666666666665555

>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=90.71  E-value=1.5  Score=29.07  Aligned_cols=124  Identities=9%  Similarity=-0.182  Sum_probs=81.0

Q ss_pred             hhHHHHHHHHhHHcCCCccHHH-H---HHHHHHhcCCC-------chHHHHHH-h---hhhhcchhhHHHHHHHHHhcCC
Q 039275           11 FNEALEPFGKLESLGVHTDEVT-M---VVVLTASSGPG-------AWILAKEL-Q---IELDLSSYSLSSKTSRYAHSGR   75 (153)
Q Consensus        11 ~~~a~~~~~~m~~~g~~p~~~~-~---~~ll~~~~~~~-------~~~~a~~~-~---~~~~~~~~~~~~ll~~~~~~g~   75 (153)
                      .++|++++++..+.  .|+..+ |   ..++..+...+       .+++|..+ +   ...+.+...|..+...+...+.
T Consensus        45 ~~~al~~~~~~l~~--~P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~pk~~~~~~~~~~~~~~~~~  122 (334)
T d1dcea1          45 DESVLELTSQILGA--NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPE  122 (334)
T ss_dssp             SHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCSS
T ss_pred             cHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhCCCcHHHHHHhhHHHHHhcc
Confidence            48999999998763  465443 2   23344444443       45666666 1   2223355566667667767665


Q ss_pred             --ccccc------------hHHHHHHHH-HHHHhcCChHHHHHHHHHHHHcCCCC-ChhhHHHHHHHhcCCCccccchh
Q 039275           76 --IRLAR------------DPVSCKAMI-SGYSQAGRFNEALEPFGKLESLGVHT-DEVTMVVVLAASSGPGALDFGKS  138 (153)
Q Consensus        76 --~~~a~------------~~~~~~~li-~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~g~~~~a~~  138 (153)
                        .++|.            ....|...+ ..+...++.++|...++......  | +...|..+-..+.+.|++++|..
T Consensus       123 ~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~--p~~~~a~~~l~~~~~~~~~~~~A~~  199 (334)
T d1dcea1         123 PNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN--FSNYSSWHYRSCLLPQLHPQPDSGP  199 (334)
T ss_dssp             CCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT--CCCHHHHHHHHHHHHHHSCCCCSSS
T ss_pred             ccHHHHHHHHHHHHhhCchhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHhcCHHHHHH
Confidence              44554            344554444 56667899999999998887554  4 56678888888889999988877

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.30  E-value=0.59  Score=25.28  Aligned_cols=66  Identities=14%  Similarity=0.017  Sum_probs=42.3

Q ss_pred             HHHHHhcCCCchHHHHHH-hhhh--hcc-hhhHHHHHHHHHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHHH
Q 039275           35 VVLTASSGPGAWILAKEL-QIEL--DLS-SYSLSSKTSRYAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLES  110 (153)
Q Consensus        35 ~ll~~~~~~~~~~~a~~~-~~~~--~~~-~~~~~~ll~~~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  110 (153)
                      -+=..+.+.|++++|..+ +.-+  .|+ ......               ...+++.|-.++.+.|++++|.+.+++..+
T Consensus        10 ~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~---------------~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~   74 (95)
T d1tjca_          10 ELGKVAYTEADYYHTELWMEQALRQLDEGEISTID---------------KVSVLDYLSYAVYQQGDLDKALLLTKKLLE   74 (95)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSC---------------HHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCcc---------------HHHHHHHHhhHHHhcCChHHHHHHHHHHHH
Confidence            445566778888888877 1111  111 100000               246788888999999999999999999876


Q ss_pred             cCCCCCh
Q 039275          111 LGVHTDE  117 (153)
Q Consensus       111 ~g~~p~~  117 (153)
                      .  .|+.
T Consensus        75 l--~P~~   79 (95)
T d1tjca_          75 L--DPEH   79 (95)
T ss_dssp             H--CTTC
T ss_pred             h--CcCC
Confidence            4  4653

>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=87.67  E-value=0.039  Score=36.73  Aligned_cols=40  Identities=20%  Similarity=0.042  Sum_probs=25.2

Q ss_pred             cCCCchHHHHHH-hhhh--h-cchhhHHHHHHHHHhcCCccccc
Q 039275           41 SGPGAWILAKEL-QIEL--D-LSSYSLSSKTSRYAHSGRIRLAR   80 (153)
Q Consensus        41 ~~~~~~~~a~~~-~~~~--~-~~~~~~~~ll~~~~~~g~~~~a~   80 (153)
                      .+.|++++|.+. +.-+  . .|...+..+...|+..|++++|.
T Consensus         7 L~~G~l~eAl~~l~~al~~~P~d~~ar~~La~lL~~~G~~e~A~   50 (264)
T d1zbpa1           7 LSEGQLQQALELLIEAIKASPKDASLRSSFIELLCIDGDFERAD   50 (264)
T ss_dssp             TTTTCHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHH
Confidence            456888888888 2222  3 34456666666666666666666

>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=87.54  E-value=1  Score=26.39  Aligned_cols=111  Identities=9%  Similarity=-0.009  Sum_probs=60.2

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCc----------hHHHHHH-hhh--hhcc-hhhHHHHHHH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGA----------WILAKEL-QIE--LDLS-SYSLSSKTSR   69 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~----------~~~a~~~-~~~--~~~~-~~~~~~ll~~   69 (153)
                      .|-+.+.+++|++.|++..+.. |.++..+..+=.++...++          +++|.+. +.-  +.|+ ...|..+-..
T Consensus         6 ~~~r~~~fe~A~~~~e~al~~~-P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~P~~~~a~~~lG~~   84 (145)
T d1zu2a1           6 EFDRILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNA   84 (145)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHccHHHHHHHHHHHHhhC-CcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhcchhhHHHhhHHHH
Confidence            4667788999999999987753 4455566555555554433          3444444 222  2232 2233333333


Q ss_pred             HHhcCCccccchHHHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCChhhHHHHHHHhc
Q 039275           70 YAHSGRIRLARDPVSCKAMISGYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLAASS  128 (153)
Q Consensus        70 ~~~~g~~~~a~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~  128 (153)
                      |...|.+....  .         ...+++++|.+.|+...+  +.|+...+..-+..+-
T Consensus        85 y~~~g~~~~~~--~---------~~~~~~~~A~~~~~kal~--l~P~~~~~~~~L~~~~  130 (145)
T d1zu2a1          85 YTSFAFLTPDE--T---------EAKHNFDLATQFFQQAVD--EQPDNTHYLKSLEMTA  130 (145)
T ss_dssp             HHHHHHHCCCH--H---------HHHHHHHHHHHHHHHHHH--HCTTCHHHHHHHHHHH
T ss_pred             HHHcccchhhH--H---------HHHHhHHHhhhhhhcccc--cCCCHHHHHHHHHHHH
Confidence            33333222111  0         011245778888877764  4688777777666553

>d1u9pa1 a.43.1.1 (A:72-107) Arc repressor {Salmonella bacteriophage P22 [TaxId: 10754]}

class: All alpha proteins
fold: Ribbon-helix-helix
superfamily: Ribbon-helix-helix
family: Arc/Mnt-like phage repressors
domain: Arc repressor
species: Salmonella bacteriophage P22 [TaxId: 10754]

Probab=86.89  E-value=0.33  Score=20.81  Aligned_cols=33  Identities=21%  Similarity=0.229  Sum_probs=23.9

Q ss_pred             HHHHHHHHh-HHcCCCccHHHHHHHHHHhcCCCc
Q 039275           13 EALEPFGKL-ESLGVHTDEVTMVVVLTASSGPGA   45 (153)
Q Consensus        13 ~a~~~~~~m-~~~g~~p~~~~~~~ll~~~~~~~~   45 (153)
                      +.+++.++. ..+|...|...|..++.++-+.|+
T Consensus         2 evldlvrkvaeeng~s~ns~iy~~vmes~kkegr   35 (36)
T d1u9pa1           2 EVLDLVRKVAEENGRSVNSEIYQRVMESFKKEGR   35 (36)
T ss_dssp             HHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTC
T ss_pred             cHHHHHHHHHHHcCcchhHHHHHHHHHHHHHccC
Confidence            345555555 567888888889888888877765

>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=85.02  E-value=4.9  Score=28.44  Aligned_cols=102  Identities=6%  Similarity=-0.132  Sum_probs=67.7

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHHHHHH-hhhh---hcchhhHHHHHHHHHhcCCcccc
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWILAKEL-QIEL---DLSSYSLSSKTSRYAHSGRIRLA   79 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~a~~~-~~~~---~~~~~~~~~ll~~~~~~g~~~~a   79 (153)
                      .+...|++++|...|++..+. .+-+...|+.+=..+...|+..+|... .+.+   +|....+..|...|.+.....++
T Consensus       161 l~~~~~~~~~A~~~y~~A~~l-~P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~~~~~~a~~nL~~~~~~~~~~~~~  239 (497)
T d1ya0a1         161 IARYRNQTSQAESYYRHAAQL-VPSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVKFPFPAASTNLQKALSKALESRDE  239 (497)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH-CTTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSSBCCHHHHHHHHHHHHHHTTSCCC
T ss_pred             HHHHcccHHHHHHHHHHHHHH-CCCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhhhhh
Confidence            456778899999999888764 233457888888888888998888877 2222   45667788888888777665544


Q ss_pred             c--------hHHHHHHHHHHHHhcCChHHHHHHHH
Q 039275           80 R--------DPVSCKAMISGYSQAGRFNEALEPFG  106 (153)
Q Consensus        80 ~--------~~~~~~~li~~~~~~g~~~~a~~~~~  106 (153)
                      .        -...+-.+...+.....++...++.+
T Consensus       240 ~~~~~~~~~~~~~f~~~~~~l~~~~~~~~~~~~~~  274 (497)
T d1ya0a1         240 VKTKWGVSDFIKAFIKFHGHVYLSKSLEKLSPLRE  274 (497)
T ss_dssp             CCSSCCHHHHHHHHHHHHHHHHHTCCGGGHHHHHH
T ss_pred             hccccccchHHHHHHHHHHHHHhCCchhhHHHHHH
Confidence            4        23344445555556666555444433

>d1sxjd1 a.80.1.1 (D:263-353) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: post-AAA+ oligomerization domain-like
superfamily: post-AAA+ oligomerization domain-like
family: DNA polymerase III clamp loader subunits, C-terminal domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=81.92  E-value=2.4  Score=22.69  Aligned_cols=44  Identities=9%  Similarity=0.024  Sum_probs=30.4

Q ss_pred             hHhhcCChhHHHHHHHHhHHcCCCccHHHHHHHHHHhcCCCchHH
Q 039275            4 GYSQAGRFNEALEPFGKLESLGVHTDEVTMVVVLTASSGPGAWIL   48 (153)
Q Consensus         4 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~   48 (153)
                      ..+.+|++++|.+..+.+...|+.+. ...+.+.........+++
T Consensus        11 ~~~~~~~f~~a~~~i~~l~~~Gys~~-dIl~~l~~~vv~~~~i~~   54 (91)
T d1sxjd1          11 EKVKSGDFDEIKKYVNTFMKSGWSAA-SVVNQLHEYYITNDNFDT   54 (91)
T ss_dssp             HHHHSCCHHHHHHHHHHHHHTSCCCT-THHHHHHHHHHHCSSSCH
T ss_pred             HHHHcCCHHHHHHHHHHHHHcCCCHH-HHHHHHHHHHHhcCCCCH
Confidence            35678999999999999999998776 444555544333333333