Citrus Sinensis ID: 044084

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340---
Protein Sequence
TNSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccEEEHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccccHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccccHHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHcccccHHHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHccccccc
Coil and Loop (DISEMBL)
TNSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECEsrkldltpsstHMYKILCDSLGKSGRAFEILKFFRDMKekgiledpsVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISqgcipgqvTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKmkpkgcepnvwIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRmnggvidrAMAGIMVGVFSKLSQIEEL
Flexible Loop (DISEMBL)
TNSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKldltpssthMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSklsqieel
Low Complexity Region (SEG)
TNSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL
Disordered region (IsUnstruct)
*******HYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSK*******
Disordered Region (DISOPRED)
TNSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL
Disordered Region (DISEMBL)
TNSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL
Disordered Region (DISPRO)
TNSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQ****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
TNSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL
Positional Conservation
no confident homologs detected

---

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	343	2.2.26 [Sep-21-2011]
Q66GP4	609	Pentatricopeptide repeat-	yes	no	0.988	0.556	0.551	1e-106
Q8S8P6	624	Pentatricopeptide repeat-	no	no	0.921	0.506	0.267	3e-26
Q8L844	709	Pentatricopeptide repeat-	no	no	0.798	0.386	0.25	3e-24
Q9SIC9	918	Pentatricopeptide repeat-	no	no	0.816	0.305	0.259	5e-24
Q9M9X9	987	Pentatricopeptide repeat-	no	no	0.766	0.266	0.257	3e-23
Q9LSL9	915	Pentatricopeptide repeat-	no	no	0.655	0.245	0.287	7e-22
Q76C99	791	Protein Rf1, mitochondria	N/A	no	0.766	0.332	0.248	8e-21
Q9FLL3	527	Pentatricopeptide repeat-	no	no	0.600	0.390	0.263	1e-20
Q9LYZ9	819	Pentatricopeptide repeat-	no	no	0.810	0.339	0.252	1e-20
Q9SXD1	630	Pentatricopeptide repeat-	no	no	0.813	0.442	0.256	4e-20

>sp|Q66GP4|PP379_ARATH Pentatricopeptide repeat-containing protein At5g13770, chloroplastic OS=Arabidopsis thaliana GN=At5g13770 PE=2 SV=1

 Score =  385 bits (989), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 197/357 (55%), Positives = 257/357 (71%), Gaps = 18/357 (5%)

Query: 5   SKLHYYEKMK-SAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLD-LTPSSTHM 62
           S +  ++++K S G+    GCYC+IMEA  KIG++ KV  LF E +S++L  L   S  +
Sbjct: 191 STIQVFDRLKQSVGVEPSPGCYCRIMEAHEKIGENHKVVELFQEFKSQRLSFLAKESGSI 250

Query: 63  YKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAE 122
           Y I+C SL KSGRAFE L+   +MK+KGI E   +Y+ LI +FA   EV + E+LFKEA 
Sbjct: 251 YTIVCSSLAKSGRAFEALEVLEEMKDKGIPESSELYSMLIRAFAEAREVVITEKLFKEAG 310

Query: 123 EKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYW 182
            K +L+D E+ LK+VLMY+ EG +E TLEVV +M+ AEL ++DCI C IVNGFSK+R + 
Sbjct: 311 GKKLLKDPEMCLKVVLMYVREGNMETTLEVVAAMRKAELKVTDCILCAIVNGFSKQRGFA 370

Query: 183 AAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMV 242
            AVKVYE  + + C  GQVTYA  INAYCR+  Y+KAE +F EM +KGFDKCVVAYS+++
Sbjct: 371 EAVKVYEWAMKEECEAGQVTYAIAINAYCRLEKYNKAEMLFDEMVKKGFDKCVVAYSNIM 430

Query: 243 AMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK----------- 291
            MYGKT R+ DA+RL+AKMK +GC+PN+WIYNSL+DMHGRA +LR+ EK           
Sbjct: 431 DMYGKTRRLSDAVRLMAKMKQRGCKPNIWIYNSLIDMHGRAMDLRRAEKIWKEMKRAKVL 490

Query: 292 -----YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL 343
                YT++ISAYN ++E + CV+ Y EFRMN G IDRAMAGIMVGVFSK S+I+EL
Sbjct: 491 PDKVSYTSMISAYNRSKELERCVELYQEFRMNRGKIDRAMAGIMVGVFSKTSRIDEL 547

Arabidopsis thaliana (taxid: 3702)

>sp|Q8S8P6|PP180_ARATH Pentatricopeptide repeat-containing protein At2g32630 OS=Arabidopsis thaliana GN=At2g32630 PE=3 SV=1

 Score =  119 bits (298), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 90/337 (26%), Positives = 155/337 (45%), Gaps = 21/337 (6%)

Query: 13  MKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGK 72
           MK  G+V +   Y  +ME   K G       LF E   R ++   S  H+Y  L     +
Sbjct: 285 MKKDGVVYNKVTYTLLMELSVKNGKMSDAEKLFDEMRERGIE---SDVHVYTSLISWNCR 341

Query: 73  SGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEV 132
            G        F ++ EKG+      Y +LI     + E+  AE L  E + KG+     V
Sbjct: 342 KGNMKRAFLLFDELTEKGLSPSSYTYGALIDGVCKVGEMGAAEILMNEMQSKGVNITQVV 401

Query: 133 FLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISC-VIVNGFSKRRAYWAAVKVYEQL 191
           F  L+  Y  +GMV++   + + M+      +D  +C  I + F++ + Y  A +   ++
Sbjct: 402 FNTLIDGYCRKGMVDEASMIYDVMEQKGFQ-ADVFTCNTIASCFNRLKRYDEAKQWLFRM 460

Query: 192 ISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRI 251
           +  G     V+Y ++I+ YC+ G   +A+++F+EM  KG     + Y+ M+  Y K G+I
Sbjct: 461 MEGGVKLSTVSYTNLIDVYCKEGNVEEAKRLFVEMSSKGVQPNAITYNVMIYAYCKQGKI 520

Query: 252 RDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKN------------LRQLEK----YTTV 295
           ++A +L A M+  G +P+ + Y SL+     A N            L+ L++    YT +
Sbjct: 521 KEARKLRANMEANGMDPDSYTYTSLIHGECIADNVDEAMRLFSEMGLKGLDQNSVTYTVM 580

Query: 296 ISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVG 332
           IS  + A + D     Y+E +  G  ID  +   ++G
Sbjct: 581 ISGLSKAGKSDEAFGLYDEMKRKGYTIDNKVYTALIG 617

Arabidopsis thaliana (taxid: 3702)

>sp|Q8L844|PP413_ARATH Pentatricopeptide repeat-containing protein At5g42310, mitochondrial OS=Arabidopsis thaliana GN=At5g42310 PE=2 SV=1

 Score =  112 bits (281), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 78/312 (25%), Positives = 150/312 (48%), Gaps = 38/312 (12%)

Query: 7   LHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKIL 66
           L  Y++++   + LD      I+  F K GD  K  AL L   ++   L+  +  +  I+
Sbjct: 254 LRLYKEIERDKLELDVQLVNDIIMGFAKSGDPSK--ALQLLGMAQATGLSAKTATLVSII 311

Query: 67  CDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGM 126
             +L  SGR  E    F ++++ GI      Y +L+  +     +K AE +  E E++G+
Sbjct: 312 S-ALADSGRTLEAEALFEELRQSGIKPRTRAYNALLKGYVKTGPLKDAESMVSEMEKRGV 370

Query: 127 --------------------------LRDLE---------VFLKLVLMYIEEGMVEKTLE 151
                                     L+++E         VF +L+  + + G  +KT +
Sbjct: 371 SPDEHTYSLLIDAYVNAGRWESARIVLKEMEAGDVQPNSFVFSRLLAGFRDRGEWQKTFQ 430

Query: 152 VVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYC 211
           V++ MK+  +        V+++ F K      A+  +++++S+G  P +VT+ ++I+ +C
Sbjct: 431 VLKEMKSIGVKPDRQFYNVVIDTFGKFNCLDHAMTTFDRMLSEGIEPDRVTWNTLIDCHC 490

Query: 212 RIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVW 271
           + G +  AE++F  M+++G   C   Y+ M+  YG   R  D  RL+ KMK +G  PNV 
Sbjct: 491 KHGRHIVAEEMFEAMERRGCLPCATTYNIMINSYGDQERWDDMKRLLGKMKSQGILPNVV 550

Query: 272 IYNSLMDMHGRA 283
            + +L+D++G++
Sbjct: 551 THTTLVDVYGKS 562

Arabidopsis thaliana (taxid: 3702)

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

 Score =  112 bits (279), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 75/289 (25%), Positives = 141/289 (48%), Gaps = 9/289 (3%)

Query: 9   YYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCD 68
           ++++M+  G+  D   +  ++    + G  E    LF E  +R+++        Y  L D
Sbjct: 326 FFDEMQRNGVQPDRITFNSLLAVCSRGGLWEAARNLFDEMTNRRIE---QDVFSYNTLLD 382

Query: 69  SLGKSGR---AFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKG 125
           ++ K G+   AFEIL     M  K I+ +   Y+++I  FA       A  LF E    G
Sbjct: 383 AICKGGQMDLAFEILA---QMPVKRIMPNVVSYSTVIDGFAKAGRFDEALNLFGEMRYLG 439

Query: 126 MLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAV 185
           +  D   +  L+ +Y + G  E+ L+++  M +  +         ++ G+ K+  Y    
Sbjct: 440 IALDRVSYNTLLSIYTKVGRSEEALDILREMASVGIKKDVVTYNALLGGYGKQGKYDEVK 499

Query: 186 KVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMY 245
           KV+ ++  +  +P  +TY+++I+ Y + GLY +A ++F E +  G    VV YS+++   
Sbjct: 500 KVFTEMKREHVLPNLLTYSTLIDGYSKGGLYKEAMEIFREFKSAGLRADVVLYSALIDAL 559

Query: 246 GKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTT 294
            K G +  A+ L+ +M  +G  PNV  YNS++D  GR+  + +   Y+ 
Sbjct: 560 CKNGLVGSAVSLIDEMTKEGISPNVVTYNSIIDAFGRSATMDRSADYSN 608

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M9X9|PPR18_ARATH Pentatricopeptide repeat-containing protein At1g06710, mitochondrial OS=Arabidopsis thaliana GN=At1g06710 PE=2 SV=1

 Score =  109 bits (272), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 73/284 (25%), Positives = 136/284 (47%), Gaps = 21/284 (7%)

Query: 12  KMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLG 71
           +M   G + D+  Y +++     + ++ K+   FL  E  K     +  + Y I+ DS  
Sbjct: 473 EMIGQGFIPDTSTYSKVLNY---LCNASKMELAFLLFEEMKRGGLVADVYTYTIMVDSFC 529

Query: 72  KSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLE 131
           K+G   +  K+F +M+E G   +   Y +LI ++    +V  A ELF+    +G L ++ 
Sbjct: 530 KAGLIEQARKWFNEMREVGCTPNVVTYTALIHAYLKAKKVSYANELFETMLSEGCLPNIV 589

Query: 132 VFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDC-----------------ISCVIVNG 174
            +  L+  + + G VEK  ++ E M  ++ ++ D                      +++G
Sbjct: 590 TYSALIDGHCKAGQVEKACQIFERMCGSK-DVPDVDMYFKQYDDNSERPNVVTYGALLDG 648

Query: 175 FSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKC 234
           F K      A K+ + +  +GC P Q+ Y ++I+  C++G   +A++V  EM + GF   
Sbjct: 649 FCKSHRVEEARKLLDAMSMEGCEPNQIVYDALIDGLCKVGKLDEAQEVKTEMSEHGFPAT 708

Query: 235 VVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMD 278
           +  YSS++  Y K  R   A ++++KM    C PNV IY  ++D
Sbjct: 709 LYTYSSLIDRYFKVKRQDLASKVLSKMLENSCAPNVVIYTEMID 752

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LSL9|PP445_ARATH Pentatricopeptide repeat-containing protein At5g65560 OS=Arabidopsis thaliana GN=At5g65560 PE=2 SV=1

 Score =  105 bits (261), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 65/226 (28%), Positives = 117/226 (51%), Gaps = 1/226 (0%)

Query: 58  SSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEEL 117
            +   Y +L  SL  S R  E L   ++M+E GI  +   Y  LI S  S  + + A EL
Sbjct: 321 PTVRTYTVLIKSLCGSERKSEALNLVKEMEETGIKPNIHTYTVLIDSLCSQCKFEKAREL 380

Query: 118 FKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSK 177
             +  EKG++ ++  +  L+  Y + GM+E  ++VVE M++ +L+ +      ++ G+ K
Sbjct: 381 LGQMLEKGLMPNVITYNALINGYCKRGMIEDAVDVVELMESRKLSPNTRTYNELIKGYCK 440

Query: 178 RRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVA 237
              +  A+ V  +++ +  +P  VTY S+I+  CR G +  A ++   M  +G       
Sbjct: 441 SNVH-KAMGVLNKMLERKVLPDVVTYNSLIDGQCRSGNFDSAYRLLSLMNDRGLVPDQWT 499

Query: 238 YSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRA 283
           Y+SM+    K+ R+ +A  L   ++ KG  PNV +Y +L+D + +A
Sbjct: 500 YTSMIDSLCKSKRVEEACDLFDSLEQKGVNPNVVMYTALIDGYCKA 545

Arabidopsis thaliana (taxid: 3702)

>sp|Q76C99|RF1_ORYSI Protein Rf1, mitochondrial OS=Oryza sativa subsp. indica GN=Rf1 PE=2 SV=1

 Score =  101 bits (251), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 66/266 (24%), Positives = 123/266 (46%), Gaps = 3/266 (1%)

Query: 13  MKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGK 72
           M   G++ D   Y  I+  +   G  ++      +  S   D        Y +L D L K
Sbjct: 257 MVKNGVMPDCMTYNSILHGYCSSGQPKEAIGFLKKMRS---DGVEPDVVTYSLLMDYLCK 313

Query: 73  SGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEV 132
           +GR  E  K F  M ++G+  + + Y +L+  +A+   +     L       G+  D  V
Sbjct: 314 NGRCMEARKIFDSMTKRGLKPEITTYGTLLQGYATKGALVEMHGLLDLMVRNGIHPDHYV 373

Query: 133 FLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLI 192
           F  L+  Y ++G V++ + V   M+   LN +      ++    K      A+  +EQ+I
Sbjct: 374 FSILICAYAKQGKVDQAMLVFSKMRQQGLNPNAVTYGAVIGILCKSGRVEDAMLYFEQMI 433

Query: 193 SQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIR 252
            +G  PG + Y S+I+  C    + +AE++ +EM  +G     + ++S++  + K GR+ 
Sbjct: 434 DEGLSPGNIVYNSLIHGLCTCNKWERAEELILEMLDRGICLNTIFFNSIIDSHCKEGRVI 493

Query: 253 DAMRLVAKMKPKGCEPNVWIYNSLMD 278
           ++ +L   M   G +PNV  YN+L++
Sbjct: 494 ESEKLFELMVRIGVKPNVITYNTLIN 519

Reduces the expression of the cytoplasmic male sterility (CMS)-associated mitochondrial gene ORF79, encoding a cytotoxic peptide. Can restore male fertility by blocking ORF79 production via endonucleolytic cleavage of dicistronic ATP6/ORF79 mRNA. Promotes the editing of ATP6 mRNAs independently of its cleavage function.

Oryza sativa subsp. indica (taxid: 39946)

>sp|Q9FLL3|PP412_ARATH Pentatricopeptide repeat-containing protein At5g41170, mitochondrial OS=Arabidopsis thaliana GN=At5g41170 PE=2 SV=1

 Score =  101 bits (251), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 57/216 (26%), Positives = 102/216 (47%)

Query: 62  MYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEA 121
           MY  + DSL K+G     L  F  M+  GI  D  +Y SL+    +    + A+ L +  
Sbjct: 179 MYTTIIDSLCKNGHVNYALSLFDQMENYGIRPDVVMYTSLVNGLCNSGRWRDADSLLRGM 238

Query: 122 EEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAY 181
            ++ +  D+  F  L+  +++EG      E+   M    +  +      ++NGF      
Sbjct: 239 TKRKIKPDVITFNALIDAFVKEGKFLDAEELYNEMIRMSIAPNIFTYTSLINGFCMEGCV 298

Query: 182 WAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSM 241
             A +++  + ++GC P  V Y S+IN +C+      A K+F EM QKG     + Y+++
Sbjct: 299 DEARQMFYLMETKGCFPDVVAYTSLINGFCKCKKVDDAMKIFYEMSQKGLTGNTITYTTL 358

Query: 242 VAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLM 277
           +  +G+ G+   A  + + M  +G  PN+  YN L+
Sbjct: 359 IQGFGQVGKPNVAQEVFSHMVSRGVPPNIRTYNVLL 394

Arabidopsis thaliana (taxid: 3702)

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

 Score =  100 bits (250), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 71/281 (25%), Positives = 128/281 (45%), Gaps = 3/281 (1%)

Query: 11  EKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSL 70
           EKMKS GI  D+  Y  ++    +    ++ A +F E ++        +   Y  L D  
Sbjct: 268 EKMKSDGIAPDAYTYNTLITCCKRGSLHQEAAQVFEEMKAAGFSYDKVT---YNALLDVY 324

Query: 71  GKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDL 130
           GKS R  E +K   +M   G       Y SLI ++A    +  A EL  +  EKG   D+
Sbjct: 325 GKSHRPKEAMKVLNEMVLNGFSPSIVTYNSLISAYARDGMLDEAMELKNQMAEKGTKPDV 384

Query: 131 EVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQ 190
             +  L+  +   G VE  + + E M+NA    + C     +  +  R  +   +K++++
Sbjct: 385 FTYTTLLSGFERAGKVESAMSIFEEMRNAGCKPNICTFNAFIKMYGNRGKFTEMMKIFDE 444

Query: 191 LISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGR 250
           +   G  P  VT+ +++  + + G+ S+   VF EM++ GF      ++++++ Y + G 
Sbjct: 445 INVCGLSPDIVTWNTLLAVFGQNGMDSEVSGVFKEMKRAGFVPERETFNTLISAYSRCGS 504

Query: 251 IRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK 291
              AM +  +M   G  P++  YN+++    R     Q EK
Sbjct: 505 FEQAMTVYRRMLDAGVTPDLSTYNTVLAALARGGMWEQSEK 545

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SXD1|PPR91_ARATH Pentatricopeptide repeat-containing protein At1g62670, mitochondrial OS=Arabidopsis thaliana GN=At1g62670 PE=2 SV=2

 Score = 99.4 bits (246), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 73/285 (25%), Positives = 131/285 (45%), Gaps = 6/285 (2%)

Query: 11  EKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSL 70
           ++M + G   D   Y  ++    K GD++    L  + E  KL+       +Y  + D L
Sbjct: 210 DRMVAKGCQPDLVTYGVVVNGLCKRGDTDLAFNLLNKMEQGKLE---PGVLIYNTIIDGL 266

Query: 71  GKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDL 130
            K     + L  F++M+ KGI  +   Y+SLI    +      A  L  +  E+ +  D+
Sbjct: 267 CKYKHMDDALNLFKEMETKGIRPNVVTYSSLISCLCNYGRWSDASRLLSDMIERKINPDV 326

Query: 131 EVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQ 190
             F  L+  +++EG + +  ++ + M    ++ S      ++NGF        A +++E 
Sbjct: 327 FTFSALIDAFVKEGKLVEAEKLYDEMVKRSIDPSIVTYSSLINGFCMHDRLDEAKQMFEF 386

Query: 191 LISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGR 250
           ++S+ C P  VTY ++I  +C+     +  +VF EM Q+G     V Y+ ++    + G 
Sbjct: 387 MVSKHCFPDVVTYNTLIKGFCKYKRVEEGMEVFREMSQRGLVGNTVTYNILIQGLFQAGD 446

Query: 251 IRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTV 295
              A  +  +M   G  PN+  YN+L+D  G  KN  +LEK   V
Sbjct: 447 CDMAQEIFKEMVSDGVPPNIMTYNTLLD--GLCKN-GKLEKAMVV 488

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	343
297738294	552	unnamed protein product [Vitis vinifera]	0.988	0.614	0.676	1e-137
225425981	603	PREDICTED: pentatricopeptide repeat-cont	0.988	0.562	0.676	1e-137
297736068	568	unnamed protein product [Vitis vinifera]	0.988	0.596	0.664	1e-136
359484961	609	PREDICTED: pentatricopeptide repeat-cont	0.988	0.556	0.664	1e-135
224108157	525	predicted protein [Populus trichocarpa]	0.988	0.645	0.675	1e-135
224101979	404	predicted protein [Populus trichocarpa]	0.988	0.839	0.652	1e-132
449530158	608	PREDICTED: pentatricopeptide repeat-cont	0.991	0.559	0.617	1e-128
449466949	608	PREDICTED: pentatricopeptide repeat-cont	0.991	0.559	0.615	1e-127
356575210	609	PREDICTED: pentatricopeptide repeat-cont	0.991	0.558	0.598	1e-118
356521196	601	PREDICTED: pentatricopeptide repeat-cont	0.991	0.565	0.590	1e-118

>gi|297738294|emb|CBI27495.3| unnamed protein product [Vitis vinifera]

 Score =  495 bits (1274), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 240/355 (67%), Positives = 292/355 (82%), Gaps = 16/355 (4%)

Query: 5   SKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYK 64
           S +  Y++MKSAG+V +S  Y +IMEA+ KI D EKV  LF E ESRK+D +P ST +Y+
Sbjct: 142 STIAVYDRMKSAGVVPNSESYYRIMEAYIKIRDYEKVVTLFQEFESRKIDSSPFSTQIYR 201

Query: 65  ILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEK 124
           ILC+SLGK GRAFE L+FFRDM +KGILED +VY+SLICSFASI EVKVAEELF+EAEEK
Sbjct: 202 ILCESLGKMGRAFEALEFFRDMTKKGILEDSAVYSSLICSFASIREVKVAEELFREAEEK 261

Query: 125 GMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAA 184
            +LRD EVFLKLVLMY+EEG++E+TLE+V++MKN E+ +SDCI C IVNGF+K+R   AA
Sbjct: 262 KILRDPEVFLKLVLMYVEEGLMERTLEIVKAMKNVEIRVSDCIFCAIVNGFAKKRGLRAA 321

Query: 185 VKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAM 244
            KVY++LI QGC PGQVTYASIIN YCR+ LYSKAE VF EM++KGF+KCVVAYSSMV M
Sbjct: 322 AKVYDELILQGCEPGQVTYASIINVYCRMELYSKAEMVFSEMEKKGFNKCVVAYSSMVVM 381

Query: 245 YGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK------------- 291
           YGKTGR+R+AMRLVAKMK +GCEPNVW+YNSLMDMHGR KNLRQ+EK             
Sbjct: 382 YGKTGRLREAMRLVAKMKERGCEPNVWVYNSLMDMHGRVKNLRQVEKLWKEMKRKKVVPD 441

Query: 292 ---YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL 343
              YT+VISAY+ A +F+ C++FY+EFRMNGGVIDR +AGIMVG+FSK  +++EL
Sbjct: 442 RVSYTSVISAYSKAGDFETCMRFYHEFRMNGGVIDRVIAGIMVGIFSKSGRVDEL 496

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225425981|ref|XP_002269531.1| PREDICTED: pentatricopeptide repeat-containing protein At5g13770, chloroplastic-like [Vitis vinifera]

 Score =  494 bits (1272), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 240/355 (67%), Positives = 292/355 (82%), Gaps = 16/355 (4%)

Query: 5   SKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYK 64
           S +  Y++MKSAG+V +S  Y +IMEA+ KI D EKV  LF E ESRK+D +P ST +Y+
Sbjct: 204 STIAVYDRMKSAGVVPNSESYYRIMEAYIKIRDYEKVVTLFQEFESRKIDSSPFSTQIYR 263

Query: 65  ILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEK 124
           ILC+SLGK GRAFE L+FFRDM +KGILED +VY+SLICSFASI EVKVAEELF+EAEEK
Sbjct: 264 ILCESLGKMGRAFEALEFFRDMTKKGILEDSAVYSSLICSFASIREVKVAEELFREAEEK 323

Query: 125 GMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAA 184
            +LRD EVFLKLVLMY+EEG++E+TLE+V++MKN E+ +SDCI C IVNGF+K+R   AA
Sbjct: 324 KILRDPEVFLKLVLMYVEEGLMERTLEIVKAMKNVEIRVSDCIFCAIVNGFAKKRGLRAA 383

Query: 185 VKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAM 244
            KVY++LI QGC PGQVTYASIIN YCR+ LYSKAE VF EM++KGF+KCVVAYSSMV M
Sbjct: 384 AKVYDELILQGCEPGQVTYASIINVYCRMELYSKAEMVFSEMEKKGFNKCVVAYSSMVVM 443

Query: 245 YGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK------------- 291
           YGKTGR+R+AMRLVAKMK +GCEPNVW+YNSLMDMHGR KNLRQ+EK             
Sbjct: 444 YGKTGRLREAMRLVAKMKERGCEPNVWVYNSLMDMHGRVKNLRQVEKLWKEMKRKKVVPD 503

Query: 292 ---YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL 343
              YT+VISAY+ A +F+ C++FY+EFRMNGGVIDR +AGIMVG+FSK  +++EL
Sbjct: 504 RVSYTSVISAYSKAGDFETCMRFYHEFRMNGGVIDRVIAGIMVGIFSKSGRVDEL 558

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297736068|emb|CBI24106.3| unnamed protein product [Vitis vinifera]

 Score =  490 bits (1261), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 236/355 (66%), Positives = 292/355 (82%), Gaps = 16/355 (4%)

Query: 5   SKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYK 64
           S +  Y++MKSAG+V +S  Y +IMEA+ KI D EKV  LF E ESRK+D +P ST +Y+
Sbjct: 128 STIAVYDRMKSAGVVPNSESYYRIMEAYIKIRDYEKVVTLFQEFESRKIDSSPFSTQIYR 187

Query: 65  ILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEK 124
           ILC+SLGK GRAFE L+FFRDM +KGILED +VY+SLICSFASI EVKVAEELF+EAEEK
Sbjct: 188 ILCESLGKMGRAFEALEFFRDMTKKGILEDSAVYSSLICSFASIREVKVAEELFREAEEK 247

Query: 125 GMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAA 184
            +LRD EVFLKLVLMY+EEG++E+T+E+V++MKN ++ +SDCI C IVNGF+K+R   AA
Sbjct: 248 KILRDPEVFLKLVLMYVEEGLMERTIEIVKAMKNVKIRVSDCIFCAIVNGFAKKRGLRAA 307

Query: 185 VKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAM 244
            KVY++LI QGC PGQVTYASIIN YCR+ LYSKAE +F EM++KGF+KCVVAYSSMV M
Sbjct: 308 AKVYDELILQGCEPGQVTYASIINVYCRMELYSKAEMMFSEMEKKGFNKCVVAYSSMVVM 367

Query: 245 YGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK------------- 291
           YGKTGR+R+AMRLVAKMK +GC+PNVW+YNSLMDMHGR KNLRQ+EK             
Sbjct: 368 YGKTGRLREAMRLVAKMKERGCKPNVWVYNSLMDMHGRVKNLRQVEKLWKEMKRKKVVPD 427

Query: 292 ---YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL 343
              YT+VISAY+ A +F+ C++FY+EFRMNGGVIDR +AGIMVG+FSK  +++EL
Sbjct: 428 RVSYTSVISAYSKAGDFETCMRFYHEFRMNGGVIDRVIAGIMVGIFSKSGRVDEL 482

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359484961|ref|XP_002273494.2| PREDICTED: pentatricopeptide repeat-containing protein At5g13770, chloroplastic-like [Vitis vinifera]

 Score =  488 bits (1255), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 236/355 (66%), Positives = 292/355 (82%), Gaps = 16/355 (4%)

Query: 5   SKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYK 64
           S +  Y++MKSAG+V +S  Y +IMEA+ KI D EKV  LF E ESRK+D +P ST +Y+
Sbjct: 205 STIAVYDRMKSAGVVPNSESYYRIMEAYIKIRDYEKVVTLFQEFESRKIDSSPFSTQIYR 264

Query: 65  ILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEK 124
           ILC+SLGK GRAFE L+FFRDM +KGILED +VY+SLICSFASI EVKVAEELF+EAEEK
Sbjct: 265 ILCESLGKMGRAFEALEFFRDMTKKGILEDSAVYSSLICSFASIREVKVAEELFREAEEK 324

Query: 125 GMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAA 184
            +LRD EVFLKLVLMY+EEG++E+T+E+V++MKN ++ +SDCI C IVNGF+K+R   AA
Sbjct: 325 KILRDPEVFLKLVLMYVEEGLMERTIEIVKAMKNVKIRVSDCIFCAIVNGFAKKRGLRAA 384

Query: 185 VKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAM 244
            KVY++LI QGC PGQVTYASIIN YCR+ LYSKAE +F EM++KGF+KCVVAYSSMV M
Sbjct: 385 AKVYDELILQGCEPGQVTYASIINVYCRMELYSKAEMMFSEMEKKGFNKCVVAYSSMVVM 444

Query: 245 YGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK------------- 291
           YGKTGR+R+AMRLVAKMK +GC+PNVW+YNSLMDMHGR KNLRQ+EK             
Sbjct: 445 YGKTGRLREAMRLVAKMKERGCKPNVWVYNSLMDMHGRVKNLRQVEKLWKEMKRKKVVPD 504

Query: 292 ---YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL 343
              YT+VISAY+ A +F+ C++FY+EFRMNGGVIDR +AGIMVG+FSK  +++EL
Sbjct: 505 RVSYTSVISAYSKAGDFETCMRFYHEFRMNGGVIDRVIAGIMVGIFSKSGRVDEL 559

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224108157|ref|XP_002314741.1| predicted protein [Populus trichocarpa] gi|222863781|gb|EEF00912.1| predicted protein [Populus trichocarpa]

 Score =  486 bits (1252), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 246/364 (67%), Positives = 294/364 (80%), Gaps = 25/364 (6%)

Query: 5   SKLHYY-------EKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTP 57
           +KLH Y       EKM  AGI LDS CYCQIM+A+YK+GD+EKV ALF E ESRKLD  P
Sbjct: 118 NKLHMYGSTISVHEKMILAGIPLDSRCYCQIMKAYYKLGDAEKVVALFNEFESRKLDSKP 177

Query: 58  S-STHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEE 116
                ++KILC SLG+SG+AF+ L++ RDM++KGILED S+Y+SLICSFA+I EV+VAEE
Sbjct: 178 MILRQIFKILCLSLGRSGQAFQALEYSRDMRKKGILEDSSIYSSLICSFANIREVEVAEE 237

Query: 117 LFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMK-NAELNISDCISCVIVNGF 175
           LFKEA EK MLRD E+ L+LVLMYIEEG +EKT+E+V+ MK  A L +SDCI C IVNGF
Sbjct: 238 LFKEALEKRMLRDPEIVLRLVLMYIEEGQMEKTIEIVKVMKGTANLKVSDCIFCAIVNGF 297

Query: 176 SKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCV 235
           SKRR + AAVKVYE+L   GC PGQVTYAS+INAYCR GLYSKAE VF EM++KGFDKCV
Sbjct: 298 SKRRGFSAAVKVYEELKYDGCDPGQVTYASVINAYCRAGLYSKAEMVFSEMEEKGFDKCV 357

Query: 236 VAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK---- 291
           VAYSSM++MYGKTGR RDA RLVAKMK KGCEPNVWIYNSL+DMHGRAKNLRQ+EK    
Sbjct: 358 VAYSSMISMYGKTGRARDATRLVAKMKLKGCEPNVWIYNSLLDMHGRAKNLRQVEKLWKE 417

Query: 292 ------------YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQ 339
                       Y++VISAYN ++E++MCV++Y+E+R+NGGVID AMAGIM GVFSK+S+
Sbjct: 418 MKRRKVAPDKVTYSSVISAYNKSKEYEMCVRYYHEYRINGGVIDGAMAGIMAGVFSKISR 477

Query: 340 IEEL 343
           I+EL
Sbjct: 478 IDEL 481

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224101979|ref|XP_002312498.1| predicted protein [Populus trichocarpa] gi|222852318|gb|EEE89865.1| predicted protein [Populus trichocarpa]

 Score =  476 bits (1225), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 233/357 (65%), Positives = 293/357 (82%), Gaps = 18/357 (5%)

Query: 5   SKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSS-THMY 63
           S L  +EKMK AGI LDSGCY Q M+A +K+GD+E+V  +F E ESRK+D  P   + MY
Sbjct: 12  STLSVHEKMKLAGIPLDSGCYFQTMKARHKLGDAERVVEMFNEFESRKIDSKPMILSQMY 71

Query: 64  KILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEE 123
           KILC+SLG+SG+ FE L++FRDMK+KGILED S+Y+SLICS  +I EVK+AEEL+KEA+E
Sbjct: 72  KILCESLGRSGQVFEALEYFRDMKKKGILEDSSMYSSLICSLVNIREVKLAEELYKEAQE 131

Query: 124 KGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMK-NAELNISDCISCVIVNGFSKRRAYW 182
           K ML+D E FLKLVL+Y+EEG +EKT+E+V+ MK  A+L +SDCI C +VNGFSKRR + 
Sbjct: 132 KRMLKDPETFLKLVLIYMEEGQMEKTVEIVKEMKGTAKLKVSDCIFCAVVNGFSKRRGFD 191

Query: 183 AAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMV 242
           AAVKVYE+L   GC PGQVTYAS+INAYCR+GLYSKAE VF EM+ KGFDKCVVAYSS++
Sbjct: 192 AAVKVYEELKYDGCEPGQVTYASVINAYCRVGLYSKAEVVFFEMEAKGFDKCVVAYSSII 251

Query: 243 AMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK----------- 291
           +MYGKTGR RDAMRLVAKMK KGC+PN WIYNSL+DMHGRAK+LR++EK           
Sbjct: 252 SMYGKTGRPRDAMRLVAKMKLKGCQPNTWIYNSLVDMHGRAKDLRRVEKLWKEMKRRKVA 311

Query: 292 -----YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL 343
                YT++ISAY+ ++E++MCV+F++E+R+NGGVID A+AGIMVGVFSK+S+I+EL
Sbjct: 312 PDKVTYTSIISAYSKSKEYEMCVRFFHEYRINGGVIDGAIAGIMVGVFSKISRIDEL 368

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449530158|ref|XP_004172063.1| PREDICTED: pentatricopeptide repeat-containing protein At5g13770, chloroplastic-like [Cucumis sativus]

 Score =  464 bits (1195), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 220/356 (61%), Positives = 284/356 (79%), Gaps = 16/356 (4%)

Query: 4   QSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMY 63
           +S +  ++++KSA I  DSGCYC++MEA+ K+GDSE+V  LF E ESR  D TP ST +Y
Sbjct: 204 KSTIMVFQRLKSARIEADSGCYCRVMEAYLKLGDSERVMELFNEVESRISDSTPFSTKIY 263

Query: 64  KILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEE 123
            ILC+SL KSGR FE L+FFRDM++KGI ED ++Y++LIC+FASI EVK+AE+L+ EA+ 
Sbjct: 264 GILCESLAKSGRVFESLEFFRDMRKKGIAEDYTIYSALICTFASIQEVKLAEDLYNEAKA 323

Query: 124 KGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWA 183
           K +LRD  +FLKL+LMY+++G +EK LE+VE MK+ ++ +SDCI C IVNG++ RR Y A
Sbjct: 324 KKLLRDPAMFLKLILMYVQQGSLEKALEIVEVMKDFKIGVSDCIFCAIVNGYATRRGYEA 383

Query: 184 AVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVA 243
           AVKVYE+LI  GC PGQVTYAS INAYCR+GLYSKAE +F EM++KGFDKCVVAYSS+++
Sbjct: 384 AVKVYEKLIEDGCEPGQVTYASAINAYCRVGLYSKAEDIFGEMEEKGFDKCVVAYSSLIS 443

Query: 244 MYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK------------ 291
           MYGKTGR++DAMRL+AKMK KGC+PNVWIYN LM+MHG+AKNL+Q+EK            
Sbjct: 444 MYGKTGRLKDAMRLLAKMKEKGCQPNVWIYNILMEMHGKAKNLKQVEKLWKEMKRKKIAP 503

Query: 292 ----YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL 343
               YT++ISAY  A EF+ C ++Y EFRMNGG ID+A  GIMVGVFSK S+++EL
Sbjct: 504 DKVSYTSIISAYVKASEFEKCEQYYREFRMNGGTIDKAFGGIMVGVFSKTSRVDEL 559

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449466949|ref|XP_004151188.1| PREDICTED: pentatricopeptide repeat-containing protein At5g13770, chloroplastic-like [Cucumis sativus]

 Score =  461 bits (1185), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 219/356 (61%), Positives = 283/356 (79%), Gaps = 16/356 (4%)

Query: 4   QSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMY 63
           +S +  ++++KSA I  DSGCYC++MEA+ K+GDSE+V  LF E ESR    TP ST +Y
Sbjct: 204 KSTIMVFQRLKSARIEADSGCYCRVMEAYLKLGDSERVMELFNEVESRISVSTPFSTKIY 263

Query: 64  KILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEE 123
            ILC+SL KSGR FE L+FFRDM++KGI ED ++Y++LIC+FASI EVK+AE+L+ EA+ 
Sbjct: 264 GILCESLAKSGRVFESLEFFRDMRKKGIAEDYTIYSALICTFASIQEVKLAEDLYNEAKA 323

Query: 124 KGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWA 183
           K +LRD  +FLKL+LMY+++G +EK LE+VE MK+ ++ +SDCI C IVNG++ RR Y A
Sbjct: 324 KKLLRDPAMFLKLILMYVQQGSLEKALEIVEVMKDFKIGVSDCIFCAIVNGYATRRGYEA 383

Query: 184 AVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVA 243
           AVKVYE+LI  GC PGQVTYAS INAYCR+GLYSKAE +F EM++KGFDKCVVAYSS+++
Sbjct: 384 AVKVYEKLIEDGCEPGQVTYASAINAYCRVGLYSKAEDIFGEMEEKGFDKCVVAYSSLIS 443

Query: 244 MYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK------------ 291
           MYGKTGR++DAMRL+AKMK KGC+PNVWIYN LM+MHG+AKNL+Q+EK            
Sbjct: 444 MYGKTGRLKDAMRLLAKMKEKGCQPNVWIYNILMEMHGKAKNLKQVEKLWKEMKRKKIAP 503

Query: 292 ----YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL 343
               YT++ISAY  A EF+ C ++Y EFRMNGG ID+A  GIMVGVFSK S+++EL
Sbjct: 504 DKVSYTSIISAYVKASEFEKCEQYYREFRMNGGTIDKAFGGIMVGVFSKTSRVDEL 559

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356575210|ref|XP_003555735.1| PREDICTED: pentatricopeptide repeat-containing protein At5g13770, chloroplastic-like [Glycine max]

 Score =  432 bits (1110), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 218/364 (59%), Positives = 278/364 (76%), Gaps = 24/364 (6%)

Query: 3   SQSKLH-------YYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDL 55
           S +KLH        +E+MKS+ +VLDS  Y  IMEA+ K+ + EKV  LF E ESRKL  
Sbjct: 202 SYNKLHMFRNTVLVFERMKSSNVVLDSRGYLHIMEAYSKLNECEKVVQLFREFESRKLRG 261

Query: 56  TPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAE 115
           +     +Y ILC+SL + GRAFE L FF +M +KGI E  S+Y+ LI SFAS+ EV VAE
Sbjct: 262 SSYLAQIYVILCESLARHGRAFEALDFFTEMAKKGISEY-SIYSKLIYSFASLREVVVAE 320

Query: 116 ELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGF 175
           EL +EA+ K  ++D EV+LKLV MYIEEG++EKTLEVV+ M++A++ +SDCI C +VNGF
Sbjct: 321 ELLREAKGKMTIKDPEVYLKLVHMYIEEGLLEKTLEVVKEMEDADVKVSDCILCTVVNGF 380

Query: 176 SKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCV 235
           SK+R + AAVKV+E+LIS+G   GQVTYAS+INAY R+G YSKAE+VF+EM+QKGFDKCV
Sbjct: 381 SKKRGFLAAVKVFEELISKGYESGQVTYASVINAYWRLGQYSKAEEVFLEMEQKGFDKCV 440

Query: 236 VAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK---- 291
            AYS+M+ MYG+TGR+R AM+LVAKMK +GC+PNVWIYNSL+DMHGR KNL+QLEK    
Sbjct: 441 YAYSTMIVMYGRTGRVRSAMKLVAKMKERGCKPNVWIYNSLIDMHGRDKNLKQLEKLWKE 500

Query: 292 ------------YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQ 339
                       YT++I AY+ A EF+ CVKF+NE+RMNGG+IDRAMAGIMVGVFSK+  
Sbjct: 501 MKRRRVAPDKVSYTSIIGAYSKAGEFETCVKFFNEYRMNGGLIDRAMAGIMVGVFSKVGL 560

Query: 340 IEEL 343
           ++EL
Sbjct: 561 VDEL 564

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356521196|ref|XP_003529243.1| PREDICTED: pentatricopeptide repeat-containing protein At5g13770, chloroplastic-like [Glycine max]

 Score =  431 bits (1109), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 215/364 (59%), Positives = 279/364 (76%), Gaps = 24/364 (6%)

Query: 3   SQSKLH-------YYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDL 55
           S +KLH        +E+++S+ +VLDS  Y  IMEA+ K+ + EKV  LF E ESRKL  
Sbjct: 194 SYNKLHMFRNTVLVFERIRSSNVVLDSRGYLHIMEAYSKLNECEKVVQLFREFESRKLRG 253

Query: 56  TPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAE 115
                 +Y+ILC+SL + GRA E L +FR+M +KGI E  S+Y+ LI SFAS+ EV VAE
Sbjct: 254 PTCLAQIYEILCESLARCGRASEALDYFREMTKKGISEY-SIYSKLIYSFASLGEVDVAE 312

Query: 116 ELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGF 175
           EL +EA+ K  ++D EV+LKLV MYIEEG++EKTLEVV+ M++A++ +SDCI C +VNGF
Sbjct: 313 ELVREAKGKTTIKDPEVYLKLVHMYIEEGLLEKTLEVVKEMEDADVKVSDCILCTVVNGF 372

Query: 176 SKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCV 235
           SK+R + AAVKV+E+LIS+G  PGQVTYAS+INAY R+G YSKAE+VF+EM+QKGFDKCV
Sbjct: 373 SKKRGFSAAVKVFEELISKGNEPGQVTYASVINAYWRLGQYSKAEEVFLEMEQKGFDKCV 432

Query: 236 VAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK---- 291
            AYS+M+ MYG+TGR+R AM+LVAKMK +GC+PNVWIYNSL+DMHGR KNL+QLEK    
Sbjct: 433 YAYSTMIVMYGRTGRVRSAMKLVAKMKERGCKPNVWIYNSLIDMHGRDKNLKQLEKLWKE 492

Query: 292 ------------YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQ 339
                       YT++I AY+ A EF+ CVK +NE+RMNGG+IDRA+AGIMVGVFSK+ Q
Sbjct: 493 MKRRRVAPDKVSYTSIIGAYSKAGEFETCVKLFNEYRMNGGLIDRALAGIMVGVFSKVGQ 552

Query: 340 IEEL 343
           ++EL
Sbjct: 553 VDEL 556

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	343
TAIR|locus:2177115	609	AT5G13770 "AT5G13770" [Arabido	0.988	0.556	0.551	9.4e-98
TAIR|locus:2060226	624	AT2G32630 "AT2G32630" [Arabido	0.915	0.503	0.271	1.4e-27
TAIR|locus:2077061	619	AT3G22470 "AT3G22470" [Arabido	0.860	0.476	0.256	1.5e-24
TAIR|locus:2061310	918	GUN1 "AT2G31400" [Arabidopsis	0.810	0.302	0.262	5.8e-24
TAIR|locus:2157607	709	AT5G42310 [Arabidopsis thalian	0.778	0.376	0.259	1.2e-23
TAIR|locus:2026192	630	RPF2 "rna processing factor 2"	0.862	0.469	0.254	2.3e-22
TAIR|locus:2044430	822	AT2G18940 [Arabidopsis thalian	0.763	0.318	0.255	2.5e-22
TAIR|locus:2174008	974	AT5G61990 "AT5G61990" [Arabido	0.938	0.330	0.238	6.9e-22
TAIR|locus:2097395	638	AT3G49730 [Arabidopsis thalian	0.897	0.482	0.238	8.4e-22
TAIR|locus:2175443	952	AT5G04810 [Arabidopsis thalian	0.822	0.296	0.268	8.5e-22

TAIR|locus:2177115 AT5G13770 "AT5G13770" [Arabidopsis thaliana (taxid:3702)]

 Score = 971 (346.9 bits), Expect = 9.4e-98, P = 9.4e-98
 Identities = 197/357 (55%), Positives = 257/357 (71%)

Query:     5 SKLHYYEKMK-SAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLD-LTPSSTHM 62
             S +  ++++K S G+    GCYC+IMEA  KIG++ KV  LF E +S++L  L   S  +
Sbjct:   191 STIQVFDRLKQSVGVEPSPGCYCRIMEAHEKIGENHKVVELFQEFKSQRLSFLAKESGSI 250

Query:    63 YKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAE 122
             Y I+C SL KSGRAFE L+   +MK+KGI E   +Y+ LI +FA   EV + E+LFKEA 
Sbjct:   251 YTIVCSSLAKSGRAFEALEVLEEMKDKGIPESSELYSMLIRAFAEAREVVITEKLFKEAG 310

Query:   123 EKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYW 182
              K +L+D E+ LK+VLMY+ EG +E TLEVV +M+ AEL ++DCI C IVNGFSK+R + 
Sbjct:   311 GKKLLKDPEMCLKVVLMYVREGNMETTLEVVAAMRKAELKVTDCILCAIVNGFSKQRGFA 370

Query:   183 AAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMV 242
              AVKVYE  + + C  GQVTYA  INAYCR+  Y+KAE +F EM +KGFDKCVVAYS+++
Sbjct:   371 EAVKVYEWAMKEECEAGQVTYAIAINAYCRLEKYNKAEMLFDEMVKKGFDKCVVAYSNIM 430

Query:   243 AMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK----------- 291
              MYGKT R+ DA+RL+AKMK +GC+PN+WIYNSL+DMHGRA +LR+ EK           
Sbjct:   431 DMYGKTRRLSDAVRLMAKMKQRGCKPNIWIYNSLIDMHGRAMDLRRAEKIWKEMKRAKVL 490

Query:   292 -----YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL 343
                  YT++ISAYN ++E + CV+ Y EFRMN G IDRAMAGIMVGVFSK S+I+EL
Sbjct:   491 PDKVSYTSMISAYNRSKELERCVELYQEFRMNRGKIDRAMAGIMVGVFSKTSRIDEL 547

GO:0003674 "molecular_function" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0009658 "chloroplast organization" evidence=IMP

TAIR|locus:2060226 AT2G32630 "AT2G32630" [Arabidopsis thaliana (taxid:3702)]

 Score = 316 (116.3 bits), Expect = 1.4e-27, P = 1.4e-27
 Identities = 92/339 (27%), Positives = 157/339 (46%)

Query:    13 MKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGK 72
             MK  G+V +   Y  +ME   K G       LF E   R ++   S  H+Y  L     +
Sbjct:   285 MKKDGVVYNKVTYTLLMELSVKNGKMSDAEKLFDEMRERGIE---SDVHVYTSLISWNCR 341

Query:    73 SGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEV 132
              G        F ++ EKG+      Y +LI     + E+  AE L  E + KG+     V
Sbjct:   342 KGNMKRAFLLFDELTEKGLSPSSYTYGALIDGVCKVGEMGAAEILMNEMQSKGVNITQVV 401

Query:   133 FLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISC-VIVNGFSKRRAYWAAVKVYEQL 191
             F  L+  Y  +GMV++   + + M+      +D  +C  I + F++ + Y  A +   ++
Sbjct:   402 FNTLIDGYCRKGMVDEASMIYDVMEQKGFQ-ADVFTCNTIASCFNRLKRYDEAKQWLFRM 460

Query:   192 ISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRI 251
             +  G     V+Y ++I+ YC+ G   +A+++F+EM  KG     + Y+ M+  Y K G+I
Sbjct:   461 MEGGVKLSTVSYTNLIDVYCKEGNVEEAKRLFVEMSSKGVQPNAITYNVMIYAYCKQGKI 520

Query:   252 RDAMRLVAKMKPKGCEPNVWIYNSLMDMHGR--AKN------------LRQLEK----YT 293
             ++A +L A M+  G +P+ + Y SL+  HG   A N            L+ L++    YT
Sbjct:   521 KEARKLRANMEANGMDPDSYTYTSLI--HGECIADNVDEAMRLFSEMGLKGLDQNSVTYT 578

Query:   294 TVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVG 332
              +IS  + A + D     Y+E +  G  ID  +   ++G
Sbjct:   579 VMISGLSKAGKSDEAFGLYDEMKRKGYTIDNKVYTALIG 617

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 288 (106.4 bits), Expect = 1.5e-24, P = 1.5e-24
 Identities = 78/304 (25%), Positives = 145/304 (47%)

Query:    11 EKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSL 70
             ++M   G   D   Y  ++    K G+S     LF + E R +    +S   Y I+ DSL
Sbjct:   199 DRMVEYGFQPDEVTYGPVLNRLCKSGNSALALDLFRKMEERNIK---ASVVQYSIVIDSL 255

Query:    71 GKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDL 130
              K G   + L  F +M+ KGI  D   Y+SLI    +  +     ++ +E   + ++ D+
Sbjct:   256 CKDGSFDDALSLFNEMEMKGIKADVVTYSSLIGGLCNDGKWDDGAKMLREMIGRNIIPDV 315

Query:   131 EVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISC-VIVNGFSKRRAYWAAVKVYE 189
               F  L+ ++++EG + +  E+   M    +   D I+   +++GF K      A ++++
Sbjct:   316 VTFSALIDVFVKEGKLLEAKELYNEMITRGI-APDTITYNSLIDGFCKENCLHEANQMFD 374

Query:   190 QLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTG 249
              ++S+GC P  VTY+ +IN+YC+        ++F E+  KG     + Y+++V  + ++G
Sbjct:   375 LMVSKGCEPDIVTYSILINSYCKAKRVDDGMRLFREISSKGLIPNTITYNTLVLGFCQSG 434

Query:   250 RIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCV 309
             ++  A  L  +M  +G  P+V  Y  L+D  G   N  +L K   +      +R   + +
Sbjct:   435 KLNAAKELFQEMVSRGVPPSVVTYGILLD--GLCDN-GELNKALEIFEKMQKSR-MTLGI 490

Query:   310 KFYN 313
               YN
Sbjct:   491 GIYN 494

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2061310 GUN1 "AT2G31400" [Arabidopsis thaliana (taxid:3702)]

 Score = 286 (105.7 bits), Expect = 5.8e-24, P = 5.8e-24
 Identities = 76/289 (26%), Positives = 144/289 (49%)

Query:     9 YYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCD 68
             ++++M+  G+  D   +  ++    + G  E    LF E  +R+++        Y  L D
Sbjct:   326 FFDEMQRNGVQPDRITFNSLLAVCSRGGLWEAARNLFDEMTNRRIE---QDVFSYNTLLD 382

Query:    69 SLGKSGR---AFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKG 125
             ++ K G+   AFEIL     M  K I+ +   Y+++I  FA       A  LF E    G
Sbjct:   383 AICKGGQMDLAFEILA---QMPVKRIMPNVVSYSTVIDGFAKAGRFDEALNLFGEMRYLG 439

Query:   126 MLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISC-VIVNGFSKRRAYWAA 184
             +  D   +  L+ +Y + G  E+ L+++  M +  +   D ++   ++ G+ K+  Y   
Sbjct:   440 IALDRVSYNTLLSIYTKVGRSEEALDILREMASVGIK-KDVVTYNALLGGYGKQGKYDEV 498

Query:   185 VKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAM 244
              KV+ ++  +  +P  +TY+++I+ Y + GLY +A ++F E +  G    VV YS+++  
Sbjct:   499 KKVFTEMKREHVLPNLLTYSTLIDGYSKGGLYKEAMEIFREFKSAGLRADVVLYSALIDA 558

Query:   245 YGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYT 293
               K G +  A+ L+ +M  +G  PNV  YNS++D  GR+  + +   Y+
Sbjct:   559 LCKNGLVGSAVSLIDEMTKEGISPNVVTYNSIIDAFGRSATMDRSADYS 607

GO:0003677 "DNA binding" evidence=IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0031930 "mitochondria-nucleus signaling pathway" evidence=IMP

GO:0010019 "chloroplast-nucleus signaling pathway" evidence=IMP

TAIR|locus:2157607 AT5G42310 [Arabidopsis thaliana (taxid:3702)]

 Score = 281 (104.0 bits), Expect = 1.2e-23, P = 1.2e-23
 Identities = 70/270 (25%), Positives = 138/270 (51%)

Query:    14 KSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKS 73
             ++ G+   +     I+ A    G + +  ALF E   R+  + P  T  Y  L     K+
Sbjct:   296 QATGLSAKTATLVSIISALADSGRTLEAEALFEEL--RQSGIKPR-TRAYNALLKGYVKT 352

Query:    74 GRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVF 133
             G   +      +M+++G+  D   Y+ LI ++ +    + A  + KE E   +  +  VF
Sbjct:   353 GPLKDAESMVSEMEKRGVSPDEHTYSLLIDAYVNAGRWESARIVLKEMEAGDVQPNSFVF 412

Query:   134 LKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLIS 193
              +L+  + + G  +KT +V++ MK+  +        V+++ F K      A+  +++++S
Sbjct:   413 SRLLAGFRDRGEWQKTFQVLKEMKSIGVKPDRQFYNVVIDTFGKFNCLDHAMTTFDRMLS 472

Query:   194 QGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRD 253
             +G  P +VT+ ++I+ +C+ G +  AE++F  M+++G   C   Y+ M+  YG   R  D
Sbjct:   473 EGIEPDRVTWNTLIDCHCKHGRHIVAEEMFEAMERRGCLPCATTYNIMINSYGDQERWDD 532

Query:   254 AMRLVAKMKPKGCEPNVWIYNSLMDMHGRA 283
               RL+ KMK +G  PNV  + +L+D++G++
Sbjct:   533 MKRLLGKMKSQGILPNVVTHTTLVDVYGKS 562

GO:0005739 "mitochondrion" evidence=ISM

GO:0009507 "chloroplast" evidence=IDA

TAIR|locus:2026192 RPF2 "rna processing factor 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 268 (99.4 bits), Expect = 2.3e-22, P = 2.3e-22
 Identities = 77/303 (25%), Positives = 139/303 (45%)

Query:    11 EKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSL 70
             ++M + G   D   Y  ++    K GD++    L  + E  KL+  P    +Y  + D L
Sbjct:   210 DRMVAKGCQPDLVTYGVVVNGLCKRGDTDLAFNLLNKMEQGKLE--PGVL-IYNTIIDGL 266

Query:    71 GKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDL 130
              K     + L  F++M+ KGI  +   Y+SLI    +      A  L  +  E+ +  D+
Sbjct:   267 CKYKHMDDALNLFKEMETKGIRPNVVTYSSLISCLCNYGRWSDASRLLSDMIERKINPDV 326

Query:   131 EVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQ 190
               F  L+  +++EG + +  ++ + M    ++ S      ++NGF        A +++E 
Sbjct:   327 FTFSALIDAFVKEGKLVEAEKLYDEMVKRSIDPSIVTYSSLINGFCMHDRLDEAKQMFEF 386

Query:   191 LISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGR 250
             ++S+ C P  VTY ++I  +C+     +  +VF EM Q+G     V Y+ ++    + G 
Sbjct:   387 MVSKHCFPDVVTYNTLIKGFCKYKRVEEGMEVFREMSQRGLVGNTVTYNILIQGLFQAGD 446

Query:   251 IRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVK 310
                A  +  +M   G  PN+  YN+L+D  G  KN  +LEK   V+  Y    + +  + 
Sbjct:   447 CDMAQEIFKEMVSDGVPPNIMTYNTLLD--GLCKN-GKLEK-AMVVFEYLQRSKMEPTIY 502

Query:   311 FYN 313
              YN
Sbjct:   503 TYN 505

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0000966 "RNA 5'-end processing" evidence=IMP

GO:0003723 "RNA binding" evidence=IDA

TAIR|locus:2044430 AT2G18940 [Arabidopsis thaliana (taxid:3702)]

 Score = 270 (100.1 bits), Expect = 2.5e-22, P = 2.5e-22
 Identities = 71/278 (25%), Positives = 142/278 (51%)

Query:    11 EKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHM-YKILCDS 69
             +K+     +LD   Y  I+ A+ + G  EK   LF     R  ++ PS T + Y ++ D 
Sbjct:   199 DKIPLQEYLLDVRAYTTILHAYSRTGKYEKAIDLF----ERMKEMGPSPTLVTYNVILDV 254

Query:    70 LGKSGRAF-EILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLR 128
              GK GR++ +IL    +M+ KG+  D    ++++ + A    ++ A+E F E +  G   
Sbjct:   255 FGKMGRSWRKILGVLDEMRSKGLKFDEFTCSTVLSACAREGLLREAKEFFAELKSCGYEP 314

Query:   129 DLEVFLKLVLMYIEEGMVEKTLEVVESMK-NA----ELNISDCISCVIVNGFSKRRAYWA 183
                 +  L+ ++ + G+  + L V++ M+ N+     +  ++ ++  +  GFSK      
Sbjct:   315 GTVTYNALLQVFGKAGVYTEALSVLKEMEENSCPADSVTYNELVAAYVRAGFSKE----- 369

Query:   184 AVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVA 243
             A  V E +  +G +P  +TY ++I+AY + G   +A K+F  M++ G       Y+++++
Sbjct:   370 AAGVIEMMTKKGVMPNAITYTTVIDAYGKAGKEDEALKLFYSMKEAGCVPNTCTYNAVLS 429

Query:   244 MYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHG 281
             + GK  R  + ++++  MK  GC PN   +N+++ + G
Sbjct:   430 LLGKKSRSNEMIKMLCDMKSNGCSPNRATWNTMLALCG 467

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 267 (99.0 bits), Expect = 6.9e-22, P = 6.9e-22
 Identities = 78/327 (23%), Positives = 137/327 (41%)

Query:     2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTH 61
             N    L   E M   G+V     Y  +++   KI   E   +L +E +S  + L     H
Sbjct:   257 NVDGALKLKESMICKGLVPLKYTYDVLIDGLCKIKRLEDAKSLLVEMDSLGVSL---DNH 313

Query:    62 MYKILCDSLGKSGRAFEILK-FFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKE 120
              Y +L D L K GR  +  K    +M   GI   P +Y   IC  +    ++ A+ LF  
Sbjct:   314 TYSLLIDGLLK-GRNADAAKGLVHEMVSHGINIKPYMYDCCICVMSKEGVMEKAKALFDG 372

Query:   121 AEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRA 180
                 G++   + +  L+  Y  E  V +  E++  MK   + IS      +V G      
Sbjct:   373 MIASGLIPQAQAYASLIEGYCREKNVRQGYELLVEMKKRNIVISPYTYGTVVKGMCSSGD 432

Query:   181 YWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSS 240
                A  + +++I+ GC P  V Y ++I  + +   +  A +V  EM+++G    +  Y+S
Sbjct:   433 LDGAYNIVKEMIASGCRPNVVIYTTLIKTFLQNSRFGDAMRVLKEMKEQGIAPDIFCYNS 492

Query:   241 MVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYN 300
             ++    K  R+ +A   + +M   G +PN + Y + +  +  A      +KY   +    
Sbjct:   493 LIIGLSKAKRMDEARSFLVEMVENGLKPNAFTYGAFISGYIEASEFASADKYVKEMRECG 552

Query:   301 MAREFDMCVKFYNEFRMNGGVIDRAMA 327
             +     +C    NE+   G VI+   A
Sbjct:   553 VLPNKVLCTGLINEYCKKGKVIEACSA 579

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2097395 AT3G49730 [Arabidopsis thaliana (taxid:3702)]

 Score = 263 (97.6 bits), Expect = 8.4e-22, P = 8.4e-22
 Identities = 75/315 (23%), Positives = 149/315 (47%)

Query:    11 EKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSL 70
             E  K+   +++   +  +M  F    +  K A   L+ E  K  L P   +++  L D+L
Sbjct:   156 EMRKTNPELIEPELFVVLMRRFAS-ANMVKKAVEVLD-EMPKYGLEPDE-YVFGCLLDAL 212

Query:    71 GKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDL 130
              K+G   E  K F DM+EK    +   + SL+  +    ++  A+E+  + +E G+  D+
Sbjct:   213 CKNGSVKEASKVFEDMREK-FPPNLRYFTSLLYGWCREGKLMEAKEVLVQMKEAGLEPDI 271

Query:   131 EVFLKLVLMYIEEGMVEKTLEVVESMKNA--ELNISDCISCVIVNGFSKRRAYWAAVKVY 188
              VF  L+  Y   G +    +++  M+    E N++ C + +I       +    A++V+
Sbjct:   272 VVFTNLLSGYAHAGKMADAYDLMNDMRKRGFEPNVN-CYTVLIQALCRTEKRMDEAMRVF 330

Query:   189 EQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKT 248
              ++   GC    VTY ++I+ +C+ G+  K   V  +M++KG     V Y  ++  + K 
Sbjct:   331 VEMERYGCEADIVTYTALISGFCKWGMIDKGYSVLDDMRKKGVMPSQVTYMQIMVAHEKK 390

Query:   249 GRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMC 308
              +  + + L+ KMK +GC P++ IYN ++ +  +   +++  +    + A  ++   D  
Sbjct:   391 EQFEECLELIEKMKRRGCHPDLLIYNVVIRLACKLGEVKEAVRLWNEMEANGLSPGVDTF 450

Query:   309 VKFYNEFRMNGGVID 323
             V   N F   G +I+
Sbjct:   451 VIMINGFTSQGFLIE 465

GO:0005739 "mitochondrion" evidence=ISM

GO:0007131 "reciprocal meiotic recombination" evidence=RCA

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

GO:0009691 "cytokinin biosynthetic process" evidence=RCA

TAIR|locus:2175443 AT5G04810 [Arabidopsis thaliana (taxid:3702)]

 Score = 266 (98.7 bits), Expect = 8.5e-22, P = 8.5e-22
 Identities = 79/294 (26%), Positives = 147/294 (50%)

Query:    12 KMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKIL---CD 68
             KMK  GI +    Y  I+  F K G +E  AA +   E++++  T +++   KI+   C 
Sbjct:   369 KMKEEGIEMSLVTYSVIVGGFSKAGHAE--AADYWFDEAKRIHKTLNASIYGKIIYAHCQ 426

Query:    69 SLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLR 128
             +     RA E L   R+M+E+GI    ++Y +++  +  +A+ K    +FK  +E G   
Sbjct:   427 TCNME-RA-EAL--VREMEEEGIDAPIAIYHTMMDGYTMVADEKKGLVVFKRLKECGFTP 482

Query:   129 DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVY 188
              +  +  L+ +Y + G + K LEV   MK   +  +     +++NGF K + +  A  V+
Sbjct:   483 TVVTYGCLINLYTKVGKISKALEVSRVMKEEGVKHNLKTYSMMINGFVKLKDWANAFAVF 542

Query:   189 EQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKT 248
             E ++ +G  P  + Y +II+A+C +G   +A +   EMQ+         +  ++  Y K+
Sbjct:   543 EDMVKEGMKPDVILYNNIISAFCGMGNMDRAIQTVKEMQKLRHRPTTRTFMPIIHGYAKS 602

Query:   249 GRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMA 302
             G +R ++ +   M+  GC P V  +N L++  G  +  RQ+EK   ++    +A
Sbjct:   603 GDMRRSLEVFDMMRRCGCVPTVHTFNGLIN--GLVEK-RQMEKAVEILDEMTLA 653

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00035162001 SubName- Full=Chromosome chr1 scaffold_75, whole genome shotgun sequence; (571 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	343
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	1e-10
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	2e-09
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-09
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	8e-09
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	4e-08
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-07
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	3e-07
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	5e-07
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	1e-06
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	1e-06
pfam12854	34	pfam12854, PPR_1, PPR repeat	2e-06
pfam01535	31	pfam01535, PPR, PPR repeat	1e-05
pfam13041	50	pfam13041, PPR_2, PPR repeat family	3e-05
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	2e-04
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	8e-04
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	0.001
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	0.002

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

 Score = 62.2 bits (151), Expect = 1e-10
 Identities = 57/253 (22%), Positives = 118/253 (46%), Gaps = 19/253 (7%)

Query: 40  KVAALFLEC----ESRKL-DLTPS-STHMYKILCDSLGKSGRAFEILKFFRDMKEKGILE 93
           +V  + ++C    ++R+L D  P  +   +  +   L  +G   E    FR+M E G   
Sbjct: 163 RVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDA 222

Query: 94  DPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVV 153
           +P  +  ++ + A +   +  ++L     + G++ D  V   L+ MY + G +E    V 
Sbjct: 223 EPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVF 282

Query: 154 ESMKNAE-LNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCR 212
           + M     +  +  ++   ++G+S+      A+ +Y ++   G    Q T++ +I  + R
Sbjct: 283 DGMPEKTTVAWNSMLAGYALHGYSEE-----ALCLYYEMRDSGVSIDQFTFSIMIRIFSR 337

Query: 213 IGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWI 272
           + L   A++    + + GF   +VA +++V +Y K GR+ DA  +  +M  K    N+  
Sbjct: 338 LALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRK----NLIS 393

Query: 273 YNSLM---DMHGR 282
           +N+L+     HGR
Sbjct: 394 WNALIAGYGNHGR 406

Length = 697

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

 Score = 58.7 bits (142), Expect = 2e-09
 Identities = 57/260 (21%), Positives = 117/260 (45%), Gaps = 19/260 (7%)

Query: 16  AGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGR 75
            G+V D+   C +++ + K GD E    +F +    K      +T  +  +       G 
Sbjct: 253 TGVVGDTFVSCALIDMYSKCGDIEDARCVF-DGMPEK------TTVAWNSMLAGYALHGY 305

Query: 76  AFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLK 135
           + E L  + +M++ G+  D   ++ +I  F+ +A ++ A++        G   D+     
Sbjct: 306 SEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTA 365

Query: 136 LVLMYIEEGMVEKTLEVVESMKNAELNISDCISC-VIVNGFSKRRAYWAAVKVYEQLISQ 194
           LV +Y + G +E    V + M    L     IS   ++ G+        AV+++E++I++
Sbjct: 366 LVDLYSKWGRMEDARNVFDRMPRKNL-----ISWNALIAGYGNHGRGTKAVEMFERMIAE 420

Query: 195 GCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQ-KGFDKCVVAYSSMVAMYGKTGRIRD 253
           G  P  VT+ ++++A    GL  +  ++F  M +        + Y+ M+ + G+ G + +
Sbjct: 421 GVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDE 480

Query: 254 AMRLV--AKMKPKGCEPNVW 271
           A  ++  A  KP     N+W
Sbjct: 481 AYAMIRRAPFKPTV---NMW 497

Length = 697

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

 Score = 52.4 bits (127), Expect = 2e-09
 Identities = 17/50 (34%), Positives = 33/50 (66%)

Query: 233 KCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGR 282
             VV Y++++  Y K G++ +A++L  +MK +G +PNV+ Y+ L+D   +
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

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

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

 Score = 56.8 bits (137), Expect = 8e-09
 Identities = 50/227 (22%), Positives = 101/227 (44%), Gaps = 10/227 (4%)

Query: 67  CDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGM 126
           C + G+  RA E+   ++ + E  I   P VY   + S +   +   A  ++ + ++KG+
Sbjct: 589 CANAGQVDRAKEV---YQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGV 645

Query: 127 LRDLEVFLK-LVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAV 185
             D EVF   LV +    G ++K  E+++  +   + +       ++   S  + +  A+
Sbjct: 646 KPD-EVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKAL 704

Query: 186 KVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMY 245
           ++YE + S    P   T  ++I A C      KA +V  EM++ G     + YS ++   
Sbjct: 705 ELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVAS 764

Query: 246 GKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKY 292
            +       + L+++ K  G +PN+ +   +  +      LR+ EK 
Sbjct: 765 ERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGL-----CLRRFEKA 806

Length = 1060

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

 Score = 54.9 bits (132), Expect = 4e-08
 Identities = 58/272 (21%), Positives = 118/272 (43%), Gaps = 15/272 (5%)

Query: 13  MKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFL---ECESRKLDLTPSSTHMYKILCDS 69
           ++ AG+  D   Y  ++    K G   KV A+F    E  +  ++   ++ H +  L D 
Sbjct: 463 VQEAGLKADCKLYTTLISTCAKSG---KVDAMFEVFHEMVNAGVE---ANVHTFGALIDG 516

Query: 70  LGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKE--AEEKGML 127
             ++G+  +    +  M+ K +  D  V+ +LI +      V  A ++  E  AE   + 
Sbjct: 517 CARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPID 576

Query: 128 RDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISC--VIVNGFSKRRAYWAAV 185
            D      L+      G V++  EV + +   E NI        + VN  S++  +  A+
Sbjct: 577 PDHITVGALMKACANAGQVDRAKEVYQMIH--EYNIKGTPEVYTIAVNSCSQKGDWDFAL 634

Query: 186 KVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMY 245
            +Y+ +  +G  P +V ++++++     G   KA ++  + +++G     V+YSS++   
Sbjct: 635 SIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGAC 694

Query: 246 GKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLM 277
                 + A+ L   +K     P V   N+L+
Sbjct: 695 SNAKNWKKALELYEDIKSIKLRPTVSTMNALI 726

Length = 1060

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

 Score = 46.6 bits (112), Expect = 2e-07
 Identities = 18/50 (36%), Positives = 29/50 (58%)

Query: 198 PGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGK 247
           P  VTY ++I+ YC+ G   +A K+F EM+++G    V  YS ++    K
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

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

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

 Score = 51.8 bits (124), Expect = 3e-07
 Identities = 42/194 (21%), Positives = 84/194 (43%), Gaps = 6/194 (3%)

Query: 72  KSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLE 131
           ++G   E L+ F  M+E  +  D     S+I +   + + ++  E+     + G   D+ 
Sbjct: 265 ENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVS 324

Query: 132 VFLKLVLMYIEEGMVEKTLEVVESMKNAEL-NISDCISCVIVNGFSKRRAYWAAVKVYEQ 190
           V   L+ MY+  G   +  +V   M+  +  + +  IS    NG   +     A++ Y  
Sbjct: 325 VCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDK-----ALETYAL 379

Query: 191 LISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGR 250
           +      P ++T AS+++A   +G      K+    ++KG    VV  ++++ MY K   
Sbjct: 380 MEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKC 439

Query: 251 IRDAMRLVAKMKPK 264
           I  A+ +   +  K
Sbjct: 440 IDKALEVFHNIPEK 453

Length = 857

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

 Score = 51.4 bits (123), Expect = 5e-07
 Identities = 47/200 (23%), Positives = 92/200 (46%), Gaps = 12/200 (6%)

Query: 75  RAFEILKFFRDMKEKGILEDPSV-YASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVF 133
           R FE L FFR M     L+  SV   + + + A I  +   +E+       G+  D  + 
Sbjct: 470 RCFEALIFFRQML--LTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLP 527

Query: 134 LKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISC-VIVNGFSKRRAYWAAVKVYEQLI 192
             L+ +Y+  G +        S +       D +S  +++ G+        AV+++ +++
Sbjct: 528 NALLDLYVRCGRMNYAWNQFNSHEK------DVVSWNILLTGYVAHGKGSMAVELFNRMV 581

Query: 193 SQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQK-GFDKCVVAYSSMVAMYGKTGRI 251
             G  P +VT+ S++ A  R G+ ++  + F  M++K      +  Y+ +V + G+ G++
Sbjct: 582 ESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKL 641

Query: 252 RDAMRLVAKMKPKGCEPNVW 271
            +A   + KM P   +P VW
Sbjct: 642 TEAYNFINKM-PITPDPAVW 660

Length = 857

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

 Score = 49.9 bits (119), Expect = 1e-06
 Identities = 52/269 (19%), Positives = 110/269 (40%), Gaps = 28/269 (10%)

Query: 74  GRAFEILKFFRDMKEKGILEDP-SVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEV 132
           GR  E L+ F  ++       P S Y +L+ +  ++  ++  + ++   E  G   D  +
Sbjct: 101 GRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYM 160

Query: 133 FLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLI 192
             +++LM+++ GM+     + + M   E N++   +  I+ G      Y  A  ++ ++ 
Sbjct: 161 MNRVLLMHVKCGMLIDARRLFDEM--PERNLASWGT--IIGGLVDAGNYREAFALFREMW 216

Query: 193 SQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIR 252
             G      T+  ++ A   +G     +++   + + G         +++ MY K G I 
Sbjct: 217 EDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIE 276

Query: 253 DAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFY 312
           DA  +   M  K        +NS                   +++ Y +    +  +  Y
Sbjct: 277 DARCVFDGMPEK----TTVAWNS-------------------MLAGYALHGYSEEALCLY 313

Query: 313 NEFRMNGGVIDRAMAGIMVGVFSKLSQIE 341
            E R +G  ID+    IM+ +FS+L+ +E
Sbjct: 314 YEMRDSGVSIDQFTFSIMIRIFSRLALLE 342

Length = 697

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

 Score = 50.3 bits (120), Expect = 1e-06
 Identities = 64/307 (20%), Positives = 124/307 (40%), Gaps = 30/307 (9%)

Query: 1   TNSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIG--DSEKV--AALFLECESR----- 51
             S   +  Y ++   G + D      ++E   K G  D +K+  A  F  C+ +     
Sbjct: 368 RKSPEYIDAYNRLLRDGRIKDC---IDLLEDMEKRGLLDMDKIYHAKFFKACKKQRAVKE 424

Query: 52  -----KLDLTPSSTH--MYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICS 104
                KL   P+ +   M   +C S      A  +L   R ++E G+  D  +Y +LI +
Sbjct: 425 AFRFAKLIRNPTLSTFNMLMSVCASSQDIDGALRVL---RLVQEAGLKADCKLYTTLIST 481

Query: 105 FASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNIS 164
            A   +V    E+F E    G+  ++  F  L+      G V K       M++  +   
Sbjct: 482 CAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPD 541

Query: 165 DCISCVIVNGFSKRRAYWAAVKVYEQLI--SQGCIPGQVTYASIINAYCRIGLYSKAEKV 222
             +   +++   +  A   A  V  ++   +    P  +T  +++ A    G   +A++V
Sbjct: 542 RVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEV 601

Query: 223 FIEMQQ---KGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDM 279
           +  + +   KG  +    Y+  V    + G    A+ +   MK KG +P+   +++L+D+
Sbjct: 602 YQMIHEYNIKGTPEV---YTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDV 658

Query: 280 HGRAKNL 286
            G A +L
Sbjct: 659 AGHAGDL 665

Length = 1060

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

 Score = 43.1 bits (103), Expect = 2e-06
 Identities = 12/34 (35%), Positives = 20/34 (58%)

Query: 194 QGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQ 227
           +G  P  VTY ++I+  CR G   +A ++  EM+
Sbjct: 1   KGLKPDVVTYNTLIDGLCRAGRVDEAVELLDEME 34

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

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

 Score = 40.9 bits (97), Expect = 1e-05
 Identities = 14/31 (45%), Positives = 22/31 (70%)

Query: 201 VTYASIINAYCRIGLYSKAEKVFIEMQQKGF 231
           VTY S+I+ YC+ G   +A ++F EM++KG 
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

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

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

 Score = 40.5 bits (96), Expect = 3e-05
 Identities = 10/43 (23%), Positives = 25/43 (58%)

Query: 170 VIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCR 212
            +++G+ K+     A+K++ ++  +G  P   TY+ +I+  C+
Sbjct: 8   TLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

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

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

 Score = 37.8 bits (89), Expect = 2e-04
 Identities = 11/31 (35%), Positives = 21/31 (67%)

Query: 201 VTYASIINAYCRIGLYSKAEKVFIEMQQKGF 231
           VTY ++I+  C+ G   +A ++F EM+++G 
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGI 31

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

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

 Score = 41.0 bits (96), Expect = 8e-04
 Identities = 47/236 (19%), Positives = 95/236 (40%), Gaps = 23/236 (9%)

Query: 63  YKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAE 122
           + +L     K+G   E L  +  M   G+  D   +  ++ +   I ++    E+     
Sbjct: 155 WNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVV 214

Query: 123 EKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISC-VIVNGFSKRRAY 181
             G   D++V   L+ MY++ G V     V + M        DCIS   +++G+ +    
Sbjct: 215 RFGFELDVDVVNALITMYVKCGDVVSARLVFDRMP-----RRDCISWNAMISGYFENGEC 269

Query: 182 WAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSM 241
              ++++  +      P  +T  S+I+A   +G      ++   + + GF   V   +S+
Sbjct: 270 LEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSL 329

Query: 242 VAMYGKTGRIRDAMRLVAKMKPK----------GCEPN------VWIYNSLMDMHG 281
           + MY   G   +A ++ ++M+ K          G E N      +  Y +LM+   
Sbjct: 330 IQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETY-ALMEQDN 384

Length = 857

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

 Score = 35.5 bits (83), Expect = 0.001
 Identities = 13/35 (37%), Positives = 23/35 (65%)

Query: 236 VAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNV 270
           V Y++++    K GR+ +A+ L  +MK +G EP+V
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

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

>gnl|CDD|205985 pfam13812, PPR_3, Pentatricopeptide repeat domain

 Score = 34.8 bits (81), Expect = 0.002
 Identities = 9/30 (30%), Positives = 14/30 (46%)

Query: 201 VTYASIINAYCRIGLYSKAEKVFIEMQQKG 230
            TY +++ A  + G    A  V  EM+  G
Sbjct: 2   ETYNALLLALAKAGDPDLALAVLEEMKASG 31

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	343
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.95
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.95
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.94
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.92
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.9
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.9
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.88
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.86
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.84
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.83
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.83
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.82
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.81
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.79
PRK14574	822	hmsH outer membrane protein; Provisional	99.78
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.77
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.76
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.75
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.74
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.72
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.72
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.71
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.71
PRK14574	822	hmsH outer membrane protein; Provisional	99.71
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.7
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.7
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.7
KOG1126	638	consensus DNA-binding cell division cycle control	99.68
KOG2076	895	consensus RNA polymerase III transcription factor	99.67
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.65
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.6
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.59
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.59
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.58
KOG2076	895	consensus RNA polymerase III transcription factor	99.58
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.58
KOG1126	638	consensus DNA-binding cell division cycle control	99.57
PRK12370	553	invasion protein regulator; Provisional	99.57
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.55
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.55
PRK12370	553	invasion protein regulator; Provisional	99.55
KOG2003	840	consensus TPR repeat-containing protein [General f	99.54
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.53
PF13041	50	PPR_2: PPR repeat family	99.48
KOG2003	840	consensus TPR repeat-containing protein [General f	99.48
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.48
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.47
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.47
PF13041	50	PPR_2: PPR repeat family	99.44
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	99.43
KOG1129	478	consensus TPR repeat-containing protein [General f	99.43
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	99.43
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.4
KOG1129	478	consensus TPR repeat-containing protein [General f	99.39
PRK11189	296	lipoprotein NlpI; Provisional	99.38
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.37
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.34
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	99.34
PRK11189	296	lipoprotein NlpI; Provisional	99.34
KOG0547	606	consensus Translocase of outer mitochondrial membr	99.33
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.31
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	99.31
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	99.3
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	99.26
KOG0547	606	consensus Translocase of outer mitochondrial membr	99.25
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	99.21
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	99.2
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	99.2
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.11
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	99.1
KOG2376	652	consensus Signal recognition particle, subunit Srp	99.08
KOG3785	557	consensus Uncharacterized conserved protein [Funct	99.06
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	99.05
PLN02789	320	farnesyltranstransferase	99.04
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	99.04
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	99.04
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	99.03
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	99.02
KOG4340	459	consensus Uncharacterized conserved protein [Funct	99.02
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	99.0
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	99.0
KOG1125	579	consensus TPR repeat-containing protein [General f	98.92
PRK04841	903	transcriptional regulator MalT; Provisional	98.92
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.9
PF12854	34	PPR_1: PPR repeat	98.9
PF12854	34	PPR_1: PPR repeat	98.89
KOG1125	579	consensus TPR repeat-containing protein [General f	98.88
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.87
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.84
PLN02789	320	farnesyltranstransferase	98.82
KOG4340	459	consensus Uncharacterized conserved protein [Funct	98.81
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.8
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.8
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.8
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.79
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	98.79
PRK04841	903	transcriptional regulator MalT; Provisional	98.79
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.75
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	98.75
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.74
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	98.74
KOG2047	835	consensus mRNA splicing factor [RNA processing and	98.73
KOG2047	835	consensus mRNA splicing factor [RNA processing and	98.73
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.72
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.71
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	98.7
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.69
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.69
KOG3616	1636	consensus Selective LIM binding factor [Transcript	98.68
KOG3785	557	consensus Uncharacterized conserved protein [Funct	98.68
PRK15359	144	type III secretion system chaperone protein SscB;	98.67
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.66
PRK15359	144	type III secretion system chaperone protein SscB;	98.66
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.66
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	98.64
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.63
KOG3060	289	consensus Uncharacterized conserved protein [Funct	98.62
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	98.59
KOG3060	289	consensus Uncharacterized conserved protein [Funct	98.59
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.56
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	98.54
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.52
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	98.5
KOG3616	1636	consensus Selective LIM binding factor [Transcript	98.48
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.42
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.42
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.4
KOG2376	652	consensus Signal recognition particle, subunit Srp	98.39
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	98.39
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.38
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.37
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.36
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.36
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.36
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.35
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.34
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.33
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.33
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	98.32
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.29
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	98.24
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	98.2
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	98.15
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	98.15
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	98.11
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	98.1
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.1
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	98.08
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	98.06
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	98.06
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	98.03
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.03
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	98.02
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	98.01
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.99
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.98
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.97
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	97.96
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.95
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.94
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.94
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.93
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.9
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.88
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.87
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.86
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.86
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.85
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.79
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.79
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.76
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	97.75
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.74
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	97.7
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.68
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	97.67
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.64
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	97.63
KOG0553	304	consensus TPR repeat-containing protein [General f	97.59
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.58
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.58
PF12688	120	TPR_5: Tetratrico peptide repeat	97.57
PF12688	120	TPR_5: Tetratrico peptide repeat	97.55
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	97.54
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	97.54
KOG0553	304	consensus TPR repeat-containing protein [General f	97.53
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.51
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	97.48
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.4
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	97.4
COG4700	251	Uncharacterized protein conserved in bacteria cont	97.4
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.35
KOG2796	366	consensus Uncharacterized conserved protein [Funct	97.32
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	97.31
PRK10803	263	tol-pal system protein YbgF; Provisional	97.31
PRK10803	263	tol-pal system protein YbgF; Provisional	97.28
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	97.23
PF13371	73	TPR_9: Tetratricopeptide repeat	97.21
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.14
KOG2041	1189	consensus WD40 repeat protein [General function pr	97.11
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.11
KOG2796	366	consensus Uncharacterized conserved protein [Funct	97.1
PF13371	73	TPR_9: Tetratricopeptide repeat	97.1
COG4700	251	Uncharacterized protein conserved in bacteria cont	97.09
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.09
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	97.05
PRK15331	165	chaperone protein SicA; Provisional	97.04
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	97.02
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	96.95
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	96.94
PRK15331	165	chaperone protein SicA; Provisional	96.89
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	96.83
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	96.74
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.74
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	96.65
COG3898	531	Uncharacterized membrane-bound protein [Function u	96.61
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	96.59
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	96.56
KOG2041	1189	consensus WD40 repeat protein [General function pr	96.52
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	96.48
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	96.42
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	96.41
smart00299	140	CLH Clathrin heavy chain repeat homology.	96.38
KOG3941	406	consensus Intermediate in Toll signal transduction	96.37
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	96.36
KOG2610	491	consensus Uncharacterized conserved protein [Funct	96.34
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	96.3
smart00299	140	CLH Clathrin heavy chain repeat homology.	96.27
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	96.16
KOG3941	406	consensus Intermediate in Toll signal transduction	96.14
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	96.02
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	95.99
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	95.92
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	95.91
PF13512	142	TPR_18: Tetratricopeptide repeat	95.88
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	95.85
COG3118	304	Thioredoxin domain-containing protein [Posttransla	95.83
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	95.79
COG3629	280	DnrI DNA-binding transcriptional activator of the	95.65
PF13428	44	TPR_14: Tetratricopeptide repeat	95.63
PF13428	44	TPR_14: Tetratricopeptide repeat	95.55
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	95.54
COG4105	254	ComL DNA uptake lipoprotein [General function pred	95.51
KOG4555	175	consensus TPR repeat-containing protein [Function	95.47
COG3629	280	DnrI DNA-binding transcriptional activator of the	95.42
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	95.42
COG3118	304	Thioredoxin domain-containing protein [Posttransla	95.35
KOG1941	518	consensus Acetylcholine receptor-associated protei	95.27
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	95.23
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	95.22
PF13512	142	TPR_18: Tetratricopeptide repeat	95.22
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	95.19
COG0457	291	NrfG FOG: TPR repeat [General function prediction	95.19
KOG4555	175	consensus TPR repeat-containing protein [Function	95.09
KOG2610	491	consensus Uncharacterized conserved protein [Funct	94.86
PRK11906	458	transcriptional regulator; Provisional	94.74
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	94.38
KOG4570	418	consensus Uncharacterized conserved protein [Funct	94.36
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	94.35
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	94.28
PRK11906	458	transcriptional regulator; Provisional	94.23
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	94.23
PF13431	34	TPR_17: Tetratricopeptide repeat	94.21
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	94.19
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	94.18
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	94.05
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	94.01
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	93.9
COG4105	254	ComL DNA uptake lipoprotein [General function pred	93.84
KOG4570	418	consensus Uncharacterized conserved protein [Funct	93.77
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	93.66
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	93.64
KOG1941	518	consensus Acetylcholine receptor-associated protei	93.63
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	93.43
KOG1585	308	consensus Protein required for fusion of vesicles	93.41
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	93.23
COG0457	291	NrfG FOG: TPR repeat [General function prediction	93.23
COG3898	531	Uncharacterized membrane-bound protein [Function u	93.18
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	92.77
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	92.38
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	92.36
KOG1550	552	consensus Extracellular protein SEL-1 and related	92.28
KOG1586	288	consensus Protein required for fusion of vesicles	92.12
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	91.93
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	91.67
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	91.46
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	91.45
PF13431	34	TPR_17: Tetratricopeptide repeat	91.39
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	91.1
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	91.07
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	91.0
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	90.84
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	90.55
KOG4234	271	consensus TPR repeat-containing protein [General f	90.39
KOG1585	308	consensus Protein required for fusion of vesicles	89.66
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	89.65
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	89.62
KOG1550	552	consensus Extracellular protein SEL-1 and related	89.6
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	89.37
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	89.3
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	88.8
cd08819	88	CARD_MDA5_2 Caspase activation and recruitment dom	88.52
PF13929	292	mRNA_stabil: mRNA stabilisation	88.16
PRK09687	280	putative lyase; Provisional	87.89
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	87.89
COG4455	273	ImpE Protein of avirulence locus involved in tempe	87.68
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	87.62
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	87.59
KOG4648	536	consensus Uncharacterized conserved protein, conta	87.55
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	87.43
COG3947	361	Response regulator containing CheY-like receiver a	87.39
COG4455	273	ImpE Protein of avirulence locus involved in tempe	87.33
PF07163	309	Pex26: Pex26 protein; InterPro: IPR010797 This fam	87.24
PF07163	309	Pex26: Pex26 protein; InterPro: IPR010797 This fam	87.22
cd08819	88	CARD_MDA5_2 Caspase activation and recruitment dom	86.9
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	86.88
PHA02875	413	ankyrin repeat protein; Provisional	86.73
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	86.3
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	86.22
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	85.98
PF04097	613	Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic9	85.94
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	85.6
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	85.58
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	85.44
PF10366	108	Vps39_1: Vacuolar sorting protein 39 domain 1; Int	85.38
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	84.8
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	84.44
COG1747	711	Uncharacterized N-terminal domain of the transcrip	84.38
KOG1464	440	consensus COP9 signalosome, subunit CSN2 [Posttran	83.6
PRK15180	831	Vi polysaccharide biosynthesis protein TviD; Provi	82.79
KOG4234	271	consensus TPR repeat-containing protein [General f	82.44
KOG1464	440	consensus COP9 signalosome, subunit CSN2 [Posttran	82.38
PF13929	292	mRNA_stabil: mRNA stabilisation	82.24
KOG1258	577	consensus mRNA processing protein [RNA processing	82.2
PRK15180	831	Vi polysaccharide biosynthesis protein TviD; Provi	82.16
cd00280	200	TRFH Telomeric Repeat binding Factor or TTAGGG Rep	81.89
KOG4648	536	consensus Uncharacterized conserved protein, conta	81.71
PF11848	48	DUF3368: Domain of unknown function (DUF3368); Int	81.68
PRK09687	280	putative lyase; Provisional	81.47
KOG2063	877	consensus Vacuolar assembly/sorting proteins VPS39	80.97
TIGR02508	115	type_III_yscG type III secretion protein, YscG fam	80.57
PF10345	608	Cohesin_load: Cohesin loading factor; InterPro: IP	80.52
PF06552	186	TOM20_plant: Plant specific mitochondrial import r	80.49

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=1.7e-59  Score=427.21  Aligned_cols=320  Identities=17%  Similarity=0.253  Sum_probs=176.2

Q ss_pred             CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHH
Q 044084           20 LDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYA   99 (343)
Q Consensus        20 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~   99 (343)
                      |+..+|+.++.+|++.|+++.|.++|++|.+.|+.|+   ..+|+.||.+|++.|++++|.++|++|.+.|+.||..+|+
T Consensus       435 pd~~Tyn~LL~a~~k~g~~e~A~~lf~~M~~~Gl~pD---~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTyn  511 (1060)
T PLN03218        435 PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKAD---CKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFG  511 (1060)
T ss_pred             CCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            4445555555555555555555555555555555544   4555555555555555555555555555555555555555


Q ss_pred             HHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHh--cCCCCchhhHHHHHHHHhc
Q 044084          100 SLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKN--AELNISDCISCVIVNGFSK  177 (343)
Q Consensus       100 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~~~~~l~~~~~~  177 (343)
                      .+|.+|++.|++++|.++|++|.+.|+.||..+|+.|+.+|++.|++++|.++|++|..  .++.||..+|+.+|.+|++
T Consensus       512 aLI~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k  591 (1060)
T PLN03218        512 ALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACAN  591 (1060)
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHH
Confidence            55555555555555555555555555555555555555555555555555555555543  3444555555555555555


Q ss_pred             CCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHH
Q 044084          178 RRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRL  257 (343)
Q Consensus       178 ~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  257 (343)
                      .|++++|.++|++|.+.|+.|+..+|+.+|.+|++.|++++|.++|++|.+.|+.||..+|+.++.+|++.|++++|.++
T Consensus       592 ~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l  671 (1060)
T PLN03218        592 AGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEI  671 (1060)
T ss_pred             CCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHH
Confidence            55555555555555555555555555555555555555555555555555555555555555555555555555555555


Q ss_pred             HHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh----------------HHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 044084          258 VAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK----------------YTTVISAYNMAREFDMCVKFYNEFRMNGGV  321 (343)
Q Consensus       258 ~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~----------------~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~  321 (343)
                      +++|.+.|+.||..+|+.++.+|++.|++++|.+                |+.|+.+|++.|++++|.++|++|...|+.
T Consensus       672 ~~eM~k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~  751 (1060)
T PLN03218        672 LQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLC  751 (1060)
T ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCC
Confidence            5555555555555555555555555555555544                555555555555555555555555555555


Q ss_pred             ccHHHHHHHHHHHhccccccc
Q 044084          322 IDRAMAGIMVGVFSKLSQIEE  342 (343)
Q Consensus       322 p~~~~~~~l~~~~~~~g~~~~  342 (343)
                      ||..||++++.+|++.|++++
T Consensus       752 Pd~~Ty~sLL~a~~k~G~le~  772 (1060)
T PLN03218        752 PNTITYSILLVASERKDDADV  772 (1060)
T ss_pred             CCHHHHHHHHHHHHHCCCHHH
Confidence            555555555555555555443

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=8.4e-59  Score=422.71  Aligned_cols=331  Identities=18%  Similarity=0.293  Sum_probs=323.2

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      ++++|+++|++|.+.|+.||..+|+.+|.+|++.|++++|.++|++|.+.|+.|+   ..+|+.+|.+|++.|++++|.+
T Consensus       452 ~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~Pd---vvTynaLI~gy~k~G~~eeAl~  528 (1060)
T PLN03218        452 DIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEAN---VHTFGALIDGCARAGQVAKAFG  528 (1060)
T ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHHHHCcCHHHHHH
Confidence            5789999999999999999999999999999999999999999999999999888   8999999999999999999999


Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHH--cCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhc
Q 044084           82 FFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEE--KGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNA  159 (343)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  159 (343)
                      +|++|.+.|+.||..+|+.+|.+|++.|++++|.++|++|.+  .|+.||..+|+.++.+|++.|++++|.++|+.|.+.
T Consensus       529 lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~  608 (1060)
T PLN03218        529 AYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEY  608 (1060)
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHc
Confidence            999999999999999999999999999999999999999987  678999999999999999999999999999999999


Q ss_pred             CCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHH
Q 044084          160 ELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYS  239 (343)
Q Consensus       160 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  239 (343)
                      ++.|+..+|+.+|.+|++.|++++|.++|++|.+.|+.||..+|+.++.+|++.|++++|.++|+.|.+.|+.||..+|+
T Consensus       609 gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~~pd~~tyn  688 (1060)
T PLN03218        609 NIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYS  688 (1060)
T ss_pred             CCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh----------------HHHHHHHHHhcC
Q 044084          240 SMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK----------------YTTVISAYNMAR  303 (343)
Q Consensus       240 ~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~----------------~~~l~~~~~~~g  303 (343)
                      .+|.+|++.|++++|.++|++|.+.|+.||..+|+.||.+|++.|++++|.+                |+.++.+|++.|
T Consensus       689 sLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~Ty~sLL~a~~k~G  768 (1060)
T PLN03218        689 SLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKD  768 (1060)
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCC
Confidence            9999999999999999999999999999999999999999999999999987                999999999999


Q ss_pred             CHHHHHHHHHHHHhCCCCccHHHHHHHHHHHh
Q 044084          304 EFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFS  335 (343)
Q Consensus       304 ~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~  335 (343)
                      ++++|.+++++|.+.|+.||..+|++++..|.
T Consensus       769 ~le~A~~l~~~M~k~Gi~pd~~tynsLIglc~  800 (1060)
T PLN03218        769 DADVGLDLLSQAKEDGIKPNLVMCRCITGLCL  800 (1060)
T ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            99999999999999999999999999987643

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

Probab=100.00  E-value=1.9e-53  Score=384.23  Aligned_cols=326  Identities=19%  Similarity=0.269  Sum_probs=186.0

Q ss_pred             hhhHHHHHHHHHhCC-CCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            3 SQSKLHYYEKMKSAG-IVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         3 ~~~A~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      +++|+++|++|...+ ..||..+|+.++.+|++.++++.+.+++..|.+.|+.|+   ..+|+.|+.+|++.|+++.|.+
T Consensus       103 ~~~Al~~f~~m~~~~~~~~~~~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~---~~~~n~Li~~y~k~g~~~~A~~  179 (697)
T PLN03081        103 HREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPD---QYMMNRVLLMHVKCGMLIDARR  179 (697)
T ss_pred             HHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcc---hHHHHHHHHHHhcCCCHHHHHH
Confidence            455555666555543 445555555555555555555555555555555555544   4455555555555555555555


Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCC----------------------------------
Q 044084           82 FFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGML----------------------------------  127 (343)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~----------------------------------  127 (343)
                      +|++|.    .||..+|+.++.+|++.|++++|.++|++|.+.|+.                                  
T Consensus       180 lf~~m~----~~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~~~~~~~~l~~~~~~~g~  255 (697)
T PLN03081        180 LFDEMP----ERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGV  255 (697)
T ss_pred             HHhcCC----CCCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHHHhcCCcHHHHHHHHHHHHHhCC
Confidence            555553    245555555555555555555555555555555444                                  


Q ss_pred             -CCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHH
Q 044084          128 -RDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASI  206 (343)
Q Consensus       128 -~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l  206 (343)
                       ||..+|+.|+.+|++.|++++|.++|+.|..    +|..+|+.+|.+|++.|++++|.++|++|.+.|+.||..||+.+
T Consensus       256 ~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~----~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~l  331 (697)
T PLN03081        256 VGDTFVSCALIDMYSKCGDIEDARCVFDGMPE----KTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIM  331 (697)
T ss_pred             CccceeHHHHHHHHHHCCCHHHHHHHHHhCCC----CChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence             4555555555555566666666666655532    34455666666666666666666666666555555666666666


Q ss_pred             HHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccCh
Q 044084          207 INAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNL  286 (343)
Q Consensus       207 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~  286 (343)
                      +.+|++.|++++|.+++..|.+.|++||..+|+.|+.+|++.|++++|.++|++|.+    ||..+|+.||.+|++.|+.
T Consensus       332 l~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~----~d~~t~n~lI~~y~~~G~~  407 (697)
T PLN03081        332 IRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPR----KNLISWNALIAGYGNHGRG  407 (697)
T ss_pred             HHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCC----CCeeeHHHHHHHHHHcCCH
Confidence            666666666666666666666555556666666666666666666666666655542    4555566666666666665


Q ss_pred             hHHHh----------------HHHHHHHHHhcCCHHHHHHHHHHHHh-CCCCccHHHHHHHHHHHhcccccccC
Q 044084          287 RQLEK----------------YTTVISAYNMAREFDMCVKFYNEFRM-NGGVIDRAMAGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       287 ~~a~~----------------~~~l~~~~~~~g~~~~a~~~~~~m~~-~~~~p~~~~~~~l~~~~~~~g~~~~a  343 (343)
                      ++|.+                |+.++.+|.+.|.+++|.++|+.|.+ .|+.|+..+|++++++|++.|++++|
T Consensus       408 ~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~~l~r~G~~~eA  481 (697)
T PLN03081        408 TKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEA  481 (697)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHHHHHhcCCHHHH
Confidence            55554                55555666666666666666666543 35556666666666666666655543

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

Probab=100.00  E-value=6.1e-54  Score=387.35  Aligned_cols=324  Identities=19%  Similarity=0.231  Sum_probs=297.1

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      +++.|.+++..|.+.|+.||..+|+.++..|++.|++++|.++|++|.+    ++   ..+|+.+|.+|++.|++++|++
T Consensus       138 ~~~~a~~l~~~m~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~----~~---~~t~n~li~~~~~~g~~~~A~~  210 (697)
T PLN03081        138 SIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPE----RN---LASWGTIIGGLVDAGNYREAFA  210 (697)
T ss_pred             CHHHHHHHHHHHHHhCCCcchHHHHHHHHHHhcCCCHHHHHHHHhcCCC----CC---eeeHHHHHHHHHHCcCHHHHHH
Confidence            4567888999999999889999999999999999999999999988854    33   5779999999999999999999


Q ss_pred             HHHHHHhcCCCCCh-----------------------------------HhHHHHHHHHhcccCHHHHHHHHHHHHHcCC
Q 044084           82 FFRDMKEKGILEDP-----------------------------------SVYASLICSFASIAEVKVAEELFKEAEEKGM  126 (343)
Q Consensus        82 ~~~~~~~~~~~~~~-----------------------------------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  126 (343)
                      +|++|.+.|+.|+.                                   .+|+.|+.+|++.|++++|.++|+.|.+   
T Consensus       211 lf~~M~~~g~~p~~~t~~~ll~a~~~~~~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~---  287 (697)
T PLN03081        211 LFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPE---  287 (697)
T ss_pred             HHHHHHHhCCCCChhhHHHHHHHHhcCCcHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCC---
Confidence            99998776665554                                   4557778889999999999999998853   


Q ss_pred             CCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHH
Q 044084          127 LRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASI  206 (343)
Q Consensus       127 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l  206 (343)
                       +|..+|+.++.+|++.|++++|.++|++|.+.|+.||..||+.++.+|++.|++++|.+++..|.+.|+.||..+|+.+
T Consensus       288 -~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~L  366 (697)
T PLN03081        288 -KTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTAL  366 (697)
T ss_pred             -CChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHH
Confidence             6999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccCh
Q 044084          207 INAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNL  286 (343)
Q Consensus       207 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~  286 (343)
                      +.+|++.|++++|.++|++|.+    ||..+||.||.+|++.|+.++|.++|++|.+.|+.||..||+.++.+|.+.|..
T Consensus       367 i~~y~k~G~~~~A~~vf~~m~~----~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~  442 (697)
T PLN03081        367 VDLYSKWGRMEDARNVFDRMPR----KNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLS  442 (697)
T ss_pred             HHHHHHCCCHHHHHHHHHhCCC----CCeeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcH
Confidence            9999999999999999999864    789999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHh-----------------HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHhcccccccC
Q 044084          287 RQLEK-----------------YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       287 ~~a~~-----------------~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~g~~~~a  343 (343)
                      ++|.+                 |+.++.+|++.|++++|.+++++|   ++.|+..+|++|+.+|...|+++.+
T Consensus       443 ~~a~~~f~~m~~~~g~~p~~~~y~~li~~l~r~G~~~eA~~~~~~~---~~~p~~~~~~~Ll~a~~~~g~~~~a  513 (697)
T PLN03081        443 EQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRA---PFKPTVNMWAALLTACRIHKNLELG  513 (697)
T ss_pred             HHHHHHHHHHHHhcCCCCCccchHhHHHHHHhcCCHHHHHHHHHHC---CCCCCHHHHHHHHHHHHHcCCcHHH
Confidence            99877                 999999999999999999999876   6789999999999999999998753

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=9.5e-53  Score=388.05  Aligned_cols=331  Identities=18%  Similarity=0.255  Sum_probs=279.4

Q ss_pred             chhhHHHHHHHHHhCCCCCChhh-----------------------------------HHHHHHHHHhcCCHHHHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGC-----------------------------------YCQIMEAFYKIGDSEKVAALFL   46 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~-----------------------------------~~~l~~~~~~~~~~~~a~~~~~   46 (343)
                      ++++|+++|++|.+.|+.||..|                                   |+.|+.+|++.|++++|.++|+
T Consensus       167 ~~~~A~~~f~~M~~~g~~Pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~  246 (857)
T PLN03077        167 YFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFD  246 (857)
T ss_pred             CHHHHHHHHHHHHHcCCCCChhHHHHHHHHhCCccchhhHHHHHHHHHHcCCCcccchHhHHHHHHhcCCCHHHHHHHHh
Confidence            45667777777776666665555                                   4666677778888888888888


Q ss_pred             HHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCC
Q 044084           47 ECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGM  126 (343)
Q Consensus        47 ~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  126 (343)
                      +|...    +   ..+||.+|.+|++.|++++|+++|++|.+.|+.||..||+.++.+|++.|+.+.+.+++..+.+.|+
T Consensus       247 ~m~~~----d---~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~  319 (857)
T PLN03077        247 RMPRR----D---CISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGF  319 (857)
T ss_pred             cCCCC----C---cchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCC
Confidence            87532    2   5789999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHH
Q 044084          127 LRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASI  206 (343)
Q Consensus       127 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l  206 (343)
                      .||..+|+.|+.+|++.|++++|.++|++|..    ||..+|+.+|.+|++.|++++|.++|++|.+.|+.||..||+.+
T Consensus       320 ~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~----~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~l  395 (857)
T PLN03077        320 AVDVSVCNSLIQMYLSLGSWGEAEKVFSRMET----KDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASV  395 (857)
T ss_pred             ccchHHHHHHHHHHHhcCCHHHHHHHHhhCCC----CCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHH
Confidence            99999999999999999999999999999864    67789999999999999999999999999999999999999999


Q ss_pred             HHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhC----------------------
Q 044084          207 INAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK----------------------  264 (343)
Q Consensus       207 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~----------------------  264 (343)
                      +.+|++.|+++.|.++++.+.+.|+.|+..+|+.|+.+|++.|++++|.++|++|.+.                      
T Consensus       396 l~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~vs~~~mi~~~~~~g~~~eA~  475 (857)
T PLN03077        396 LSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEAL  475 (857)
T ss_pred             HHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHCCCHHHHH
Confidence            9999999999999999999999888888888888888888888777777777766542                      


Q ss_pred             --------CCCchHHHHHHHHH-----------------------------------HHhcccChhHHHh----------
Q 044084          265 --------GCEPNVWIYNSLMD-----------------------------------MHGRAKNLRQLEK----------  291 (343)
Q Consensus       265 --------~~~p~~~~~~~l~~-----------------------------------~~~~~~~~~~a~~----------  291 (343)
                              ++.||..||+.++.                                   +|++.|++++|..          
T Consensus       476 ~lf~~m~~~~~pd~~t~~~lL~a~~~~g~l~~~~~i~~~~~~~g~~~~~~~~naLi~~y~k~G~~~~A~~~f~~~~~d~~  555 (857)
T PLN03077        476 IFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSHEKDVV  555 (857)
T ss_pred             HHHHHHHhCCCCCHhHHHHHHHHHhhhchHHHhHHHHHHHHHhCCCccceechHHHHHHHHcCCHHHHHHHHHhcCCChh
Confidence                    35677776665554                                   4444455555543          


Q ss_pred             -HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHhcccccccC
Q 044084          292 -YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       292 -~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~g~~~~a  343 (343)
                       |+.++.+|++.|+.++|+++|++|.+.|+.||..||+.++.+|.+.|++++|
T Consensus       556 s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~v~ea  608 (857)
T PLN03077        556 SWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQG  608 (857)
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCcccHHHHHHHHhhcChHHHH
Confidence             8888899999999999999999999999999999999999999998888764

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=4.4e-51  Score=377.00  Aligned_cols=328  Identities=14%  Similarity=0.168  Sum_probs=270.2

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCc-----------------------
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPS-----------------------   58 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-----------------------   58 (343)
                      +++.|+++|++|.+    ||..+|+.+|.+|++.|++++|.++|++|...|+.|+..                       
T Consensus       136 ~~~~A~~~f~~m~~----~d~~~~n~li~~~~~~g~~~~A~~~f~~M~~~g~~Pd~~t~~~ll~~~~~~~~~~~~~~~~~  211 (857)
T PLN03077        136 ELVHAWYVFGKMPE----RDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHA  211 (857)
T ss_pred             ChHHHHHHHhcCCC----CCeeEHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHhCCccchhhHHHHHH
Confidence            56889999999974    789999999999999999999999999999999887721                       


Q ss_pred             ---------hHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCC
Q 044084           59 ---------STHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRD  129 (343)
Q Consensus        59 ---------~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  129 (343)
                               +..+|+.||.+|++.|+++.|.++|++|.    .||..+|+.+|.+|++.|++++|.++|.+|.+.|+.||
T Consensus       212 ~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~----~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd  287 (857)
T PLN03077        212 HVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMP----RRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPD  287 (857)
T ss_pred             HHHHcCCCcccchHhHHHHHHhcCCCHHHHHHHHhcCC----CCCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCC
Confidence                     12345666666667777777777777764    35667777777777777777777777777777777778


Q ss_pred             HHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHH
Q 044084          130 LEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINA  209 (343)
Q Consensus       130 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~  209 (343)
                      ..+|+.++.++++.|+.+.|.+++..+.+.|+.||..+|+.++.+|++.|++++|.++|++|.    .||..+|+.++.+
T Consensus       288 ~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~----~~d~~s~n~li~~  363 (857)
T PLN03077        288 LMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRME----TKDAVSWTAMISG  363 (857)
T ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCC----CCCeeeHHHHHHH
Confidence            778888888887777777788888777777777788888888888888888888888888775    4677788888888


Q ss_pred             HHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHH
Q 044084          210 YCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQL  289 (343)
Q Consensus       210 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a  289 (343)
                      |++.|++++|.++|++|.+.|+.||..+|+.++.+|++.|+++.|.++++.|.+.|+.|+..+++.|+++|++.|++++|
T Consensus       364 ~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A  443 (857)
T PLN03077        364 YEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKA  443 (857)
T ss_pred             HHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCHHHH
Confidence            88888888888888888888888888888888888888888888888888888888888888999999999999999988


Q ss_pred             Hh------------HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHhccccccc
Q 044084          290 EK------------YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEE  342 (343)
Q Consensus       290 ~~------------~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~g~~~~  342 (343)
                      .+            |+.++.+|++.|+.++|+.+|++|.. ++.||..||++++.+|++.|.+++
T Consensus       444 ~~vf~~m~~~d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~-~~~pd~~t~~~lL~a~~~~g~l~~  507 (857)
T PLN03077        444 LEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLL-TLKPNSVTLIAALSACARIGALMC  507 (857)
T ss_pred             HHHHHhCCCCCeeeHHHHHHHHHHCCCHHHHHHHHHHHHh-CCCCCHhHHHHHHHHHhhhchHHH
Confidence            87            99999999999999999999999986 588999998888877777666543

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

Probab=99.95  E-value=1.8e-24  Score=203.61  Aligned_cols=327  Identities=13%  Similarity=0.098  Sum_probs=239.0

Q ss_pred             hhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHH
Q 044084            3 SQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKF   82 (343)
Q Consensus         3 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~   82 (343)
                      .++|...|+++.+.+. .+...+..++..+.+.|++++|..+++.+.+..    |.+..+|..+...+...|++++|+..
T Consensus       549 ~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~----~~~~~~~~~l~~~~~~~~~~~~A~~~  623 (899)
T TIGR02917       549 EEEAVAWLEKAAELNP-QEIEPALALAQYYLGKGQLKKALAILNEAADAA----PDSPEAWLMLGRAQLAAGDLNKAVSS  623 (899)
T ss_pred             HHHHHHHHHHHHHhCc-cchhHHHHHHHHHHHCCCHHHHHHHHHHHHHcC----CCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            3455555555554432 344445555556666666666666666655433    12245666667777777777777777


Q ss_pred             HHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCC
Q 044084           83 FRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELN  162 (343)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  162 (343)
                      |+++.+.. +.+...+..+...+.+.|++++|..+++++.+..+ .+..++..++..+...|++++|.++++.+.+..+ 
T Consensus       624 ~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-  700 (899)
T TIGR02917       624 FKKLLALQ-PDSALALLLLADAYAVMKNYAKAITSLKRALELKP-DNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQHP-  700 (899)
T ss_pred             HHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCc-
Confidence            77666543 22445566666666677777777777777666543 2566677777777777777777777777766654 


Q ss_pred             CchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHH
Q 044084          163 ISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMV  242 (343)
Q Consensus       163 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  242 (343)
                      .+...+..+...+...|++++|.+.|+++...+  |+..++..+..++.+.|++++|.+.++.+.+.. +.+...+..+.
T Consensus       701 ~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~-~~~~~~~~~la  777 (899)
T TIGR02917       701 KAALGFELEGDLYLRQKDYPAAIQAYRKALKRA--PSSQNAIKLHRALLASGNTAEAVKTLEAWLKTH-PNDAVLRTALA  777 (899)
T ss_pred             CChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--CCchHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHH
Confidence            455667777778888888888888888887763  555677778888888889999988888888765 56788888999


Q ss_pred             HHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh---------------HHHHHHHHHhcCCHHH
Q 044084          243 AMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK---------------YTTVISAYNMAREFDM  307 (343)
Q Consensus       243 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~---------------~~~l~~~~~~~g~~~~  307 (343)
                      ..|...|++++|...|+++.+.. +++..++..+...+...|+ .+|..               +..+...+...|++++
T Consensus       778 ~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~-~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  855 (899)
T TIGR02917       778 ELYLAQKDYDKAIKHYRTVVKKA-PDNAVVLNNLAWLYLELKD-PRALEYAEKALKLAPNIPAILDTLGWLLVEKGEADR  855 (899)
T ss_pred             HHHHHCcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCc-HHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHH
Confidence            99999999999999999998864 4577888899999999988 66666               5677888999999999


Q ss_pred             HHHHHHHHHhCCCCccHHHHHHHHHHHhcccccccC
Q 044084          308 CVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       308 a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~g~~~~a  343 (343)
                      |.++++++.+.+.. ++.++..+..++.+.|+.++|
T Consensus       856 A~~~~~~a~~~~~~-~~~~~~~l~~~~~~~g~~~~A  890 (899)
T TIGR02917       856 ALPLLRKAVNIAPE-AAAIRYHLALALLATGRKAEA  890 (899)
T ss_pred             HHHHHHHHHhhCCC-ChHHHHHHHHHHHHcCCHHHH
Confidence            99999999998754 888999999999999998875

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

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.95  E-value=1.1e-24  Score=185.42  Aligned_cols=310  Identities=10%  Similarity=0.049  Sum_probs=206.1

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      ++++|+..|.++.+.++ .+..++..+...+.+.|++++|..+++.+......+.......+..++..+...|++++|..
T Consensus        50 ~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g~~~~A~~  128 (389)
T PRK11788         50 QPDKAIDLFIEMLKVDP-ETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAGLLDRAEE  128 (389)
T ss_pred             ChHHHHHHHHHHHhcCc-ccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHH
Confidence            45677777777777643 34556777777777777777777777777654322211112456677777777777777777


Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCC----HHHHHHHHHHHHhcCcHhHHHHHHHHHH
Q 044084           82 FFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRD----LEVFLKLVLMYIEEGMVEKTLEVVESMK  157 (343)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~  157 (343)
                      +|+++.+.. +++..++..++..+.+.|++++|.+.++.+.+.+..+.    ...+..+...+.+.|++++|...|+++.
T Consensus       129 ~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al  207 (389)
T PRK11788        129 LFLQLVDEG-DFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDLDAARALLKKAL  207 (389)
T ss_pred             HHHHHHcCC-cchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence            777776642 23556677777777777777777777777776553322    1234556666777777777777777776


Q ss_pred             hcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhh
Q 044084          158 NAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVA  237 (343)
Q Consensus       158 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  237 (343)
                      +... .+...+..+...+...|++++|.++++++...+......++..+..+|...|++++|...++.+.+..  |+...
T Consensus       208 ~~~p-~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~--p~~~~  284 (389)
T PRK11788        208 AADP-QCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRALEEY--PGADL  284 (389)
T ss_pred             hHCc-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCchH
Confidence            6543 33445666777777777777777777777765322223456677777777777777777777777653  45555


Q ss_pred             HHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 044084          238 YSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRM  317 (343)
Q Consensus       238 ~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~~  317 (343)
                      +..++..+.+.|++++|..+++++.+.  .|+..++..++..+...                ...|+.++++.++++|.+
T Consensus       285 ~~~la~~~~~~g~~~~A~~~l~~~l~~--~P~~~~~~~l~~~~~~~----------------~~~g~~~~a~~~~~~~~~  346 (389)
T PRK11788        285 LLALAQLLEEQEGPEAAQALLREQLRR--HPSLRGFHRLLDYHLAE----------------AEEGRAKESLLLLRDLVG  346 (389)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHh--CcCHHHHHHHHHHhhhc----------------cCCccchhHHHHHHHHHH
Confidence            677777777777777777777777664  56666666555443321                114577889999999999


Q ss_pred             CCCCccHHHHHHHHHHHhccccc
Q 044084          318 NGGVIDRAMAGIMVGVFSKLSQI  340 (343)
Q Consensus       318 ~~~~p~~~~~~~l~~~~~~~g~~  340 (343)
                      .++.|++..      +|..||-.
T Consensus       347 ~~~~~~p~~------~c~~cg~~  363 (389)
T PRK11788        347 EQLKRKPRY------RCRNCGFT  363 (389)
T ss_pred             HHHhCCCCE------ECCCCCCC
Confidence            888888773      46666644

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

Probab=99.94  E-value=5e-23  Score=193.80  Aligned_cols=325  Identities=12%  Similarity=0.103  Sum_probs=174.9

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      ++++|+.+++.+.... +++..++..+...+...|++++|.+.|+++.+...    .+...+..+...+...|++++|.+
T Consensus       446 ~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~----~~~~~~~~la~~~~~~g~~~~A~~  520 (899)
T TIGR02917       446 QFDKALAAAKKLEKKQ-PDNASLHNLLGAIYLGKGDLAKAREAFEKALSIEP----DFFPAAANLARIDIQEGNPDDAIQ  520 (899)
T ss_pred             CHHHHHHHHHHHHHhC-CCCcHHHHHHHHHHHhCCCHHHHHHHHHHHHhhCC----CcHHHHHHHHHHHHHCCCHHHHHH
Confidence            3456666666665542 23455566666666666666666666666554331    112344445555555555555555


Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHh----------------------------------cccCHHHHHHHHHHHHHcCCC
Q 044084           82 FFRDMKEKGILEDPSVYASLICSFA----------------------------------SIAEVKVAEELFKEAEEKGML  127 (343)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~l~~~~~----------------------------------~~~~~~~a~~~~~~~~~~~~~  127 (343)
                      .++++...+ +.+..++..+...+.                                  ..|++++|..+++.+.+... 
T Consensus       521 ~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-  598 (899)
T TIGR02917       521 RFEKVLTID-PKNLRAILALAGLYLRTGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEAADAAP-  598 (899)
T ss_pred             HHHHHHHhC-cCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchhHHHHHHHHHHHCCCHHHHHHHHHHHHHcCC-
Confidence            555554432 113334444444444                                  44444444444444443322 


Q ss_pred             CCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHH
Q 044084          128 RDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASII  207 (343)
Q Consensus       128 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll  207 (343)
                      .+..+|..+...+...|++++|...|+++.+..+ .+...+..+..++...|++++|..+++++.+.. +.+..++..+.
T Consensus       599 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~  676 (899)
T TIGR02917       599 DSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQP-DSALALLLLADAYAVMKNYAKAITSLKRALELK-PDNTEAQIGLA  676 (899)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHH
Confidence            2444555555555555555555555555544332 233344455555555555555555555555432 22344555555


Q ss_pred             HHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChh
Q 044084          208 NAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLR  287 (343)
Q Consensus       208 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~  287 (343)
                      ..+...|++++|..+++.+.+.+ +.+...+..+...+...|++++|...|+++...  .|+..++..+..++.+.|+++
T Consensus       677 ~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~  753 (899)
T TIGR02917       677 QLLLAAKRTESAKKIAKSLQKQH-PKAALGFELEGDLYLRQKDYPAAIQAYRKALKR--APSSQNAIKLHRALLASGNTA  753 (899)
T ss_pred             HHHHHcCCHHHHHHHHHHHHhhC-cCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhh--CCCchHHHHHHHHHHHCCCHH
Confidence            55555555555555555555543 334555556666666666666666666666654  334455555666666666666


Q ss_pred             HHHh---------------HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHhcccc
Q 044084          288 QLEK---------------YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQ  339 (343)
Q Consensus       288 ~a~~---------------~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~g~  339 (343)
                      +|..               +..+...|...|++++|.+.|+++.+... ++...++.+..++.+.|+
T Consensus       754 ~A~~~~~~~l~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p-~~~~~~~~l~~~~~~~~~  819 (899)
T TIGR02917       754 EAVKTLEAWLKTHPNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKAP-DNAVVLNNLAWLYLELKD  819 (899)
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhcCc
Confidence            6654               55556666667777777777777766542 345556666666666555

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

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.92  E-value=2.6e-21  Score=164.86  Aligned_cols=284  Identities=12%  Similarity=0.093  Sum_probs=228.4

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCC---hHhHHH
Q 044084           24 CYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILED---PSVYAS  100 (343)
Q Consensus        24 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~  100 (343)
                      ........+...|++++|...|.++.+.+    |.+..++..+...+...|++++|..+++.+...+..++   ...+..
T Consensus        37 ~~y~~g~~~~~~~~~~~A~~~~~~al~~~----p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~  112 (389)
T PRK11788         37 RDYFKGLNFLLNEQPDKAIDLFIEMLKVD----PETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQE  112 (389)
T ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHhcC----cccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence            33344556778899999999999998864    33467899999999999999999999999987542222   245778


Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCch----hhHHHHHHHHh
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISD----CISCVIVNGFS  176 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~  176 (343)
                      +...+.+.|+++.|..+|+++.+... .+..++..++..+.+.|++++|.+.++.+.+.+..+..    ..+..+...+.
T Consensus       113 La~~~~~~g~~~~A~~~~~~~l~~~~-~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~  191 (389)
T PRK11788        113 LGQDYLKAGLLDRAEELFLQLVDEGD-FAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQAL  191 (389)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHcCCc-chHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHH
Confidence            88999999999999999999988643 46889999999999999999999999999876643321    23556777888


Q ss_pred             cCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHH
Q 044084          177 KRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMR  256 (343)
Q Consensus       177 ~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  256 (343)
                      ..|++++|.+.|+++.+.. +.+...+..+...+.+.|++++|.++++++.+.+......+++.++.+|...|++++|..
T Consensus       192 ~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~  270 (389)
T PRK11788        192 ARGDLDAARALLKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLE  270 (389)
T ss_pred             hCCCHHHHHHHHHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHH
Confidence            9999999999999998864 334567778889999999999999999999986533335678899999999999999999


Q ss_pred             HHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHhc
Q 044084          257 LVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSK  336 (343)
Q Consensus       257 ~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~  336 (343)
                      .++++.+.  .|+...+..+                   +..+.+.|++++|..+++++.+.  .|+..++..++..+..
T Consensus       271 ~l~~~~~~--~p~~~~~~~l-------------------a~~~~~~g~~~~A~~~l~~~l~~--~P~~~~~~~l~~~~~~  327 (389)
T PRK11788        271 FLRRALEE--YPGADLLLAL-------------------AQLLEEQEGPEAAQALLREQLRR--HPSLRGFHRLLDYHLA  327 (389)
T ss_pred             HHHHHHHh--CCCchHHHHH-------------------HHHHHHhCCHHHHHHHHHHHHHh--CcCHHHHHHHHHHhhh
Confidence            99999876  4665544333                   44566678888999999998875  5888888888877664

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

Probab=99.90  E-value=3e-19  Score=160.06  Aligned_cols=331  Identities=10%  Similarity=0.008  Sum_probs=256.6

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      ++++|+..|++.++.  .|+...|..+..+|.+.|++++|++.++...+.+    |....+|..+..++...|++++|+.
T Consensus       142 ~~~~Ai~~y~~al~~--~p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l~----p~~~~a~~~~a~a~~~lg~~~eA~~  215 (615)
T TIGR00990       142 DFNKAIKLYSKAIEC--KPDPVYYSNRAACHNALGDWEKVVEDTTAALELD----PDYSKALNRRANAYDGLGKYADALL  215 (615)
T ss_pred             CHHHHHHHHHHHHhc--CCchHHHHHHHHHHHHhCCHHHHHHHHHHHHHcC----CCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            678999999999875  4677889999999999999999999999987764    3346789999999999999999987


Q ss_pred             HHHHHHhcCC----------------------------CC-ChHhHHHHHH-----------------------------
Q 044084           82 FFRDMKEKGI----------------------------LE-DPSVYASLIC-----------------------------  103 (343)
Q Consensus        82 ~~~~~~~~~~----------------------------~~-~~~~~~~l~~-----------------------------  103 (343)
                      .|......+.                            .| +...+..+..                             
T Consensus       216 ~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  295 (615)
T TIGR00990       216 DLTASCIIDGFRNEQSAQAVERLLKKFAESKAKEILETKPENLPSVTFVGNYLQSFRPKPRPAGLEDSNELDEETGNGQL  295 (615)
T ss_pred             HHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHccCCcchhhhhcccccccccccchH
Confidence            6654432110                            00 0000100000                             


Q ss_pred             -HH------hcccCHHHHHHHHHHHHHcC-CCC-CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHH
Q 044084          104 -SF------ASIAEVKVAEELFKEAEEKG-MLR-DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNG  174 (343)
Q Consensus       104 -~~------~~~~~~~~a~~~~~~~~~~~-~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  174 (343)
                       ..      ...+++++|...|+...+.+ ..| ....+..+...+...|++++|+..|++..+..+ .....|..+...
T Consensus       296 ~l~~~~~e~~~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~P-~~~~~~~~la~~  374 (615)
T TIGR00990       296 QLGLKSPESKADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELDP-RVTQSYIKRASM  374 (615)
T ss_pred             HHHHHHHHhhhhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC-CcHHHHHHHHHH
Confidence             00      11256888999999988764 223 466788889999999999999999999987654 345578888889


Q ss_pred             HhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHH
Q 044084          175 FSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDA  254 (343)
Q Consensus       175 ~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  254 (343)
                      +...|++++|...|++..+.. +.+...+..+...+...|++++|...|+...+.. +.+...+..+...+.+.|++++|
T Consensus       375 ~~~~g~~~eA~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~-P~~~~~~~~la~~~~~~g~~~eA  452 (615)
T TIGR00990       375 NLELGDPDKAEEDFDKALKLN-SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLD-PDFIFSHIQLGVTQYKEGSIASS  452 (615)
T ss_pred             HHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-ccCHHHHHHHHHHHHHCCCHHHH
Confidence            999999999999999998774 3456788888999999999999999999999875 44677888899999999999999


Q ss_pred             HHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh----------------------HHHHHHHHHhcCCHHHHHHHH
Q 044084          255 MRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK----------------------YTTVISAYNMAREFDMCVKFY  312 (343)
Q Consensus       255 ~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~----------------------~~~l~~~~~~~g~~~~a~~~~  312 (343)
                      ...|++..+.. +.+...+..+...+...|++++|..                      ++.....+...|++++|.+++
T Consensus       453 ~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~~~~~eA~~~~  531 (615)
T TIGR00990       453 MATFRRCKKNF-PEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWKQDFIEAENLC  531 (615)
T ss_pred             HHHHHHHHHhC-CCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHhhhHHHHHHHH
Confidence            99999998752 3356788889999999999999976                      111122233469999999999


Q ss_pred             HHHHhCCCCccHHHHHHHHHHHhcccccccC
Q 044084          313 NEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       313 ~~m~~~~~~p~~~~~~~l~~~~~~~g~~~~a  343 (343)
                      ++...... .+...+..+..++.+.|++++|
T Consensus       532 ~kAl~l~p-~~~~a~~~la~~~~~~g~~~eA  561 (615)
T TIGR00990       532 EKALIIDP-ECDIAVATMAQLLLQQGDVDEA  561 (615)
T ss_pred             HHHHhcCC-CcHHHHHHHHHHHHHccCHHHH
Confidence            99887642 2344688899999999998875

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.90  E-value=6.1e-19  Score=157.82  Aligned_cols=307  Identities=9%  Similarity=0.032  Sum_probs=241.2

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      ++++|+.+++......+. +...+..++......|++++|...|+++....    |.+...+..+...+...|++++|+.
T Consensus        57 ~~~~A~~l~~~~l~~~p~-~~~~l~~l~~~~l~~g~~~~A~~~l~~~l~~~----P~~~~a~~~la~~l~~~g~~~~Ai~  131 (656)
T PRK15174         57 ETDVGLTLLSDRVLTAKN-GRDLLRRWVISPLASSQPDAVLQVVNKLLAVN----VCQPEDVLLVASVLLKSKQYATVAD  131 (656)
T ss_pred             CcchhHHHhHHHHHhCCC-chhHHHHHhhhHhhcCCHHHHHHHHHHHHHhC----CCChHHHHHHHHHHHHcCCHHHHHH
Confidence            467888888888887543 45566666677778999999999999998765    3335788888999999999999999


Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCC
Q 044084           82 FFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAEL  161 (343)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  161 (343)
                      .+++..+.. +.+...+..+...+...|++++|...++.+....+. +...+..+ ..+...|++++|...++.+.+...
T Consensus       132 ~l~~Al~l~-P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~P~-~~~a~~~~-~~l~~~g~~~eA~~~~~~~l~~~~  208 (656)
T PRK15174        132 LAEQAWLAF-SGNSQIFALHLRTLVLMDKELQAISLARTQAQEVPP-RGDMIATC-LSFLNKSRLPEDHDLARALLPFFA  208 (656)
T ss_pred             HHHHHHHhC-CCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCCC-CHHHHHHH-HHHHHcCCHHHHHHHHHHHHhcCC
Confidence            999998763 224667888888999999999999999988776544 33444333 347888999999999999877654


Q ss_pred             CCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhH----HHHHHHHHHHcCCCcChhh
Q 044084          162 NISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSK----AEKVFIEMQQKGFDKCVVA  237 (343)
Q Consensus       162 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~----a~~~~~~~~~~~~~~~~~~  237 (343)
                      .++...+..+...+...|++++|...+++..... +.+...+..+...+...|++++    |...|+...+.. +.+...
T Consensus       209 ~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~-p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l~-P~~~~a  286 (656)
T PRK15174        209 LERQESAGLAVDTLCAVGKYQEAIQTGESALARG-LDGAALRRSLGLAYYQSGRSREAKLQAAEHWRHALQFN-SDNVRI  286 (656)
T ss_pred             CcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHhhC-CCCHHH
Confidence            3444455566778889999999999999988774 3456677788888999999885    789999988875 446778


Q ss_pred             HHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh---------------HHHHHHHHHhc
Q 044084          238 YSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK---------------YTTVISAYNMA  302 (343)
Q Consensus       238 ~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~---------------~~~l~~~~~~~  302 (343)
                      +..+...+...|++++|...+++..+.. +.+...+..+..++.+.|++++|..               +..+..++...
T Consensus       287 ~~~lg~~l~~~g~~~eA~~~l~~al~l~-P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~~P~~~~~~~~~a~al~~~  365 (656)
T PRK15174        287 VTLYADALIRTGQNEKAIPLLQQSLATH-PDLPYVRAMYARALRQVGQYTAASDEFVQLAREKGVTSKWNRYAAAALLQA  365 (656)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHC
Confidence            8899999999999999999999988763 2245567778888999999998876               33345678889


Q ss_pred             CCHHHHHHHHHHHHhCC
Q 044084          303 REFDMCVKFYNEFRMNG  319 (343)
Q Consensus       303 g~~~~a~~~~~~m~~~~  319 (343)
                      |++++|+..|++..+..
T Consensus       366 G~~deA~~~l~~al~~~  382 (656)
T PRK15174        366 GKTSEAESVFEHYIQAR  382 (656)
T ss_pred             CCHHHHHHHHHHHHHhC
Confidence            99999999999987754

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.88  E-value=8e-19  Score=157.07  Aligned_cols=307  Identities=10%  Similarity=0.025  Sum_probs=249.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHH
Q 044084           25 YCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICS  104 (343)
Q Consensus        25 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  104 (343)
                      ...++..+.+.|++++|..+++.........    ...+..++.+....|++++|+..++++..... .+...+..+...
T Consensus        45 ~~~~~~~~~~~g~~~~A~~l~~~~l~~~p~~----~~~l~~l~~~~l~~g~~~~A~~~l~~~l~~~P-~~~~a~~~la~~  119 (656)
T PRK15174         45 IILFAIACLRKDETDVGLTLLSDRVLTAKNG----RDLLRRWVISPLASSQPDAVLQVVNKLLAVNV-CQPEDVLLVASV  119 (656)
T ss_pred             HHHHHHHHHhcCCcchhHHHhHHHHHhCCCc----hhHHHHHhhhHhhcCCHHHHHHHHHHHHHhCC-CChHHHHHHHHH
Confidence            4456677889999999999999998876544    35677777888889999999999999998742 256678888899


Q ss_pred             HhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHH
Q 044084          105 FASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAA  184 (343)
Q Consensus       105 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  184 (343)
                      +...|++++|...++++.+..+. +...+..+...+...|++++|...++.+....+.+ ...+..+ ..+...|++++|
T Consensus       120 l~~~g~~~~Ai~~l~~Al~l~P~-~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~P~~-~~a~~~~-~~l~~~g~~~eA  196 (656)
T PRK15174        120 LLKSKQYATVADLAEQAWLAFSG-NSQIFALHLRTLVLMDKELQAISLARTQAQEVPPR-GDMIATC-LSFLNKSRLPED  196 (656)
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCCCC-HHHHHHH-HHHHHcCCHHHH
Confidence            99999999999999999986543 68889999999999999999999999887665533 3334333 347889999999


Q ss_pred             HHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHH----HHHHHHH
Q 044084          185 VKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRD----AMRLVAK  260 (343)
Q Consensus       185 ~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~----a~~~~~~  260 (343)
                      ...++.+.+....++...+..+..++.+.|++++|...++...+.. +.+...+..+...+...|++++    |...|++
T Consensus       197 ~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~-p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~  275 (656)
T PRK15174        197 HDLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARG-LDGAALRRSLGLAYYQSGRSREAKLQAAEHWRH  275 (656)
T ss_pred             HHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCchhhHHHHHHHHHH
Confidence            9999998876433444555566788899999999999999999875 4567788899999999999986    8999999


Q ss_pred             HhhCCCCchHHHHHHHHHHHhcccChhHHHh---------------HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHH
Q 044084          261 MKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK---------------YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRA  325 (343)
Q Consensus       261 m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~---------------~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~  325 (343)
                      ..+.. +.+...+..+...+...|++++|..               +..+..++.+.|++++|+..++++...+  |+..
T Consensus       276 Al~l~-P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~~--P~~~  352 (656)
T PRK15174        276 ALQFN-SDNVRIVTLYADALIRTGQNEKAIPLLQQSLATHPDLPYVRAMYARALRQVGQYTAASDEFVQLAREK--GVTS  352 (656)
T ss_pred             HHhhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--ccch
Confidence            98763 2356788899999999999999987               6778889999999999999999998864  4443


Q ss_pred             H-HHHHHHHHhcccccccC
Q 044084          326 M-AGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       326 ~-~~~l~~~~~~~g~~~~a  343 (343)
                      . +..+..++...|+.++|
T Consensus       353 ~~~~~~a~al~~~G~~deA  371 (656)
T PRK15174        353 KWNRYAAAALLQAGKTSEA  371 (656)
T ss_pred             HHHHHHHHHHHHCCCHHHH
Confidence            3 44457788899988764

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.86  E-value=2.3e-17  Score=157.34  Aligned_cols=334  Identities=10%  Similarity=0.006  Sum_probs=234.3

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHH------------HHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYK------------ILCDS   69 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~------------~li~~   69 (343)
                      ++++|+..|++..+..+ .+...+..+..++.+.|++++|...|++..+.......  ...|.            .....
T Consensus       284 ~~~~A~~~l~~aL~~~P-~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~--~~~~~~ll~~~~~~~~~~~g~~  360 (1157)
T PRK11447        284 QGGKAIPELQQAVRANP-KDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSN--RDKWESLLKVNRYWLLIQQGDA  360 (1157)
T ss_pred             CHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccc--hhHHHHHHHhhhHHHHHHHHHH
Confidence            57889999999888653 36788889999999999999999999998776543221  11121            22446


Q ss_pred             hhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHH-------------
Q 044084           70 LGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKL-------------  136 (343)
Q Consensus        70 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l-------------  136 (343)
                      +.+.|++++|+..|++..+... .+...+..+...+...|++++|++.|+++.+.... +...+..+             
T Consensus       361 ~~~~g~~~eA~~~~~~Al~~~P-~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~p~-~~~a~~~L~~l~~~~~~~~A~  438 (1157)
T PRK11447        361 ALKANNLAQAERLYQQARQVDN-TDSYAVLGLGDVAMARKDYAAAERYYQQALRMDPG-NTNAVRGLANLYRQQSPEKAL  438 (1157)
T ss_pred             HHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhcCHHHHH
Confidence            6788999999999999988642 35566777888899999999999999998876432 33333322             


Q ss_pred             -----------------------------HHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHH
Q 044084          137 -----------------------------VLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKV  187 (343)
Q Consensus       137 -----------------------------~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  187 (343)
                                                   ...+...|++++|++.|++..+..+ -+...+..+...|...|++++|...
T Consensus       439 ~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~P-~~~~~~~~LA~~~~~~G~~~~A~~~  517 (1157)
T PRK11447        439 AFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLALDP-GSVWLTYRLAQDLRQAGQRSQADAL  517 (1157)
T ss_pred             HHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHH
Confidence                                         2334567888888888888877664 3555677788888888999999988


Q ss_pred             HHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHc--------------------------------------
Q 044084          188 YEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQK--------------------------------------  229 (343)
Q Consensus       188 ~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~--------------------------------------  229 (343)
                      ++++.+.. +.+...+..+...+...++.++|...++.+...                                      
T Consensus       518 l~~al~~~-P~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~~l  596 (1157)
T PRK11447        518 MRRLAQQK-PNDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEALL  596 (1157)
T ss_pred             HHHHHHcC-CCCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHHHH
Confidence            88887653 112222222222233334444443333321100                                      


Q ss_pred             -CCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh---------------HH
Q 044084          230 -GFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK---------------YT  293 (343)
Q Consensus       230 -~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~---------------~~  293 (343)
                       ..+.+...+..+...+.+.|++++|+..|++..+.. +.+...+..+...+...|+.++|..               +.
T Consensus       597 ~~~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~-P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~~p~~~~~~~  675 (1157)
T PRK11447        597 RQQPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTRE-PGNADARLGLIEVDIAQGDLAAARAQLAKLPATANDSLNTQR  675 (1157)
T ss_pred             HhCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhccCCCChHHHH
Confidence             124455667778888899999999999999998763 3357788889999999999999987               55


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCC--c---cHHHHHHHHHHHhcccccccC
Q 044084          294 TVISAYNMAREFDMCVKFYNEFRMNGGV--I---DRAMAGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       294 ~l~~~~~~~g~~~~a~~~~~~m~~~~~~--p---~~~~~~~l~~~~~~~g~~~~a  343 (343)
                      .+..++...|++++|.++++++......  |   +...+..+...+.+.|+.++|
T Consensus       676 ~la~~~~~~g~~~eA~~~~~~al~~~~~~~~~~~~a~~~~~~a~~~~~~G~~~~A  730 (1157)
T PRK11447        676 RVALAWAALGDTAAAQRTFNRLIPQAKSQPPSMESALVLRDAARFEAQTGQPQQA  730 (1157)
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHhhhCccCCcchhhHHHHHHHHHHHHHcCCHHHH
Confidence            6677888999999999999998775332  2   224566667788888887654

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

Probab=99.84  E-value=2.2e-18  Score=143.31  Aligned_cols=184  Identities=18%  Similarity=0.210  Sum_probs=80.0

Q ss_pred             HHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCC
Q 044084          100 SLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRR  179 (343)
Q Consensus       100 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  179 (343)
                      .|.-.+-..|+.-.|++.|++..+..+. =...|-.|...|...+.++.|+..|.+.....+ .....+..+...|..+|
T Consensus       223 nLg~~f~~~Gei~~aiq~y~eAvkldP~-f~dAYiNLGnV~ke~~~~d~Avs~Y~rAl~lrp-n~A~a~gNla~iYyeqG  300 (966)
T KOG4626|consen  223 NLGCVFNAQGEIWLAIQHYEEAVKLDPN-FLDAYINLGNVYKEARIFDRAVSCYLRALNLRP-NHAVAHGNLACIYYEQG  300 (966)
T ss_pred             hcchHHhhcchHHHHHHHHHHhhcCCCc-chHHHhhHHHHHHHHhcchHHHHHHHHHHhcCC-cchhhccceEEEEeccc
Confidence            3333334444444445544444443211 134444555555555555555555554443322 22233444444444445


Q ss_pred             cHHHHHHHHHHHHHcCCCCC-HhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHH
Q 044084          180 AYWAAVKVYEQLISQGCIPG-QVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLV  258 (343)
Q Consensus       180 ~~~~a~~~~~~~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  258 (343)
                      ..+.|++.|++..+.  .|+ ...|+.|..++-..|++.+|.+.+....... +......+.|...|...|.++.|..+|
T Consensus       301 ~ldlAI~~Ykral~~--~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l~-p~hadam~NLgni~~E~~~~e~A~~ly  377 (966)
T KOG4626|consen  301 LLDLAIDTYKRALEL--QPNFPDAYNNLANALKDKGSVTEAVDCYNKALRLC-PNHADAMNNLGNIYREQGKIEEATRLY  377 (966)
T ss_pred             cHHHHHHHHHHHHhc--CCCchHHHhHHHHHHHhccchHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhccchHHHHHH
Confidence            555555555544443  222 2344445555444455555555444444432 222334444444444444444444444


Q ss_pred             HHHhhCCCCchH-HHHHHHHHHHhcccChhHHH
Q 044084          259 AKMKPKGCEPNV-WIYNSLMDMHGRAKNLRQLE  290 (343)
Q Consensus       259 ~~m~~~~~~p~~-~~~~~l~~~~~~~~~~~~a~  290 (343)
                      ....+-  .|.- ...+.|...|.+.|++++|.
T Consensus       378 ~~al~v--~p~~aaa~nNLa~i~kqqgnl~~Ai  408 (966)
T KOG4626|consen  378 LKALEV--FPEFAAAHNNLASIYKQQGNLDDAI  408 (966)
T ss_pred             HHHHhh--ChhhhhhhhhHHHHHHhcccHHHHH
Confidence            444432  2221 23344444444444444443

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

Probab=99.83  E-value=3.9e-16  Score=140.14  Aligned_cols=313  Identities=10%  Similarity=-0.024  Sum_probs=235.5

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC--------------------------
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDL--------------------------   55 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--------------------------   55 (343)
                      ++++|+..++..++.++ .+...|..+..+|...|++++|..-|......+...                          
T Consensus       175 ~~~~Ai~~~~~al~l~p-~~~~a~~~~a~a~~~lg~~~eA~~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~~~~~l~~  253 (615)
T TIGR00990       175 DWEKVVEDTTAALELDP-DYSKALNRRANAYDGLGKYADALLDLTASCIIDGFRNEQSAQAVERLLKKFAESKAKEILET  253 (615)
T ss_pred             CHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            57889999999998753 467789999999999999999987664432211000                          


Q ss_pred             CCchHHHHHHH---------------------------------HHH---hhccCcHHHHHHHHHHHHhcC-CCC-ChHh
Q 044084           56 TPSSTHMYKIL---------------------------------CDS---LGKSGRAFEILKFFRDMKEKG-ILE-DPSV   97 (343)
Q Consensus        56 ~~~~~~~~~~l---------------------------------i~~---~~~~~~~~~a~~~~~~~~~~~-~~~-~~~~   97 (343)
                      .|.....+..+                                 ...   ....+++++|.+.|+.....+ ..| ....
T Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~~~~~~a~a  333 (615)
T TIGR00990       254 KPENLPSVTFVGNYLQSFRPKPRPAGLEDSNELDEETGNGQLQLGLKSPESKADESYEEAARAFEKALDLGKLGEKEAIA  333 (615)
T ss_pred             CCCCCCCHHHHHHHHHHccCCcchhhhhcccccccccccchHHHHHHHHHhhhhhhHHHHHHHHHHHHhcCCCChhhHHH
Confidence            00000000000                                 000   012257889999999998764 233 3456


Q ss_pred             HHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhc
Q 044084           98 YASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSK  177 (343)
Q Consensus        98 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  177 (343)
                      +..+...+...|++++|...+++..+..+. ....|..+...+...|++++|...|++..+.++ .+..+|..+...+..
T Consensus       334 ~~~lg~~~~~~g~~~eA~~~~~kal~l~P~-~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~p-~~~~~~~~lg~~~~~  411 (615)
T TIGR00990       334 LNLRGTFKCLKGKHLEALADLSKSIELDPR-VTQSYIKRASMNLELGDPDKAEEDFDKALKLNS-EDPDIYYHRAQLHFI  411 (615)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHH
Confidence            777888888999999999999999986532 577888999999999999999999999987764 456788899999999


Q ss_pred             CCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHH
Q 044084          178 RRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRL  257 (343)
Q Consensus       178 ~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  257 (343)
                      .|++++|...|++..+.. +.+...+..+..++.+.|++++|...|+...+.. +.+...++.+...+...|++++|...
T Consensus       412 ~g~~~~A~~~~~kal~l~-P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~A~~~  489 (615)
T TIGR00990       412 KGEFAQAGKDYQKSIDLD-PDFIFSHIQLGVTQYKEGSIASSMATFRRCKKNF-PEAPDVYNYYGELLLDQNKFDEAIEK  489 (615)
T ss_pred             cCCHHHHHHHHHHHHHcC-ccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHccCHHHHHHH
Confidence            999999999999998874 3456677788888999999999999999998864 55678899999999999999999999


Q ss_pred             HHHHhhCCCCchH-----H-HHHHHHHHHhcccChhHHHh---------------HHHHHHHHHhcCCHHHHHHHHHHHH
Q 044084          258 VAKMKPKGCEPNV-----W-IYNSLMDMHGRAKNLRQLEK---------------YTTVISAYNMAREFDMCVKFYNEFR  316 (343)
Q Consensus       258 ~~~m~~~~~~p~~-----~-~~~~l~~~~~~~~~~~~a~~---------------~~~l~~~~~~~g~~~~a~~~~~~m~  316 (343)
                      |++..+.....+.     . .++.....+...|++++|..               +..+...+.+.|++++|++.|++..
T Consensus       490 ~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~~~~~eA~~~~~kAl~l~p~~~~a~~~la~~~~~~g~~~eAi~~~e~A~  569 (615)
T TIGR00990       490 FDTAIELEKETKPMYMNVLPLINKALALFQWKQDFIEAENLCEKALIIDPECDIAVATMAQLLLQQGDVDEALKLFERAA  569 (615)
T ss_pred             HHHHHhcCCccccccccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            9998875221111     1 11222223334578887776               7788999999999999999999987


Q ss_pred             hCC
Q 044084          317 MNG  319 (343)
Q Consensus       317 ~~~  319 (343)
                      +..
T Consensus       570 ~l~  572 (615)
T TIGR00990       570 ELA  572 (615)
T ss_pred             HHh
Confidence            653

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.83  E-value=4.3e-16  Score=148.76  Aligned_cols=227  Identities=11%  Similarity=0.038  Sum_probs=157.4

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCC-ChHhHH------
Q 044084           27 QIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILE-DPSVYA------   99 (343)
Q Consensus        27 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~------   99 (343)
                      .....+...|++++|...|++..+..    |.+..++..+...+.+.|++++|+..|++..+..... ....+.      
T Consensus       274 ~~G~~~~~~g~~~~A~~~l~~aL~~~----P~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~  349 (1157)
T PRK11447        274 AQGLAAVDSGQGGKAIPELQQAVRAN----PKDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVN  349 (1157)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhC----CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhh
Confidence            34567788999999999999998765    3336789999999999999999999999998764322 111121      


Q ss_pred             ------HHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHH
Q 044084          100 ------SLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVN  173 (343)
Q Consensus       100 ------~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  173 (343)
                            .....+.+.|++++|...|+++.+..+. +...+..+...+...|++++|++.|++..+..+ .+...+..+..
T Consensus       350 ~~~~~~~~g~~~~~~g~~~eA~~~~~~Al~~~P~-~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~p-~~~~a~~~L~~  427 (1157)
T PRK11447        350 RYWLLIQQGDAALKANNLAQAERLYQQARQVDNT-DSYAVLGLGDVAMARKDYAAAERYYQQALRMDP-GNTNAVRGLAN  427 (1157)
T ss_pred             hHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHH
Confidence                  1234567889999999999999997643 677888899999999999999999999987654 23333333322


Q ss_pred             ------------------------------------------HHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHH
Q 044084          174 ------------------------------------------GFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYC  211 (343)
Q Consensus       174 ------------------------------------------~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~  211 (343)
                                                                .+...|++++|.+.|++..+.. +-+...+..+...|.
T Consensus       428 l~~~~~~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~-P~~~~~~~~LA~~~~  506 (1157)
T PRK11447        428 LYRQQSPEKALAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLALD-PGSVWLTYRLAQDLR  506 (1157)
T ss_pred             HHHhcCHHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH
Confidence                                                      3345677777777777776653 223445556667777


Q ss_pred             ccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHH
Q 044084          212 RIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKM  261 (343)
Q Consensus       212 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m  261 (343)
                      +.|++++|...++.+.+.. +.+...+..+...+...++.++|...++.+
T Consensus       507 ~~G~~~~A~~~l~~al~~~-P~~~~~~~a~al~l~~~~~~~~Al~~l~~l  555 (1157)
T PRK11447        507 QAGQRSQADALMRRLAQQK-PNDPEQVYAYGLYLSGSDRDRAALAHLNTL  555 (1157)
T ss_pred             HcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHhCCCHHHHHHHHHhC
Confidence            7777777777777776643 223333433334444555555555555544

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

Probab=99.82  E-value=9e-18  Score=139.77  Aligned_cols=309  Identities=14%  Similarity=0.124  Sum_probs=250.6

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHh-HH
Q 044084           21 DSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSV-YA   99 (343)
Q Consensus        21 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~~   99 (343)
                      -..+|..+...+-..|++++|+.+++.+.+..    |.....|..+..++...|+.+.|...|.+.++.  .|+... .+
T Consensus       115 ~ae~ysn~aN~~kerg~~~~al~~y~~aiel~----p~fida~inla~al~~~~~~~~a~~~~~~alql--nP~l~ca~s  188 (966)
T KOG4626|consen  115 GAEAYSNLANILKERGQLQDALALYRAAIELK----PKFIDAYINLAAALVTQGDLELAVQCFFEALQL--NPDLYCARS  188 (966)
T ss_pred             HHHHHHHHHHHHHHhchHHHHHHHHHHHHhcC----chhhHHHhhHHHHHHhcCCCcccHHHHHHHHhc--Ccchhhhhc
Confidence            45688889999999999999999999887755    444688999999999999999999999888775  454432 33


Q ss_pred             HHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCC
Q 044084          100 SLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRR  179 (343)
Q Consensus       100 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  179 (343)
                      .+....-..|..++|...+.+.++..+. =...|+.|...+...|+...|++.|++....++ .-...|-.|...|...+
T Consensus       189 ~lgnLlka~Grl~ea~~cYlkAi~~qp~-fAiawsnLg~~f~~~Gei~~aiq~y~eAvkldP-~f~dAYiNLGnV~ke~~  266 (966)
T KOG4626|consen  189 DLGNLLKAEGRLEEAKACYLKAIETQPC-FAIAWSNLGCVFNAQGEIWLAIQHYEEAVKLDP-NFLDAYINLGNVYKEAR  266 (966)
T ss_pred             chhHHHHhhcccchhHHHHHHHHhhCCc-eeeeehhcchHHhhcchHHHHHHHHHHhhcCCC-cchHHHhhHHHHHHHHh
Confidence            3445555678889999998888876432 356788899999999999999999999887654 22346888888888899


Q ss_pred             cHHHHHHHHHHHHHcCCCCC-HhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHH
Q 044084          180 AYWAAVKVYEQLISQGCIPG-QVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLV  258 (343)
Q Consensus       180 ~~~~a~~~~~~~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  258 (343)
                      .+++|...|.+....  .|+ ...+..+...|-.+|.++-|+..+++..+.. +.=...|+.|..++-..|+..+|.+.|
T Consensus       267 ~~d~Avs~Y~rAl~l--rpn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~~-P~F~~Ay~NlanALkd~G~V~ea~~cY  343 (966)
T KOG4626|consen  267 IFDRAVSCYLRALNL--RPNHAVAHGNLACIYYEQGLLDLAIDTYKRALELQ-PNFPDAYNNLANALKDKGSVTEAVDCY  343 (966)
T ss_pred             cchHHHHHHHHHHhc--CCcchhhccceEEEEeccccHHHHHHHHHHHHhcC-CCchHHHhHHHHHHHhccchHHHHHHH
Confidence            999999998887776  454 5677788888899999999999999998864 223678999999999999999999999


Q ss_pred             HHHhhCCCCchHHHHHHHHHHHhcccChhHHHh---------------HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcc
Q 044084          259 AKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK---------------YTTVISAYNMAREFDMCVKFYNEFRMNGGVID  323 (343)
Q Consensus       259 ~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~---------------~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~  323 (343)
                      ++..... .--....+.|...|...|.+++|..               ++.|...|-+.|++++|+..|++.++  ++|+
T Consensus       344 nkaL~l~-p~hadam~NLgni~~E~~~~e~A~~ly~~al~v~p~~aaa~nNLa~i~kqqgnl~~Ai~~Ykealr--I~P~  420 (966)
T KOG4626|consen  344 NKALRLC-PNHADAMNNLGNIYREQGKIEEATRLYLKALEVFPEFAAAHNNLASIYKQQGNLDDAIMCYKEALR--IKPT  420 (966)
T ss_pred             HHHHHhC-CccHHHHHHHHHHHHHhccchHHHHHHHHHHhhChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHh--cCch
Confidence            9998762 2245678889999999999999887               88999999999999999999999887  6777


Q ss_pred             HH-HHHHHHHHHhcccccccC
Q 044084          324 RA-MAGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       324 ~~-~~~~l~~~~~~~g~~~~a  343 (343)
                      .. .|+.+...|...|+++.|
T Consensus       421 fAda~~NmGnt~ke~g~v~~A  441 (966)
T KOG4626|consen  421 FADALSNMGNTYKEMGDVSAA  441 (966)
T ss_pred             HHHHHHhcchHHHHhhhHHHH
Confidence            64 488888888888887653

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.81  E-value=1.2e-15  Score=139.67  Aligned_cols=331  Identities=12%  Similarity=0.075  Sum_probs=239.1

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      +.++|++++.+..... +.+...+..+...+.+.|++++|..+|++..+..    |.+...+..++..+...|++++|+.
T Consensus        30 ~~~~A~~~~~~~~~~~-~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~----P~~~~a~~~la~~l~~~g~~~eA~~  104 (765)
T PRK10049         30 QDAEVITVYNRYRVHM-QLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLE----PQNDDYQRGLILTLADAGQYDEALV  104 (765)
T ss_pred             CHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC----CCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            5678899998888633 3455578899999999999999999999987764    3334677788889999999999999


Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHH-------
Q 044084           82 FFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVE-------  154 (343)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~-------  154 (343)
                      .+++..+.. +.+.. +..+..++...|+.++|...++++.+..+. +...+..+...+...+..++|++.++       
T Consensus       105 ~l~~~l~~~-P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~P~-~~~~~~~la~~l~~~~~~e~Al~~l~~~~~~p~  181 (765)
T PRK10049        105 KAKQLVSGA-PDKAN-LLALAYVYKRAGRHWDELRAMTQALPRAPQ-TQQYPTEYVQALRNNRLSAPALGAIDDANLTPA  181 (765)
T ss_pred             HHHHHHHhC-CCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCChHHHHHHHHhCCCCHH
Confidence            999998863 23455 778888889999999999999999987654 56666666666666666555544443       


Q ss_pred             ---------------------------------------HHHhc-CCCCchh-hHH----HHHHHHhcCCcHHHHHHHHH
Q 044084          155 ---------------------------------------SMKNA-ELNISDC-ISC----VIVNGFSKRRAYWAAVKVYE  189 (343)
Q Consensus       155 ---------------------------------------~~~~~-~~~~~~~-~~~----~l~~~~~~~~~~~~a~~~~~  189 (343)
                                                             .+.+. ...|+.. .+.    ..+..+...|++++|...|+
T Consensus       182 ~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l~~Ll~~g~~~eA~~~~~  261 (765)
T PRK10049        182 EKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQRARIDRLGALLARDRYKDVISEYQ  261 (765)
T ss_pred             HHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence                                                   33322 1112111 111    11234567789999999999


Q ss_pred             HHHHcCCC-CCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCc---ChhhHHHHHHHHHccCChHHHHHHHHHHhhCC
Q 044084          190 QLISQGCI-PGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDK---CVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKG  265 (343)
Q Consensus       190 ~~~~~~~~-p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~  265 (343)
                      .+.+.+.. |+. ....+..+|...|++++|+.+|+.+.+.....   .......+..++...|++++|..+++.+.+..
T Consensus       262 ~ll~~~~~~P~~-a~~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~~l~~~~~~~  340 (765)
T PRK10049        262 RLKAEGQIIPPW-AQRWVASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLESENYPGALTVTAHTINNS  340 (765)
T ss_pred             HhhccCCCCCHH-HHHHHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccHHHHHHHHHHHhhcC
Confidence            99887532 322 22335678899999999999999987653111   12456667778889999999999999988652


Q ss_pred             C-----------Cch---HHHHHHHHHHHhcccChhHHHh---------------HHHHHHHHHhcCCHHHHHHHHHHHH
Q 044084          266 C-----------EPN---VWIYNSLMDMHGRAKNLRQLEK---------------YTTVISAYNMAREFDMCVKFYNEFR  316 (343)
Q Consensus       266 ~-----------~p~---~~~~~~l~~~~~~~~~~~~a~~---------------~~~l~~~~~~~g~~~~a~~~~~~m~  316 (343)
                      .           .|+   ...+..+...+...|+.++|+.               +..+...+...|++++|++.+++..
T Consensus       341 P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~P~n~~l~~~lA~l~~~~g~~~~A~~~l~~al  420 (765)
T PRK10049        341 PPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNAPGNQGLRIDYASVLQARGWPRAAENELKKAE  420 (765)
T ss_pred             CceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            1           123   2344567778888999999887               7788888899999999999999988


Q ss_pred             hCCCCcc-HHHHHHHHHHHhcccccccC
Q 044084          317 MNGGVID-RAMAGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       317 ~~~~~p~-~~~~~~l~~~~~~~g~~~~a  343 (343)
                      ...  |+ ...+......+.+.|++++|
T Consensus       421 ~l~--Pd~~~l~~~~a~~al~~~~~~~A  446 (765)
T PRK10049        421 VLE--PRNINLEVEQAWTALDLQEWRQM  446 (765)
T ss_pred             hhC--CCChHHHHHHHHHHHHhCCHHHH
Confidence            854  54 45566677788888887654

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.79  E-value=2e-15  Score=120.73  Aligned_cols=294  Identities=13%  Similarity=0.112  Sum_probs=226.4

Q ss_pred             CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhH
Q 044084           19 VLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVY   98 (343)
Q Consensus        19 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~   98 (343)
                      +.+..+|.++|.+.++....++|.+++++.........   ..+||.+|.+-.-...    .+++.+|.+..+.||..|+
T Consensus       204 PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~---~~aFN~lI~~~S~~~~----K~Lv~EMisqkm~Pnl~Tf  276 (625)
T KOG4422|consen  204 PKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVY---REAFNGLIGASSYSVG----KKLVAEMISQKMTPNLFTF  276 (625)
T ss_pred             CCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheee---HHhhhhhhhHHHhhcc----HHHHHHHHHhhcCCchHhH
Confidence            45778999999999999999999999999988877777   8899999876543332    7789999999999999999


Q ss_pred             HHHHHHHhcccCHHHH----HHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhH-HHHHHHHHHh----cCCCC----ch
Q 044084           99 ASLICSFASIAEVKVA----EELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEK-TLEVVESMKN----AELNI----SD  165 (343)
Q Consensus        99 ~~l~~~~~~~~~~~~a----~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~----~~~~~----~~  165 (343)
                      |+++++..+.|+++.+    .+++.+|.+.|+.|+..+|..+|..+++.++..+ |..++.++..    ..++|    +.
T Consensus       277 NalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~  356 (625)
T KOG4422|consen  277 NALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDN  356 (625)
T ss_pred             HHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchh
Confidence            9999999999987654    5678889999999999999999999999888754 4555555543    22222    33


Q ss_pred             hhHHHHHHHHhcCCcHHHHHHHHHHHHHcC----CCCCH---hhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhH
Q 044084          166 CISCVIVNGFSKRRAYWAAVKVYEQLISQG----CIPGQ---VTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAY  238 (343)
Q Consensus       166 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~p~~---~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  238 (343)
                      ..|..-+..|.+..+.+-|.++..-+....    +.|+.   .-|..+..+.|.....+.....++.|.-.-.-|+..+.
T Consensus       357 ~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lVP~~y~p~~~~m  436 (625)
T KOG4422|consen  357 KFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLVPSAYFPHSQTM  436 (625)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceecCCchhH
Confidence            446667788888888888888877665431    33432   23556777788888899999999999888777899999


Q ss_pred             HHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhccc-Ch--------hHHHh------------------
Q 044084          239 SSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAK-NL--------RQLEK------------------  291 (343)
Q Consensus       239 ~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~-~~--------~~a~~------------------  291 (343)
                      ..++++....|+++-..++|..++..|...+...-.-++..+++.. ..        ..+..                  
T Consensus       437 ~~~lrA~~v~~~~e~ipRiw~D~~~~ght~r~~l~eeil~~L~~~k~hp~tp~r~Ql~~~~ak~aad~~e~~e~~~~R~r  516 (625)
T KOG4422|consen  437 IHLLRALDVANRLEVIPRIWKDSKEYGHTFRSDLREEILMLLARDKLHPLTPEREQLQVAFAKCAADIKEAYESQPIRQR  516 (625)
T ss_pred             HHHHHHHhhcCcchhHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHHHHHhhHHHHH
Confidence            9999999999999999999999988875555554444444444433 11        00000                  


Q ss_pred             --------HHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 044084          292 --------YTTVISAYNMAREFDMCVKFYNEFRMNG  319 (343)
Q Consensus       292 --------~~~l~~~~~~~g~~~~a~~~~~~m~~~~  319 (343)
                              .+...-.+.+.|+.++|.+++..+.+.+
T Consensus       517 ~~~~~~t~l~~ia~Ll~R~G~~qkA~e~l~l~~~~~  552 (625)
T KOG4422|consen  517 AQDWPATSLNCIAILLLRAGRTQKAWEMLGLFLRKH  552 (625)
T ss_pred             hccCChhHHHHHHHHHHHcchHHHHHHHHHHHHhcC
Confidence                    6777777889999999999999986554

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.78  E-value=1.4e-14  Score=130.84  Aligned_cols=306  Identities=11%  Similarity=0.049  Sum_probs=183.2

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcc
Q 044084           29 MEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASI  108 (343)
Q Consensus        29 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  108 (343)
                      ...+...|++++|.++|+++.+...    .+...+..++..+...++.++|++.++++...  .|+...+..++..+...
T Consensus       109 A~ly~~~gdyd~Aiely~kaL~~dP----~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~--dp~~~~~l~layL~~~~  182 (822)
T PRK14574        109 ARAYRNEKRWDQALALWQSSLKKDP----TNPDLISGMIMTQADAGRGGVVLKQATELAER--DPTVQNYMTLSYLNRAT  182 (822)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhhCC----CCHHHHHHHHHHHhhcCCHHHHHHHHHHhccc--CcchHHHHHHHHHHHhc
Confidence            3345555666666666665554432    12344445555555556666666665555543  23333333332333233


Q ss_pred             cCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHH----------------------------------
Q 044084          109 AEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVE----------------------------------  154 (343)
Q Consensus       109 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~----------------------------------  154 (343)
                      ++..+|++.++++.+..+. +...+..+...+.+.|-...|.++..                                  
T Consensus       183 ~~~~~AL~~~ekll~~~P~-n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~f~~~~~~~l~~~~~a~~vr~a~~~~~~~~  261 (822)
T PRK14574        183 DRNYDALQASSEAVRLAPT-SEEVLKNHLEILQRNRIVEPALRLAKENPNLVSAEHYRQLERDAAAEQVRMAVLPTRSET  261 (822)
T ss_pred             chHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCcHHHHHHHHhCccccCHHHHHHHHHHHHHHHHhhcccccccch
Confidence            4444466666666655432 44555555555544443333333222                                  


Q ss_pred             --------------HHHhc-CCCCch-hhH----HHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccC
Q 044084          155 --------------SMKNA-ELNISD-CIS----CVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIG  214 (343)
Q Consensus       155 --------------~~~~~-~~~~~~-~~~----~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~  214 (343)
                                    .+... +..|.. ..|    --.+-++...|+..++++.|+.+...+.+....+-..+..+|...+
T Consensus       262 ~r~~~~d~ala~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~  341 (822)
T PRK14574        262 ERFDIADKALADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRR  341 (822)
T ss_pred             hhHHHHHHHHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcC
Confidence                          11110 000111 111    1234456667788888888888888776555667788888999999


Q ss_pred             ChhHHHHHHHHHHHcC-----CCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCC-------------CchHHH-HHH
Q 044084          215 LYSKAEKVFIEMQQKG-----FDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGC-------------EPNVWI-YNS  275 (343)
Q Consensus       215 ~~~~a~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~-------------~p~~~~-~~~  275 (343)
                      ++++|+.++..+....     .+++......|.-+|...+++++|..+++++.+.-.             .||-.. ...
T Consensus       342 ~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l  421 (822)
T PRK14574        342 LPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTL  421 (822)
T ss_pred             CcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHH
Confidence            9999999999886643     123444457788888999999999999999887311             122222 344


Q ss_pred             HHHHHhcccChhHHHh---------------HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcc-HHHHHHHHHHHhcccc
Q 044084          276 LMDMHGRAKNLRQLEK---------------YTTVISAYNMAREFDMCVKFYNEFRMNGGVID-RAMAGIMVGVFSKLSQ  339 (343)
Q Consensus       276 l~~~~~~~~~~~~a~~---------------~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~-~~~~~~l~~~~~~~g~  339 (343)
                      ++..+...|++.+|++               ...+...+...|.+.+|.+.++.....  .|+ ..+......++.+.|+
T Consensus       422 ~a~~~~~~gdl~~Ae~~le~l~~~aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l--~P~~~~~~~~~~~~al~l~e  499 (822)
T PRK14574        422 LVQSLVALNDLPTAQKKLEDLSSTAPANQNLRIALASIYLARDLPRKAEQELKAVESL--APRSLILERAQAETAMALQE  499 (822)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhh--CCccHHHHHHHHHHHHhhhh
Confidence            5667788888888887               777788888899999999999777665  344 4456667777777777


Q ss_pred             cccC
Q 044084          340 IEEL  343 (343)
Q Consensus       340 ~~~a  343 (343)
                      +++|
T Consensus       500 ~~~A  503 (822)
T PRK14574        500 WHQM  503 (822)
T ss_pred             HHHH
Confidence            7653

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

Probab=99.77  E-value=4.9e-15  Score=114.21  Aligned_cols=295  Identities=11%  Similarity=0.077  Sum_probs=206.8

Q ss_pred             CchhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHH
Q 044084            1 TNSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEIL   80 (343)
Q Consensus         1 ~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~   80 (343)
                      +++++|.++|-+|.+.+. -+..+.-+|.+.|.+.|..++|+++.+.+.++.--+...-..+...|.+-|...|-+|.|.
T Consensus        49 ~Q~dKAvdlF~e~l~~d~-~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DRAE  127 (389)
T COG2956          49 NQPDKAVDLFLEMLQEDP-ETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDRAE  127 (389)
T ss_pred             cCcchHHHHHHHHHhcCc-hhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhHHH
Confidence            467888898888888543 3556677788888888999999998887765432222111344556777888888899999


Q ss_pred             HHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCC----HHHHHHHHHHHHhcCcHhHHHHHHHHH
Q 044084           81 KFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRD----LEVFLKLVLMYIEEGMVEKTLEVVESM  156 (343)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~  156 (343)
                      ++|..+.+.+. .-......|+..|-...+|++|.++-+++.+.+..+.    ...|.-|...+....+++.|..++.+.
T Consensus       128 ~~f~~L~de~e-fa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~kA  206 (389)
T COG2956         128 DIFNQLVDEGE-FAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLKKA  206 (389)
T ss_pred             HHHHHHhcchh-hhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHH
Confidence            99888877542 2345677788888888889999888888888765543    344666777777778888888888888


Q ss_pred             HhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChh
Q 044084          157 KNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVV  236 (343)
Q Consensus       157 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  236 (343)
                      .+.+. -++..--.+.+.....|+++.|.+.++...+.+..--..+...+..+|...|+.++....+..+.+..  +...
T Consensus       207 lqa~~-~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~--~g~~  283 (389)
T COG2956         207 LQADK-KCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETN--TGAD  283 (389)
T ss_pred             HhhCc-cceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHcc--CCcc
Confidence            87765 34444445667788888999999999888888644445677788888888999988888888888764  3333


Q ss_pred             hHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 044084          237 AYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFR  316 (343)
Q Consensus       237 ~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~  316 (343)
                      .-..+.+......-.+.|...+.+-...  +|+...+..+++......                ..|...+-+.++++|.
T Consensus       284 ~~l~l~~lie~~~G~~~Aq~~l~~Ql~r--~Pt~~gf~rl~~~~l~da----------------eeg~~k~sL~~lr~mv  345 (389)
T COG2956         284 AELMLADLIELQEGIDAAQAYLTRQLRR--KPTMRGFHRLMDYHLADA----------------EEGRAKESLDLLRDMV  345 (389)
T ss_pred             HHHHHHHHHHHhhChHHHHHHHHHHHhh--CCcHHHHHHHHHhhhccc----------------cccchhhhHHHHHHHH
Confidence            3344444444444456666666555554  788888888887654322                2345566666777775


Q ss_pred             hC
Q 044084          317 MN  318 (343)
Q Consensus       317 ~~  318 (343)
                      ..
T Consensus       346 ge  347 (389)
T COG2956         346 GE  347 (389)
T ss_pred             HH
Confidence            43

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.76  E-value=4.8e-14  Score=129.16  Aligned_cols=314  Identities=9%  Similarity=-0.010  Sum_probs=227.4

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      ++++|..++++..+..+ .+...+..+...+.+.|++++|...++++.+..    |.+.. +..+..++...|++++|+.
T Consensus        64 ~~~~A~~~~~~al~~~P-~~~~a~~~la~~l~~~g~~~eA~~~l~~~l~~~----P~~~~-~~~la~~l~~~g~~~~Al~  137 (765)
T PRK10049         64 QWQNSLTLWQKALSLEP-QNDDYQRGLILTLADAGQYDEALVKAKQLVSGA----PDKAN-LLALAYVYKRAGRHWDELR  137 (765)
T ss_pred             CHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC----CCCHH-HHHHHHHHHHCCCHHHHHH
Confidence            56789999999888643 456677888889999999999999999988764    33345 8888889999999999999


Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHhcccCHHH----------------------------------------------HH
Q 044084           82 FFRDMKEKGILEDPSVYASLICSFASIAEVKV----------------------------------------------AE  115 (343)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~----------------------------------------------a~  115 (343)
                      .++++.+.... +...+..+..++...+..+.                                              |.
T Consensus       138 ~l~~al~~~P~-~~~~~~~la~~l~~~~~~e~Al~~l~~~~~~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al  216 (765)
T PRK10049        138 AMTQALPRAPQ-TQQYPTEYVQALRNNRLSAPALGAIDDANLTPAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRAL  216 (765)
T ss_pred             HHHHHHHhCCC-CHHHHHHHHHHHHHCCChHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHH
Confidence            99999886432 34444455555555455443                                              33


Q ss_pred             HHHHHHHHc-CCCCCHH-HH----HHHHHHHHhcCcHhHHHHHHHHHHhcCCC-CchhhHHHHHHHHhcCCcHHHHHHHH
Q 044084          116 ELFKEAEEK-GMLRDLE-VF----LKLVLMYIEEGMVEKTLEVVESMKNAELN-ISDCISCVIVNGFSKRRAYWAAVKVY  188 (343)
Q Consensus       116 ~~~~~~~~~-~~~~~~~-~~----~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~  188 (343)
                      ..++.+.+. ...|+.. .+    ...+..+...|++++|+..|+.+.+.+.+ |+. .-..+...|...|++++|...|
T Consensus       217 ~~~~~ll~~~~~~p~~~~~~~~a~~d~l~~Ll~~g~~~eA~~~~~~ll~~~~~~P~~-a~~~la~~yl~~g~~e~A~~~l  295 (765)
T PRK10049        217 AQYDALEALWHDNPDATADYQRARIDRLGALLARDRYKDVISEYQRLKAEGQIIPPW-AQRWVASAYLKLHQPEKAQSIL  295 (765)
T ss_pred             HHHHHHHhhcccCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhccCCCCCHH-HHHHHHHHHHhcCCcHHHHHHH
Confidence            344444432 1122211 11    11133456779999999999999887642 322 2233577899999999999999


Q ss_pred             HHHHHcCCCC---CHhhHHHHHHHHHccCChhHHHHHHHHHHHcCC-----------CcC---hhhHHHHHHHHHccCCh
Q 044084          189 EQLISQGCIP---GQVTYASIINAYCRIGLYSKAEKVFIEMQQKGF-----------DKC---VVAYSSMVAMYGKTGRI  251 (343)
Q Consensus       189 ~~~~~~~~~p---~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~-----------~~~---~~~~~~l~~~~~~~~~~  251 (343)
                      +++.......   .......+..++...|++++|..+++.+.+...           .|+   ...+..+...+...|++
T Consensus       296 ~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~  375 (765)
T PRK10049        296 TELFYHPETIADLSDEELADLFYSLLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDL  375 (765)
T ss_pred             HHHhhcCCCCCCCChHHHHHHHHHHHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCH
Confidence            9988653111   123456667788999999999999999987631           122   23456677888999999


Q ss_pred             HHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh---------------HHHHHHHHHhcCCHHHHHHHHHHHH
Q 044084          252 RDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK---------------YTTVISAYNMAREFDMCVKFYNEFR  316 (343)
Q Consensus       252 ~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~---------------~~~l~~~~~~~g~~~~a~~~~~~m~  316 (343)
                      ++|+++++++.... +.+...+..+...+...|++++|+.               +...+..+...|++++|..++++++
T Consensus       376 ~eA~~~l~~al~~~-P~n~~l~~~lA~l~~~~g~~~~A~~~l~~al~l~Pd~~~l~~~~a~~al~~~~~~~A~~~~~~ll  454 (765)
T PRK10049        376 PQAEMRARELAYNA-PGNQGLRIDYASVLQARGWPRAAENELKKAEVLEPRNINLEVEQAWTALDLQEWRQMDVLTDDVV  454 (765)
T ss_pred             HHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            99999999998762 4467788889999999999999988               4556667889999999999999999


Q ss_pred             hCCCCccHHH
Q 044084          317 MNGGVIDRAM  326 (343)
Q Consensus       317 ~~~~~p~~~~  326 (343)
                      +.  .|+...
T Consensus       455 ~~--~Pd~~~  462 (765)
T PRK10049        455 AR--EPQDPG  462 (765)
T ss_pred             Hh--CCCCHH
Confidence            85  344443

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

Probab=99.75  E-value=2.7e-17  Score=133.22  Aligned_cols=256  Identities=15%  Similarity=0.186  Sum_probs=107.4

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHh
Q 044084           27 QIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFA  106 (343)
Q Consensus        27 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  106 (343)
                      .+...+.+.|++++|+++++.......+  |.+...|..+.......++++.|.+.++++...+.. ++..+..++.. .
T Consensus        13 ~~A~~~~~~~~~~~Al~~L~~~~~~~~~--~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~~~-~~~~~~~l~~l-~   88 (280)
T PF13429_consen   13 RLARLLYQRGDYEKALEVLKKAAQKIAP--PDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASDKA-NPQDYERLIQL-L   88 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccc--cccccccccccccccccccccccccccccccccccc-ccccccccccc-c
Confidence            5577888899999999998654433311  222456777777777888899999999998876533 55567777766 6


Q ss_pred             cccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcC-CCCchhhHHHHHHHHhcCCcHHHHH
Q 044084          107 SIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAE-LNISDCISCVIVNGFSKRRAYWAAV  185 (343)
Q Consensus       107 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~  185 (343)
                      ..+++++|..++....+..  +++..+..++..+.+.++++++.++++.+.... .+.+...|..+...+.+.|++++|.
T Consensus        89 ~~~~~~~A~~~~~~~~~~~--~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~  166 (280)
T PF13429_consen   89 QDGDPEEALKLAEKAYERD--GDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKAL  166 (280)
T ss_dssp             -------------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHH
T ss_pred             ccccccccccccccccccc--cccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHH
Confidence            8888999988887766543  466677788888889999999999998876533 3356667888888888999999999


Q ss_pred             HHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCC
Q 044084          186 KVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKG  265 (343)
Q Consensus       186 ~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~  265 (343)
                      +.+++..+.. +-|......++..+...|+.+++..++....+.. +.|+..+..+..+|...|+.++|..+|++.....
T Consensus       167 ~~~~~al~~~-P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~  244 (280)
T PF13429_consen  167 RDYRKALELD-PDDPDARNALAWLLIDMGDYDEAREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKALKLN  244 (280)
T ss_dssp             HHHHHHHHH--TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHcC-CCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-cCHHHHHHHHHHHhcccccccccccccccccccc
Confidence            9999988873 2246677788888888899999888888887764 5667778888999999999999999999988752


Q ss_pred             CCchHHHHHHHHHHHhcccChhHHHh
Q 044084          266 CEPNVWIYNSLMDMHGRAKNLRQLEK  291 (343)
Q Consensus       266 ~~p~~~~~~~l~~~~~~~~~~~~a~~  291 (343)
                       +.|+.+...+.+++...|+.++|..
T Consensus       245 -p~d~~~~~~~a~~l~~~g~~~~A~~  269 (280)
T PF13429_consen  245 -PDDPLWLLAYADALEQAGRKDEALR  269 (280)
T ss_dssp             -TT-HHHHHHHHHHHT----------
T ss_pred             -ccccccccccccccccccccccccc
Confidence             3377778888889999999988876

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.74  E-value=3.1e-14  Score=114.04  Aligned_cols=285  Identities=13%  Similarity=0.128  Sum_probs=215.4

Q ss_pred             hhhHHHHHHHHHhCCCCCChhhHHHHHHHHH--hcCCHHHH-HHHHHHHHhCCCCC----------------CCchHHHH
Q 044084            3 SQSKLHYYEKMKSAGIVLDSGCYCQIMEAFY--KIGDSEKV-AALFLECESRKLDL----------------TPSSTHMY   63 (343)
Q Consensus         3 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~--~~~~~~~a-~~~~~~~~~~~~~~----------------~~~~~~~~   63 (343)
                      .+.+.-+++.|.+.|++.+...-..|+...+  ...++.-| ++.|-.|...+-..                .|.+..++
T Consensus       131 vKDs~ilY~~m~~e~~~vS~kvq~~L~~LV~~~Ns~~~~~~E~~~Fv~~~~~~E~S~~sWK~G~vAdL~~E~~PKT~et~  210 (625)
T KOG4422|consen  131 VKDSCILYERMRSENVDVSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFGEDSTSSWKSGAVADLLFETLPKTDETV  210 (625)
T ss_pred             cchhHHHHHHHHhcCCCCCHHHHHHHHHHHHhhcCCCCcchhHHHHhhccccccccccccccccHHHHHHhhcCCCchhH
Confidence            4567778999999998888877776665433  32222211 22232332222111                13335889


Q ss_pred             HHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Q 044084           64 KILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEE  143 (343)
Q Consensus        64 ~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  143 (343)
                      .++|.++++....+.|.+++++......+.+..+||.+|.+-.-..+    .+++.+|......||..|+|+++.+..+.
T Consensus       211 s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~----K~Lv~EMisqkm~Pnl~TfNalL~c~akf  286 (625)
T KOG4422|consen  211 SIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVG----KKLVAEMISQKMTPNLFTFNALLSCAAKF  286 (625)
T ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhcc----HHHHHHHHHhhcCCchHhHHHHHHHHHHh
Confidence            99999999999999999999999988888899999999976543333    78899999999999999999999999999


Q ss_pred             CcHhH----HHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHH-HHHHHHHHHHc----CCCC----CHhhHHHHHHHH
Q 044084          144 GMVEK----TLEVVESMKNAELNISDCISCVIVNGFSKRRAYWA-AVKVYEQLISQ----GCIP----GQVTYASIINAY  210 (343)
Q Consensus       144 ~~~~~----a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~~----~~~p----~~~~~~~ll~~~  210 (343)
                      |+++.    |.+++.+|++.|+.|+..+|..+|..+++.+++.+ +..++.++...    .++|    |...|...+..|
T Consensus       287 g~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~~FF~~AM~Ic  366 (625)
T KOG4422|consen  287 GKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDNKFFQSAMSIC  366 (625)
T ss_pred             cchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchhHHHHHHHHHH
Confidence            98765    56778889999999999999999999999887744 55555555543    2332    445677788888


Q ss_pred             HccCChhHHHHHHHHHHHc----CCCcC---hhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcc
Q 044084          211 CRIGLYSKAEKVFIEMQQK----GFDKC---VVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRA  283 (343)
Q Consensus       211 ~~~~~~~~a~~~~~~~~~~----~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~  283 (343)
                      .+..+.+-|.++..-+...    -+.|+   ..-|..+....++....+....+|+.|+-.-+-|+..+...++++....
T Consensus       367 ~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lVP~~y~p~~~~m~~~lrA~~v~  446 (625)
T KOG4422|consen  367 SSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLVPSAYFPHSQTMIHLLRALDVA  446 (625)
T ss_pred             HHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceecCCchhHHHHHHHHhhc
Confidence            8999999998887766542    12233   2346677888888889999999999999888899999999999999988


Q ss_pred             cChhHHHh
Q 044084          284 KNLRQLEK  291 (343)
Q Consensus       284 ~~~~~a~~  291 (343)
                      |.++-..+
T Consensus       447 ~~~e~ipR  454 (625)
T KOG4422|consen  447 NRLEVIPR  454 (625)
T ss_pred             CcchhHHH
Confidence            88876655

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

Probab=99.72  E-value=1e-16  Score=129.87  Aligned_cols=253  Identities=16%  Similarity=0.165  Sum_probs=115.3

Q ss_pred             CchhhHHHHHHHHHhCC-CCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHH
Q 044084            1 TNSQSKLHYYEKMKSAG-IVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEI   79 (343)
Q Consensus         1 ~~~~~A~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a   79 (343)
                      .++++|+++++...... .+.+...|..+...+...++++.|.+.++++...+..    +...+..++.. ...+++++|
T Consensus        22 ~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~~~----~~~~~~~l~~l-~~~~~~~~A   96 (280)
T PF13429_consen   22 GDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASDKA----NPQDYERLIQL-LQDGDPEEA   96 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccccccccccc----ccccccccccc-ccccccccc
Confidence            36789999997665544 3345566677777888899999999999999776533    24567777777 789999999


Q ss_pred             HHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHh
Q 044084           80 LKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKG-MLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKN  158 (343)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  158 (343)
                      .+++....+..  +++..+..++..+.+.++++.+..+++.+.... .+.+...|..+...+.+.|+.++|++.+++..+
T Consensus        97 ~~~~~~~~~~~--~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~  174 (280)
T PF13429_consen   97 LKLAEKAYERD--GDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKALE  174 (280)
T ss_dssp             -----------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHH
T ss_pred             ccccccccccc--cccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            99998776653  466677888888999999999999999987543 345788899999999999999999999999998


Q ss_pred             cCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhH
Q 044084          159 AELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAY  238 (343)
Q Consensus       159 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  238 (343)
                      ..+ .+......++..+...|+.+++..+++...+.. +.|...+..+..+|...|+.++|...|+...+.. +.|+...
T Consensus       175 ~~P-~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~-p~d~~~~  251 (280)
T PF13429_consen  175 LDP-DDPDARNALAWLLIDMGDYDEAREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKALKLN-PDDPLWL  251 (280)
T ss_dssp             H-T-T-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHS-TT-HHHH
T ss_pred             cCC-CCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-cCHHHHHHHHHHHhcccccccccccccccccccc-ccccccc
Confidence            875 467778889999999999999999999888774 4556677888999999999999999999998875 5688889


Q ss_pred             HHHHHHHHccCChHHHHHHHHHHhh
Q 044084          239 SSMVAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       239 ~~l~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                      ..+..++...|+.++|.++..+...
T Consensus       252 ~~~a~~l~~~g~~~~A~~~~~~~~~  276 (280)
T PF13429_consen  252 LAYADALEQAGRKDEALRLRRQALR  276 (280)
T ss_dssp             HHHHHHHT-----------------
T ss_pred             ccccccccccccccccccccccccc
Confidence            9999999999999999999887654

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.72  E-value=1.2e-13  Score=117.09  Aligned_cols=254  Identities=7%  Similarity=0.006  Sum_probs=118.8

Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHH
Q 044084           33 YKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVK  112 (343)
Q Consensus        33 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  112 (343)
                      .+.|+++.|.+.+.++.+......   ..........+...|+++.|...++++.+.... ++.....+...|.+.|+++
T Consensus       129 ~~~g~~~~A~~~l~~A~~~~~~~~---~~~~l~~a~l~l~~g~~~~Al~~l~~~~~~~P~-~~~al~ll~~~~~~~gdw~  204 (398)
T PRK10747        129 QQRGDEARANQHLERAAELADNDQ---LPVEITRVRIQLARNENHAARHGVDKLLEVAPR-HPEVLRLAEQAYIRTGAWS  204 (398)
T ss_pred             HHCCCHHHHHHHHHHHHhcCCcch---HHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHHHhHH
Confidence            455555555555555543321111   011112234445555555555555555544311 3444445555555555555


Q ss_pred             HHHHHHHHHHHcCCCCCH-------HHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHH
Q 044084          113 VAEELFKEAEEKGMLRDL-------EVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAV  185 (343)
Q Consensus       113 ~a~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  185 (343)
                      .+..++..+.+.+..++.       .+|..++.......+.+...++++.+...- +.+......+...+...|+.++|.
T Consensus       205 ~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~~-~~~~~~~~~~A~~l~~~g~~~~A~  283 (398)
T PRK10747        205 SLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQSRKT-RHQVALQVAMAEHLIECDDHDTAQ  283 (398)
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHHH-hCCHHHHHHHHHHHHHCCCHHHHH
Confidence            555555555554433111       112222222222333334444444433221 123334445555555555555555


Q ss_pred             HHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCC
Q 044084          186 KVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKG  265 (343)
Q Consensus       186 ~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~  265 (343)
                      +++++..+.  +|+...  .++.+....++.+++.+..+...+.. +-|...+..+...+.+.+++++|.+.|+...+. 
T Consensus       284 ~~L~~~l~~--~~~~~l--~~l~~~l~~~~~~~al~~~e~~lk~~-P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~-  357 (398)
T PRK10747        284 QIILDGLKR--QYDERL--VLLIPRLKTNNPEQLEKVLRQQIKQH-GDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQ-  357 (398)
T ss_pred             HHHHHHHhc--CCCHHH--HHHHhhccCCChHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc-
Confidence            555555543  233311  11222233455555555555555443 334444555555555555555555555555543 


Q ss_pred             CCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 044084          266 CEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRM  317 (343)
Q Consensus       266 ~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~~  317 (343)
                       .|+..++..                   +...+.+.|+.++|.+++++-..
T Consensus       358 -~P~~~~~~~-------------------La~~~~~~g~~~~A~~~~~~~l~  389 (398)
T PRK10747        358 -RPDAYDYAW-------------------LADALDRLHKPEEAAAMRRDGLM  389 (398)
T ss_pred             -CCCHHHHHH-------------------HHHHHHHcCCHHHHHHHHHHHHh
Confidence             455555444                   44555566666777777776543

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

Probab=99.71  E-value=9.5e-14  Score=112.20  Aligned_cols=304  Identities=13%  Similarity=0.108  Sum_probs=236.6

Q ss_pred             hhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHH-HHHH
Q 044084            3 SQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAF-EILK   81 (343)
Q Consensus         3 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~-~a~~   81 (343)
                      .+++++-.+.+.+.|.+-+...-+....+.....++++|+.+|+++.+.. +-.-.+..+|+.++-.--.+.+.. -|..
T Consensus       243 ~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knD-PYRl~dmdlySN~LYv~~~~skLs~LA~~  321 (559)
T KOG1155|consen  243 HEEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKND-PYRLDDMDLYSNVLYVKNDKSKLSYLAQN  321 (559)
T ss_pred             HHHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcC-CCcchhHHHHhHHHHHHhhhHHHHHHHHH
Confidence            45667777777888886666666666677778889999999999998874 333444678887765543322221 2222


Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCC
Q 044084           82 FFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAEL  161 (343)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  161 (343)
                      +++    - -+--+.|...+.+-|+-.++.+.|...|++..+.++. ....|+.+..-|....+...|.+.++...+.++
T Consensus       322 v~~----i-dKyR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLNp~-~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~p  395 (559)
T KOG1155|consen  322 VSN----I-DKYRPETCCIIANYYSLRSEHEKAVMYFKRALKLNPK-YLSAWTLMGHEYVEMKNTHAAIESYRRAVDINP  395 (559)
T ss_pred             HHH----h-ccCCccceeeehhHHHHHHhHHHHHHHHHHHHhcCcc-hhHHHHHhhHHHHHhcccHHHHHHHHHHHhcCc
Confidence            221    1 1234567888888888889999999999999997754 678899999999999999999999999998877


Q ss_pred             CCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHH
Q 044084          162 NISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSM  241 (343)
Q Consensus       162 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  241 (343)
                       .|-..|-.+.++|.-.+.+.-|+-.|++..... +-|...|.+|..+|.+.++.++|++-|......| ..+...+..|
T Consensus       396 -~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~k-PnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~-dte~~~l~~L  472 (559)
T KOG1155|consen  396 -RDYRAWYGLGQAYEIMKMHFYALYYFQKALELK-PNDSRLWVALGECYEKLNRLEEAIKCYKRAILLG-DTEGSALVRL  472 (559)
T ss_pred             -hhHHHHhhhhHHHHHhcchHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHhccHHHHHHHHHHHHhcc-ccchHHHHHH
Confidence             688889999999999999999999999998874 5678899999999999999999999999999887 4466889999


Q ss_pred             HHHHHccCChHHHHHHHHHHhhC----CC-Cch-HHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHHH
Q 044084          242 VAMYGKTGRIRDAMRLVAKMKPK----GC-EPN-VWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEF  315 (343)
Q Consensus       242 ~~~~~~~~~~~~a~~~~~~m~~~----~~-~p~-~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m  315 (343)
                      .+.|-+.++..+|...|.+-++.    |. .|. ...-.-|..-+.+.+++++|..|......+  ....++|..++++.
T Consensus       473 akLye~l~d~~eAa~~yek~v~~~~~eg~~~~~t~ka~~fLA~~f~k~~~~~~As~Ya~~~~~~--~~e~eeak~LlRei  550 (559)
T KOG1155|consen  473 AKLYEELKDLNEAAQYYEKYVEVSELEGEIDDETIKARLFLAEYFKKMKDFDEASYYATLVLKG--ETECEEAKALLREI  550 (559)
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHhhcchHHHHHHHHHHhcC--CchHHHHHHHHHHH
Confidence            99999999999999988877652    33 331 222233555678899999998877766655  56778899999988


Q ss_pred             HhC
Q 044084          316 RMN  318 (343)
Q Consensus       316 ~~~  318 (343)
                      ++.
T Consensus       551 r~~  553 (559)
T KOG1155|consen  551 RKI  553 (559)
T ss_pred             HHh
Confidence            765

>TIGR00540 hemY_coli hemY protein

Probab=99.71  E-value=1.8e-13  Score=116.67  Aligned_cols=278  Identities=9%  Similarity=0.005  Sum_probs=182.6

Q ss_pred             chhhHHHHHHHHHhCCCCCChh-hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSG-CYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEIL   80 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~   80 (343)
                      +++.|.+.+.+..+..  |+.. .+-....+..+.|+++.|.+.+.+..+....+.   ....-.....+...|+++.|.
T Consensus        99 ~~~~A~~~l~~~~~~~--~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~---l~~~~~~a~l~l~~~~~~~Al  173 (409)
T TIGR00540        99 DYAKAEKLIAKNADHA--AEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDN---ILVEIARTRILLAQNELHAAR  173 (409)
T ss_pred             CHHHHHHHHHHHhhcC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCc---hHHHHHHHHHHHHCCCHHHHH
Confidence            6778888887776653  4433 344456677888999999999988766543222   123334577778889999999


Q ss_pred             HHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHH-HHHHH---HHhcCcHhHHHHHHHHH
Q 044084           81 KFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFL-KLVLM---YIEEGMVEKTLEVVESM  156 (343)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~l~~~---~~~~~~~~~a~~~~~~~  156 (343)
                      ..++.+.+..+. +...+..+...+...|+++.+.+.+..+.+.+.. +...+. .-...   ....+..+++.+.+..+
T Consensus       174 ~~l~~l~~~~P~-~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~-~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~  251 (409)
T TIGR00540       174 HGVDKLLEMAPR-HKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLF-DDEEFADLEQKAEIGLLDEAMADEGIDGLLNW  251 (409)
T ss_pred             HHHHHHHHhCCC-CHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHH
Confidence            999998887532 5567778888889999999999999998888654 333332 11111   12223333333444444


Q ss_pred             HhcCC---CCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhH---HHHHHHHHccCChhHHHHHHHHHHHcC
Q 044084          157 KNAEL---NISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTY---ASIINAYCRIGLYSKAEKVFIEMQQKG  230 (343)
Q Consensus       157 ~~~~~---~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~---~~ll~~~~~~~~~~~a~~~~~~~~~~~  230 (343)
                      .+..+   +.+...+..+...+...|++++|.+++++..+.  .||....   ....-.....++.+.+.+.++...+..
T Consensus       252 ~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~--~pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk~~  329 (409)
T TIGR00540       252 WKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKK--LGDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAKNV  329 (409)
T ss_pred             HHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhh--CCCcccchhHHHHHhhhcCCCChHHHHHHHHHHHHhC
Confidence            43322   125667788888889999999999999998886  3444321   111122234577788888888777653


Q ss_pred             CCcCh--hhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHH
Q 044084          231 FDKCV--VAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQL  289 (343)
Q Consensus       231 ~~~~~--~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a  289 (343)
                       +-|+  ....++...+.+.|++++|.+.|+........|+...+..+...+.+.|+.++|
T Consensus       330 -p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A  389 (409)
T TIGR00540       330 -DDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEA  389 (409)
T ss_pred             -CCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHH
Confidence             3344  566788888899999999999998544433478887776666665555544433

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.

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.71  E-value=6.9e-13  Score=120.04  Aligned_cols=310  Identities=10%  Similarity=0.031  Sum_probs=233.0

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      ++++|+++|+++.+..+ -+...+..++..+.+.++.++|++.++.+......     ...+..++..+...++..+|++
T Consensus       117 dyd~Aiely~kaL~~dP-~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~dp~-----~~~~l~layL~~~~~~~~~AL~  190 (822)
T PRK14574        117 RWDQALALWQSSLKKDP-TNPDLISGMIMTQADAGRGGVVLKQATELAERDPT-----VQNYMTLSYLNRATDRNYDALQ  190 (822)
T ss_pred             CHHHHHHHHHHHHhhCC-CCHHHHHHHHHHHhhcCCHHHHHHHHHHhcccCcc-----hHHHHHHHHHHHhcchHHHHHH
Confidence            67899999999999865 35677778889999999999999999998765432     2344444455545666767999


Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHH------------------------------------------
Q 044084           82 FFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFK------------------------------------------  119 (343)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~------------------------------------------  119 (343)
                      .++++.+.. +-+...+..+..++.+.|-...|.++..                                          
T Consensus       191 ~~ekll~~~-P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~f~~~~~~~l~~~~~a~~vr~a~~~~~~~~~r~~~~d~  269 (822)
T PRK14574        191 ASSEAVRLA-PTSEEVLKNHLEILQRNRIVEPALRLAKENPNLVSAEHYRQLERDAAAEQVRMAVLPTRSETERFDIADK  269 (822)
T ss_pred             HHHHHHHhC-CCCHHHHHHHHHHHHHcCCcHHHHHHHHhCccccCHHHHHHHHHHHHHHHHhhcccccccchhhHHHHHH
Confidence            999999974 2256666777777777765544443332                                          


Q ss_pred             ------HHHHc-CCCCCH-HH----HHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHH
Q 044084          120 ------EAEEK-GMLRDL-EV----FLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKV  187 (343)
Q Consensus       120 ------~~~~~-~~~~~~-~~----~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  187 (343)
                            .+... +..|.. ..    .--.+-++...+++.++++.|+.+...+.+....+-..+.++|...+++++|..+
T Consensus       270 ala~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l  349 (822)
T PRK14574        270 ALADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPI  349 (822)
T ss_pred             HHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHH
Confidence                  11110 111221 11    1223456778899999999999999888665666788999999999999999999


Q ss_pred             HHHHHHcC-----CCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCC-----------CcCh---hhHHHHHHHHHcc
Q 044084          188 YEQLISQG-----CIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGF-----------DKCV---VAYSSMVAMYGKT  248 (343)
Q Consensus       188 ~~~~~~~~-----~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~-----------~~~~---~~~~~l~~~~~~~  248 (343)
                      |+.+....     .+++......|.-+|...+++++|..+++.+.+...           .||.   ..+..++..+...
T Consensus       350 ~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~  429 (822)
T PRK14574        350 LSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVAL  429 (822)
T ss_pred             HHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHHHHHc
Confidence            99997653     123444457889999999999999999999998421           1221   2345567888999


Q ss_pred             CChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh---------------HHHHHHHHHhcCCHHHHHHHHH
Q 044084          249 GRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK---------------YTTVISAYNMAREFDMCVKFYN  313 (343)
Q Consensus       249 ~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~---------------~~~l~~~~~~~g~~~~a~~~~~  313 (343)
                      |++.+|++.++++.... +-|......+.+.+...|.++.|+.               ....+.++...|++++|..+.+
T Consensus       430 gdl~~Ae~~le~l~~~a-P~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l~P~~~~~~~~~~~~al~l~e~~~A~~~~~  508 (822)
T PRK14574        430 NDLPTAQKKLEDLSSTA-PANQNLRIALASIYLARDLPRKAEQELKAVESLAPRSLILERAQAETAMALQEWHQMELLTD  508 (822)
T ss_pred             CCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhCCccHHHHHHHHHHHHhhhhHHHHHHHHH
Confidence            99999999999998763 4488889999999999999999988               5666777888899999999999


Q ss_pred             HHHhCC
Q 044084          314 EFRMNG  319 (343)
Q Consensus       314 ~m~~~~  319 (343)
                      ...+..
T Consensus       509 ~l~~~~  514 (822)
T PRK14574        509 DVISRS  514 (822)
T ss_pred             HHHhhC
Confidence            887753

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.70  E-value=1e-13  Score=117.47  Aligned_cols=274  Identities=10%  Similarity=0.052  Sum_probs=200.0

Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHH--HHHHHHhcccCHH
Q 044084           35 IGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYA--SLICSFASIAEVK  112 (343)
Q Consensus        35 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~--~l~~~~~~~~~~~  112 (343)
                      .|++++|.+.+....+....|    ...|.....+..+.|+++.|.+.+.++.+.  .|+.....  .....+...|+++
T Consensus        97 eGd~~~A~k~l~~~~~~~~~p----~l~~llaA~aA~~~g~~~~A~~~l~~A~~~--~~~~~~~~~l~~a~l~l~~g~~~  170 (398)
T PRK10747         97 EGDYQQVEKLMTRNADHAEQP----VVNYLLAAEAAQQRGDEARANQHLERAAEL--ADNDQLPVEITRVRIQLARNENH  170 (398)
T ss_pred             CCCHHHHHHHHHHHHhcccch----HHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHCCCHH
Confidence            489999998887765543222    234544456668899999999999998775  44543332  3356788889999


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCch-------hhHHHHHHHHhcCCcHHHHH
Q 044084          113 VAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISD-------CISCVIVNGFSKRRAYWAAV  185 (343)
Q Consensus       113 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~  185 (343)
                      .|...++++.+..+. ++.....+...|.+.|++++|.+++..+.+....++.       .+|..++.......+.+...
T Consensus       171 ~Al~~l~~~~~~~P~-~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~  249 (398)
T PRK10747        171 AARHGVDKLLEVAPR-HPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLK  249 (398)
T ss_pred             HHHHHHHHHHhcCCC-CHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHH
Confidence            999999999887754 7888899999999999999999999999887764322       12333344444455667777


Q ss_pred             HHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCC
Q 044084          186 KVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKG  265 (343)
Q Consensus       186 ~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~  265 (343)
                      ++++.+.+. .+.+......+..++...|+.++|..++++..+.  +++...  .++.+....++.+++.+..+...+. 
T Consensus       250 ~~w~~lp~~-~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~l--~~l~~~l~~~~~~~al~~~e~~lk~-  323 (398)
T PRK10747        250 RWWKNQSRK-TRHQVALQVAMAEHLIECDDHDTAQQIILDGLKR--QYDERL--VLLIPRLKTNNPEQLEKVLRQQIKQ-  323 (398)
T ss_pred             HHHHhCCHH-HhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHH--HHHHhhccCCChHHHHHHHHHHHhh-
Confidence            777776554 2456777888889999999999999999988874  445432  2334444568899999999888876 


Q ss_pred             CCchH-HHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHhcccccccC
Q 044084          266 CEPNV-WIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       266 ~~p~~-~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~g~~~~a  343 (343)
                       .|+. .....+                   ...+.+.|++++|.+.|+...+.  .|+..++..+..++.+.|+.++|
T Consensus       324 -~P~~~~l~l~l-------------------grl~~~~~~~~~A~~~le~al~~--~P~~~~~~~La~~~~~~g~~~~A  380 (398)
T PRK10747        324 -HGDTPLLWSTL-------------------GQLLMKHGEWQEASLAFRAALKQ--RPDAYDYAWLADALDRLHKPEEA  380 (398)
T ss_pred             -CCCCHHHHHHH-------------------HHHHHHCCCHHHHHHHHHHHHhc--CCCHHHHHHHHHHHHHcCCHHHH
Confidence             4444 333333                   44566778888999999999884  68999988999999999998764

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.70  E-value=5.2e-13  Score=123.25  Aligned_cols=220  Identities=8%  Similarity=-0.020  Sum_probs=91.7

Q ss_pred             HHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 044084           61 HMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMY  140 (343)
Q Consensus        61 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  140 (343)
                      ..|..+..++.. +++++|+..+.+....  .|+......+...+...|++++|...++++...  .|+...+..+...+
T Consensus       478 ~a~~~LG~~l~~-~~~~eAi~a~~~Al~~--~Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~--~p~~~a~~~la~al  552 (987)
T PRK09782        478 AAWNRLAKCYRD-TLPGVALYAWLQAEQR--QPDAWQHRAVAYQAYQVEDYATALAAWQKISLH--DMSNEDLLAAANTA  552 (987)
T ss_pred             HHHHHHHHHHHh-CCcHHHHHHHHHHHHh--CCchHHHHHHHHHHHHCCCHHHHHHHHHHHhcc--CCCcHHHHHHHHHH
Confidence            344444444443 4444444444444332  233222222222223445555555555444332  12222333444444


Q ss_pred             HhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHH
Q 044084          141 IEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAE  220 (343)
Q Consensus       141 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~  220 (343)
                      .+.|+.++|...+++..+.++ .+...+..+.......|++++|...+++..+.  .|+...+..+..++.+.|++++|.
T Consensus       553 l~~Gd~~eA~~~l~qAL~l~P-~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l--~P~~~a~~~LA~~l~~lG~~deA~  629 (987)
T PRK09782        553 QAAGNGAARDRWLQQAEQRGL-GDNALYWWLHAQRYIPGQPELALNDLTRSLNI--APSANAYVARATIYRQRHNVPAAV  629 (987)
T ss_pred             HHCCCHHHHHHHHHHHHhcCC-ccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHh--CCCHHHHHHHHHHHHHCCCHHHHH
Confidence            445555555555554444332 11111222222222335555555555554443  233444444444455555555555


Q ss_pred             HHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHH
Q 044084          221 KVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLE  290 (343)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~  290 (343)
                      ..++...+.. |.+...++.+...+...|++++|...+++..+.. +-+...+..+..++...|++++|+
T Consensus       630 ~~l~~AL~l~-Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l~-P~~~~a~~nLA~al~~lGd~~eA~  697 (987)
T PRK09782        630 SDLRAALELE-PNNSNYQAALGYALWDSGDIAQSREMLERAHKGL-PDDPALIRQLAYVNQRLDDMAATQ  697 (987)
T ss_pred             HHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHH
Confidence            5555544443 2233444444444445555555555555444431 112333444444444444444443

>TIGR00540 hemY_coli hemY protein

Probab=99.70  E-value=1.4e-13  Score=117.30  Aligned_cols=282  Identities=11%  Similarity=-0.001  Sum_probs=188.9

Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHH
Q 044084           33 YKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVK  112 (343)
Q Consensus        33 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  112 (343)
                      ...|+++.|.+.+....+....|    ...+-....+..+.|+++.|.+.+.+..+....+.....-.....+...|+++
T Consensus        95 ~~~g~~~~A~~~l~~~~~~~~~~----~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~~~~~~  170 (409)
T TIGR00540        95 LAEGDYAKAEKLIAKNADHAAEP----VLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRILLAQNELH  170 (409)
T ss_pred             HhCCCHHHHHHHHHHHhhcCCCC----HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHHHHCCCHH
Confidence            45689999999998876654322    24555566778888999999999999876532222223333567788899999


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHH-HHHHHH---hcCCcHHHHHHHH
Q 044084          113 VAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISC-VIVNGF---SKRRAYWAAVKVY  188 (343)
Q Consensus       113 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~l~~~~---~~~~~~~~a~~~~  188 (343)
                      .|...++.+.+..+. ++.+...+...+...|++++|.+.+..+.+.++. +...+. .-..++   ...+..+...+.+
T Consensus       171 ~Al~~l~~l~~~~P~-~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~-~~~~~~~l~~~a~~~~l~~~~~~~~~~~L  248 (409)
T TIGR00540       171 AARHGVDKLLEMAPR-HKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLF-DDEEFADLEQKAEIGLLDEAMADEGIDGL  248 (409)
T ss_pred             HHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHHHHHHHHHhcCHHHH
Confidence            999999999998754 7788889999999999999999999999988763 333231 111111   2222333333344


Q ss_pred             HHHHHcC---CCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhh---HHHHHHHHHccCChHHHHHHHHHHh
Q 044084          189 EQLISQG---CIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVA---YSSMVAMYGKTGRIRDAMRLVAKMK  262 (343)
Q Consensus       189 ~~~~~~~---~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~~~l~~~~~~~~~~~~a~~~~~~m~  262 (343)
                      ..+.+..   .+.+...+..+...+...|+.++|.+++++..+..  ||...   ...........++.+.+.+.+++..
T Consensus       249 ~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~--pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~l  326 (409)
T TIGR00540       249 LNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKL--GDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQA  326 (409)
T ss_pred             HHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhC--CCcccchhHHHHHhhhcCCCChHHHHHHHHHHH
Confidence            4444431   11367778888889999999999999999998865  33321   1111222234567788888888777


Q ss_pred             hCCCCchHH---HHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHhcccc
Q 044084          263 PKGCEPNVW---IYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQ  339 (343)
Q Consensus       263 ~~~~~p~~~---~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~g~  339 (343)
                      +.  .|+..   ...++                   ...+.+.|++++|.+.|+........|+...+..+..++.+.|+
T Consensus       327 k~--~p~~~~~~ll~sL-------------------g~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~  385 (409)
T TIGR00540       327 KN--VDDKPKCCINRAL-------------------GQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGD  385 (409)
T ss_pred             Hh--CCCChhHHHHHHH-------------------HHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCC
Confidence            65  44443   32333                   34455677778888888854444456788777788888888888


Q ss_pred             cccC
Q 044084          340 IEEL  343 (343)
Q Consensus       340 ~~~a  343 (343)
                      .++|
T Consensus       386 ~~~A  389 (409)
T TIGR00540       386 KAEA  389 (409)
T ss_pred             HHHH
Confidence            7654

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.

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

Probab=99.68  E-value=1.6e-14  Score=121.57  Aligned_cols=276  Identities=13%  Similarity=0.092  Sum_probs=205.4

Q ss_pred             hhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHH
Q 044084            3 SQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKF   82 (343)
Q Consensus         3 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~   82 (343)
                      .++|+..|..+.++ +.-+......+..+|...+++++|.++|+.+.+...-- -...++|.+.+..+-+.-    ++..
T Consensus       335 ~~~A~~~~~klp~h-~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~r-v~~meiyST~LWHLq~~v----~Ls~  408 (638)
T KOG1126|consen  335 CREALNLFEKLPSH-HYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYR-VKGMEIYSTTLWHLQDEV----ALSY  408 (638)
T ss_pred             HHHHHHHHHhhHHh-cCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccc-ccchhHHHHHHHHHHhhH----HHHH
Confidence            57899999995554 44455777889999999999999999999997764322 223577887776543321    2222


Q ss_pred             H-HHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCC
Q 044084           83 F-RDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAEL  161 (343)
Q Consensus        83 ~-~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  161 (343)
                      + +.+.... +-.+.+|.++.++|.-.++.+.|++.|++..+.... ...+|+.+..-+.....+|.|...|+.....++
T Consensus       409 Laq~Li~~~-~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQldp~-faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~~  486 (638)
T KOG1126|consen  409 LAQDLIDTD-PNSPESWCALGNCFSLQKDHDTAIKCFKRAIQLDPR-FAYAYTLLGHESIATEEFDKAMKSFRKALGVDP  486 (638)
T ss_pred             HHHHHHhhC-CCCcHHHHHhcchhhhhhHHHHHHHHHHHhhccCCc-cchhhhhcCChhhhhHHHHhHHHHHHhhhcCCc
Confidence            2 2233322 335778999999999999999999999998885532 678888888888888999999999988876543


Q ss_pred             CCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHH
Q 044084          162 NISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSM  241 (343)
Q Consensus       162 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  241 (343)
                       -.-.+|--+.-.|.+.++++.|.-.|++..+-+ +-+.+....+...+.+.|+.|+|++++++....+ +.|+..--..
T Consensus       487 -rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~IN-P~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld-~kn~l~~~~~  563 (638)
T KOG1126|consen  487 -RHYNAWYGLGTVYLKQEKLEFAEFHFQKAVEIN-PSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLD-PKNPLCKYHR  563 (638)
T ss_pred             -hhhHHHHhhhhheeccchhhHHHHHHHhhhcCC-ccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcC-CCCchhHHHH
Confidence             233344456677889999999999999888765 3345556667777888899999999999888776 4456666666


Q ss_pred             HHHHHccCChHHHHHHHHHHhhCCCCch-HHHHHHHHHHHhcccChhHHHh
Q 044084          242 VAMYGKTGRIRDAMRLVAKMKPKGCEPN-VWIYNSLMDMHGRAKNLRQLEK  291 (343)
Q Consensus       242 ~~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~~~~~l~~~~~~~~~~~~a~~  291 (343)
                      +..+...+++++|+..++++++.  .|+ ...+..+...|.+.|+.+.|..
T Consensus       564 ~~il~~~~~~~eal~~LEeLk~~--vP~es~v~~llgki~k~~~~~~~Al~  612 (638)
T KOG1126|consen  564 ASILFSLGRYVEALQELEELKEL--VPQESSVFALLGKIYKRLGNTDLALL  612 (638)
T ss_pred             HHHHHhhcchHHHHHHHHHHHHh--CcchHHHHHHHHHHHHHHccchHHHH
Confidence            77778889999999999998875  454 4567777788999999888876

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

Probab=99.67  E-value=2.1e-12  Score=112.57  Aligned_cols=334  Identities=12%  Similarity=0.101  Sum_probs=241.0

Q ss_pred             CchhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHH
Q 044084            1 TNSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEIL   80 (343)
Q Consensus         1 ~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~   80 (343)
                      ++.++|..++.+.++..+ .....|..|...|-+.|+.+++...+-.+...+    |.+...|..+.....+.|.+++|.
T Consensus       153 g~~eeA~~i~~EvIkqdp-~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~----p~d~e~W~~ladls~~~~~i~qA~  227 (895)
T KOG2076|consen  153 GDLEEAEEILMEVIKQDP-RNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLN----PKDYELWKRLADLSEQLGNINQAR  227 (895)
T ss_pred             CCHHHHHHHHHHHHHhCc-cchhhHHHHHHHHHHcccHHHHHHHHHHHHhcC----CCChHHHHHHHHHHHhcccHHHHH
Confidence            367889999999998764 477789999999999999999988776554433    223478999999999999999999


Q ss_pred             HHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHH----HHHHHHHHhcCcHhHHHHHHHHH
Q 044084           81 KFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVF----LKLVLMYIEEGMVEKTLEVVESM  156 (343)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~----~~l~~~~~~~~~~~~a~~~~~~~  156 (343)
                      -.|.+..+.. +++...+---...|-+.|+...|...|.++....++.|..-+    ...++.+...++.+.|.+.++..
T Consensus       228 ~cy~rAI~~~-p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~~e~a~~~le~~  306 (895)
T KOG2076|consen  228 YCYSRAIQAN-PSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNERERAAKALEGA  306 (895)
T ss_pred             HHHHHHHhcC-CcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            9999998874 334444445567788899999999999999887653333322    23455667777778888888877


Q ss_pred             Hhc-CCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcC---------------------------CCCCHhhHHHHHH
Q 044084          157 KNA-ELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQG---------------------------CIPGQVTYASIIN  208 (343)
Q Consensus       157 ~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---------------------------~~p~~~~~~~ll~  208 (343)
                      ... +-..+...++.++..+.+...++.+......+....                           ..++...+ .++-
T Consensus       307 ~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l~v~-rl~i  385 (895)
T KOG2076|consen  307 LSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYDLRVI-RLMI  385 (895)
T ss_pred             HhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCccchhH-hHhh
Confidence            652 122455568888888899889998888887776611                           11222221 1222


Q ss_pred             HHHccCChhHHHHHHHHHHHcC--CCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccCh
Q 044084          209 AYCRIGLYSKAEKVFIEMQQKG--FDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNL  286 (343)
Q Consensus       209 ~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~  286 (343)
                      ++.+....+....+...+.+..  +.-+...|.-+..+|...|++.+|+.+|..+...-..-+...|-.+..+|...|..
T Consensus       386 cL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~l~e~  465 (895)
T KOG2076|consen  386 CLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYMELGEY  465 (895)
T ss_pred             hhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHHHHhhH
Confidence            3344455555555555566655  33356788889999999999999999999998774445677899999999999999


Q ss_pred             hHHHh---------------HHHHHHHHHhcCCHHHHHHHHHHHH--------hCCCCccHHHHHHHHHHHhcccccc
Q 044084          287 RQLEK---------------YTTVISAYNMAREFDMCVKFYNEFR--------MNGGVIDRAMAGIMVGVFSKLSQIE  341 (343)
Q Consensus       287 ~~a~~---------------~~~l~~~~~~~g~~~~a~~~~~~m~--------~~~~~p~~~~~~~l~~~~~~~g~~~  341 (343)
                      ++|.+               -..|...+-+.|+.++|.+.+..+.        ..+..|+........+.|...|+.+
T Consensus       466 e~A~e~y~kvl~~~p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~~D~~~~e~~a~~~e~ri~~~r~d~l~~~gk~E  543 (895)
T KOG2076|consen  466 EEAIEFYEKVLILAPDNLDARITLASLYQQLGNHEKALETLEQIINPDGRNAEACAWEPERRILAHRCDILFQVGKRE  543 (895)
T ss_pred             HHHHHHHHHHHhcCCCchhhhhhHHHHHHhcCCHHHHHHHHhcccCCCccchhhccccHHHHHHHHHHHHHHHhhhHH
Confidence            99987               4566677888999999999998853        3345556666566667777777655

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.65  E-value=1.1e-11  Score=114.73  Aligned_cols=305  Identities=11%  Similarity=0.006  Sum_probs=218.7

Q ss_pred             hhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCc---HHHHH
Q 044084            4 QSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGR---AFEIL   80 (343)
Q Consensus         4 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~---~~~a~   80 (343)
                      .+|...+..|.+... -+....-.+.....+.|+.++|.++|............ +...-..|+..+.+.+.   ..++.
T Consensus       359 ~~~~~~~~~~y~~~~-~~~~~l~q~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~l~~~l~~~~~~~~~~~~~~~~~  436 (987)
T PRK09782        359 AEALRLARLLYQQEP-ANLTRLDQLTWQLMQNGQSREAADLLLQRYPFQGDARL-SQTLMARLASLLESHPYLATPAKVA  436 (987)
T ss_pred             hHHHHHHHHHHhcCC-CCHHHHHHHHHHHHHcccHHHHHHHHHHhcCCCccccc-CHHHHHHHHHHHHhCCcccchHHHH
Confidence            455566666666522 35666666777788999999999999988663211111 13345567777777665   33332


Q ss_pred             HH----------------------HHHHHhc-CC-CC--ChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHH
Q 044084           81 KF----------------------FRDMKEK-GI-LE--DPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFL  134 (343)
Q Consensus        81 ~~----------------------~~~~~~~-~~-~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  134 (343)
                      .+                      ++..... +. ++  +...|..+..++.. ++.++|...+.+.....  |+.....
T Consensus       437 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~al~~~p~~~~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~~--Pd~~~~L  513 (987)
T PRK09782        437 ILSKPLPLAEQRQWQSQLPGIADNCPAIVRLLGDMSPSYDAAAWNRLAKCYRD-TLPGVALYAWLQAEQRQ--PDAWQHR  513 (987)
T ss_pred             HhccccccchhHHHHhhhhhhhhhHHHHHHhcccCCCCCCHHHHHHHHHHHHh-CCcHHHHHHHHHHHHhC--CchHHHH
Confidence            22                      2222111 11 23  45667777777766 78888999888877654  5554444


Q ss_pred             HHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccC
Q 044084          135 KLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIG  214 (343)
Q Consensus       135 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~  214 (343)
                      .+...+...|++++|...|+++....  |+...+..+...+...|++++|...+++..+.. +++...+..+.......|
T Consensus       514 ~lA~al~~~Gr~eeAi~~~rka~~~~--p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~-P~~~~l~~~La~~l~~~G  590 (987)
T PRK09782        514 AVAYQAYQVEDYATALAAWQKISLHD--MSNEDLLAAANTAQAAGNGAARDRWLQQAEQRG-LGDNALYWWLHAQRYIPG  590 (987)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHhccC--CCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHhCC
Confidence            55556678999999999999986543  334456677788889999999999999998874 223333333344455669


Q ss_pred             ChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh---
Q 044084          215 LYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK---  291 (343)
Q Consensus       215 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~---  291 (343)
                      ++++|...++...+..  |+...+..+..++.+.|++++|...+++..... +.+...+..+..++...|+.++|..   
T Consensus       591 r~~eAl~~~~~AL~l~--P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~-Pd~~~a~~nLG~aL~~~G~~eeAi~~l~  667 (987)
T PRK09782        591 QPELALNDLTRSLNIA--PSANAYVARATIYRQRHNVPAAVSDLRAALELE-PNNSNYQAALGYALWDSGDIAQSREMLE  667 (987)
T ss_pred             CHHHHHHHHHHHHHhC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            9999999999999865  578889999999999999999999999999863 2255677778788999999998876   


Q ss_pred             ------------HHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 044084          292 ------------YTTVISAYNMAREFDMCVKFYNEFRMNG  319 (343)
Q Consensus       292 ------------~~~l~~~~~~~g~~~~a~~~~~~m~~~~  319 (343)
                                  +..+..++...|++++|+..+++..+..
T Consensus       668 ~AL~l~P~~~~a~~nLA~al~~lGd~~eA~~~l~~Al~l~  707 (987)
T PRK09782        668 RAHKGLPDDPALIRQLAYVNQRLDDMAATQHYARLVIDDI  707 (987)
T ss_pred             HHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC
Confidence                        7888899999999999999999998753

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

Probab=99.60  E-value=1.2e-11  Score=95.90  Aligned_cols=230  Identities=13%  Similarity=0.133  Sum_probs=182.5

Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCC---hHhHHHHHHHHhcccC
Q 044084           34 KIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILED---PSVYASLICSFASIAE  110 (343)
Q Consensus        34 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~  110 (343)
                      -..+.++|.++|-+|.+..    |.+..+--+|.+.|-+.|..+.|+.+.+.+.++.-.+.   ......|..-|...|-
T Consensus        47 Ls~Q~dKAvdlF~e~l~~d----~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl  122 (389)
T COG2956          47 LSNQPDKAVDLFLEMLQED----PETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGL  122 (389)
T ss_pred             hhcCcchHHHHHHHHHhcC----chhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhh
Confidence            4567899999999997743    55568888999999999999999999999987521111   1223456677889999


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCch----hhHHHHHHHHhcCCcHHHHHH
Q 044084          111 VKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISD----CISCVIVNGFSKRRAYWAAVK  186 (343)
Q Consensus       111 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~  186 (343)
                      +|.|+.+|..+.+.+. .-......|+..|-...+|++|+++-+++...+..+..    ..|.-+...+....+.+.|..
T Consensus       123 ~DRAE~~f~~L~de~e-fa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~  201 (389)
T COG2956         123 LDRAEDIFNQLVDEGE-FAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARE  201 (389)
T ss_pred             hhHHHHHHHHHhcchh-hhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHH
Confidence            9999999999988553 35678889999999999999999999998877655432    246677777777899999999


Q ss_pred             HHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCC
Q 044084          187 VYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGC  266 (343)
Q Consensus       187 ~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~  266 (343)
                      ++.+..+.+ +-.+..--.+.+.....|+++.|.+.++.+.+.+...-..+...|..+|.+.|+.++....+.++.+...
T Consensus       202 ~l~kAlqa~-~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~~  280 (389)
T COG2956         202 LLKKALQAD-KKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETNT  280 (389)
T ss_pred             HHHHHHhhC-ccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHccC
Confidence            999998874 2233333455678889999999999999999987555567888999999999999999999999988643


Q ss_pred             Cch
Q 044084          267 EPN  269 (343)
Q Consensus       267 ~p~  269 (343)
                      .++
T Consensus       281 g~~  283 (389)
T COG2956         281 GAD  283 (389)
T ss_pred             Ccc
Confidence            333

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

Probab=99.59  E-value=3.1e-13  Score=117.34  Aligned_cols=259  Identities=15%  Similarity=0.189  Sum_probs=186.1

Q ss_pred             HHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHH
Q 044084            8 HYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMK   87 (343)
Q Consensus         8 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~   87 (343)
                      .++-.+...|+.|+..||..+|.-|+..|+++.|- +|.-|.-+..+..   ...|+.++.+..+.++.+.+.       
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~---e~vf~~lv~sh~~And~Enpk-------   79 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVR---EGVFRGLVASHKEANDAENPK-------   79 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhccccccc---chhHHHHHhcccccccccCCC-------
Confidence            46677888999999999999999999999999998 9998887777655   678999999999999887765       


Q ss_pred             hcCCCCChHhHHHHHHHHhcccCHHH---HHHHHHHHH----HcCCCCCHHHH---------------HHHHHHHHhcCc
Q 044084           88 EKGILEDPSVYASLICSFASIAEVKV---AEELFKEAE----EKGMLRDLEVF---------------LKLVLMYIEEGM  145 (343)
Q Consensus        88 ~~~~~~~~~~~~~l~~~~~~~~~~~~---a~~~~~~~~----~~~~~~~~~~~---------------~~l~~~~~~~~~  145 (343)
                          .|-..||..|..+|...||...   +.+.+..+.    ..|.. ....+               ...+......|-
T Consensus        80 ----ep~aDtyt~Ll~ayr~hGDli~fe~veqdLe~i~~sfs~~Gvg-s~e~~fl~k~~c~p~~lpda~n~illlv~egl  154 (1088)
T KOG4318|consen   80 ----EPLADTYTNLLKAYRIHGDLILFEVVEQDLESINQSFSDHGVG-SPERWFLMKIHCCPHSLPDAENAILLLVLEGL  154 (1088)
T ss_pred             ----CCchhHHHHHHHHHHhccchHHHHHHHHHHHHHHhhhhhhccC-cHHHHHHhhcccCcccchhHHHHHHHHHHHHH
Confidence                6788899999999999999655   333222222    22321 11111               122333344455


Q ss_pred             HhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCC-cHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHH
Q 044084          146 VEKTLEVVESMKNAELNISDCISCVIVNGFSKRR-AYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFI  224 (343)
Q Consensus       146 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~  224 (343)
                      ++.+++++..+....-..   .+..+++-+.... .+++...+-+...+   .|+..+|..++.+-...|+.+.|..++.
T Consensus       155 waqllkll~~~Pvsa~~~---p~~vfLrqnv~~ntpvekLl~~cksl~e---~~~s~~l~a~l~~alaag~~d~Ak~ll~  228 (1088)
T KOG4318|consen  155 WAQLLKLLAKVPVSAWNA---PFQVFLRQNVVDNTPVEKLLNMCKSLVE---APTSETLHAVLKRALAAGDVDGAKNLLY  228 (1088)
T ss_pred             HHHHHHHHhhCCcccccc---hHHHHHHHhccCCchHHHHHHHHHHhhc---CCChHHHHHHHHHHHhcCchhhHHHHHH
Confidence            566666555543221100   1112344444332 23333333333332   5899999999999999999999999999


Q ss_pred             HHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh
Q 044084          225 EMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK  291 (343)
Q Consensus       225 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~  291 (343)
                      +|.+.|++.+.+-|..|+-+   .++...+..+++-|.+.|+.|+..|+...+..+...|....+..
T Consensus       229 emke~gfpir~HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~~t~~~~e  292 (1088)
T KOG4318|consen  229 EMKEKGFPIRAHYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNGQTKYGEE  292 (1088)
T ss_pred             HHHHcCCCcccccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcchhhhhccc
Confidence            99999999999888888766   78888899999999999999999999988888877665444443

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

Probab=99.59  E-value=3.7e-11  Score=95.83  Aligned_cols=273  Identities=10%  Similarity=0.042  Sum_probs=138.8

Q ss_pred             CCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHH
Q 044084           36 GDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAE  115 (343)
Q Consensus        36 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  115 (343)
                      |+|.+|+++..+-.+.+..|    ...|..-..+.-+.|+.+.+-.++.+.-+....++...+-+........|+.+.|.
T Consensus        98 G~~~qAEkl~~rnae~~e~p----~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~~aA~  173 (400)
T COG3071          98 GDFQQAEKLLRRNAEHGEQP----VLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAAR  173 (400)
T ss_pred             CcHHHHHHHHHHhhhcCcch----HHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHH
Confidence            66666666666655544433    24455555555666666666666666655433334444555555556666666666


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCch-------hhHHHHHHHHhcCCcHHHHHHHH
Q 044084          116 ELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISD-------CISCVIVNGFSKRRAYWAAVKVY  188 (343)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~  188 (343)
                      .-++++.+.++. ++.+.....++|.+.|++.....++..+.+.+.-.+.       .+|..+++-....+..+.-...|
T Consensus       174 ~~v~~ll~~~pr-~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W  252 (400)
T COG3071         174 ENVDQLLEMTPR-HPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWW  252 (400)
T ss_pred             HHHHHHHHhCcC-ChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHH
Confidence            666666665543 4555666666666666666666666666665542222       13444555444444455544555


Q ss_pred             HHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhC-CCC
Q 044084          189 EQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK-GCE  267 (343)
Q Consensus       189 ~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~-~~~  267 (343)
                      ++..+. .+-++..-..++.-+.+.|+.++|.++..+..+++..|+.   .. .-.+.+-++.+.-.+..++-.+. +..
T Consensus       253 ~~~pr~-lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L---~~-~~~~l~~~d~~~l~k~~e~~l~~h~~~  327 (400)
T COG3071         253 KNQPRK-LRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRL---CR-LIPRLRPGDPEPLIKAAEKWLKQHPED  327 (400)
T ss_pred             HhccHH-hhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhH---HH-HHhhcCCCCchHHHHHHHHHHHhCCCC
Confidence            554433 2233444444555555666666666666665555544431   11 11223344444444444333322 222


Q ss_pred             chHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHhcccccc
Q 044084          268 PNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIE  341 (343)
Q Consensus       268 p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~g~~~  341 (343)
                        +-.+                   ..+...|.+.+.|.+|...|+...+  ..|+..+|+.+..++.+.|+..
T Consensus       328 --p~L~-------------------~tLG~L~~k~~~w~kA~~~leaAl~--~~~s~~~~~~la~~~~~~g~~~  378 (400)
T COG3071         328 --PLLL-------------------STLGRLALKNKLWGKASEALEAALK--LRPSASDYAELADALDQLGEPE  378 (400)
T ss_pred             --hhHH-------------------HHHHHHHHHhhHHHHHHHHHHHHHh--cCCChhhHHHHHHHHHHcCChH
Confidence              2333                   3334444444555555555554443  2455555555555555555443

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

Probab=99.58  E-value=4.1e-11  Score=95.55  Aligned_cols=276  Identities=12%  Similarity=0.023  Sum_probs=215.5

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      ++.+|.++..+-.+++-.| ...|..-..+.-+.|+.+.+-..+.+..+...++.   ....-+..+.....|+++.|..
T Consensus        99 ~~~qAEkl~~rnae~~e~p-~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~---l~v~ltrarlll~~~d~~aA~~  174 (400)
T COG3071          99 DFQQAEKLLRRNAEHGEQP-VLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDT---LAVELTRARLLLNRRDYPAARE  174 (400)
T ss_pred             cHHHHHHHHHHhhhcCcch-HHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCch---HHHHHHHHHHHHhCCCchhHHH
Confidence            6788999998888877543 44566677788899999999999999877644443   5677788889999999999999


Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCH-------HHHHHHHHHHHhcCcHhHHHHHHH
Q 044084           82 FFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDL-------EVFLKLVLMYIEEGMVEKTLEVVE  154 (343)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~  154 (343)
                      -+.++.+.+.. ++........+|.+.|++..+..++..+.+.|.-.+.       .+|..+++-....+..+.-...++
T Consensus       175 ~v~~ll~~~pr-~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~  253 (400)
T COG3071         175 NVDQLLEMTPR-HPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWK  253 (400)
T ss_pred             HHHHHHHhCcC-ChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHH
Confidence            99999887644 6677888999999999999999999999998876543       457777776666666666666777


Q ss_pred             HHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcC
Q 044084          155 SMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKC  234 (343)
Q Consensus       155 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~  234 (343)
                      .....- +.+...-.+++.-+.+.|+.++|.++..+..+.+..|+   ...+ -.+.+-++.+.-++..+.-.+.. +-+
T Consensus       254 ~~pr~l-r~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~---L~~~-~~~l~~~d~~~l~k~~e~~l~~h-~~~  327 (400)
T COG3071         254 NQPRKL-RNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPR---LCRL-IPRLRPGDPEPLIKAAEKWLKQH-PED  327 (400)
T ss_pred             hccHHh-hcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChh---HHHH-HhhcCCCCchHHHHHHHHHHHhC-CCC
Confidence            765432 23444667788889999999999999999999876666   2222 23566788888777777766553 455


Q ss_pred             hhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHH
Q 044084          235 VVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLE  290 (343)
Q Consensus       235 ~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~  290 (343)
                      +..+.+|...|.+.+.+.+|...|+...+.  .|+..+|+-+.+++.+.|+..+|.
T Consensus       328 p~L~~tLG~L~~k~~~w~kA~~~leaAl~~--~~s~~~~~~la~~~~~~g~~~~A~  381 (400)
T COG3071         328 PLLLSTLGRLALKNKLWGKASEALEAALKL--RPSASDYAELADALDQLGEPEEAE  381 (400)
T ss_pred             hhHHHHHHHHHHHhhHHHHHHHHHHHHHhc--CCChhhHHHHHHHHHHcCChHHHH
Confidence            688999999999999999999999987765  889999888877777666555443

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

Probab=99.58  E-value=3.6e-11  Score=105.05  Aligned_cols=306  Identities=12%  Similarity=0.139  Sum_probs=231.4

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcc
Q 044084           29 MEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASI  108 (343)
Q Consensus        29 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  108 (343)
                      .....-.|++++|.+++.++.++...    ....|.+|...|-+.|+.+++...+-..-... +-|...|..+.....+.
T Consensus       146 AN~lfarg~~eeA~~i~~EvIkqdp~----~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~-p~d~e~W~~ladls~~~  220 (895)
T KOG2076|consen  146 ANNLFARGDLEEAEEILMEVIKQDPR----NPIAYYTLGEIYEQRGDIEKALNFWLLAAHLN-PKDYELWKRLADLSEQL  220 (895)
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHhCcc----chhhHHHHHHHHHHcccHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHhc
Confidence            33344459999999999999887643    35899999999999999999988775554443 33667899999999999


Q ss_pred             cCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHH----HHHHHHhcCCcHHHH
Q 044084          109 AEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISC----VIVNGFSKRRAYWAA  184 (343)
Q Consensus       109 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~----~l~~~~~~~~~~~~a  184 (343)
                      |.++.|.-+|.+.++..+. +...+-.-+..|-+.|+...|.+.|.++.+..++.+..-+.    .++..+...++.+.|
T Consensus       221 ~~i~qA~~cy~rAI~~~p~-n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~~e~a  299 (895)
T KOG2076|consen  221 GNINQARYCYSRAIQANPS-NWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNERERA  299 (895)
T ss_pred             ccHHHHHHHHHHHHhcCCc-chHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHHHHH
Confidence            9999999999999998753 66666677888999999999999999999877633333222    345667777888999


Q ss_pred             HHHHHHHHHc-CCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHc---------------------------CCCcChh
Q 044084          185 VKVYEQLISQ-GCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQK---------------------------GFDKCVV  236 (343)
Q Consensus       185 ~~~~~~~~~~-~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~---------------------------~~~~~~~  236 (343)
                      .+.+...... +-..+...++.++..|.+...++.+..........                           +++++..
T Consensus       300 ~~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l~  379 (895)
T KOG2076|consen  300 AKALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYDLR  379 (895)
T ss_pred             HHHHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCccch
Confidence            9999887763 23455667888888899989999988887777662                           1223333


Q ss_pred             hHHHHHHHHHccCChHHHHHHHHHHhhCC--CCchHHHHHHHHHHHhcccChhHHHh----------------HHHHHHH
Q 044084          237 AYSSMVAMYGKTGRIRDAMRLVAKMKPKG--CEPNVWIYNSLMDMHGRAKNLRQLEK----------------YTTVISA  298 (343)
Q Consensus       237 ~~~~l~~~~~~~~~~~~a~~~~~~m~~~~--~~p~~~~~~~l~~~~~~~~~~~~a~~----------------~~~l~~~  298 (343)
                      ++ .++-++...+..+....+.....+..  +.-+...|.-+.++|...|++.+|..                |..+..+
T Consensus       380 v~-rl~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c  458 (895)
T KOG2076|consen  380 VI-RLMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARC  458 (895)
T ss_pred             hH-hHhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHH
Confidence            31 23334455555555555555566655  33456778889999999999999988                8899999


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCccH-HHHHHHHHHHhcccccccC
Q 044084          299 YNMAREFDMCVKFYNEFRMNGGVIDR-AMAGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       299 ~~~~g~~~~a~~~~~~m~~~~~~p~~-~~~~~l~~~~~~~g~~~~a  343 (343)
                      |...|.+++|++.|+..+...  |+. ..-.+|...+.+.|+.|+|
T Consensus       459 ~~~l~e~e~A~e~y~kvl~~~--p~~~D~Ri~Lasl~~~~g~~Eka  502 (895)
T KOG2076|consen  459 YMELGEYEEAIEFYEKVLILA--PDNLDARITLASLYQQLGNHEKA  502 (895)
T ss_pred             HHHHhhHHHHHHHHHHHHhcC--CCchhhhhhHHHHHHhcCCHHHH
Confidence            999999999999999998853  443 3345677888888887764

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

Probab=99.58  E-value=5e-11  Score=96.78  Aligned_cols=315  Identities=12%  Similarity=0.138  Sum_probs=199.6

Q ss_pred             CCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHH----------------------------
Q 044084           17 GIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCD----------------------------   68 (343)
Q Consensus        17 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~----------------------------   68 (343)
                      +...|...+-.....+-+.|....|.+.|......-+-.    -.+|..|..                            
T Consensus       159 ~~~~D~fllYL~Gvv~k~~~~~s~A~~sfv~~v~~~P~~----W~AWleL~~lit~~e~~~~l~~~l~~~~h~M~~~F~~  234 (559)
T KOG1155|consen  159 GGEKDEFLLYLYGVVLKELGLLSLAIDSFVEVVNRYPWF----WSAWLELSELITDIEILSILVVGLPSDMHWMKKFFLK  234 (559)
T ss_pred             cccchhHHHHHHHHHHHhhchHHHHHHHHHHHHhcCCcc----hHHHHHHHHhhchHHHHHHHHhcCcccchHHHHHHHH
Confidence            444566666666667778888898988887765533211    122322222                            


Q ss_pred             -HhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCC--CCHHHHHHHHHHHHhcCc
Q 044084           69 -SLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGML--RDLEVFLKLVLMYIEEGM  145 (343)
Q Consensus        69 -~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~  145 (343)
                       ++-...+.++++.-.+.+...|.+-+...-+....+.-...|++.|+.+|+++.+..+-  -|..+|..++-.-....+
T Consensus       235 ~a~~el~q~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~sk  314 (559)
T KOG1155|consen  235 KAYQELHQHEEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSK  314 (559)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHH
Confidence             22222344445554555555554433333333334445566777777777777776321  145566555432221111


Q ss_pred             Hh-HHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHH
Q 044084          146 VE-KTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFI  224 (343)
Q Consensus       146 ~~-~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~  224 (343)
                      +. -|..++. +  ..  --..|..++...|+-.++.++|...|++..+.+ +-....|+.+.+-|....+...|.+-++
T Consensus       315 Ls~LA~~v~~-i--dK--yR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLN-p~~~~aWTLmGHEyvEmKNt~AAi~sYR  388 (559)
T KOG1155|consen  315 LSYLAQNVSN-I--DK--YRPETCCIIANYYSLRSEHEKAVMYFKRALKLN-PKYLSAWTLMGHEYVEMKNTHAAIESYR  388 (559)
T ss_pred             HHHHHHHHHH-h--cc--CCccceeeehhHHHHHHhHHHHHHHHHHHHhcC-cchhHHHHHhhHHHHHhcccHHHHHHHH
Confidence            11 1111111 1  11  122356667777777888888888888888775 3445678888888888888888888888


Q ss_pred             HHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh-------------
Q 044084          225 EMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK-------------  291 (343)
Q Consensus       225 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~-------------  291 (343)
                      ..++.. |.|-..|-.|.++|.-.+...-|+-.|++..+.. +-|...|.+|.++|.+.++.++|++             
T Consensus       389 rAvdi~-p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~k-PnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dte~  466 (559)
T KOG1155|consen  389 RAVDIN-PRDYRAWYGLGQAYEIMKMHFYALYYFQKALELK-PNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDTEG  466 (559)
T ss_pred             HHHhcC-chhHHHHhhhhHHHHHhcchHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccccch
Confidence            888876 6678888888888888888888888888888752 3367888888888888888888887             


Q ss_pred             --HHHHHHHHHhcCCHHHHHHHHHHHHh----CCCCcc-H-HHHHHHHHHHhcccccccC
Q 044084          292 --YTTVISAYNMAREFDMCVKFYNEFRM----NGGVID-R-AMAGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       292 --~~~l~~~~~~~g~~~~a~~~~~~m~~----~~~~p~-~-~~~~~l~~~~~~~g~~~~a  343 (343)
                        +..+...|-+.++.++|.+.|.+.++    .|..-+ . ...--|..-+.+.+++++|
T Consensus       467 ~~l~~LakLye~l~d~~eAa~~yek~v~~~~~eg~~~~~t~ka~~fLA~~f~k~~~~~~A  526 (559)
T KOG1155|consen  467 SALVRLAKLYEELKDLNEAAQYYEKYVEVSELEGEIDDETIKARLFLAEYFKKMKDFDEA  526 (559)
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHhhcchHHH
Confidence              77888888888999999888887655    233222 1 1222255566777777654

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

Probab=99.57  E-value=2.7e-12  Score=108.46  Aligned_cols=271  Identities=9%  Similarity=0.060  Sum_probs=189.0

Q ss_pred             CHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcC--CCCChHhHHHHHHHHhcccCHHHH
Q 044084           37 DSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKG--ILEDPSVYASLICSFASIAEVKVA  114 (343)
Q Consensus        37 ~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a  114 (343)
                      +..+|...|..+.++....    ......+.++|...+++++|.++|+.+.+..  ..-+..+|++.+--+-   + +-+
T Consensus       334 ~~~~A~~~~~klp~h~~nt----~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq---~-~v~  405 (638)
T KOG1126|consen  334 NCREALNLFEKLPSHHYNT----GWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQ---D-EVA  405 (638)
T ss_pred             HHHHHHHHHHhhHHhcCCc----hHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHH---h-hHH
Confidence            4578888888866554322    3666778899999999999999999998753  1125667777664332   2 222


Q ss_pred             HHHH-HHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHH
Q 044084          115 EELF-KEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLIS  193 (343)
Q Consensus       115 ~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  193 (343)
                      +..+ +.+.+... -.+.+|.++..+|.-.++.+.|++.|++..+.++ -...+|+.+..-+.....+|.|...|+....
T Consensus       406 Ls~Laq~Li~~~~-~sPesWca~GNcfSLQkdh~~Aik~f~RAiQldp-~faYayTLlGhE~~~~ee~d~a~~~fr~Al~  483 (638)
T KOG1126|consen  406 LSYLAQDLIDTDP-NSPESWCALGNCFSLQKDHDTAIKCFKRAIQLDP-RFAYAYTLLGHESIATEEFDKAMKSFRKALG  483 (638)
T ss_pred             HHHHHHHHHhhCC-CCcHHHHHhcchhhhhhHHHHHHHHHHHhhccCC-ccchhhhhcCChhhhhHHHHhHHHHHHhhhc
Confidence            3333 34444432 3789999999999999999999999999988775 3667888888888888999999999998775


Q ss_pred             cCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHH
Q 044084          194 QGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIY  273 (343)
Q Consensus       194 ~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~  273 (343)
                      .. +-+-..|--+.-.|.+.++++.|+-.|+...+.+ |.+.+....+...+-+.|+.++|++++++......+ |+-.-
T Consensus       484 ~~-~rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~IN-P~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~k-n~l~~  560 (638)
T KOG1126|consen  484 VD-PRHYNAWYGLGTVYLKQEKLEFAEFHFQKAVEIN-PSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPK-NPLCK  560 (638)
T ss_pred             CC-chhhHHHHhhhhheeccchhhHHHHHHHhhhcCC-ccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCC-CchhH
Confidence            41 1122344456677899999999999999998876 556777778888889999999999999999876332 32222


Q ss_pred             HHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHH-HHHHHHHHHhcccccc
Q 044084          274 NSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRA-MAGIMVGVFSKLSQIE  341 (343)
Q Consensus       274 ~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~-~~~~l~~~~~~~g~~~  341 (343)
                      -.-+.                   .+...+++++|+..++++++.  .|+.. .|..+...|.+.|+.+
T Consensus       561 ~~~~~-------------------il~~~~~~~eal~~LEeLk~~--vP~es~v~~llgki~k~~~~~~  608 (638)
T KOG1126|consen  561 YHRAS-------------------ILFSLGRYVEALQELEELKEL--VPQESSVFALLGKIYKRLGNTD  608 (638)
T ss_pred             HHHHH-------------------HHHhhcchHHHHHHHHHHHHh--CcchHHHHHHHHHHHHHHccch
Confidence            22222                   233455666666666666653  34443 3555666666666544

>PRK12370 invasion protein regulator; Provisional

Probab=99.57  E-value=7.2e-12  Score=110.89  Aligned_cols=260  Identities=13%  Similarity=0.043  Sum_probs=178.5

Q ss_pred             CChhhHHHHHHHHH-----hcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhh---------ccCcHHHHHHHHHH
Q 044084           20 LDSGCYCQIMEAFY-----KIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLG---------KSGRAFEILKFFRD   85 (343)
Q Consensus        20 ~~~~~~~~l~~~~~-----~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~---------~~~~~~~a~~~~~~   85 (343)
                      .+...|...+.+-.     ..+++++|..+|++..+..    |.....|..+..++.         ..+++++|...+++
T Consensus       254 ~~~da~~~~lrg~~~~~~~~~~~~~~A~~~~~~Al~ld----P~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~  329 (553)
T PRK12370        254 NSIDSTMVYLRGKHELNQYTPYSLQQALKLLTQCVNMS----PNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIK  329 (553)
T ss_pred             CChHHHHHHHHhHHHHHccCHHHHHHHHHHHHHHHhcC----CccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHH
Confidence            45555555555432     2256899999999987654    333566766665443         33458899999999


Q ss_pred             HHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCch
Q 044084           86 MKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISD  165 (343)
Q Consensus        86 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  165 (343)
                      ..+.+.. +...+..+...+...|++++|...+++..+..+. +...+..+...+...|++++|...+++..+.++. +.
T Consensus       330 Al~ldP~-~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~-~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~-~~  406 (553)
T PRK12370        330 ATELDHN-NPQALGLLGLINTIHSEYIVGSLLFKQANLLSPI-SADIKYYYGWNLFMAGQLEEALQTINECLKLDPT-RA  406 (553)
T ss_pred             HHhcCCC-CHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC-Ch
Confidence            8887532 5677777888888899999999999999987643 6778888899999999999999999999887653 22


Q ss_pred             hhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCC-CHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHH
Q 044084          166 CISCVIVNGFSKRRAYWAAVKVYEQLISQGCIP-GQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAM  244 (343)
Q Consensus       166 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  244 (343)
                      ..+..++..+...|++++|...++++.... .| +...+..+..++...|+.++|...+..+.... +.+....+.+...
T Consensus       407 ~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~-~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~~-~~~~~~~~~l~~~  484 (553)
T PRK12370        407 AAGITKLWITYYHTGIDDAIRLGDELRSQH-LQDNPILLSMQVMFLSLKGKHELARKLTKEISTQE-ITGLIAVNLLYAE  484 (553)
T ss_pred             hhHHHHHHHHHhccCHHHHHHHHHHHHHhc-cccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhcc-chhHHHHHHHHHH
Confidence            233344445666889999999999987664 24 34456667778888999999999998876653 2334455666667


Q ss_pred             HHccCChHHHHHHHHHHhhC-CCCchHHHHHHHHHHHhcccChhHHHhH
Q 044084          245 YGKTGRIRDAMRLVAKMKPK-GCEPNVWIYNSLMDMHGRAKNLRQLEKY  292 (343)
Q Consensus       245 ~~~~~~~~~a~~~~~~m~~~-~~~p~~~~~~~l~~~~~~~~~~~~a~~~  292 (343)
                      |...|  ++|...++.+.+. ...|....+..++  +.-.|+.+.+..|
T Consensus       485 ~~~~g--~~a~~~l~~ll~~~~~~~~~~~~~~~~--~~~~g~~~~~~~~  529 (553)
T PRK12370        485 YCQNS--ERALPTIREFLESEQRIDNNPGLLPLV--LVAHGEAIAEKMW  529 (553)
T ss_pred             HhccH--HHHHHHHHHHHHHhhHhhcCchHHHHH--HHHHhhhHHHHHH
Confidence            77777  4777777776653 2233333333333  3334454444433

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.55  E-value=1.3e-11  Score=97.45  Aligned_cols=200  Identities=15%  Similarity=0.101  Sum_probs=143.5

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLM  139 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  139 (343)
                      ...+..+...+...|++++|.+.+++..+.. +.+...+..+...+...|++++|.+.+++..+.... +...+..+...
T Consensus        31 ~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~-~~~~~~~~~~~  108 (234)
T TIGR02521        31 AKIRVQLALGYLEQGDLEVAKENLDKALEHD-PDDYLAYLALALYYQQLGELEKAEDSFRRALTLNPN-NGDVLNNYGTF  108 (234)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-CHHHHHHHHHH
Confidence            4567777788888888888888888877653 224556677777788888888888888887776543 56677777788


Q ss_pred             HHhcCcHhHHHHHHHHHHhcCC-CCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhH
Q 044084          140 YIEEGMVEKTLEVVESMKNAEL-NISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSK  218 (343)
Q Consensus       140 ~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~  218 (343)
                      +...|++++|.+.+++...... +.....+..+..++...|++++|...+++..... +.+...+..+...+...|++++
T Consensus       109 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~  187 (234)
T TIGR02521       109 LCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQID-PQRPESLLELAELYYLRGQYKD  187 (234)
T ss_pred             HHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCChHHHHHHHHHHHHcCCHHH
Confidence            8888888888888888765422 1223356666777778888888888888877653 2345566777777888888888


Q ss_pred             HHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhh
Q 044084          219 AEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       219 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                      |...+++..+. .+.+...+..+...+...|+.++|..+.+.+..
T Consensus       188 A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  231 (234)
T TIGR02521       188 ARAYLERYQQT-YNQTAESLWLGIRIARALGDVAAAQRYGAQLQK  231 (234)
T ss_pred             HHHHHHHHHHh-CCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            88888887776 244556666777777778888888877776654

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=99.55  E-value=1.3e-11  Score=97.37  Aligned_cols=202  Identities=13%  Similarity=0.051  Sum_probs=167.8

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHH
Q 044084           21 DSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYAS  100 (343)
Q Consensus        21 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  100 (343)
                      ....+..+...+...|++++|.+.+++..+..    |.+...+..+...+...|++++|.+.+++..+... .+...+..
T Consensus        30 ~~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~----p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~-~~~~~~~~  104 (234)
T TIGR02521        30 AAKIRVQLALGYLEQGDLEVAKENLDKALEHD----PDDYLAYLALALYYQQLGELEKAEDSFRRALTLNP-NNGDVLNN  104 (234)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC----cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC-CCHHHHHH
Confidence            35678888999999999999999999987654    33357888899999999999999999999988643 35567778


Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCC
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGML-RDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRR  179 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  179 (343)
                      +...+...|++++|...+++..+.... .....+..+...+...|++++|...+++...... .+...+..+...+...|
T Consensus       105 ~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~la~~~~~~~  183 (234)
T TIGR02521       105 YGTFLCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDP-QRPESLLELAELYYLRG  183 (234)
T ss_pred             HHHHHHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-CChHHHHHHHHHHHHcC
Confidence            888999999999999999999875322 2456777888999999999999999999987654 34567888899999999


Q ss_pred             cHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHc
Q 044084          180 AYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       180 ~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  229 (343)
                      ++++|...+++..+. .+.+...+..+...+...|+.++|..+.+.+...
T Consensus       184 ~~~~A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  232 (234)
T TIGR02521       184 QYKDARAYLERYQQT-YNQTAESLWLGIRIARALGDVAAAQRYGAQLQKL  232 (234)
T ss_pred             CHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhh
Confidence            999999999998887 3445667777788888999999999988877653

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.

>PRK12370 invasion protein regulator; Provisional

Probab=99.55  E-value=1.1e-11  Score=109.78  Aligned_cols=233  Identities=12%  Similarity=0.000  Sum_probs=169.7

Q ss_pred             HHHHHHHHHHHhcCCCCChHhHHHHHHHHh---------cccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHh
Q 044084           77 FEILKFFRDMKEKGILEDPSVYASLICSFA---------SIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVE  147 (343)
Q Consensus        77 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~---------~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  147 (343)
                      ++|+..|++..+.... +...|..+..++.         ..+++++|...+++..+..+. +...+..+...+...|+++
T Consensus       278 ~~A~~~~~~Al~ldP~-~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~ldP~-~~~a~~~lg~~~~~~g~~~  355 (553)
T PRK12370        278 QQALKLLTQCVNMSPN-SIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATELDHN-NPQALGLLGLINTIHSEYI  355 (553)
T ss_pred             HHHHHHHHHHHhcCCc-cHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHccCHH
Confidence            7899999998886422 3445555544433         234589999999999987754 7888989999999999999


Q ss_pred             HHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCH-hhHHHHHHHHHccCChhHHHHHHHHH
Q 044084          148 KTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQ-VTYASIINAYCRIGLYSKAEKVFIEM  226 (343)
Q Consensus       148 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~-~~~~~ll~~~~~~~~~~~a~~~~~~~  226 (343)
                      +|...|++..+.++ .+...+..+...+...|++++|...+++..+..  |+. ..+..++..+...|++++|...++++
T Consensus       356 ~A~~~~~~Al~l~P-~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~--P~~~~~~~~~~~~~~~~g~~eeA~~~~~~~  432 (553)
T PRK12370        356 VGSLLFKQANLLSP-ISADIKYYYGWNLFMAGQLEEALQTINECLKLD--PTRAAAGITKLWITYYHTGIDDAIRLGDEL  432 (553)
T ss_pred             HHHHHHHHHHHhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CCChhhHHHHHHHHHhccCHHHHHHHHHHH
Confidence            99999999988875 456678888899999999999999999998874  432 23334444566689999999999998


Q ss_pred             HHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHH-HHHHHHHHhcccChhHHHh--------------
Q 044084          227 QQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWI-YNSLMDMHGRAKNLRQLEK--------------  291 (343)
Q Consensus       227 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~-~~~l~~~~~~~~~~~~a~~--------------  291 (343)
                      .+...+-++..+..+..++...|+.++|...+.++...  .|+..+ .+.+...|...|+  .+..              
T Consensus       433 l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~--~a~~~l~~ll~~~~~~~~  508 (553)
T PRK12370        433 RSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQ--EITGLIAVNLLYAEYCQNSE--RALPTIREFLESEQRIDN  508 (553)
T ss_pred             HHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhc--cchhHHHHHHHHHHHhccHH--HHHHHHHHHHHHhhHhhc
Confidence            87642334556777888899999999999999987665  444433 4445556676664  3322              


Q ss_pred             -HHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 044084          292 -YTTVISAYNMAREFDMCVKFYNEFRMNG  319 (343)
Q Consensus       292 -~~~l~~~~~~~g~~~~a~~~~~~m~~~~  319 (343)
                       ....-..|.-.|+.+.+..+ +++.+.|
T Consensus       509 ~~~~~~~~~~~~g~~~~~~~~-~~~~~~~  536 (553)
T PRK12370        509 NPGLLPLVLVAHGEAIAEKMW-NKFKNED  536 (553)
T ss_pred             CchHHHHHHHHHhhhHHHHHH-HHhhccc
Confidence             22244445556776666665 7776654

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

Probab=99.54  E-value=6.8e-12  Score=101.71  Aligned_cols=157  Identities=11%  Similarity=0.154  Sum_probs=104.2

Q ss_pred             CCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHH
Q 044084          178 RRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRL  257 (343)
Q Consensus       178 ~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  257 (343)
                      .|++++|.+.|++.......-....|++-+ .+-..|++++|+..|-.+... +..+..+...+...|-...+...|.++
T Consensus       503 ngd~dka~~~ykeal~ndasc~ealfnigl-t~e~~~~ldeald~f~klh~i-l~nn~evl~qianiye~led~aqaie~  580 (840)
T KOG2003|consen  503 NGDLDKAAEFYKEALNNDASCTEALFNIGL-TAEALGNLDEALDCFLKLHAI-LLNNAEVLVQIANIYELLEDPAQAIEL  580 (840)
T ss_pred             cCcHHHHHHHHHHHHcCchHHHHHHHHhcc-cHHHhcCHHHHHHHHHHHHHH-HHhhHHHHHHHHHHHHHhhCHHHHHHH
Confidence            467778888888777654333333444333 345678888888877766543 123566677777888888888888888


Q ss_pred             HHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh----------------------------------------------
Q 044084          258 VAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK----------------------------------------------  291 (343)
Q Consensus       258 ~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~----------------------------------------------  291 (343)
                      +-+.... ++.|+.....|.+.|-+.|+-..|.+                                              
T Consensus       581 ~~q~~sl-ip~dp~ilskl~dlydqegdksqafq~~ydsyryfp~nie~iewl~ayyidtqf~ekai~y~ekaaliqp~~  659 (840)
T KOG2003|consen  581 LMQANSL-IPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRYFPCNIETIEWLAAYYIDTQFSEKAINYFEKAALIQPNQ  659 (840)
T ss_pred             HHHhccc-CCCCHHHHHHHHHHhhcccchhhhhhhhhhcccccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHhcCccH
Confidence            8777654 55577888888889999998888876                                              


Q ss_pred             --HHHHHHHH-HhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHhccc
Q 044084          292 --YTTVISAY-NMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLS  338 (343)
Q Consensus       292 --~~~l~~~~-~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~g  338 (343)
                        |..|+..| .+.|++++|.++|++.... ++.|.....-|++.+...|
T Consensus       660 ~kwqlmiasc~rrsgnyqka~d~yk~~hrk-fpedldclkflvri~~dlg  708 (840)
T KOG2003|consen  660 SKWQLMIASCFRRSGNYQKAFDLYKDIHRK-FPEDLDCLKFLVRIAGDLG  708 (840)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHHh-CccchHHHHHHHHHhcccc
Confidence              55554333 4556677777766666554 3445556666666655544

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

Probab=99.53  E-value=5.4e-11  Score=104.74  Aligned_cols=334  Identities=13%  Similarity=0.140  Sum_probs=173.3

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccC----cHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSG----RAF   77 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~----~~~   77 (343)
                      |+++|...|-+..+....--...+--|.+.+.+.|+++.+...|+.+....    |.+..+...|...|...+    ..+
T Consensus       322 d~ekA~~yY~~s~k~~~d~~~l~~~GlgQm~i~~~dle~s~~~fEkv~k~~----p~~~etm~iLG~Lya~~~~~~~~~d  397 (1018)
T KOG2002|consen  322 DFEKAFKYYMESLKADNDNFVLPLVGLGQMYIKRGDLEESKFCFEKVLKQL----PNNYETMKILGCLYAHSAKKQEKRD  397 (1018)
T ss_pred             cHHHHHHHHHHHHccCCCCccccccchhHHHHHhchHHHHHHHHHHHHHhC----cchHHHHHHHHhHHHhhhhhhHHHH
Confidence            566777777555554321112334456677777777777777777776654    333456666666665553    345


Q ss_pred             HHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHH----HHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHH
Q 044084           78 EILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEA----EEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVV  153 (343)
Q Consensus        78 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~----~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  153 (343)
                      .|..++.+..+.. +.|...|-.+...+-...-+ .++..+..+    ...+-.+-+...|.+...+...|++++|...|
T Consensus       398 ~a~~~l~K~~~~~-~~d~~a~l~laql~e~~d~~-~sL~~~~~A~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~~f  475 (1018)
T KOG2002|consen  398 KASNVLGKVLEQT-PVDSEAWLELAQLLEQTDPW-ASLDAYGNALDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHF  475 (1018)
T ss_pred             HHHHHHHHHHhcc-cccHHHHHHHHHHHHhcChH-HHHHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHH
Confidence            5555555554442 22455555555444433322 224444332    23344455666666666666666666666666


Q ss_pred             HHHHhc---CCCCch------hhHHHHHHHHhcCCcHHHHHHHHHHHHHcC-----------------------------
Q 044084          154 ESMKNA---ELNISD------CISCVIVNGFSKRRAYWAAVKVYEQLISQG-----------------------------  195 (343)
Q Consensus       154 ~~~~~~---~~~~~~------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-----------------------------  195 (343)
                      ......   ...++.      .+--.+...+-..++.+.|.++|..+.+..                             
T Consensus       476 ~~A~~~~~~~~n~de~~~~~lt~~YNlarl~E~l~~~~~A~e~Yk~Ilkehp~YId~ylRl~~ma~~k~~~~ea~~~lk~  555 (1018)
T KOG2002|consen  476 KSALGKLLEVANKDEGKSTNLTLKYNLARLLEELHDTEVAEEMYKSILKEHPGYIDAYLRLGCMARDKNNLYEASLLLKD  555 (1018)
T ss_pred             HHHhhhhhhhcCccccccchhHHHHHHHHHHHhhhhhhHHHHHHHHHHHHCchhHHHHHHhhHHHHhccCcHHHHHHHHH
Confidence            655433   111111      111122233333334444444444433321                             


Q ss_pred             ----CCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHc-CCCcChhhHHHHHHHHHc------------cCChHHHHHHH
Q 044084          196 ----CIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQK-GFDKCVVAYSSMVAMYGK------------TGRIRDAMRLV  258 (343)
Q Consensus       196 ----~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~------------~~~~~~a~~~~  258 (343)
                          ...++..++.+...+.+...+..|.+-|+.+.+. ...+|+.+.-+|...|.+            .+..++|+++|
T Consensus       556 ~l~~d~~np~arsl~G~~~l~k~~~~~a~k~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y  635 (1018)
T KOG2002|consen  556 ALNIDSSNPNARSLLGNLHLKKSEWKPAKKKFETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLY  635 (1018)
T ss_pred             HHhcccCCcHHHHHHHHHHHhhhhhcccccHHHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHH
Confidence                0112222222333344444444444444333322 112344444444443332            13346677777


Q ss_pred             HHHhhCCCCchHHHHHHHHHHHhcccChhHHHh---------------HHHHHHHHHhcCCHHHHHHHHHHHHhC-CCCc
Q 044084          259 AKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK---------------YTTVISAYNMAREFDMCVKFYNEFRMN-GGVI  322 (343)
Q Consensus       259 ~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~---------------~~~l~~~~~~~g~~~~a~~~~~~m~~~-~~~p  322 (343)
                      .+..+.. +-|.+.-+.+.-.++..|++.+|..               |..+..+|...|+|..|+++|+.-.+. +..-
T Consensus       636 ~kvL~~d-pkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~~~~  714 (1018)
T KOG2002|consen  636 GKVLRND-PKNMYAANGIGIVLAEKGRFSEARDIFSQVREATSDFEDVWLNLAHCYVEQGQYRLAIQMYENCLKKFYKKN  714 (1018)
T ss_pred             HHHHhcC-cchhhhccchhhhhhhccCchHHHHHHHHHHHHHhhCCceeeeHHHHHHHHHHHHHHHHHHHHHHHHhcccC
Confidence            7766652 2355666666667777777777766               667777777888888888887765443 3344


Q ss_pred             cHHHHHHHHHHHhccccccc
Q 044084          323 DRAMAGIMVGVFSKLSQIEE  342 (343)
Q Consensus       323 ~~~~~~~l~~~~~~~g~~~~  342 (343)
                      +......|.+++.++|++.+
T Consensus       715 ~~~vl~~Lara~y~~~~~~e  734 (1018)
T KOG2002|consen  715 RSEVLHYLARAWYEAGKLQE  734 (1018)
T ss_pred             CHHHHHHHHHHHHHhhhHHH
Confidence            55567777777777777654

>PF13041 PPR_2: PPR repeat family

Probab=99.48  E-value=1.2e-13  Score=79.56  Aligned_cols=50  Identities=30%  Similarity=0.637  Sum_probs=33.9

Q ss_pred             cChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhc
Q 044084          233 KCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGR  282 (343)
Q Consensus       233 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~  282 (343)
                      ||+.+||++|.+|++.|++++|.++|++|.+.|+.||..||+.++++|++
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            56666666666666666666666666666666666666666666666653

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

Probab=99.48  E-value=6.6e-11  Score=96.11  Aligned_cols=251  Identities=14%  Similarity=0.084  Sum_probs=162.8

Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhc--cCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcc
Q 044084           31 AFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGK--SGRAFEILKFFRDMKEKGILEDPSVYASLICSFASI  108 (343)
Q Consensus        31 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~--~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  108 (343)
                      .+.++|+++.|.+++.-+.+++....   ..+-+.|-..+.-  -.++..|.+.-+..+..+ .-+......-.+.....
T Consensus       428 ~~lk~~d~~~aieilkv~~~kdnk~~---saaa~nl~~l~flqggk~~~~aqqyad~aln~d-ryn~~a~~nkgn~~f~n  503 (840)
T KOG2003|consen  428 ELLKNGDIEGAIEILKVFEKKDNKTA---SAAANNLCALRFLQGGKDFADAQQYADIALNID-RYNAAALTNKGNIAFAN  503 (840)
T ss_pred             HHHhccCHHHHHHHHHHHHhccchhh---HHHhhhhHHHHHHhcccchhHHHHHHHHHhccc-ccCHHHhhcCCceeeec
Confidence            47788999999999888877654433   2233333322222  335666766666554432 11222222222334456


Q ss_pred             cCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHH
Q 044084          109 AEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVY  188 (343)
Q Consensus       109 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  188 (343)
                      |+++.|...+++.......-....| .+.-.+-..|++++|++.|-++...-. .+......+...|-...++.+|++++
T Consensus       504 gd~dka~~~ykeal~ndasc~ealf-niglt~e~~~~ldeald~f~klh~il~-nn~evl~qianiye~led~aqaie~~  581 (840)
T KOG2003|consen  504 GDLDKAAEFYKEALNNDASCTEALF-NIGLTAEALGNLDEALDCFLKLHAILL-NNAEVLVQIANIYELLEDPAQAIELL  581 (840)
T ss_pred             CcHHHHHHHHHHHHcCchHHHHHHH-HhcccHHHhcCHHHHHHHHHHHHHHHH-hhHHHHHHHHHHHHHhhCHHHHHHHH
Confidence            8888888888888765432222222 234456677888888888877654322 34455666777777778888888888


Q ss_pred             HHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCc
Q 044084          189 EQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEP  268 (343)
Q Consensus       189 ~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p  268 (343)
                      .+.... ++.|+.....+...|-+.|+-..|.+.+-+--+. ++-+..+..-|...|....-++++...|++..-  +.|
T Consensus       582 ~q~~sl-ip~dp~ilskl~dlydqegdksqafq~~ydsyry-fp~nie~iewl~ayyidtqf~ekai~y~ekaal--iqp  657 (840)
T KOG2003|consen  582 MQANSL-IPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRY-FPCNIETIEWLAAYYIDTQFSEKAINYFEKAAL--IQP  657 (840)
T ss_pred             HHhccc-CCCCHHHHHHHHHHhhcccchhhhhhhhhhcccc-cCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHh--cCc
Confidence            776554 4556777788888888888888877765443332 566777777788888888788888888887654  478


Q ss_pred             hHHHHHHHHHHH-hcccChhHHHh
Q 044084          269 NVWIYNSLMDMH-GRAKNLRQLEK  291 (343)
Q Consensus       269 ~~~~~~~l~~~~-~~~~~~~~a~~  291 (343)
                      +..-|..++..| .+.|++..|..
T Consensus       658 ~~~kwqlmiasc~rrsgnyqka~d  681 (840)
T KOG2003|consen  658 NQSKWQLMIASCFRRSGNYQKAFD  681 (840)
T ss_pred             cHHHHHHHHHHHHHhcccHHHHHH
Confidence            888888777654 45788887766

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

Probab=99.48  E-value=2.3e-09  Score=91.09  Aligned_cols=305  Identities=10%  Similarity=0.080  Sum_probs=152.5

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHH
Q 044084           24 CYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLIC  103 (343)
Q Consensus        24 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  103 (343)
                      +|..-.+.|.+.+.++-|..+|....+--    |.....|......--..|..++...+|++....- +-....|-....
T Consensus       518 tw~~da~~~~k~~~~~carAVya~alqvf----p~k~slWlra~~~ek~hgt~Esl~Allqkav~~~-pkae~lwlM~ak  592 (913)
T KOG0495|consen  518 TWLDDAQSCEKRPAIECARAVYAHALQVF----PCKKSLWLRAAMFEKSHGTRESLEALLQKAVEQC-PKAEILWLMYAK  592 (913)
T ss_pred             HHhhhHHHHHhcchHHHHHHHHHHHHhhc----cchhHHHHHHHHHHHhcCcHHHHHHHHHHHHHhC-CcchhHHHHHHH
Confidence            44444555555555555555555443322    2223445444444444455555555555554431 112233333344


Q ss_pred             HHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHH
Q 044084          104 SFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWA  183 (343)
Q Consensus       104 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  183 (343)
                      .+...|+...|..++.+..+..+. +...|-.-+..-.....++.|..+|.+.....  |+...|.--+....-.+..++
T Consensus       593 e~w~agdv~~ar~il~~af~~~pn-seeiwlaavKle~en~e~eraR~llakar~~s--gTeRv~mKs~~~er~ld~~ee  669 (913)
T KOG0495|consen  593 EKWKAGDVPAARVILDQAFEANPN-SEEIWLAAVKLEFENDELERARDLLAKARSIS--GTERVWMKSANLERYLDNVEE  669 (913)
T ss_pred             HHHhcCCcHHHHHHHHHHHHhCCC-cHHHHHHHHHHhhccccHHHHHHHHHHHhccC--CcchhhHHHhHHHHHhhhHHH
Confidence            444445555555555555544332 44445555555555555555555555444322  233333333333333344444


Q ss_pred             HHHHHHHHHHc---------------------------------CCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcC
Q 044084          184 AVKVYEQLISQ---------------------------------GCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKG  230 (343)
Q Consensus       184 a~~~~~~~~~~---------------------------------~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  230 (343)
                      |.+++++..+.                                 .++-....|..+.+.=-+.|.+-.|..+++...-.+
T Consensus       670 A~rllEe~lk~fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~cP~~ipLWllLakleEk~~~~~rAR~ildrarlkN  749 (913)
T KOG0495|consen  670 ALRLLEEALKSFPDFHKLWLMLGQIEEQMENIEMAREAYLQGTKKCPNSIPLWLLLAKLEEKDGQLVRARSILDRARLKN  749 (913)
T ss_pred             HHHHHHHHHHhCCchHHHHHHHhHHHHHHHHHHHHHHHHHhccccCCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhcC
Confidence            44444443332                                 012222334444444444555666666666655544


Q ss_pred             CCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh-----------HHHHHHHH
Q 044084          231 FDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK-----------YTTVISAY  299 (343)
Q Consensus       231 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~-----------~~~l~~~~  299 (343)
                       +.+...|-..|++-.+.|+.+.|..+..+..+. ++.+...|..-|....+.++-..+..           ...+...|
T Consensus       750 -Pk~~~lwle~Ir~ElR~gn~~~a~~lmakALQe-cp~sg~LWaEaI~le~~~~rkTks~DALkkce~dphVllaia~lf  827 (913)
T KOG0495|consen  750 -PKNALLWLESIRMELRAGNKEQAELLMAKALQE-CPSSGLLWAEAIWLEPRPQRKTKSIDALKKCEHDPHVLLAIAKLF  827 (913)
T ss_pred             -CCcchhHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCccchhHHHHHHhccCcccchHHHHHHHhccCCchhHHHHHHHH
Confidence             445566666666666666666666666555554 23334444444444443333222211           55566677


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHhcccc
Q 044084          300 NMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQ  339 (343)
Q Consensus       300 ~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~g~  339 (343)
                      ....+++.|.+.|.+.+..+.. +..+|.-+..-+.+.|.
T Consensus       828 w~e~k~~kar~Wf~Ravk~d~d-~GD~wa~fykfel~hG~  866 (913)
T KOG0495|consen  828 WSEKKIEKAREWFERAVKKDPD-NGDAWAWFYKFELRHGT  866 (913)
T ss_pred             HHHHHHHHHHHHHHHHHccCCc-cchHHHHHHHHHHHhCC
Confidence            7788899999999998876432 33556666666666663

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

Probab=99.47  E-value=4.2e-09  Score=89.51  Aligned_cols=232  Identities=8%  Similarity=0.054  Sum_probs=128.4

Q ss_pred             HHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcH
Q 044084          102 ICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAY  181 (343)
Q Consensus       102 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  181 (343)
                      ...|.+.+.++-+..+|....+--+ .+...|......=-..|..+....+|++....-+ -....|......+-..|+.
T Consensus       523 a~~~~k~~~~~carAVya~alqvfp-~k~slWlra~~~ek~hgt~Esl~Allqkav~~~p-kae~lwlM~ake~w~agdv  600 (913)
T KOG0495|consen  523 AQSCEKRPAIECARAVYAHALQVFP-CKKSLWLRAAMFEKSHGTRESLEALLQKAVEQCP-KAEILWLMYAKEKWKAGDV  600 (913)
T ss_pred             HHHHHhcchHHHHHHHHHHHHhhcc-chhHHHHHHHHHHHhcCcHHHHHHHHHHHHHhCC-cchhHHHHHHHHHHhcCCc
Confidence            3334444444444444444444321 1334444444443444455555555555544332 2233444444555556666


Q ss_pred             HHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHH
Q 044084          182 WAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKM  261 (343)
Q Consensus       182 ~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m  261 (343)
                      ..|..++.+..+.. +.+...|-.-++.-.....++.|..+|......  .|+...|..-+....-.++.++|.+++++.
T Consensus       601 ~~ar~il~~af~~~-pnseeiwlaavKle~en~e~eraR~llakar~~--sgTeRv~mKs~~~er~ld~~eeA~rllEe~  677 (913)
T KOG0495|consen  601 PAARVILDQAFEAN-PNSEEIWLAAVKLEFENDELERARDLLAKARSI--SGTERVWMKSANLERYLDNVEEALRLLEEA  677 (913)
T ss_pred             HHHHHHHHHHHHhC-CCcHHHHHHHHHHhhccccHHHHHHHHHHHhcc--CCcchhhHHHhHHHHHhhhHHHHHHHHHHH
Confidence            66666666666653 224455555566666666666676666666553  355666666666556666677777777666


Q ss_pred             hhCCCCchH-HHHHHHHHHHhcccChhHHHh---------------HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHH
Q 044084          262 KPKGCEPNV-WIYNSLMDMHGRAKNLRQLEK---------------YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRA  325 (343)
Q Consensus       262 ~~~~~~p~~-~~~~~l~~~~~~~~~~~~a~~---------------~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~  325 (343)
                      .+.  .|+- ..|..+.+.+-+.++.+.|..               |..+...--+.|.+-+|..++++.+-.+.+ +..
T Consensus       678 lk~--fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~cP~~ipLWllLakleEk~~~~~rAR~ildrarlkNPk-~~~  754 (913)
T KOG0495|consen  678 LKS--FPDFHKLWLMLGQIEEQMENIEMAREAYLQGTKKCPNSIPLWLLLAKLEEKDGQLVRARSILDRARLKNPK-NAL  754 (913)
T ss_pred             HHh--CCchHHHHHHHhHHHHHHHHHHHHHHHHHhccccCCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhcCCC-cch
Confidence            654  3333 455666666666666666665               555555555666666777777766665533 445


Q ss_pred             HHHHHHHHHhcccccc
Q 044084          326 MAGIMVGVFSKLSQIE  341 (343)
Q Consensus       326 ~~~~l~~~~~~~g~~~  341 (343)
                      .|-..++.=.|.|..+
T Consensus       755 lwle~Ir~ElR~gn~~  770 (913)
T KOG0495|consen  755 LWLESIRMELRAGNKE  770 (913)
T ss_pred             hHHHHHHHHHHcCCHH
Confidence            5666666655555544

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

Probab=99.47  E-value=2.4e-10  Score=100.81  Aligned_cols=266  Identities=13%  Similarity=0.119  Sum_probs=174.2

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhc---CCCCCh------HhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCH
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEK---GILEDP------SVYASLICSFASIAEVKVAEELFKEAEEKGMLRDL  130 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---~~~~~~------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  130 (343)
                      .+..|.+...+...|.+..|...|.+.+..   ...++.      .+--.+....-..++.+.|.+.|..+.+..+. -+
T Consensus       452 ~E~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YNlarl~E~l~~~~~A~e~Yk~Ilkehp~-YI  530 (1018)
T KOG2002|consen  452 PEVLNNVASLHFRLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYNLARLLEELHDTEVAEEMYKSILKEHPG-YI  530 (1018)
T ss_pred             HHHHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHHHHHHHHhhhhhhHHHHHHHHHHHHCch-hH
Confidence            356666666666667777666666665543   112222      11112334444555666666666666664321 23


Q ss_pred             HHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcC-CCCCHhhHHHHHHH
Q 044084          131 EVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQG-CIPGQVTYASIINA  209 (343)
Q Consensus       131 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~p~~~~~~~ll~~  209 (343)
                      ..|-.++.+....+...+|...+....+.+- .+...++.+...+.....+..|.+-|....+.- ..+|.++...|.+.
T Consensus       531 d~ylRl~~ma~~k~~~~ea~~~lk~~l~~d~-~np~arsl~G~~~l~k~~~~~a~k~f~~i~~~~~~~~D~YsliaLGN~  609 (1018)
T KOG2002|consen  531 DAYLRLGCMARDKNNLYEASLLLKDALNIDS-SNPNARSLLGNLHLKKSEWKPAKKKFETILKKTSTKTDAYSLIALGNV  609 (1018)
T ss_pred             HHHHHhhHHHHhccCcHHHHHHHHHHHhccc-CCcHHHHHHHHHHHhhhhhcccccHHHHHHhhhccCCchhHHHHhhHH
Confidence            3444444344445666777777777665443 344456666667777777877877666665542 23566666666665


Q ss_pred             HHc------------cCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHH
Q 044084          210 YCR------------IGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLM  277 (343)
Q Consensus       210 ~~~------------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~  277 (343)
                      |.+            .+..++|+++|..+.+.. |.|...-|-+.-+++..|++..|..+|.+.++... -+..+|..+.
T Consensus       610 ~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~d-pkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~-~~~dv~lNla  687 (1018)
T KOG2002|consen  610 YIQALHNPSRNPEKEKKHQEKALQLYGKVLRND-PKNMYAANGIGIVLAEKGRFSEARDIFSQVREATS-DFEDVWLNLA  687 (1018)
T ss_pred             HHHHhcccccChHHHHHHHHHHHHHHHHHHhcC-cchhhhccchhhhhhhccCchHHHHHHHHHHHHHh-hCCceeeeHH
Confidence            542            234677888888888875 56778888888888999999999999999888632 2456778888


Q ss_pred             HHHhcccChhHHHh-----------------HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHH
Q 044084          278 DMHGRAKNLRQLEK-----------------YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGI  329 (343)
Q Consensus       278 ~~~~~~~~~~~a~~-----------------~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~  329 (343)
                      .+|...|++..|.+                 ...|..++.+.|.+.+|.+.+...+...+.-...-||.
T Consensus       688 h~~~e~~qy~~AIqmYe~~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~ll~a~~~~p~~~~v~FN~  756 (1018)
T KOG2002|consen  688 HCYVEQGQYRLAIQMYENCLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEALLKARHLAPSNTSVKFNL  756 (1018)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCCccchHHhHH
Confidence            88888898888887                 67788888889999999998888877654433334543

>PF13041 PPR_2: PPR repeat family

Probab=99.44  E-value=3.3e-13  Score=77.76  Aligned_cols=47  Identities=21%  Similarity=0.447  Sum_probs=19.3

Q ss_pred             chhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHH
Q 044084          164 SDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAY  210 (343)
Q Consensus       164 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~  210 (343)
                      |..+||++|.+|++.|++++|.++|++|.+.|+.||..||+.+|++|
T Consensus         2 ~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~   48 (50)
T PF13041_consen    2 DVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGL   48 (50)
T ss_pred             chHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence            33344444444444444444444444444444444444444444433

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

Probab=99.43  E-value=1.4e-09  Score=93.66  Aligned_cols=277  Identities=17%  Similarity=0.185  Sum_probs=190.9

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhcc-----CcH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKS-----GRA   76 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~-----~~~   76 (343)
                      ++++|++.++.-.+. +.............+.+.|+.++|..+|..+.+++    |.+...|..+..+....     .+.
T Consensus        19 ~~~~AL~~L~~~~~~-I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rN----Pdn~~Yy~~L~~~~g~~~~~~~~~~   93 (517)
T PF12569_consen   19 DYEEALEHLEKNEKQ-ILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRN----PDNYDYYRGLEEALGLQLQLSDEDV   93 (517)
T ss_pred             CHHHHHHHHHhhhhh-CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC----CCcHHHHHHHHHHHhhhcccccccH
Confidence            567888888765443 43445567778889999999999999999998887    44456677777666322     256


Q ss_pred             HHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCH-HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHH
Q 044084           77 FEILKFFRDMKEKGILEDPSVYASLICSFASIAEV-KVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVES  155 (343)
Q Consensus        77 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  155 (343)
                      +...++|+++...-  |.......+.-.+.....+ ..+...+..+...|++   .+++.|-..|....+.+-..+++..
T Consensus        94 ~~~~~~y~~l~~~y--p~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvP---slF~~lk~Ly~d~~K~~~i~~l~~~  168 (517)
T PF12569_consen   94 EKLLELYDELAEKY--PRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVP---SLFSNLKPLYKDPEKAAIIESLVEE  168 (517)
T ss_pred             HHHHHHHHHHHHhC--ccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCc---hHHHHHHHHHcChhHHHHHHHHHHH
Confidence            77788888887653  4333333332223322223 3445556666777753   4666777777766666666666666


Q ss_pred             HHhc----C----------CCCch--hhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCC-HhhHHHHHHHHHccCChhH
Q 044084          156 MKNA----E----------LNISD--CISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPG-QVTYASIINAYCRIGLYSK  218 (343)
Q Consensus       156 ~~~~----~----------~~~~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~-~~~~~~ll~~~~~~~~~~~  218 (343)
                      ....    +          -+|+.  +++..+...|-..|++++|++++++.++.  .|+ +..|..-.+.+-+.|++.+
T Consensus       169 ~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~h--tPt~~ely~~KarilKh~G~~~~  246 (517)
T PF12569_consen  169 YVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEH--TPTLVELYMTKARILKHAGDLKE  246 (517)
T ss_pred             HHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhc--CCCcHHHHHHHHHHHHHCCCHHH
Confidence            5432    1          12343  34456677888899999999999999987  465 5677777888999999999


Q ss_pred             HHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHH--------HHHHHHHHhcccChhHHH
Q 044084          219 AEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWI--------YNSLMDMHGRAKNLRQLE  290 (343)
Q Consensus       219 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~--------~~~l~~~~~~~~~~~~a~  290 (343)
                      |.+.++.....+ .-|...-+..+..+.++|++++|.+++......+..|-...        ......+|.+.|++..|.
T Consensus       247 Aa~~~~~Ar~LD-~~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~r~~~~~~AL  325 (517)
T PF12569_consen  247 AAEAMDEARELD-LADRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYLRQGDYGLAL  325 (517)
T ss_pred             HHHHHHHHHhCC-hhhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHhhHHHHH
Confidence            999999999886 45777778888899999999999999999887765432211        133445677777777766


Q ss_pred             h
Q 044084          291 K  291 (343)
Q Consensus       291 ~  291 (343)
                      +
T Consensus       326 k  326 (517)
T PF12569_consen  326 K  326 (517)
T ss_pred             H
Confidence            5

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 [], [].

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

Probab=99.43  E-value=2.3e-11  Score=94.58  Aligned_cols=229  Identities=13%  Similarity=0.128  Sum_probs=173.0

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhH-HHHHHH
Q 044084           26 CQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVY-ASLICS  104 (343)
Q Consensus        26 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~l~~~  104 (343)
                      +.+.++|.+.|.+.+|.+.|+...++..-+     .+|..|-++|.+-.++..|+.++.+-++.  .|-.+|| .-..+.
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q~~~~-----dTfllLskvY~ridQP~~AL~~~~~gld~--fP~~VT~l~g~ARi  299 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQFPHP-----DTFLLLSKVYQRIDQPERALLVIGEGLDS--FPFDVTYLLGQARI  299 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhcCCch-----hHHHHHHHHHHHhccHHHHHHHHhhhhhc--CCchhhhhhhhHHH
Confidence            567788888888888888888776654433     47888888888888888888888887765  4444444 345566


Q ss_pred             HhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHH
Q 044084          105 FASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAA  184 (343)
Q Consensus       105 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  184 (343)
                      +-..++.+++.++++...+.... ++.....+...|.-.++++.|+..|+++.+.|+ -+...|+.+.-+|.-.++++-+
T Consensus       300 ~eam~~~~~a~~lYk~vlk~~~~-nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~-~speLf~NigLCC~yaqQ~D~~  377 (478)
T KOG1129|consen  300 HEAMEQQEDALQLYKLVLKLHPI-NVEAIACIAVGYFYDNNPEMALRYYRRILQMGA-QSPELFCNIGLCCLYAQQIDLV  377 (478)
T ss_pred             HHHHHhHHHHHHHHHHHHhcCCc-cceeeeeeeeccccCCChHHHHHHHHHHHHhcC-CChHHHhhHHHHHHhhcchhhh
Confidence            77778888888888888876542 666666777777788888888888888888887 5667788888888888888888


Q ss_pred             HHHHHHHHHcCCCCCH--hhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHh
Q 044084          185 VKVYEQLISQGCIPGQ--VTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMK  262 (343)
Q Consensus       185 ~~~~~~~~~~~~~p~~--~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~  262 (343)
                      +.-|.+....--.|+.  .+|-.+-......|++..|.+-|+-....+ ..+...++.|.-.-.+.|++++|..+++...
T Consensus       378 L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d-~~h~ealnNLavL~~r~G~i~~Arsll~~A~  456 (478)
T KOG1129|consen  378 LPSFQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSD-AQHGEALNNLAVLAARSGDILGARSLLNAAK  456 (478)
T ss_pred             HHHHHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccC-cchHHHHHhHHHHHhhcCchHHHHHHHHHhh
Confidence            8888887765333433  456666666677888888888888877765 3456778888877788888888888888777


Q ss_pred             hC
Q 044084          263 PK  264 (343)
Q Consensus       263 ~~  264 (343)
                      ..
T Consensus       457 s~  458 (478)
T KOG1129|consen  457 SV  458 (478)
T ss_pred             hh
Confidence            54

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

Probab=99.43  E-value=1.6e-09  Score=93.38  Aligned_cols=278  Identities=17%  Similarity=0.175  Sum_probs=198.8

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhH-HHHHHH
Q 044084           26 CQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVY-ASLICS  104 (343)
Q Consensus        26 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~l~~~  104 (343)
                      -.....+...|++++|++.++.-...- ...   ..........+.+.|+.++|..+|..+...+  |+...| ..+..+
T Consensus         8 LY~~~il~e~g~~~~AL~~L~~~~~~I-~Dk---~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rN--Pdn~~Yy~~L~~~   81 (517)
T PF12569_consen    8 LYKNSILEEAGDYEEALEHLEKNEKQI-LDK---LAVLEKRAELLLKLGRKEEAEKIYRELIDRN--PDNYDYYRGLEEA   81 (517)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHhhhhhC-CCH---HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCcHHHHHHHHHH
Confidence            334566789999999999997754433 222   5677788899999999999999999999985  455544 444444


Q ss_pred             Hhc-----ccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcH-hHHHHHHHHHHhcCCCCchhhHHHHHHHHhcC
Q 044084          105 FAS-----IAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMV-EKTLEVVESMKNAELNISDCISCVIVNGFSKR  178 (343)
Q Consensus       105 ~~~-----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  178 (343)
                      ..-     ..+.+....+++++...-  |.......+.-.+..-..+ ..+...+..+...|+ |+  +|+.+-..|...
T Consensus        82 ~g~~~~~~~~~~~~~~~~y~~l~~~y--p~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~Kgv-Ps--lF~~lk~Ly~d~  156 (517)
T PF12569_consen   82 LGLQLQLSDEDVEKLLELYDELAEKY--PRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGV-PS--LFSNLKPLYKDP  156 (517)
T ss_pred             HhhhcccccccHHHHHHHHHHHHHhC--ccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCC-ch--HHHHHHHHHcCh
Confidence            422     235778888899887754  3333332232222222223 345556677788888 44  677777777766


Q ss_pred             CcHHHHHHHHHHHHHc----C----------CCCCHh--hHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHH
Q 044084          179 RAYWAAVKVYEQLISQ----G----------CIPGQV--TYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMV  242 (343)
Q Consensus       179 ~~~~~a~~~~~~~~~~----~----------~~p~~~--~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  242 (343)
                      ....-..+++......    +          -+|+..  ++.-+...|-..|++++|.++++...++. |..+..|..-.
T Consensus       157 ~K~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~ht-Pt~~ely~~Ka  235 (517)
T PF12569_consen  157 EKAAIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHT-PTLVELYMTKA  235 (517)
T ss_pred             hHHHHHHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcC-CCcHHHHHHHH
Confidence            6666666666665432    1          123332  34555677889999999999999999985 33477888999


Q ss_pred             HHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh------------------------HHHHHHH
Q 044084          243 AMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK------------------------YTTVISA  298 (343)
Q Consensus       243 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~------------------------~~~l~~~  298 (343)
                      +.+-+.|++.+|.+.++..+..... |...-+-.+..+.+.|+.++|+.                        ......+
T Consensus       236 rilKh~G~~~~Aa~~~~~Ar~LD~~-DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a  314 (517)
T PF12569_consen  236 RILKHAGDLKEAAEAMDEARELDLA-DRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEA  314 (517)
T ss_pred             HHHHHCCCHHHHHHHHHHHHhCChh-hHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHH
Confidence            9999999999999999999987543 67777778888999999999988                        4566788


Q ss_pred             HHhcCCHHHHHHHHHHHH
Q 044084          299 YNMAREFDMCVKFYNEFR  316 (343)
Q Consensus       299 ~~~~g~~~~a~~~~~~m~  316 (343)
                      |.+.|++..|++-|....
T Consensus       315 ~~r~~~~~~ALk~~~~v~  332 (517)
T PF12569_consen  315 YLRQGDYGLALKRFHAVL  332 (517)
T ss_pred             HHHHhhHHHHHHHHHHHH
Confidence            999999999887666553

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 [], [].

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.40  E-value=5.1e-10  Score=95.33  Aligned_cols=240  Identities=18%  Similarity=0.163  Sum_probs=155.5

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhC-----CCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhc-----CC
Q 044084           22 SGCYCQIMEAFYKIGDSEKVAALFLECESR-----KLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEK-----GI   91 (343)
Q Consensus        22 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-----~~   91 (343)
                      ..+...+...|...|+++.|..++.+..+.     |.. .+.-....+.+...|...+++++|..+|+++...     |-
T Consensus       199 ~~~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~-hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~  277 (508)
T KOG1840|consen  199 LRTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLK-HLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGE  277 (508)
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCcc-CHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCC
Confidence            346666888888888888888888776544     111 1222344455677788888888888888887652     21


Q ss_pred             C-C-ChHhHHHHHHHHhcccCHHHHHHHHHHHHHc-----CCC-CC-HHHHHHHHHHHHhcCcHhHHHHHHHHHHhc---
Q 044084           92 L-E-DPSVYASLICSFASIAEVKVAEELFKEAEEK-----GML-RD-LEVFLKLVLMYIEEGMVEKTLEVVESMKNA---  159 (343)
Q Consensus        92 ~-~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~~-~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---  159 (343)
                      . | -..+++.|..+|.+.|++++|...+++..+.     |.. |. ...++.+...++..+++++|..+++...+.   
T Consensus       278 ~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~  357 (508)
T KOG1840|consen  278 DHPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLD  357 (508)
T ss_pred             CCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHh
Confidence            1 1 2345666777788888888888777766541     111 11 233556667777788888888887765321   


Q ss_pred             CCCC----chhhHHHHHHHHhcCCcHHHHHHHHHHHHHcC-------CCCCHhhHHHHHHHHHccCChhHHHHHHHHHHH
Q 044084          160 ELNI----SDCISCVIVNGFSKRRAYWAAVKVYEQLISQG-------CIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQ  228 (343)
Q Consensus       160 ~~~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-------~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  228 (343)
                      -+.+    -..+++.|...|...|++++|.+++++.....       ..-....++.+...|.+.+++.+|.++|.+...
T Consensus       358 ~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~  437 (508)
T KOG1840|consen  358 APGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKD  437 (508)
T ss_pred             hccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHH
Confidence            1111    12367788888888888888888888776531       111234567777778888888888887776443


Q ss_pred             c----CC--CcChhhHHHHHHHHHccCChHHHHHHHHHHh
Q 044084          229 K----GF--DKCVVAYSSMVAMYGKTGRIRDAMRLVAKMK  262 (343)
Q Consensus       229 ~----~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~  262 (343)
                      .    |.  +-...+|..|...|.+.|+++.|.++.+...
T Consensus       438 i~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  438 IMKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             HHHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            2    21  1224577788888888888888888776665

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

Probab=99.39  E-value=1.2e-10  Score=90.66  Aligned_cols=231  Identities=10%  Similarity=0.011  Sum_probs=181.5

Q ss_pred             HHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Q 044084           64 KILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEE  143 (343)
Q Consensus        64 ~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  143 (343)
                      +.+.++|.+.|-+.+|.+.|+.-+..  .|-+.||-.|-+.|.+..++..|+.++.+-.+.-+ -++.....+.+.+-..
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q--~~~~dTfllLskvY~ridQP~~AL~~~~~gld~fP-~~VT~l~g~ARi~eam  303 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQ--FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDSFP-FDVTYLLGQARIHEAM  303 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhc--CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhcCC-chhhhhhhhHHHHHHH
Confidence            46788999999999999999988776  56677888899999999999999999988887543 3666667788888899


Q ss_pred             CcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHH
Q 044084          144 GMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVF  223 (343)
Q Consensus       144 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~  223 (343)
                      ++.++|.++|+...+... .++....++...|.-.++++.|+.+|+++.+.|+ -+...|+.+.-+|.-.+++|-+..-|
T Consensus       304 ~~~~~a~~lYk~vlk~~~-~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~-~speLf~NigLCC~yaqQ~D~~L~sf  381 (478)
T KOG1129|consen  304 EQQEDALQLYKLVLKLHP-INVEAIACIAVGYFYDNNPEMALRYYRRILQMGA-QSPELFCNIGLCCLYAQQIDLVLPSF  381 (478)
T ss_pred             HhHHHHHHHHHHHHhcCC-ccceeeeeeeeccccCCChHHHHHHHHHHHHhcC-CChHHHhhHHHHHHhhcchhhhHHHH
Confidence            999999999999887765 5666777777888888999999999999999985 46677888887888888999999888


Q ss_pred             HHHHHcCCCcC--hhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHh
Q 044084          224 IEMQQKGFDKC--VVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNM  301 (343)
Q Consensus       224 ~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~  301 (343)
                      .+....--.|+  ..+|..+-......|++..|.+.|+-....+.. +...                   ++.|.-.-.+
T Consensus       382 ~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~~-h~ea-------------------lnNLavL~~r  441 (478)
T KOG1129|consen  382 QRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSDAQ-HGEA-------------------LNNLAVLAAR  441 (478)
T ss_pred             HHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccCcc-hHHH-------------------HHhHHHHHhh
Confidence            88776543343  456778888888889999999988887765211 2333                   4444445567


Q ss_pred             cCCHHHHHHHHHHHHhCC
Q 044084          302 AREFDMCVKFYNEFRMNG  319 (343)
Q Consensus       302 ~g~~~~a~~~~~~m~~~~  319 (343)
                      .|++++|..+++......
T Consensus       442 ~G~i~~Arsll~~A~s~~  459 (478)
T KOG1129|consen  442 SGDILGARSLLNAAKSVM  459 (478)
T ss_pred             cCchHHHHHHHHHhhhhC
Confidence            888888888888877643

>PRK11189 lipoprotein NlpI; Provisional

Probab=99.38  E-value=2e-09  Score=87.62  Aligned_cols=223  Identities=11%  Similarity=-0.001  Sum_probs=157.8

Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHH
Q 044084           34 KIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKV  113 (343)
Q Consensus        34 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  113 (343)
                      ..+..+.+..-+.++.......++.....|..+...+...|++++|...|++..+... .+...|+.+...+...|+++.
T Consensus        38 ~~~~~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P-~~~~a~~~lg~~~~~~g~~~~  116 (296)
T PRK11189         38 PTLQQEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALALRP-DMADAYNYLGIYLTQAGNFDA  116 (296)
T ss_pred             CchHHHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHCCCHHH
Confidence            3456677788887777543222222246688888899999999999999999988643 357789999999999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHH
Q 044084          114 AEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLIS  193 (343)
Q Consensus       114 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  193 (343)
                      |...|++..+..+. +..++..+...+...|++++|.+.|+...+..+  +..........+...+++++|...|.+...
T Consensus       117 A~~~~~~Al~l~P~-~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~~P--~~~~~~~~~~l~~~~~~~~~A~~~l~~~~~  193 (296)
T PRK11189        117 AYEAFDSVLELDPT-YNYAYLNRGIALYYGGRYELAQDDLLAFYQDDP--NDPYRALWLYLAESKLDPKQAKENLKQRYE  193 (296)
T ss_pred             HHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC--CCHHHHHHHHHHHccCCHHHHHHHHHHHHh
Confidence            99999999986643 577888899999999999999999999887664  222122222234457789999999977654


Q ss_pred             cCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHc---CC---CcChhhHHHHHHHHHccCChHHHHHHHHHHhhCC
Q 044084          194 QGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQK---GF---DKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKG  265 (343)
Q Consensus       194 ~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~---~~---~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~  265 (343)
                      .. .|+... ..+..  ...|+...+ ..+..+.+.   ..   +.....|..+...+.+.|++++|...|++..+.+
T Consensus       194 ~~-~~~~~~-~~~~~--~~lg~~~~~-~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~~  266 (296)
T PRK11189        194 KL-DKEQWG-WNIVE--FYLGKISEE-TLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALANN  266 (296)
T ss_pred             hC-CccccH-HHHHH--HHccCCCHH-HHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            32 333222 22222  334555544 344444432   10   1124578899999999999999999999999764

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

Probab=99.37  E-value=7.5e-11  Score=102.92  Aligned_cols=256  Identities=11%  Similarity=0.042  Sum_probs=178.3

Q ss_pred             HHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHH
Q 044084           43 ALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAE  122 (343)
Q Consensus        43 ~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  122 (343)
                      .++-.+...|+.|+   ..+|..+|.-|+..|+.+.|- +|.-|.-...+.+...|+.++.+....++.+.+.       
T Consensus        11 nfla~~e~~gi~Pn---RvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk-------   79 (1088)
T KOG4318|consen   11 NFLALHEISGILPN---RVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPK-------   79 (1088)
T ss_pred             hHHHHHHHhcCCCc---hhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCC-------
Confidence            45677888899888   789999999999999999998 9999988877778889999999988888877766       


Q ss_pred             HcCCCCCHHHHHHHHHHHHhcCcHhH---HHHHHHHHH----hcCCCCchhhHH--------------HHHHHHhcCCcH
Q 044084          123 EKGMLRDLEVFLKLVLMYIEEGMVEK---TLEVVESMK----NAELNISDCISC--------------VIVNGFSKRRAY  181 (343)
Q Consensus       123 ~~~~~~~~~~~~~l~~~~~~~~~~~~---a~~~~~~~~----~~~~~~~~~~~~--------------~l~~~~~~~~~~  181 (343)
                          .|.+.+|..|..+|...||...   +.+.++.+.    ..|+-.....+-              ..+.-....|.+
T Consensus        80 ----ep~aDtyt~Ll~ayr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~eglw  155 (1088)
T KOG4318|consen   80 ----EPLADTYTNLLKAYRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVLEGLW  155 (1088)
T ss_pred             ----CCchhHHHHHHHHHHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHHHHHH
Confidence                5889999999999999999654   333222222    122211111111              122222333444


Q ss_pred             HHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHH
Q 044084          182 WAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKM  261 (343)
Q Consensus       182 ~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m  261 (343)
                      +.+.+++..+....-  +. ++..+++-+..  ...-.+++........-.|++.+|..++.+-..+|+.+.|..++.+|
T Consensus       156 aqllkll~~~Pvsa~--~~-p~~vfLrqnv~--~ntpvekLl~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll~em  230 (1088)
T KOG4318|consen  156 AQLLKLLAKVPVSAW--NA-PFQVFLRQNVV--DNTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLLYEM  230 (1088)
T ss_pred             HHHHHHHhhCCcccc--cc-hHHHHHHHhcc--CCchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHHHHH
Confidence            455554444332210  00 11112443332  23334444444443322589999999999999999999999999999


Q ss_pred             hhCCCCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHhccccc
Q 044084          262 KPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQI  340 (343)
Q Consensus       262 ~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~g~~  340 (343)
                      .+.|+..+..-|..|+-+                      .+...-+..+++.|.+.|+.|+..|+...+..+..+|..
T Consensus       231 ke~gfpir~HyFwpLl~g----------------------~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~~t  287 (1088)
T KOG4318|consen  231 KEKGFPIRAHYFWPLLLG----------------------INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNGQT  287 (1088)
T ss_pred             HHcCCCcccccchhhhhc----------------------CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcchhh
Confidence            999998888766655432                      556677889999999999999999998888887776654

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

Probab=99.34  E-value=6.7e-08  Score=79.42  Aligned_cols=305  Identities=11%  Similarity=0.048  Sum_probs=155.7

Q ss_pred             hhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHH
Q 044084            3 SQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKF   82 (343)
Q Consensus         3 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~   82 (343)
                      .+.|.++|++.+..+. .+...|-..+.+=.++..+..|..+++.....-+..    ...|-..+..=-..|+...|.++
T Consensus        89 ~~RARSv~ERALdvd~-r~itLWlkYae~Emknk~vNhARNv~dRAvt~lPRV----dqlWyKY~ymEE~LgNi~gaRqi  163 (677)
T KOG1915|consen   89 IQRARSVFERALDVDY-RNITLWLKYAEFEMKNKQVNHARNVWDRAVTILPRV----DQLWYKYIYMEEMLGNIAGARQI  163 (677)
T ss_pred             HHHHHHHHHHHHhccc-ccchHHHHHHHHHHhhhhHhHHHHHHHHHHHhcchH----HHHHHHHHHHHHHhcccHHHHHH
Confidence            4567777777776543 345556666666666666666666666654433222    23444444444444555555555


Q ss_pred             HHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHH-------
Q 044084           83 FRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVES-------  155 (343)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~-------  155 (343)
                      |++-.+-  .|+...|.+.++.=.+-+.++.|..++++.+--.  |++..|-...+.=.+.|....|..+|+.       
T Consensus       164 ferW~~w--~P~eqaW~sfI~fElRykeieraR~IYerfV~~H--P~v~~wikyarFE~k~g~~~~aR~VyerAie~~~~  239 (677)
T KOG1915|consen  164 FERWMEW--EPDEQAWLSFIKFELRYKEIERARSIYERFVLVH--PKVSNWIKYARFEEKHGNVALARSVYERAIEFLGD  239 (677)
T ss_pred             HHHHHcC--CCcHHHHHHHHHHHHHhhHHHHHHHHHHHHheec--ccHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhhh
Confidence            5544432  4555555555555555555555555555444321  3333333333333333333222222222       


Q ss_pred             ------------------------------HHhc-------------------------------------------CCC
Q 044084          156 ------------------------------MKNA-------------------------------------------ELN  162 (343)
Q Consensus       156 ------------------------------~~~~-------------------------------------------~~~  162 (343)
                                                    ..+.                                           .-+
T Consensus       240 d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~~pk~raeeL~k~~~~fEKqfGd~~gIEd~Iv~KRk~qYE~~v~~np  319 (677)
T KOG1915|consen  240 DEEAEILFVAFAEFEERQKEYERARFIYKYALDHIPKGRAEELYKKYTAFEKQFGDKEGIEDAIVGKRKFQYEKEVSKNP  319 (677)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHhcchhhhHHHHhhhhhhHHHHHHHhCC
Confidence                                          1110                                           001


Q ss_pred             CchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHh--hHHHHH----H-HH---HccCChhHHHHHHHHHHHc---
Q 044084          163 ISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQV--TYASII----N-AY---CRIGLYSKAEKVFIEMQQK---  229 (343)
Q Consensus       163 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~--~~~~ll----~-~~---~~~~~~~~a~~~~~~~~~~---  229 (343)
                      -|-.+|--.++.-...|+.+...++|++.... ++|-..  .|...|    + ++   ....+++.+.+++....+.   
T Consensus       320 ~nYDsWfdylrL~e~~g~~~~Ire~yErAIan-vpp~~ekr~W~RYIYLWinYalyeEle~ed~ertr~vyq~~l~lIPH  398 (677)
T KOG1915|consen  320 YNYDSWFDYLRLEESVGDKDRIRETYERAIAN-VPPASEKRYWRRYIYLWINYALYEELEAEDVERTRQVYQACLDLIPH  398 (677)
T ss_pred             CCchHHHHHHHHHHhcCCHHHHHHHHHHHHcc-CCchhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhcCc
Confidence            23344555556566667778888888777755 333211  111111    1 11   1345566666666554442   


Q ss_pred             ---------------------------------CCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHH
Q 044084          230 ---------------------------------GFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSL  276 (343)
Q Consensus       230 ---------------------------------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l  276 (343)
                                                       |.-|-..+|...|..-.+.++++....++++.++.+ +-|..+|...
T Consensus       399 kkFtFaKiWlmyA~feIRq~~l~~ARkiLG~AIG~cPK~KlFk~YIelElqL~efDRcRkLYEkfle~~-Pe~c~~W~ky  477 (677)
T KOG1915|consen  399 KKFTFAKIWLMYAQFEIRQLNLTGARKILGNAIGKCPKDKLFKGYIELELQLREFDRCRKLYEKFLEFS-PENCYAWSKY  477 (677)
T ss_pred             ccchHHHHHHHHHHHHHHHcccHHHHHHHHHHhccCCchhHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-hHhhHHHHHH
Confidence                                             222444555555555555566666666666666543 2245556555


Q ss_pred             HHHHhcccChhHHHh-----------------HHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 044084          277 MDMHGRAKNLRQLEK-----------------YTTVISAYNMAREFDMCVKFYNEFRMN  318 (343)
Q Consensus       277 ~~~~~~~~~~~~a~~-----------------~~~l~~~~~~~g~~~~a~~~~~~m~~~  318 (343)
                      ...=...|+.+.|..                 |...|+--...|.++.|..+++++++.
T Consensus       478 aElE~~LgdtdRaRaifelAi~qp~ldmpellwkaYIdFEi~~~E~ekaR~LYerlL~r  536 (677)
T KOG1915|consen  478 AELETSLGDTDRARAIFELAISQPALDMPELLWKAYIDFEIEEGEFEKARALYERLLDR  536 (677)
T ss_pred             HHHHHHhhhHHHHHHHHHHHhcCcccccHHHHHHHhhhhhhhcchHHHHHHHHHHHHHh
Confidence            555555566665554                 555666666777788888888877665

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

Probab=99.34  E-value=3.4e-09  Score=78.74  Aligned_cols=173  Identities=10%  Similarity=0.006  Sum_probs=75.4

Q ss_pred             HHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHH
Q 044084          103 CSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYW  182 (343)
Q Consensus       103 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  182 (343)
                      -.|...|+...|..-+++.+++.+. +..+|..+...|.+.|..+.|.+.|++..+..+ -+..+.|.....+|..|+++
T Consensus        43 l~YL~~gd~~~A~~nlekAL~~DPs-~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p-~~GdVLNNYG~FLC~qg~~~  120 (250)
T COG3063          43 LGYLQQGDYAQAKKNLEKALEHDPS-YYLAHLVRAHYYQKLGENDLADESYRKALSLAP-NNGDVLNNYGAFLCAQGRPE  120 (250)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCC-CccchhhhhhHHHHhCCChH
Confidence            3444444444444444444444322 344444444444444444444444444444333 23333444444444444455


Q ss_pred             HHHHHHHHHHHcC-CCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHH
Q 044084          183 AAVKVYEQLISQG-CIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKM  261 (343)
Q Consensus       183 ~a~~~~~~~~~~~-~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m  261 (343)
                      +|...|++....- ..-...+|..+.-+..+.|+.+.|...|++..+.. +-...+.-.+.....+.|++..|...++..
T Consensus       121 eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~d-p~~~~~~l~~a~~~~~~~~y~~Ar~~~~~~  199 (250)
T COG3063         121 EAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELD-PQFPPALLELARLHYKAGDYAPARLYLERY  199 (250)
T ss_pred             HHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhC-cCCChHHHHHHHHHHhcccchHHHHHHHHH
Confidence            5544444444331 11112334444444444455555555554444432 222333444444444455555555444444


Q ss_pred             hhCCCCchHHHHHHHHHH
Q 044084          262 KPKGCEPNVWIYNSLMDM  279 (343)
Q Consensus       262 ~~~~~~p~~~~~~~l~~~  279 (343)
                      ...+. ++..+.-..|+.
T Consensus       200 ~~~~~-~~A~sL~L~iri  216 (250)
T COG3063         200 QQRGG-AQAESLLLGIRI  216 (250)
T ss_pred             Hhccc-ccHHHHHHHHHH
Confidence            44332 344443333333

>PRK11189 lipoprotein NlpI; Provisional

Probab=99.34  E-value=1.3e-08  Score=82.88  Aligned_cols=240  Identities=12%  Similarity=0.040  Sum_probs=162.9

Q ss_pred             ccCcHHHHHHHHHHHHhcC-CCCC--hHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhH
Q 044084           72 KSGRAFEILKFFRDMKEKG-ILED--PSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEK  148 (343)
Q Consensus        72 ~~~~~~~a~~~~~~~~~~~-~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  148 (343)
                      ..+..+.++.-+.+++... ..|+  ...|..+...+...|+.+.|...|++..+..+. +...|+.+...+...|++++
T Consensus        38 ~~~~~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P~-~~~a~~~lg~~~~~~g~~~~  116 (296)
T PRK11189         38 PTLQQEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALALRPD-MADAYNYLGIYLTQAGNFDA  116 (296)
T ss_pred             CchHHHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHCCCHHH
Confidence            3456778888888887642 2222  345777778889999999999999999987653 78999999999999999999


Q ss_pred             HHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHH
Q 044084          149 TLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQ  228 (343)
Q Consensus       149 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  228 (343)
                      |.+.|++..+..+ -+..+|..+..++...|++++|.+.++...+..  |+..........+...++.++|...|.....
T Consensus       117 A~~~~~~Al~l~P-~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~~--P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~~  193 (296)
T PRK11189        117 AYEAFDSVLELDP-TYNYAYLNRGIALYYGGRYELAQDDLLAFYQDD--PNDPYRALWLYLAESKLDPKQAKENLKQRYE  193 (296)
T ss_pred             HHHHHHHHHHhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHccCCHHHHHHHHHHHHh
Confidence            9999999988765 345678888888999999999999999998863  4433222222334556789999999977654


Q ss_pred             cCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHH
Q 044084          229 KGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMC  308 (343)
Q Consensus       229 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a  308 (343)
                      .. +|+...+ .+  .....|+...+ +.+..+.+. +.-+...-..+            +..|..+...+.+.|++++|
T Consensus       194 ~~-~~~~~~~-~~--~~~~lg~~~~~-~~~~~~~~~-~~~~~~l~~~~------------~ea~~~Lg~~~~~~g~~~~A  255 (296)
T PRK11189        194 KL-DKEQWGW-NI--VEFYLGKISEE-TLMERLKAG-ATDNTELAERL------------CETYFYLAKYYLSLGDLDEA  255 (296)
T ss_pred             hC-CccccHH-HH--HHHHccCCCHH-HHHHHHHhc-CCCcHHHHHHH------------HHHHHHHHHHHHHCCCHHHH
Confidence            32 3333222 22  23345665544 345555432 11111111111            11255667778889999999


Q ss_pred             HHHHHHHHhCCCCccHHHH-HHHHHHH
Q 044084          309 VKFYNEFRMNGGVIDRAMA-GIMVGVF  334 (343)
Q Consensus       309 ~~~~~~m~~~~~~p~~~~~-~~l~~~~  334 (343)
                      +..|++..+.++ ||..-+ ..++...
T Consensus       256 ~~~~~~Al~~~~-~~~~e~~~~~~e~~  281 (296)
T PRK11189        256 AALFKLALANNV-YNFVEHRYALLELA  281 (296)
T ss_pred             HHHHHHHHHhCC-chHHHHHHHHHHHH
Confidence            999999998764 344433 3344433

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

Probab=99.33  E-value=1.4e-08  Score=83.52  Aligned_cols=181  Identities=15%  Similarity=0.175  Sum_probs=107.6

Q ss_pred             HHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHc
Q 044084          133 FLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCR  212 (343)
Q Consensus       133 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~  212 (343)
                      |-.+..+|...++.++-...|.+....++ -+..+|..-.....-.+++++|..=|++.+... +-+...|..+.-+..+
T Consensus       363 yI~~a~~y~d~~~~~~~~~~F~~A~~ldp-~n~dvYyHRgQm~flL~q~e~A~aDF~Kai~L~-pe~~~~~iQl~~a~Yr  440 (606)
T KOG0547|consen  363 YIKRAAAYADENQSEKMWKDFNKAEDLDP-ENPDVYYHRGQMRFLLQQYEEAIADFQKAISLD-PENAYAYIQLCCALYR  440 (606)
T ss_pred             HHHHHHHHhhhhccHHHHHHHHHHHhcCC-CCCchhHhHHHHHHHHHHHHHHHHHHHHHhhcC-hhhhHHHHHHHHHHHH
Confidence            44444555555556666666666555554 234445555555555556666666666655542 2233445555555556


Q ss_pred             cCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCC-----CCchHHH--HHHHHHHHhcccC
Q 044084          213 IGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKG-----CEPNVWI--YNSLMDMHGRAKN  285 (343)
Q Consensus       213 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~-----~~p~~~~--~~~l~~~~~~~~~  285 (343)
                      .++++++...|++..+. +|..+..|+.....+...+++++|.+.|+..++..     +..+..+  --.++..- -.++
T Consensus       441 ~~k~~~~m~~Fee~kkk-FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~~~~~~v~~~plV~Ka~l~~q-wk~d  518 (606)
T KOG0547|consen  441 QHKIAESMKTFEEAKKK-FPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIELEPREHLIIVNAAPLVHKALLVLQ-WKED  518 (606)
T ss_pred             HHHHHHHHHHHHHHHHh-CCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhhccccccccccchhhhhhhHhhhc-hhhh
Confidence            77777788888777765 56667778888888888888888888887776541     1111111  11111111 2255


Q ss_pred             hhHHHh---------------HHHHHHHHHhcCCHHHHHHHHHHHHh
Q 044084          286 LRQLEK---------------YTTVISAYNMAREFDMCVKFYNEFRM  317 (343)
Q Consensus       286 ~~~a~~---------------~~~l~~~~~~~g~~~~a~~~~~~m~~  317 (343)
                      +..|..               |..|...-.+.|+.++|+++|++...
T Consensus       519 ~~~a~~Ll~KA~e~Dpkce~A~~tlaq~~lQ~~~i~eAielFEksa~  565 (606)
T KOG0547|consen  519 INQAENLLRKAIELDPKCEQAYETLAQFELQRGKIDEAIELFEKSAQ  565 (606)
T ss_pred             HHHHHHHHHHHHccCchHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            555544               77788888888888888888887543

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.31  E-value=2.4e-09  Score=91.30  Aligned_cols=24  Identities=8%  Similarity=0.326  Sum_probs=15.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHH
Q 044084          292 YTTVISAYNMAREFDMCVKFYNEF  315 (343)
Q Consensus       292 ~~~l~~~~~~~g~~~~a~~~~~~m  315 (343)
                      |..|...|.+.|+++.|+++.+..
T Consensus       453 ~~nL~~~Y~~~g~~e~a~~~~~~~  476 (508)
T KOG1840|consen  453 YLNLAALYRAQGNYEAAEELEEKV  476 (508)
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHH
Confidence            555666666677777777766655

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

Probab=99.31  E-value=5.7e-09  Score=87.18  Aligned_cols=267  Identities=15%  Similarity=0.090  Sum_probs=176.8

Q ss_pred             hhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHH
Q 044084            3 SQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKF   82 (343)
Q Consensus         3 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~   82 (343)
                      +++.+.+++.+.+..+ +....+..-|.++...|+..+-..+=.++.+..    |....+|-++..-|...|+..+|.+.
T Consensus       260 f~~c~kit~~lle~dp-fh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~y----P~~a~sW~aVg~YYl~i~k~seARry  334 (611)
T KOG1173|consen  260 FKECLKITEELLEKDP-FHLPCLPLHIACLYELGKSNKLFLLSHKLVDLY----PSKALSWFAVGCYYLMIGKYSEARRY  334 (611)
T ss_pred             HHHHHHHhHHHHhhCC-CCcchHHHHHHHHHHhcccchHHHHHHHHHHhC----CCCCcchhhHHHHHHHhcCcHHHHHH
Confidence            4556667777766543 566666666777777777777666666665544    33346777777777777888888888


Q ss_pred             HHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCC
Q 044084           83 FRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELN  162 (343)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  162 (343)
                      |.+....+.. -...|-.....|+-.+..++|...+...-+.-.... .-+--+.--|.+.++.+.|.+.|.+.....+ 
T Consensus       335 ~SKat~lD~~-fgpaWl~fghsfa~e~EhdQAmaaY~tAarl~~G~h-lP~LYlgmey~~t~n~kLAe~Ff~~A~ai~P-  411 (611)
T KOG1173|consen  335 FSKATTLDPT-FGPAWLAFGHSFAGEGEHDQAMAAYFTAARLMPGCH-LPSLYLGMEYMRTNNLKLAEKFFKQALAIAP-  411 (611)
T ss_pred             HHHHhhcCcc-ccHHHHHHhHHhhhcchHHHHHHHHHHHHHhccCCc-chHHHHHHHHHHhccHHHHHHHHHHHHhcCC-
Confidence            8776554211 234677777777777888888877776665322111 1112234456777778888888877766544 


Q ss_pred             CchhhHHHHHHHHhcCCcHHHHHHHHHHHHHc----C--CCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChh
Q 044084          163 ISDCISCVIVNGFSKRRAYWAAVKVYEQLISQ----G--CIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVV  236 (343)
Q Consensus       163 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  236 (343)
                      .|+...+-+.-.....+.+.+|..+|+.....    +  ...-..+++.|..+|.+.+.+++|+..++...... +.+..
T Consensus       412 ~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~q~aL~l~-~k~~~  490 (611)
T KOG1173|consen  412 SDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYYQKALLLS-PKDAS  490 (611)
T ss_pred             CcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHHHHHHHcC-CCchh
Confidence            45555666655556677788888888776521    0  01123456777788888888888888888877764 56777


Q ss_pred             hHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHH
Q 044084          237 AYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMH  280 (343)
Q Consensus       237 ~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~  280 (343)
                      ++.++.-.|...|+++.|.+.|.+...  +.||..+...++..+
T Consensus       491 ~~asig~iy~llgnld~Aid~fhKaL~--l~p~n~~~~~lL~~a  532 (611)
T KOG1173|consen  491 THASIGYIYHLLGNLDKAIDHFHKALA--LKPDNIFISELLKLA  532 (611)
T ss_pred             HHHHHHHHHHHhcChHHHHHHHHHHHh--cCCccHHHHHHHHHH
Confidence            888888888888888888888887775  477776666665543

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

Probab=99.30  E-value=8.1e-09  Score=76.77  Aligned_cols=207  Identities=13%  Similarity=0.010  Sum_probs=162.0

Q ss_pred             HHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 044084           61 HMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMY  140 (343)
Q Consensus        61 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  140 (343)
                      .+...|.-.|...|++..|..-+++.++.+.. +..+|..+...|.+.|+.+.|.+-|++..+..+. +..+.|.....+
T Consensus        36 ~arlqLal~YL~~gd~~~A~~nlekAL~~DPs-~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p~-~GdVLNNYG~FL  113 (250)
T COG3063          36 KARLQLALGYLQQGDYAQAKKNLEKALEHDPS-YYLAHLVRAHYYQKLGENDLADESYRKALSLAPN-NGDVLNNYGAFL  113 (250)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCCC-ccchhhhhhHHH
Confidence            45667778889999999999999998887532 5667888888899999999999999998887654 788888999999


Q ss_pred             HhcCcHhHHHHHHHHHHhcCC-CCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHH
Q 044084          141 IEEGMVEKTLEVVESMKNAEL-NISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKA  219 (343)
Q Consensus       141 ~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a  219 (343)
                      |..|++++|...|++...... .....+|..+.-+..+.|+++.|...|++..+.. +-...+.-.+.+...+.|++-.|
T Consensus       114 C~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~d-p~~~~~~l~~a~~~~~~~~y~~A  192 (250)
T COG3063         114 CAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELD-PQFPPALLELARLHYKAGDYAPA  192 (250)
T ss_pred             HhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhC-cCCChHHHHHHHHHHhcccchHH
Confidence            999999999999998775432 1223478888888888999999999999988774 22345666777888888999999


Q ss_pred             HHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHH
Q 044084          220 EKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIY  273 (343)
Q Consensus       220 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~  273 (343)
                      ...++.....+. ++..+.-..|+.--..|+-+.+-+.=..+...  .|...-+
T Consensus       193 r~~~~~~~~~~~-~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r~--fP~s~e~  243 (250)
T COG3063         193 RLYLERYQQRGG-AQAESLLLGIRIAKRLGDRAAAQRYQAQLQRL--FPYSEEY  243 (250)
T ss_pred             HHHHHHHHhccc-ccHHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCcHHH
Confidence            999988888764 77777777788888888888887766666654  4544433

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

Probab=99.26  E-value=2.3e-08  Score=83.66  Aligned_cols=266  Identities=12%  Similarity=0.039  Sum_probs=205.6

Q ss_pred             HHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 044084           61 HMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMY  140 (343)
Q Consensus        61 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  140 (343)
                      ........-+...+++.+..++.+.+.+.. ++....+..-|.++...|+..+...+=.++++.-+. .+.+|-++.-.|
T Consensus       245 dll~~~ad~~y~~c~f~~c~kit~~lle~d-pfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~yP~-~a~sW~aVg~YY  322 (611)
T KOG1173|consen  245 DLLAEKADRLYYGCRFKECLKITEELLEKD-PFHLPCLPLHIACLYELGKSNKLFLLSHKLVDLYPS-KALSWFAVGCYY  322 (611)
T ss_pred             HHHHHHHHHHHHcChHHHHHHHhHHHHhhC-CCCcchHHHHHHHHHHhcccchHHHHHHHHHHhCCC-CCcchhhHHHHH
Confidence            344445556777889999999999998874 445666666677888888888888887888886543 688899999999


Q ss_pred             HhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHc--CC-CCCHhhHHHHHHHHHccCChh
Q 044084          141 IEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQ--GC-IPGQVTYASIINAYCRIGLYS  217 (343)
Q Consensus       141 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~-~p~~~~~~~ll~~~~~~~~~~  217 (343)
                      .-.|+.++|++.|.+....+.. -...|-.+...|+-.|..++|+..+...-+.  |. .|    +--+.--|.+.++.+
T Consensus       323 l~i~k~seARry~SKat~lD~~-fgpaWl~fghsfa~e~EhdQAmaaY~tAarl~~G~hlP----~LYlgmey~~t~n~k  397 (611)
T KOG1173|consen  323 LMIGKYSEARRYFSKATTLDPT-FGPAWLAFGHSFAGEGEHDQAMAAYFTAARLMPGCHLP----SLYLGMEYMRTNNLK  397 (611)
T ss_pred             HHhcCcHHHHHHHHHHhhcCcc-ccHHHHHHhHHhhhcchHHHHHHHHHHHHHhccCCcch----HHHHHHHHHHhccHH
Confidence            9999999999999988765542 2347889999999999999999998887664  21 12    122333477889999


Q ss_pred             HHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhC--CC----CchHHHHHHHHHHHhcccChhHHHh
Q 044084          218 KAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK--GC----EPNVWIYNSLMDMHGRAKNLRQLEK  291 (343)
Q Consensus       218 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~--~~----~p~~~~~~~l~~~~~~~~~~~~a~~  291 (343)
                      .|.+.|....... |.|+...+-+.-.....+.+.+|..+|+.....  .+    ..-..+++.|..+|.+.+.+++|..
T Consensus       398 LAe~Ff~~A~ai~-P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~  476 (611)
T KOG1173|consen  398 LAEKFFKQALAIA-PSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAID  476 (611)
T ss_pred             HHHHHHHHHHhcC-CCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHH
Confidence            9999999888864 667888888888888888999999999887621  11    1244567888889999999999887


Q ss_pred             ---------------HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHhc
Q 044084          292 ---------------YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSK  336 (343)
Q Consensus       292 ---------------~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~  336 (343)
                                     +.++.-.|...|+++.|++.|.+.+-  +.||..+...++..+..
T Consensus       477 ~~q~aL~l~~k~~~~~asig~iy~llgnld~Aid~fhKaL~--l~p~n~~~~~lL~~aie  534 (611)
T KOG1173|consen  477 YYQKALLLSPKDASTHASIGYIYHLLGNLDKAIDHFHKALA--LKPDNIFISELLKLAIE  534 (611)
T ss_pred             HHHHHHHcCCCchhHHHHHHHHHHHhcChHHHHHHHHHHHh--cCCccHHHHHHHHHHHH
Confidence                           88888889999999999999998876  67888777667665443

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

Probab=99.25  E-value=5e-09  Score=86.06  Aligned_cols=224  Identities=15%  Similarity=0.154  Sum_probs=169.6

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcc
Q 044084           29 MEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASI  108 (343)
Q Consensus        29 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  108 (343)
                      ...+.-.|+.-.|...|+........+.    ..|.-+...|...++.++....|+.....+.. |+.+|..-.....-.
T Consensus       333 gtF~fL~g~~~~a~~d~~~~I~l~~~~~----~lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp~-n~dvYyHRgQm~flL  407 (606)
T KOG0547|consen  333 GTFHFLKGDSLGAQEDFDAAIKLDPAFN----SLYIKRAAAYADENQSEKMWKDFNKAEDLDPE-NPDVYYHRGQMRFLL  407 (606)
T ss_pred             hhhhhhcCCchhhhhhHHHHHhcCcccc----hHHHHHHHHHhhhhccHHHHHHHHHHHhcCCC-CCchhHhHHHHHHHH
Confidence            3445556888888888888877654433    44777888888999999999999988876543 667788777777888


Q ss_pred             cCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHH
Q 044084          109 AEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVY  188 (343)
Q Consensus       109 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  188 (343)
                      +++++|..-|++.++..+. +...|-.+.-+..+.++++++...|++....-+ .....|+.....+..+++++.|.+.|
T Consensus       408 ~q~e~A~aDF~Kai~L~pe-~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkkFP-~~~Evy~~fAeiLtDqqqFd~A~k~Y  485 (606)
T KOG0547|consen  408 QQYEEAIADFQKAISLDPE-NAYAYIQLCCALYRQHKIAESMKTFEEAKKKFP-NCPEVYNLFAEILTDQQQFDKAVKQY  485 (606)
T ss_pred             HHHHHHHHHHHHHhhcChh-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CCchHHHHHHHHHhhHHhHHHHHHHH
Confidence            8999999999998886643 667777777777788899999999999887644 55668898999999999999999999


Q ss_pred             HHHHHcCCCCC---------HhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHH
Q 044084          189 EQLISQGCIPG---------QVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVA  259 (343)
Q Consensus       189 ~~~~~~~~~p~---------~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  259 (343)
                      +..++.  .|+         +.+...++-.-. .+++..|..+++...+.+ +.....|..|...-.+.|+.++|+++|+
T Consensus       486 D~ai~L--E~~~~~~~v~~~plV~Ka~l~~qw-k~d~~~a~~Ll~KA~e~D-pkce~A~~tlaq~~lQ~~~i~eAielFE  561 (606)
T KOG0547|consen  486 DKAIEL--EPREHLIIVNAAPLVHKALLVLQW-KEDINQAENLLRKAIELD-PKCEQAYETLAQFELQRGKIDEAIELFE  561 (606)
T ss_pred             HHHHhh--ccccccccccchhhhhhhHhhhch-hhhHHHHHHHHHHHHccC-chHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence            988765  222         111122222212 378889999999888876 3356688889999999999999999998


Q ss_pred             HHhh
Q 044084          260 KMKP  263 (343)
Q Consensus       260 ~m~~  263 (343)
                      +...
T Consensus       562 ksa~  565 (606)
T KOG0547|consen  562 KSAQ  565 (606)
T ss_pred             HHHH
Confidence            8654

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

Probab=99.21  E-value=1.6e-07  Score=75.91  Aligned_cols=287  Identities=10%  Similarity=0.031  Sum_probs=146.8

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHH
Q 044084           21 DSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYAS  100 (343)
Q Consensus        21 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  100 (343)
                      ++.....+.+.+...|+.++|...|++....++    .+........-.+.+.|+.+....+...+.... +.+...|-.
T Consensus       231 NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~dp----y~i~~MD~Ya~LL~~eg~~e~~~~L~~~Lf~~~-~~ta~~wfV  305 (564)
T KOG1174|consen  231 NEHLMMALGKCLYYNGDYFQAEDIFSSTLCANP----DNVEAMDLYAVLLGQEGGCEQDSALMDYLFAKV-KYTASHWFV  305 (564)
T ss_pred             cHHHHHHHhhhhhhhcCchHHHHHHHHHhhCCh----hhhhhHHHHHHHHHhccCHhhHHHHHHHHHhhh-hcchhhhhh
Confidence            444455555555555555555555555543321    111222222223334455555555444444331 112222333


Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCc
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRA  180 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  180 (343)
                      -.......+++..|+.+-++.++.... +...+-.-...+...+++++|.-.|+......+ -+...|.-++.+|...|.
T Consensus       306 ~~~~l~~~K~~~rAL~~~eK~I~~~~r-~~~alilKG~lL~~~~R~~~A~IaFR~Aq~Lap-~rL~~Y~GL~hsYLA~~~  383 (564)
T KOG1174|consen  306 HAQLLYDEKKFERALNFVEKCIDSEPR-NHEALILKGRLLIALERHTQAVIAFRTAQMLAP-YRLEIYRGLFHSYLAQKR  383 (564)
T ss_pred             hhhhhhhhhhHHHHHHHHHHHhccCcc-cchHHHhccHHHHhccchHHHHHHHHHHHhcch-hhHHHHHHHHHHHHhhch
Confidence            333334445556666655555554322 344444444556666666666666666554432 344566666666666666


Q ss_pred             HHHHHHHHHHHHHcCCCCCHhhHHHHH-HHHH-ccCChhHHHHHHHHHHHcCCCcC-hhhHHHHHHHHHccCChHHHHHH
Q 044084          181 YWAAVKVYEQLISQGCIPGQVTYASII-NAYC-RIGLYSKAEKVFIEMQQKGFDKC-VVAYSSMVAMYGKTGRIRDAMRL  257 (343)
Q Consensus       181 ~~~a~~~~~~~~~~~~~p~~~~~~~ll-~~~~-~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~  257 (343)
                      +.+|.-+-++..+. ++-+..+.+.+. ..+. ....-++|.++++.-.+..  |+ ....+.+...+...|+.+.+..+
T Consensus       384 ~kEA~~~An~~~~~-~~~sA~~LtL~g~~V~~~dp~~rEKAKkf~ek~L~~~--P~Y~~AV~~~AEL~~~Eg~~~D~i~L  460 (564)
T KOG1174|consen  384 FKEANALANWTIRL-FQNSARSLTLFGTLVLFPDPRMREKAKKFAEKSLKIN--PIYTPAVNLIAELCQVEGPTKDIIKL  460 (564)
T ss_pred             HHHHHHHHHHHHHH-hhcchhhhhhhcceeeccCchhHHHHHHHHHhhhccC--CccHHHHHHHHHHHHhhCccchHHHH
Confidence            66666655554433 122333433331 1111 1223355666666555432  32 34555666677777777777777


Q ss_pred             HHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh-HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCc
Q 044084          258 VAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK-YTTVISAYNMAREFDMCVKFYNEFRMNGGVI  322 (343)
Q Consensus       258 ~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~-~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p  322 (343)
                      +++....  .||....+.|.+.+...+.+++|.. |..   ++...-+-+.+.+=++.|.+..-.|
T Consensus       461 Le~~L~~--~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~---ALr~dP~~~~sl~Gl~~lEK~~~~~  521 (564)
T KOG1174|consen  461 LEKHLII--FPDVNLHNHLGDIMRAQNEPQKAMEYYYK---ALRQDPKSKRTLRGLRLLEKSDDES  521 (564)
T ss_pred             HHHHHhh--ccccHHHHHHHHHHHHhhhHHHHHHHHHH---HHhcCccchHHHHHHHHHHhccCCC
Confidence            7776654  6777777777777776666666655 222   2223334445555555555443333

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

Probab=99.20  E-value=1.3e-07  Score=79.88  Aligned_cols=203  Identities=8%  Similarity=-0.078  Sum_probs=136.5

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHH-
Q 044084           22 SGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYAS-  100 (343)
Q Consensus        22 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~-  100 (343)
                      ...|..+...+...|+.+.+.+.+....+..... .+...........+...|++++|.+.+++..+.. +.+...+.. 
T Consensus         6 ~~a~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~e~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~~   83 (355)
T cd05804           6 ALGHAAAALLLLLGGERPAAAAKAAAAAQALAAR-ATERERAHVEALSAWIAGDLPKALALLEQLLDDY-PRDLLALKLH   83 (355)
T ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHHHhccC-CCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHh
Confidence            3456777777778888888888887776654422 1222333344556677899999999999988763 223334432 


Q ss_pred             --HHHHHhcccCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhc
Q 044084          101 --LICSFASIAEVKVAEELFKEAEEKGMLR-DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSK  177 (343)
Q Consensus       101 --l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  177 (343)
                        ........+..+.+.+.+...  ....| .......+...+...|++++|.+.+++..+..+ .+...+..+...+..
T Consensus        84 ~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~p-~~~~~~~~la~i~~~  160 (355)
T cd05804          84 LGAFGLGDFSGMRDHVARVLPLW--APENPDYWYLLGMLAFGLEEAGQYDRAEEAARRALELNP-DDAWAVHAVAHVLEM  160 (355)
T ss_pred             HHHHHhcccccCchhHHHHHhcc--CcCCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC-CCcHHHHHHHHHHHH
Confidence              111222344555555555541  11223 344555677788899999999999999988765 455677888888999


Q ss_pred             CCcHHHHHHHHHHHHHcCC-CCCH--hhHHHHHHHHHccCChhHHHHHHHHHHHc
Q 044084          178 RRAYWAAVKVYEQLISQGC-IPGQ--VTYASIINAYCRIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       178 ~~~~~~a~~~~~~~~~~~~-~p~~--~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  229 (343)
                      .|++++|...+++...... .|+.  ..|..+...+...|++++|..+++.....
T Consensus       161 ~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~~  215 (355)
T cd05804         161 QGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHIAP  215 (355)
T ss_pred             cCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhcc
Confidence            9999999999998876532 1232  23456777888999999999999998644

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.

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

Probab=99.20  E-value=7.7e-07  Score=75.13  Aligned_cols=229  Identities=14%  Similarity=0.041  Sum_probs=145.4

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHH---HHHHhhccCcHHHHHHHHHHHHhcCCCCCh-HhHHHHHHH
Q 044084           29 MEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKI---LCDSLGKSGRAFEILKFFRDMKEKGILEDP-SVYASLICS  104 (343)
Q Consensus        29 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~---li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~  104 (343)
                      ...+...|++++|.+.+++..+..+    .+...+..   ........+....+.+.+..  .....|+. .....+...
T Consensus        50 a~~~~~~g~~~~A~~~~~~~l~~~P----~~~~a~~~~~~~~~~~~~~~~~~~~~~~l~~--~~~~~~~~~~~~~~~a~~  123 (355)
T cd05804          50 ALSAWIAGDLPKALALLEQLLDDYP----RDLLALKLHLGAFGLGDFSGMRDHVARVLPL--WAPENPDYWYLLGMLAFG  123 (355)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHCC----CcHHHHHHhHHHHHhcccccCchhHHHHHhc--cCcCCCCcHHHHHHHHHH
Confidence            4456788999999999999877642    22344442   22222234555555555554  11223332 334455567


Q ss_pred             HhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCC-Cch--hhHHHHHHHHhcCCcH
Q 044084          105 FASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELN-ISD--CISCVIVNGFSKRRAY  181 (343)
Q Consensus       105 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~--~~~~~l~~~~~~~~~~  181 (343)
                      +...|++++|...+++..+..+. +...+..+...+...|++++|...+++....... ++.  ..|..+...+...|++
T Consensus       124 ~~~~G~~~~A~~~~~~al~~~p~-~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~  202 (355)
T cd05804         124 LEEAGQYDRAEEAARRALELNPD-DAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDY  202 (355)
T ss_pred             HHHcCCHHHHHHHHHHHHhhCCC-CcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCH
Confidence            88999999999999999997643 6788889999999999999999999998765432 222  2355688889999999


Q ss_pred             HHHHHHHHHHHHcCC-CCCHhhH-H--HHHHHHHccCChhHHHHH--HHHHHHcCCCcCh--hhHHHHHHHHHccCChHH
Q 044084          182 WAAVKVYEQLISQGC-IPGQVTY-A--SIINAYCRIGLYSKAEKV--FIEMQQKGFDKCV--VAYSSMVAMYGKTGRIRD  253 (343)
Q Consensus       182 ~~a~~~~~~~~~~~~-~p~~~~~-~--~ll~~~~~~~~~~~a~~~--~~~~~~~~~~~~~--~~~~~l~~~~~~~~~~~~  253 (343)
                      ++|..++++...... .+..... +  .++.-+...|..+.+.+.  +........+...  ........++...|+.+.
T Consensus       203 ~~A~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~  282 (355)
T cd05804         203 EAALAIYDTHIAPSAESDPALDLLDAASLLWRLELAGHVDVGDRWEDLADYAAWHFPDHGLAFNDLHAALALAGAGDKDA  282 (355)
T ss_pred             HHHHHHHHHHhccccCCChHHHHhhHHHHHHHHHhcCCCChHHHHHHHHHHHHhhcCcccchHHHHHHHHHHhcCCCHHH
Confidence            999999999864422 1222111 1  223333444544433333  2111111111111  222356677888999999


Q ss_pred             HHHHHHHHhhC
Q 044084          254 AMRLVAKMKPK  264 (343)
Q Consensus       254 a~~~~~~m~~~  264 (343)
                      |..+++.+...
T Consensus       283 a~~~L~~l~~~  293 (355)
T cd05804         283 LDKLLAALKGR  293 (355)
T ss_pred             HHHHHHHHHHH
Confidence            99999998764

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

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

Probab=99.11  E-value=1.8e-06  Score=71.37  Aligned_cols=152  Identities=11%  Similarity=0.046  Sum_probs=119.5

Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHH
Q 044084           34 KIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKV  113 (343)
Q Consensus        34 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  113 (343)
                      ..+++..|..+|+.......    .+...|...+.+=.++.....|..++++....=+..| ..|-..+..=-..|++..
T Consensus        85 sq~e~~RARSv~ERALdvd~----r~itLWlkYae~Emknk~vNhARNv~dRAvt~lPRVd-qlWyKY~ymEE~LgNi~g  159 (677)
T KOG1915|consen   85 SQKEIQRARSVFERALDVDY----RNITLWLKYAEFEMKNKQVNHARNVWDRAVTILPRVD-QLWYKYIYMEEMLGNIAG  159 (677)
T ss_pred             hHHHHHHHHHHHHHHHhccc----ccchHHHHHHHHHHhhhhHhHHHHHHHHHHHhcchHH-HHHHHHHHHHHHhcccHH
Confidence            34556788889988866542    2357888889999999999999999999887522222 234445555567799999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHH
Q 044084          114 AEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLIS  193 (343)
Q Consensus       114 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  193 (343)
                      |.++|++-.+  ..|+...|++.++.=.+-+.++.|..+|++..-..  |++.+|--....-.++|....+..+|....+
T Consensus       160 aRqiferW~~--w~P~eqaW~sfI~fElRykeieraR~IYerfV~~H--P~v~~wikyarFE~k~g~~~~aR~VyerAie  235 (677)
T KOG1915|consen  160 ARQIFERWME--WEPDEQAWLSFIKFELRYKEIERARSIYERFVLVH--PKVSNWIKYARFEEKHGNVALARSVYERAIE  235 (677)
T ss_pred             HHHHHHHHHc--CCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHheec--ccHHHHHHHHHHHHhcCcHHHHHHHHHHHHH
Confidence            9999999887  46999999999999999999999999999987654  7777887777777788888888888877665


Q ss_pred             c
Q 044084          194 Q  194 (343)
Q Consensus       194 ~  194 (343)
                      .
T Consensus       236 ~  236 (677)
T KOG1915|consen  236 F  236 (677)
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=99.10  E-value=9.7e-07  Score=71.57  Aligned_cols=292  Identities=11%  Similarity=0.037  Sum_probs=198.9

Q ss_pred             CCCChhhHHHHHHHHHhc--CCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCCh
Q 044084           18 IVLDSGCYCQIMEAFYKI--GDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDP   95 (343)
Q Consensus        18 ~~~~~~~~~~l~~~~~~~--~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~   95 (343)
                      ++|...+....+.+++..  ++-..+..++-.+.....-  +.+......+...+...|+.++|+..|++....+  |+.
T Consensus       190 ~~~~~dwls~wika~Aq~~~~~hs~a~~t~l~le~~~~l--r~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~d--py~  265 (564)
T KOG1174|consen  190 VPDHFDWLSKWIKALAQMFNFKHSDASQTFLMLHDNTTL--RCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCAN--PDN  265 (564)
T ss_pred             cCCCccHHHHHHHHHHHHHhcccchhhhHHHHHHhhccC--CccHHHHHHHhhhhhhhcCchHHHHHHHHHhhCC--hhh
Confidence            344444444555555544  4444555555444444333  3346788899999999999999999999987653  332


Q ss_pred             -HhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHH
Q 044084           96 -SVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNG  174 (343)
Q Consensus        96 -~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  174 (343)
                       .......-.+.+.|+.+....+...+....- -+...|..-+.......+++.|+.+-++..+.+. -+...|-.-...
T Consensus       266 i~~MD~Ya~LL~~eg~~e~~~~L~~~Lf~~~~-~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I~~~~-r~~~alilKG~l  343 (564)
T KOG1174|consen  266 VEAMDLYAVLLGQEGGCEQDSALMDYLFAKVK-YTASHWFVHAQLLYDEKKFERALNFVEKCIDSEP-RNHEALILKGRL  343 (564)
T ss_pred             hhhHHHHHHHHHhccCHhhHHHHHHHHHhhhh-cchhhhhhhhhhhhhhhhHHHHHHHHHHHhccCc-ccchHHHhccHH
Confidence             2233333445677888888888777765421 2344455555566677889999999999887664 344455555567


Q ss_pred             HhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHH-HHHHc-cCChH
Q 044084          175 FSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMV-AMYGK-TGRIR  252 (343)
Q Consensus       175 ~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~-~~~~~-~~~~~  252 (343)
                      +...+++++|.-.|+...... +-+...|.-++.+|...|++.+|..+-+...+. ++.+..+.+.+. ..+.. ...-+
T Consensus       344 L~~~~R~~~A~IaFR~Aq~La-p~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~-~~~sA~~LtL~g~~V~~~dp~~rE  421 (564)
T KOG1174|consen  344 LIALERHTQAVIAFRTAQMLA-PYRLEIYRGLFHSYLAQKRFKEANALANWTIRL-FQNSARSLTLFGTLVLFPDPRMRE  421 (564)
T ss_pred             HHhccchHHHHHHHHHHHhcc-hhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHH-hhcchhhhhhhcceeeccCchhHH
Confidence            788899999999999988763 356789999999999999999998877776654 234555555552 33322 23347


Q ss_pred             HHHHHHHHHhhCCCCchH-HHHHHHHHHHhcccChhHHHh--------------HHHHHHHHHhcCCHHHHHHHHHHHHh
Q 044084          253 DAMRLVAKMKPKGCEPNV-WIYNSLMDMHGRAKNLRQLEK--------------YTTVISAYNMAREFDMCVKFYNEFRM  317 (343)
Q Consensus       253 ~a~~~~~~m~~~~~~p~~-~~~~~l~~~~~~~~~~~~a~~--------------~~~l~~~~~~~g~~~~a~~~~~~m~~  317 (343)
                      +|..++++-...  .|+- ...+.+...|...|....+..              .+.+.+.+...+.+++|++.|...+.
T Consensus       422 KAKkf~ek~L~~--~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~ALr  499 (564)
T KOG1174|consen  422 KAKKFAEKSLKI--NPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLIIFPDVNLHNHLGDIMRAQNEPQKAMEYYYKALR  499 (564)
T ss_pred             HHHHHHHhhhcc--CCccHHHHHHHHHHHHhhCccchHHHHHHHHHhhccccHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Confidence            888888887764  5553 344556667777777776665              67778888888888899988888877


Q ss_pred             CC
Q 044084          318 NG  319 (343)
Q Consensus       318 ~~  319 (343)
                      .+
T Consensus       500 ~d  501 (564)
T KOG1174|consen  500 QD  501 (564)
T ss_pred             cC
Confidence            54

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

Probab=99.08  E-value=4.3e-06  Score=70.87  Aligned_cols=321  Identities=10%  Similarity=0.069  Sum_probs=174.0

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHH-HHHHHHhhccCcHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMY-KILCDSLGKSGRAFEIL   80 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~-~~li~~~~~~~~~~~a~   80 (343)
                      ++++|++...++...+ +.+...+.+=+-+..+.+.+++|+.+.+.-...  ...    ..| ---..+..+.+..++|+
T Consensus        27 e~e~a~k~~~Kil~~~-pdd~~a~~cKvValIq~~ky~~ALk~ikk~~~~--~~~----~~~~fEKAYc~Yrlnk~Deal   99 (652)
T KOG2376|consen   27 EYEEAVKTANKILSIV-PDDEDAIRCKVVALIQLDKYEDALKLIKKNGAL--LVI----NSFFFEKAYCEYRLNKLDEAL   99 (652)
T ss_pred             HHHHHHHHHHHHHhcC-CCcHhhHhhhHhhhhhhhHHHHHHHHHHhcchh--hhc----chhhHHHHHHHHHcccHHHHH
Confidence            4678888888888765 345566777777888888888888665432210  000    011 11122334566677776


Q ss_pred             HHHHHHHhcCCCCC-hHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCC---------------------------CCHHH
Q 044084           81 KFFRDMKEKGILED-PSVYASLICSFASIAEVKVAEELFKEAEEKGML---------------------------RDLEV  132 (343)
Q Consensus        81 ~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---------------------------~~~~~  132 (343)
                      ..++     |..++ ..+...-...+.+.+++++|..+|+.+.+++.+                           ....+
T Consensus       100 k~~~-----~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a~l~~~~~q~v~~v~e~s  174 (652)
T KOG2376|consen  100 KTLK-----GLDRLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAAALQVQLLQSVPEVPEDS  174 (652)
T ss_pred             HHHh-----cccccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHhhhHHHHHhccCCCcch
Confidence            6666     22222 224444455566777777777777766543321                           00112


Q ss_pred             HHH---HHHHHHhcCcHhHHHHHHHHHHhc--------CCC-----Cchh-hHHHHHHHHhcCCcHHHHHHHHHHHHHcC
Q 044084          133 FLK---LVLMYIEEGMVEKTLEVVESMKNA--------ELN-----ISDC-ISCVIVNGFSKRRAYWAAVKVYEQLISQG  195 (343)
Q Consensus       133 ~~~---l~~~~~~~~~~~~a~~~~~~~~~~--------~~~-----~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  195 (343)
                      |..   ....+...|++.+|+++++...+.        +..     .... .-.-+...+-..|+.++|..++....+.+
T Consensus       175 yel~yN~Ac~~i~~gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~Gqt~ea~~iy~~~i~~~  254 (652)
T KOG2376|consen  175 YELLYNTACILIENGKYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQGQTAEASSIYVDIIKRN  254 (652)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhc
Confidence            222   223345567777777777766211        100     0000 01123334445677777777777666553


Q ss_pred             CCCCHhh-------------------------------------------------------------------------
Q 044084          196 CIPGQVT-------------------------------------------------------------------------  202 (343)
Q Consensus       196 ~~p~~~~-------------------------------------------------------------------------  202 (343)
                       .+|...                                                                         
T Consensus       255 -~~D~~~~Av~~NNLva~~~d~~~~d~~~l~~k~~~~~~l~~~~l~~Ls~~qk~~i~~N~~lL~l~tnk~~q~r~~~a~l  333 (652)
T KOG2376|consen  255 -PADEPSLAVAVNNLVALSKDQNYFDGDLLKSKKSQVFKLAEFLLSKLSKKQKQAIYRNNALLALFTNKMDQVRELSASL  333 (652)
T ss_pred             -CCCchHHHHHhcchhhhccccccCchHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHhC
Confidence             222211                                                                         


Q ss_pred             --------HHHHHHHHHc--cCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHH--------HHhhC
Q 044084          203 --------YASIINAYCR--IGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVA--------KMKPK  264 (343)
Q Consensus       203 --------~~~ll~~~~~--~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~--------~m~~~  264 (343)
                              +.+++..+.+  .....++..++...-+....-...+.-.++......|+++.|.+++.        .+.+.
T Consensus       334 p~~~p~~~~~~ll~~~t~~~~~~~~ka~e~L~~~~~~~p~~s~~v~L~~aQl~is~gn~~~A~~il~~~~~~~~ss~~~~  413 (652)
T KOG2376|consen  334 PGMSPESLFPILLQEATKVREKKHKKAIELLLQFADGHPEKSKVVLLLRAQLKISQGNPEVALEILSLFLESWKSSILEA  413 (652)
T ss_pred             CccCchHHHHHHHHHHHHHHHHHHhhhHHHHHHHhccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhhhhhhhh
Confidence                    1111111100  01122233333332222211113345566677788999999999998        55555


Q ss_pred             CCCchHHHHHHHHHHHhcccChhHHHh----------------------HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCc
Q 044084          265 GCEPNVWIYNSLMDMHGRAKNLRQLEK----------------------YTTVISAYNMAREFDMCVKFYNEFRMNGGVI  322 (343)
Q Consensus       265 ~~~p~~~~~~~l~~~~~~~~~~~~a~~----------------------~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p  322 (343)
                      +..|-.+  ..+...+.+.++.+.|..                      +..+...-.+.|.-++|..+++++.+.+ ++
T Consensus       414 ~~~P~~V--~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~~l~~~~~~aa~f~lr~G~~~ea~s~leel~k~n-~~  490 (652)
T KOG2376|consen  414 KHLPGTV--GAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGSIALLSLMREAAEFKLRHGNEEEASSLLEELVKFN-PN  490 (652)
T ss_pred             ccChhHH--HHHHHHHHhccCCccHHHHHHHHHHHHHHhcccchHHHhHHHHHhHHHHhcCchHHHHHHHHHHHHhC-Cc
Confidence            5555443  444445555555443333                      4445555567899999999999999864 57


Q ss_pred             cHHHHHHHHHHHhccc
Q 044084          323 DRAMAGIMVGVFSKLS  338 (343)
Q Consensus       323 ~~~~~~~l~~~~~~~g  338 (343)
                      |..+...++.+|++..
T Consensus       491 d~~~l~~lV~a~~~~d  506 (652)
T KOG2376|consen  491 DTDLLVQLVTAYARLD  506 (652)
T ss_pred             hHHHHHHHHHHHHhcC
Confidence            8888889999988753

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.06  E-value=7.9e-07  Score=70.69  Aligned_cols=319  Identities=11%  Similarity=0.109  Sum_probs=183.2

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      |+.-|..+++.-...+-.-...+-..+..++.+.|++++|...+.-+....-.|    ...+..|..++.-.|.+.+|..
T Consensus        37 DytGAislLefk~~~~~EEE~~~~lWia~C~fhLgdY~~Al~~Y~~~~~~~~~~----~el~vnLAcc~FyLg~Y~eA~~  112 (557)
T KOG3785|consen   37 DYTGAISLLEFKLNLDREEEDSLQLWIAHCYFHLGDYEEALNVYTFLMNKDDAP----AELGVNLACCKFYLGQYIEAKS  112 (557)
T ss_pred             cchhHHHHHHHhhccchhhhHHHHHHHHHHHHhhccHHHHHHHHHHHhccCCCC----cccchhHHHHHHHHHHHHHHHH
Confidence            456677777766654433222334445667788999999999998877654333    3677778877778888888877


Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCC
Q 044084           82 FFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAEL  161 (343)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  161 (343)
                      +-....+     ++-.-..++....+.++-++.....+.+.+.     ..---+|.....-...+.+|++++.++...+ 
T Consensus       113 ~~~ka~k-----~pL~~RLlfhlahklndEk~~~~fh~~LqD~-----~EdqLSLAsvhYmR~HYQeAIdvYkrvL~dn-  181 (557)
T KOG3785|consen  113 IAEKAPK-----TPLCIRLLFHLAHKLNDEKRILTFHSSLQDT-----LEDQLSLASVHYMRMHYQEAIDVYKRVLQDN-  181 (557)
T ss_pred             HHhhCCC-----ChHHHHHHHHHHHHhCcHHHHHHHHHHHhhh-----HHHHHhHHHHHHHHHHHHHHHHHHHHHHhcC-
Confidence            7654322     3334455666667778877777766666542     1222334444333445789999999988655 


Q ss_pred             CCchhhHHH-HHHHHhcCCcHHHHHHHHHHHHHcCCCCCH-hhHHHHHHHHHc--cCChhHHH--H----------HHHH
Q 044084          162 NISDCISCV-IVNGFSKRRAYWAAVKVYEQLISQGCIPGQ-VTYASIINAYCR--IGLYSKAE--K----------VFIE  225 (343)
Q Consensus       162 ~~~~~~~~~-l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~-~~~~~ll~~~~~--~~~~~~a~--~----------~~~~  225 (343)
                       |.-...|. +.-+|.+..-++-+.++++--.+.  .||. ...|....-..+  .|+..+.+  .          ..+.
T Consensus       182 -~ey~alNVy~ALCyyKlDYydvsqevl~vYL~q--~pdStiA~NLkacn~fRl~ngr~ae~E~k~ladN~~~~~~f~~~  258 (557)
T KOG3785|consen  182 -PEYIALNVYMALCYYKLDYYDVSQEVLKVYLRQ--FPDSTIAKNLKACNLFRLINGRTAEDEKKELADNIDQEYPFIEY  258 (557)
T ss_pred             -hhhhhhHHHHHHHHHhcchhhhHHHHHHHHHHh--CCCcHHHHHHHHHHHhhhhccchhHHHHHHHHhcccccchhHHH
Confidence             33334443 345677788888888888877765  3443 222222222111  12211111  0          1111


Q ss_pred             HHHcCC------------CcC-----hhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHH-Hhc----c
Q 044084          226 MQQKGF------------DKC-----VVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDM-HGR----A  283 (343)
Q Consensus       226 ~~~~~~------------~~~-----~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~-~~~----~  283 (343)
                      +.++++            -|.     +..--.|+-.|.+.++..+|..+.+++...  .|-......+..+ +.+    .
T Consensus       259 l~rHNLVvFrngEgALqVLP~L~~~IPEARlNL~iYyL~q~dVqeA~~L~Kdl~Pt--tP~EyilKgvv~aalGQe~gSr  336 (557)
T KOG3785|consen  259 LCRHNLVVFRNGEGALQVLPSLMKHIPEARLNLIIYYLNQNDVQEAISLCKDLDPT--TPYEYILKGVVFAALGQETGSR  336 (557)
T ss_pred             HHHcCeEEEeCCccHHHhchHHHhhChHhhhhheeeecccccHHHHHHHHhhcCCC--ChHHHHHHHHHHHHhhhhcCcH
Confidence            222110            010     223334566788999999999888776532  3333333222221 111    1


Q ss_pred             cChhHHHh---------------------------------------------------HHHHHHHHHhcCCHHHHHHHH
Q 044084          284 KNLRQLEK---------------------------------------------------YTTVISAYNMAREFDMCVKFY  312 (343)
Q Consensus       284 ~~~~~a~~---------------------------------------------------~~~l~~~~~~~g~~~~a~~~~  312 (343)
                      ....-|.+                                                   --.+..+++..|.+.+|.++|
T Consensus       337 eHlKiAqqffqlVG~Sa~ecDTIpGRQsmAs~fFL~~qFddVl~YlnSi~sYF~NdD~Fn~N~AQAk~atgny~eaEelf  416 (557)
T KOG3785|consen  337 EHLKIAQQFFQLVGESALECDTIPGRQSMASYFFLSFQFDDVLTYLNSIESYFTNDDDFNLNLAQAKLATGNYVEAEELF  416 (557)
T ss_pred             HHHHHHHHHHHHhcccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhhhHHHHHHHHhcChHHHHHHH
Confidence            11111211                                                   234667788889999999998


Q ss_pred             HHHHhCCCCccHHHH-HHHHHHHhcccccc
Q 044084          313 NEFRMNGGVIDRAMA-GIMVGVFSKLSQIE  341 (343)
Q Consensus       313 ~~m~~~~~~p~~~~~-~~l~~~~~~~g~~~  341 (343)
                      -+.....++ |..+| ..|.++|.++++.+
T Consensus       417 ~~is~~~ik-n~~~Y~s~LArCyi~nkkP~  445 (557)
T KOG3785|consen  417 IRISGPEIK-NKILYKSMLARCYIRNKKPQ  445 (557)
T ss_pred             hhhcChhhh-hhHHHHHHHHHHHHhcCCch
Confidence            877655554 44555 55666888887765

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

Probab=99.05  E-value=2.7e-06  Score=72.82  Aligned_cols=226  Identities=11%  Similarity=0.052  Sum_probs=148.1

Q ss_pred             hhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHH
Q 044084            4 QSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFF   83 (343)
Q Consensus         4 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~   83 (343)
                      ...+.+.+.+.+ +.+-...+.....-.+...|+.++|......-.+.+    +.+...|+.+.-.+....++++|++.|
T Consensus        24 kkgLK~~~~iL~-k~~eHgeslAmkGL~L~~lg~~~ea~~~vr~glr~d----~~S~vCwHv~gl~~R~dK~Y~eaiKcy   98 (700)
T KOG1156|consen   24 KKGLKLIKQILK-KFPEHGESLAMKGLTLNCLGKKEEAYELVRLGLRND----LKSHVCWHVLGLLQRSDKKYDEAIKCY   98 (700)
T ss_pred             HhHHHHHHHHHH-hCCccchhHHhccchhhcccchHHHHHHHHHHhccC----cccchhHHHHHHHHhhhhhHHHHHHHH
Confidence            344555555555 333455666666666777888888888776654433    444588888888888888899999999


Q ss_pred             HHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcC-CC
Q 044084           84 RDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAE-LN  162 (343)
Q Consensus        84 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~  162 (343)
                      +.....+. -|...+.-+.-.-++.++++.......++.+..+. ....|..+..++.-.|+...|..+++...+.. ..
T Consensus        99 ~nAl~~~~-dN~qilrDlslLQ~QmRd~~~~~~tr~~LLql~~~-~ra~w~~~Avs~~L~g~y~~A~~il~ef~~t~~~~  176 (700)
T KOG1156|consen   99 RNALKIEK-DNLQILRDLSLLQIQMRDYEGYLETRNQLLQLRPS-QRASWIGFAVAQHLLGEYKMALEILEEFEKTQNTS  176 (700)
T ss_pred             HHHHhcCC-CcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Confidence            98887643 35666766666667778888887777777765432 56678888888888888889988888877654 23


Q ss_pred             CchhhHHHHH------HHHhcCCcHHHHHHHHHHHHHcCCCCCHhhH-HHHHHHHHccCChhHHHHHHHHHHHcCCCcCh
Q 044084          163 ISDCISCVIV------NGFSKRRAYWAAVKVYEQLISQGCIPGQVTY-ASIINAYCRIGLYSKAEKVFIEMQQKGFDKCV  235 (343)
Q Consensus       163 ~~~~~~~~l~------~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~-~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~  235 (343)
                      |+...+....      ......|.++.|.+.+..-...  ..|...+ ..-...+.+.+++++|..++..+....  ||.
T Consensus       177 ~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~--i~Dkla~~e~ka~l~~kl~~lEeA~~~y~~Ll~rn--Pdn  252 (700)
T KOG1156|consen  177 PSKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNEKQ--IVDKLAFEETKADLLMKLGQLEEAVKVYRRLLERN--PDN  252 (700)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhhhH--HHHHHHHhhhHHHHHHHHhhHHhHHHHHHHHHhhC--chh
Confidence            5554444322      2344566677776666554433  1222222 233455667788888888888877764  554


Q ss_pred             hhHHH
Q 044084          236 VAYSS  240 (343)
Q Consensus       236 ~~~~~  240 (343)
                      ..|+.
T Consensus       253 ~~Yy~  257 (700)
T KOG1156|consen  253 LDYYE  257 (700)
T ss_pred             HHHHH
Confidence            44443

>PLN02789 farnesyltranstransferase

Probab=99.04  E-value=1e-06  Score=71.94  Aligned_cols=215  Identities=10%  Similarity=0.037  Sum_probs=155.9

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccC-cHHHHHHHHHHHHhcCCCCChHhHHHHH
Q 044084           24 CYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSG-RAFEILKFFRDMKEKGILEDPSVYASLI  102 (343)
Q Consensus        24 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~  102 (343)
                      ++..+-..+...+..++|+.+.+++.+.+    |.+..+|+.....+...| ++++++..++++.+.+.+ +..+|+...
T Consensus        39 a~~~~ra~l~~~e~serAL~lt~~aI~ln----P~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~npk-nyqaW~~R~  113 (320)
T PLN02789         39 AMDYFRAVYASDERSPRALDLTADVIRLN----PGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDNPK-NYQIWHHRR  113 (320)
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHC----chhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCCc-chHHhHHHH
Confidence            34455556677789999999999998765    344577887777777777 579999999999887544 555676655


Q ss_pred             HHHhcccC--HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcC--
Q 044084          103 CSFASIAE--VKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKR--  178 (343)
Q Consensus       103 ~~~~~~~~--~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--  178 (343)
                      ..+.+.|+  .+.+...++.+.+...+ +..+|+.....+...|+++++++.++++.+.++ -+..+|+.....+.+.  
T Consensus       114 ~~l~~l~~~~~~~el~~~~kal~~dpk-Ny~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~-~N~sAW~~R~~vl~~~~~  191 (320)
T PLN02789        114 WLAEKLGPDAANKELEFTRKILSLDAK-NYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDV-RNNSAWNQRYFVITRSPL  191 (320)
T ss_pred             HHHHHcCchhhHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCC-CchhHHHHHHHHHHhccc
Confidence            55555565  36778888888887764 899999999999999999999999999998887 4666777665555443  


Q ss_pred             -Cc----HHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHcc----CChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHc
Q 044084          179 -RA----YWAAVKVYEQLISQGCIPGQVTYASIINAYCRI----GLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGK  247 (343)
Q Consensus       179 -~~----~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  247 (343)
                       |.    .++..+...++.... +-+...|+-+...+...    +...+|...+.+..+.+ +.+......|++.|+.
T Consensus       192 l~~~~~~~e~el~y~~~aI~~~-P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~-~~s~~al~~l~d~~~~  267 (320)
T PLN02789        192 LGGLEAMRDSELKYTIDAILAN-PRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKD-SNHVFALSDLLDLLCE  267 (320)
T ss_pred             cccccccHHHHHHHHHHHHHhC-CCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhccc-CCcHHHHHHHHHHHHh
Confidence             22    246677776666653 44567787777777663    34466888888776654 4456778888888875

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

Probab=99.04  E-value=6.6e-06  Score=70.55  Aligned_cols=327  Identities=14%  Similarity=0.146  Sum_probs=194.2

Q ss_pred             hhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHH
Q 044084            3 SQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKF   82 (343)
Q Consensus         3 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~   82 (343)
                      .++|......-.+.++ .+...|+.+.-.+....++++|.+.|......+    +.+...|.-+.-.-++.++++.....
T Consensus        57 ~~ea~~~vr~glr~d~-~S~vCwHv~gl~~R~dK~Y~eaiKcy~nAl~~~----~dN~qilrDlslLQ~QmRd~~~~~~t  131 (700)
T KOG1156|consen   57 KEEAYELVRLGLRNDL-KSHVCWHVLGLLQRSDKKYDEAIKCYRNALKIE----KDNLQILRDLSLLQIQMRDYEGYLET  131 (700)
T ss_pred             hHHHHHHHHHHhccCc-ccchhHHHHHHHHhhhhhHHHHHHHHHHHHhcC----CCcHHHHHHHHHHHHHHHhhhhHHHH
Confidence            4567777766666554 477788888888888889999999998886644    44467777776667778888888777


Q ss_pred             HHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCC-CCCHHHHHHHH------HHHHhcCcHhHHHHHHHH
Q 044084           83 FRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGM-LRDLEVFLKLV------LMYIEEGMVEKTLEVVES  155 (343)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~------~~~~~~~~~~~a~~~~~~  155 (343)
                      ..++.+.. +.....|..+..++.-.|+...|..+++...+... .|+...+....      ....+.|..++|.+.+..
T Consensus       132 r~~LLql~-~~~ra~w~~~Avs~~L~g~y~~A~~il~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~  210 (700)
T KOG1156|consen  132 RNQLLQLR-PSQRASWIGFAVAQHLLGEYKMALEILEEFEKTQNTSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLD  210 (700)
T ss_pred             HHHHHHhh-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHh
Confidence            77777652 22345677777777778888888888888776542 35555544332      234556777777777665


Q ss_pred             HHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHH-HHHccCChhHHH-HHHHH--------
Q 044084          156 MKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIIN-AYCRIGLYSKAE-KVFIE--------  225 (343)
Q Consensus       156 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~-~~~~~~~~~~a~-~~~~~--------  225 (343)
                      ....-+ .....-..-...+.+.+++++|..++..+...  .||...|...+. ++.+..+.-++. .+|..        
T Consensus       211 ~e~~i~-Dkla~~e~ka~l~~kl~~lEeA~~~y~~Ll~r--nPdn~~Yy~~l~~~lgk~~d~~~~lk~ly~~ls~~y~r~  287 (700)
T KOG1156|consen  211 NEKQIV-DKLAFEETKADLLMKLGQLEEAVKVYRRLLER--NPDNLDYYEGLEKALGKIKDMLEALKALYAILSEKYPRH  287 (700)
T ss_pred             hhhHHH-HHHHHhhhHHHHHHHHhhHHhHHHHHHHHHhh--CchhHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhcCccc
Confidence            543221 11112233445667778888888888888877  466665554433 332222222222 33333        


Q ss_pred             --------------------------HHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHh----hCCC---------
Q 044084          226 --------------------------MQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMK----PKGC---------  266 (343)
Q Consensus       226 --------------------------~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~----~~~~---------  266 (343)
                                                +.+.|+++   ++..+...|-.-...+-..++...+.    ..|.         
T Consensus       288 e~p~Rlplsvl~~eel~~~vdkyL~~~l~Kg~p~---vf~dl~SLyk~p~k~~~le~Lvt~y~~~L~~~~~f~~~D~~~~  364 (700)
T KOG1156|consen  288 ECPRRLPLSVLNGEELKEIVDKYLRPLLSKGVPS---VFKDLRSLYKDPEKVAFLEKLVTSYQHSLSGTGMFNFLDDGKQ  364 (700)
T ss_pred             ccchhccHHHhCcchhHHHHHHHHHHHhhcCCCc---hhhhhHHHHhchhHhHHHHHHHHHHHhhcccccCCCccccccc
Confidence                                      33333322   22233332222111111111111111    1111         


Q ss_pred             -CchH--HHHHHHHHHHhcccChhHHHh---------------HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHH
Q 044084          267 -EPNV--WIYNSLMDMHGRAKNLRQLEK---------------YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAG  328 (343)
Q Consensus       267 -~p~~--~~~~~l~~~~~~~~~~~~a~~---------------~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~  328 (343)
                       +|..  .|+..+++.+-+.|+++.|..               |..-.+.+...|++++|..++++.++.+. ||...-+
T Consensus       365 E~PttllWt~y~laqh~D~~g~~~~A~~yId~AIdHTPTliEly~~KaRI~kH~G~l~eAa~~l~ea~elD~-aDR~INs  443 (700)
T KOG1156|consen  365 EPPTTLLWTLYFLAQHYDKLGDYEVALEYIDLAIDHTPTLIELYLVKARIFKHAGLLDEAAAWLDEAQELDT-ADRAINS  443 (700)
T ss_pred             CCchHHHHHHHHHHHHHHHcccHHHHHHHHHHHhccCchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhccc-hhHHHHH
Confidence             3444  344567778888999988887               55556778889999999999999887653 4555433


Q ss_pred             HHHHHHhccccccc
Q 044084          329 IMVGVFSKLSQIEE  342 (343)
Q Consensus       329 ~l~~~~~~~g~~~~  342 (343)
                      --..-..+..+.++
T Consensus       444 KcAKYmLrAn~i~e  457 (700)
T KOG1156|consen  444 KCAKYMLRANEIEE  457 (700)
T ss_pred             HHHHHHHHccccHH
Confidence            33444444444443

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

Probab=99.04  E-value=2.8e-08  Score=79.94  Aligned_cols=136  Identities=15%  Similarity=0.083  Sum_probs=57.5

Q ss_pred             HHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHc----cCC
Q 044084          140 YIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCR----IGL  215 (343)
Q Consensus       140 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~----~~~  215 (343)
                      +...|++++|++++...      .+.......+..+.+.++++.|.+.++.|.+..   +..+...+..++..    .+.
T Consensus       112 ~~~~~~~~~AL~~l~~~------~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~---eD~~l~qLa~awv~l~~g~e~  182 (290)
T PF04733_consen  112 LFHEGDYEEALKLLHKG------GSLELLALAVQILLKMNRPDLAEKELKNMQQID---EDSILTQLAEAWVNLATGGEK  182 (290)
T ss_dssp             HCCCCHHHHHHCCCTTT------TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCS---CCHHHHHHHHHHHHHHHTTTC
T ss_pred             HHHcCCHHHHHHHHHcc------CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhcC---CcHHHHHHHHHHHHHHhCchh
Confidence            33445555555544322      122233344445555555555555555554431   12222223333221    223


Q ss_pred             hhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccCh
Q 044084          216 YSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNL  286 (343)
Q Consensus       216 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~  286 (343)
                      +.+|..+|+++.+. +++++.+.+.+..++...|++++|.+++.+..+.+. -++.+...++-+....|+.
T Consensus       183 ~~~A~y~f~El~~~-~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~-~~~d~LaNliv~~~~~gk~  251 (290)
T PF04733_consen  183 YQDAFYIFEELSDK-FGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDP-NDPDTLANLIVCSLHLGKP  251 (290)
T ss_dssp             CCHHHHHHHHHHCC-S--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-C-CHHHHHHHHHHHHHHTT-T
T ss_pred             HHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhcc-CCHHHHHHHHHHHHHhCCC
Confidence            55555555554433 234445555555555555555555555555444321 1334444444444444444

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=99.03  E-value=6e-07  Score=82.94  Aligned_cols=224  Identities=11%  Similarity=0.082  Sum_probs=178.4

Q ss_pred             CchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCC-----ChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHH
Q 044084           57 PSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILE-----DPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLE  131 (343)
Q Consensus        57 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~-----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  131 (343)
                      |.+...|...|..+.+.++.+.|.++.++.+.. +.+     -...|.++++.-..-|.-+...++|+++.+..  -...
T Consensus      1455 PNSSi~WI~YMaf~LelsEiekAR~iaerAL~t-IN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqyc--d~~~ 1531 (1710)
T KOG1070|consen 1455 PNSSILWIRYMAFHLELSEIEKARKIAERALKT-INFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQYC--DAYT 1531 (1710)
T ss_pred             CCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhh-CCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHhc--chHH
Confidence            444678999999999999999999999998764 222     23457778877777788899999999999864  2366


Q ss_pred             HHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCC---HhhHHHHHH
Q 044084          132 VFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPG---QVTYASIIN  208 (343)
Q Consensus       132 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~---~~~~~~ll~  208 (343)
                      +|..|...|.+.+.+++|.++++.|.+.-- .....|...+..+.++.+-+.|..++.+..+.  -|.   .....-.+.
T Consensus      1532 V~~~L~~iy~k~ek~~~A~ell~~m~KKF~-q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~--lPk~eHv~~IskfAq 1608 (1710)
T KOG1070|consen 1532 VHLKLLGIYEKSEKNDEADELLRLMLKKFG-QTRKVWIMYADFLLRQNEAEAARELLKRALKS--LPKQEHVEFISKFAQ 1608 (1710)
T ss_pred             HHHHHHHHHHHhhcchhHHHHHHHHHHHhc-chhhHHHHHHHHHhcccHHHHHHHHHHHHHhh--cchhhhHHHHHHHHH
Confidence            789999999999999999999999987543 45568999999999999999999999998876  344   223344445


Q ss_pred             HHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchH--HHHHHHHHHHhcccCh
Q 044084          209 AYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNV--WIYNSLMDMHGRAKNL  286 (343)
Q Consensus       209 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~--~~~~~l~~~~~~~~~~  286 (343)
                      .-.+.|+.+.+..+|+...... |.-...|+.+|+.-.++|+.+.++.+|++....++.|-.  ..|...+..=.+.|+-
T Consensus      1609 LEFk~GDaeRGRtlfEgll~ay-PKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~kkmKfffKkwLeyEk~~Gde 1687 (1710)
T KOG1070|consen 1609 LEFKYGDAERGRTLFEGLLSAY-PKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSIKKMKFFFKKWLEYEKSHGDE 1687 (1710)
T ss_pred             HHhhcCCchhhHHHHHHHHhhC-ccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCChhHhHHHHHHHHHHHHhcCch
Confidence            5567899999999999998875 556789999999999999999999999999999887754  3455555544444443


Q ss_pred             h
Q 044084          287 R  287 (343)
Q Consensus       287 ~  287 (343)
                      .
T Consensus      1688 ~ 1688 (1710)
T KOG1070|consen 1688 K 1688 (1710)
T ss_pred             h
Confidence            3

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=99.02  E-value=6e-06  Score=72.15  Aligned_cols=323  Identities=11%  Similarity=0.044  Sum_probs=181.8

Q ss_pred             HHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCC
Q 044084           13 MKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGIL   92 (343)
Q Consensus        13 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~   92 (343)
                      +....+.-|...|..|.-+....|+++.+-+.|++...--...    .+.|..+...+.-.|.-..|..+++.-......
T Consensus       314 ~r~~~~qnd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~~~~----~e~w~~~als~saag~~s~Av~ll~~~~~~~~~  389 (799)
T KOG4162|consen  314 LRLKKFQNDAAIFDHLTFALSRCGQFEVLAEQFEQALPFSFGE----HERWYQLALSYSAAGSDSKAVNLLRESLKKSEQ  389 (799)
T ss_pred             HHHhhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhh----HHHHHHHHHHHHHhccchHHHHHHHhhcccccC
Confidence            3333455688889999999999999999999998875543322    477888888888888888888888776554323


Q ss_pred             CCh-HhHHHHHHHHh-cccCHHHHHHHHHHHHHc--CC--CCCHHHHHHHHHHHHhc-----------CcHhHHHHHHHH
Q 044084           93 EDP-SVYASLICSFA-SIAEVKVAEELFKEAEEK--GM--LRDLEVFLKLVLMYIEE-----------GMVEKTLEVVES  155 (343)
Q Consensus        93 ~~~-~~~~~l~~~~~-~~~~~~~a~~~~~~~~~~--~~--~~~~~~~~~l~~~~~~~-----------~~~~~a~~~~~~  155 (343)
                      |+. ..+-..-..|. +.+..++++..-.++...  +.  ...+..|..+.-+|...           ....++++.+++
T Consensus       390 ps~~s~~Lmasklc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~kslqale~  469 (799)
T KOG4162|consen  390 PSDISVLLMASKLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSERDALHKKSLQALEE  469 (799)
T ss_pred             CCcchHHHHHHHHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHHHHHHHH
Confidence            433 33332233333 335555555555554441  10  11233444444444321           113455555565


Q ss_pred             HHhcCC-CCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHc-CC--
Q 044084          156 MKNAEL-NISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQK-GF--  231 (343)
Q Consensus       156 ~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~-~~--  231 (343)
                      ..+.+. .|+...|  +.--|+..++.+.|.+..++..+.+-.-+...|..+.-.+...+++.+|+.+.+..... |.  
T Consensus       470 av~~d~~dp~~if~--lalq~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al~E~~~N~  547 (799)
T KOG4162|consen  470 AVQFDPTDPLVIFY--LALQYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAALEEFGDNH  547 (799)
T ss_pred             HHhcCCCCchHHHH--HHHHHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhhhhh
Confidence            555443 1222222  22223445566666666666665544455555555555555555555555554443321 10  


Q ss_pred             --------------------------------------------------------------------------------
Q 044084          232 --------------------------------------------------------------------------------  231 (343)
Q Consensus       232 --------------------------------------------------------------------------------  231 (343)
                                                                                                      
T Consensus       548 ~l~~~~~~i~~~~~~~e~~l~t~~~~L~~we~~~~~q~~~~~g~~~~lk~~l~la~~q~~~a~s~sr~ls~l~a~~~~~~  627 (799)
T KOG4162|consen  548 VLMDGKIHIELTFNDREEALDTCIHKLALWEAEYGVQQTLDEGKLLRLKAGLHLALSQPTDAISTSRYLSSLVASQLKSA  627 (799)
T ss_pred             hhchhhhhhhhhcccHHHHHHHHHHHHHHHHhhhhHhhhhhhhhhhhhhcccccCcccccccchhhHHHHHHHHhhhhhc
Confidence                                                                                            


Q ss_pred             -----------C--cC------hhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh-
Q 044084          232 -----------D--KC------VVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK-  291 (343)
Q Consensus       232 -----------~--~~------~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~-  291 (343)
                                 .  |+      ...|......+.+.+..++|...+.+.... ..-....|......+...|.+.+|.+ 
T Consensus       628 ~se~~Lp~s~~~~~~~~~~~~~~~lwllaa~~~~~~~~~~~a~~CL~Ea~~~-~~l~~~~~~~~G~~~~~~~~~~EA~~a  706 (799)
T KOG4162|consen  628 GSELKLPSSTVLPGPDSLWYLLQKLWLLAADLFLLSGNDDEARSCLLEASKI-DPLSASVYYLRGLLLEVKGQLEEAKEA  706 (799)
T ss_pred             ccccccCcccccCCCCchHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHhc-chhhHHHHHHhhHHHHHHHhhHHHHHH
Confidence                       0  00      112223333444444444444444444332 12233344444445555666666655 


Q ss_pred             --------------HHHHHHHHHhcCCHHHHHH--HHHHHHhCCCCccHHHHHHHHHHHhcccccccC
Q 044084          292 --------------YTTVISAYNMAREFDMCVK--FYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       292 --------------~~~l~~~~~~~g~~~~a~~--~~~~m~~~~~~p~~~~~~~l~~~~~~~g~~~~a  343 (343)
                                    ...+...+.+.|+..-|..  ++.++.+.+. -++..|..+..++.+.|+.++|
T Consensus       707 f~~Al~ldP~hv~s~~Ala~~lle~G~~~la~~~~~L~dalr~dp-~n~eaW~~LG~v~k~~Gd~~~A  773 (799)
T KOG4162|consen  707 FLVALALDPDHVPSMTALAELLLELGSPRLAEKRSLLSDALRLDP-LNHEAWYYLGEVFKKLGDSKQA  773 (799)
T ss_pred             HHHHHhcCCCCcHHHHHHHHHHHHhCCcchHHHHHHHHHHHhhCC-CCHHHHHHHHHHHHHccchHHH
Confidence                          6777888888888777777  8888888664 3667788888899888887754

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.02  E-value=3.6e-07  Score=70.84  Aligned_cols=168  Identities=11%  Similarity=0.048  Sum_probs=85.9

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHH
Q 044084           22 SGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASL  101 (343)
Q Consensus        22 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  101 (343)
                      ..-+++.+..+.+-.+++.|.+++..-.++.    |.+....+.|..+|....++..|-+.++++-..  .|...-|...
T Consensus        10 EGeftaviy~lI~d~ry~DaI~~l~s~~Er~----p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql--~P~~~qYrlY   83 (459)
T KOG4340|consen   10 EGEFTAVVYRLIRDARYADAIQLLGSELERS----PRSRAGLSLLGYCYYRLQEFALAAECYEQLGQL--HPELEQYRLY   83 (459)
T ss_pred             CCchHHHHHHHHHHhhHHHHHHHHHHHHhcC----ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--ChHHHHHHHH
Confidence            3345666666667777777777766655544    223456666677777777777777777766553  3333333221


Q ss_pred             -HHHHhcccCHHHHHHHHHHHHHcC------------------------------C-CCCHHHHHHHHHHHHhcCcHhHH
Q 044084          102 -ICSFASIAEVKVAEELFKEAEEKG------------------------------M-LRDLEVFLKLVLMYIEEGMVEKT  149 (343)
Q Consensus       102 -~~~~~~~~~~~~a~~~~~~~~~~~------------------------------~-~~~~~~~~~l~~~~~~~~~~~~a  149 (343)
                       ...+.+.+.+..|+.+...|.+..                              + +-+..+.+...-...+.|+++.|
T Consensus        84 ~AQSLY~A~i~ADALrV~~~~~D~~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en~Ad~~in~gCllykegqyEaA  163 (459)
T KOG4340|consen   84 QAQSLYKACIYADALRVAFLLLDNPALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSENEADGQINLGCLLYKEGQYEAA  163 (459)
T ss_pred             HHHHHHHhcccHHHHHHHHHhcCCHHHHHHHHHHHHHHhcccccCcchHHHHHhccCCCccchhccchheeeccccHHHH
Confidence             123334444555555544443210                              0 01222333333334455666666


Q ss_pred             HHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCC
Q 044084          150 LEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGC  196 (343)
Q Consensus       150 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  196 (343)
                      .+-|+...+.+--.+...|+.-+. ..+.|+++.|++...++.+.|+
T Consensus       164 vqkFqaAlqvsGyqpllAYniALa-Hy~~~qyasALk~iSEIieRG~  209 (459)
T KOG4340|consen  164 VQKFQAALQVSGYQPLLAYNLALA-HYSSRQYASALKHISEIIERGI  209 (459)
T ss_pred             HHHHHHHHhhcCCCchhHHHHHHH-HHhhhhHHHHHHHHHHHHHhhh
Confidence            666665544332223334543332 3345566666666666665553

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

Probab=99.00  E-value=2.9e-08  Score=79.83  Aligned_cols=226  Identities=13%  Similarity=0.161  Sum_probs=151.9

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCC-ChHhHH
Q 044084           21 DSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILE-DPSVYA   99 (343)
Q Consensus        21 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~   99 (343)
                      +......+.+++...|+++.++.   ++.... .|.   ......+...+...++-+.++.-+++.......+ +.....
T Consensus        34 ~~e~~~~~~Rs~iAlg~~~~vl~---ei~~~~-~~~---l~av~~la~y~~~~~~~e~~l~~l~~~~~~~~~~~~~~~~~  106 (290)
T PF04733_consen   34 KLERDFYQYRSYIALGQYDSVLS---EIKKSS-SPE---LQAVRLLAEYLSSPSDKESALEELKELLADQAGESNEIVQL  106 (290)
T ss_dssp             HHHHHHHHHHHHHHTT-HHHHHH---HS-TTS-SCC---CHHHHHHHHHHCTSTTHHCHHHHHHHCCCTS---CHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCChhHHHH---HhccCC-Chh---HHHHHHHHHHHhCccchHHHHHHHHHHHHhccccccHHHHH
Confidence            34456677788899998776543   333322 222   4555555555544455666666665554443332 333333


Q ss_pred             HHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHh---
Q 044084          100 SLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFS---  176 (343)
Q Consensus       100 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~---  176 (343)
                      .....+...|++++|++++...      .+.......+..|.+.++++.|.+.++.|.+.+  .| .+...+..++.   
T Consensus       107 ~~A~i~~~~~~~~~AL~~l~~~------~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~--eD-~~l~qLa~awv~l~  177 (290)
T PF04733_consen  107 LAATILFHEGDYEEALKLLHKG------GSLELLALAVQILLKMNRPDLAEKELKNMQQID--ED-SILTQLAEAWVNLA  177 (290)
T ss_dssp             HHHHHHCCCCHHHHHHCCCTTT------TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCS--CC-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHcc------CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--Cc-HHHHHHHHHHHHHH
Confidence            3335677889999999988642      367788888999999999999999999998764  23 33444444433   


Q ss_pred             -cCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCCh-HHH
Q 044084          177 -KRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRI-RDA  254 (343)
Q Consensus       177 -~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~a  254 (343)
                       ..+.+.+|..+|+++.+. ..++..+.+.+..++...|++++|+.++.+..+.+ +-++.+...++.+....|+. +.+
T Consensus       178 ~g~e~~~~A~y~f~El~~~-~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~-~~~~d~LaNliv~~~~~gk~~~~~  255 (290)
T PF04733_consen  178 TGGEKYQDAFYIFEELSDK-FGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKD-PNDPDTLANLIVCSLHLGKPTEAA  255 (290)
T ss_dssp             HTTTCCCHHHHHHHHHHCC-S--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC--CCHHHHHHHHHHHHHHTT-TCHHH
T ss_pred             hCchhHHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhc-cCCHHHHHHHHHHHHHhCCChhHH
Confidence             345789999999998765 56788889999999999999999999999987665 44667777788888888887 667


Q ss_pred             HHHHHHHhhC
Q 044084          255 MRLVAKMKPK  264 (343)
Q Consensus       255 ~~~~~~m~~~  264 (343)
                      .+.+.++...
T Consensus       256 ~~~l~qL~~~  265 (290)
T PF04733_consen  256 ERYLSQLKQS  265 (290)
T ss_dssp             HHHHHHCHHH
T ss_pred             HHHHHHHHHh
Confidence            7888888864

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.

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=99.00  E-value=2.5e-06  Score=71.47  Aligned_cols=322  Identities=13%  Similarity=0.078  Sum_probs=209.3

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      |++.|+..|.+.+...+ ++...|..-..+|+..|++++|++=-.+..+.++..    ...|+....++.-.|++++|+.
T Consensus        17 d~~~ai~~~t~ai~l~p-~nhvlySnrsaa~a~~~~~~~al~da~k~~~l~p~w----~kgy~r~Gaa~~~lg~~~eA~~   91 (539)
T KOG0548|consen   17 DFETAIRLFTEAIMLSP-TNHVLYSNRSAAYASLGSYEKALKDATKTRRLNPDW----AKGYSRKGAALFGLGDYEEAIL   91 (539)
T ss_pred             cHHHHHHHHHHHHccCC-CccchhcchHHHHHHHhhHHHHHHHHHHHHhcCCch----hhHHHHhHHHHHhcccHHHHHH
Confidence            67899999999998765 488889999999999999999998776666655444    3689999999999999999999


Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHhcc---c---------------------------------------------CHHH
Q 044084           82 FFRDMKEKGILEDPSVYASLICSFASI---A---------------------------------------------EVKV  113 (343)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~l~~~~~~~---~---------------------------------------------~~~~  113 (343)
                      .|.+-++... .+...++-+..++...   +                                             +.+.
T Consensus        92 ay~~GL~~d~-~n~~L~~gl~~a~~~~~~~~~~~~~p~~~~~l~~~p~t~~~~~~~~~~~~l~~~~~~p~~l~~~l~d~r  170 (539)
T KOG0548|consen   92 AYSEGLEKDP-SNKQLKTGLAQAYLEDYAADQLFTKPYFHEKLANLPLTNYSLSDPAYVKILEIIQKNPTSLKLYLNDPR  170 (539)
T ss_pred             HHHHHhhcCC-chHHHHHhHHHhhhHHHHhhhhccCcHHHHHhhcChhhhhhhccHHHHHHHHHhhcCcHhhhcccccHH
Confidence            9988776531 2333444444433111   0                                             0000


Q ss_pred             HHHHHHHHHH--------cC-------CCC------------C----------HHHHHHHHHHHHhcCcHhHHHHHHHHH
Q 044084          114 AEELFKEAEE--------KG-------MLR------------D----------LEVFLKLVLMYIEEGMVEKTLEVVESM  156 (343)
Q Consensus       114 a~~~~~~~~~--------~~-------~~~------------~----------~~~~~~l~~~~~~~~~~~~a~~~~~~~  156 (343)
                      ..+..-.+..        .+       ..|            |          ..-...+.+...+..+++.|++.+...
T Consensus       171 ~m~a~~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~d~~ee~~~k~~a~~ek~lgnaaykkk~f~~a~q~y~~a  250 (539)
T KOG0548|consen  171 LMKADGQLKGVDELLFYASGIEILASMAEPCKQEHNGFPIIEDNTEERRVKEKAHKEKELGNAAYKKKDFETAIQHYAKA  250 (539)
T ss_pred             HHHHHHHHhcCccccccccccccCCCCCCcccccCCCCCccchhHHHHHHHHhhhHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence            0000000000        00       001            0          011334556666666777777777777


Q ss_pred             HhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhH-------HHHHHHHHccCChhHHHHHHHHHHHc
Q 044084          157 KNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTY-------ASIINAYCRIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       157 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~-------~~ll~~~~~~~~~~~a~~~~~~~~~~  229 (343)
                      ....  -+..-++....+|...|.+..+...-....+.|. -...-|       ..+..+|.+.++++.+...|.+....
T Consensus       251 ~el~--~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gr-e~rad~klIak~~~r~g~a~~k~~~~~~ai~~~~kaLte  327 (539)
T KOG0548|consen  251 LELA--TDITYLNNIAAVYLERGKYAECIELCEKAVEVGR-ELRADYKLIAKALARLGNAYTKREDYEGAIKYYQKALTE  327 (539)
T ss_pred             HhHh--hhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhH-HHHHHHHHHHHHHHHhhhhhhhHHhHHHHHHHHHHHhhh
Confidence            6655  3444456666777777777766666555555442 111122       22344666678888888888876654


Q ss_pred             CCCcChhhH-------------------------HHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhccc
Q 044084          230 GFDKCVVAY-------------------------SSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAK  284 (343)
Q Consensus       230 ~~~~~~~~~-------------------------~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~  284 (343)
                      ...|+...-                         ..=...+.+.|++..|...|.+++... +-|...|..-.-+|.+.|
T Consensus       328 ~Rt~~~ls~lk~~Ek~~k~~e~~a~~~pe~A~e~r~kGne~Fk~gdy~~Av~~YteAIkr~-P~Da~lYsNRAac~~kL~  406 (539)
T KOG0548|consen  328 HRTPDLLSKLKEAEKALKEAERKAYINPEKAEEEREKGNEAFKKGDYPEAVKHYTEAIKRD-PEDARLYSNRAACYLKLG  406 (539)
T ss_pred             hcCHHHHHHHHHHHHHHHHHHHHHhhChhHHHHHHHHHHHHHhccCHHHHHHHHHHHHhcC-CchhHHHHHHHHHHHHHh
Confidence            433332111                         111345678899999999999999885 447788999999999999


Q ss_pred             ChhHHHh---------------HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHhccc
Q 044084          285 NLRQLEK---------------YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLS  338 (343)
Q Consensus       285 ~~~~a~~---------------~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~g  338 (343)
                      .+..|..               |..-..++....+++.|.+.|++.++.+  |+..-   +++.|.+|.
T Consensus       407 ~~~~aL~Da~~~ieL~p~~~kgy~RKg~al~~mk~ydkAleay~eale~d--p~~~e---~~~~~~rc~  470 (539)
T KOG0548|consen  407 EYPEALKDAKKCIELDPNFIKAYLRKGAALRAMKEYDKALEAYQEALELD--PSNAE---AIDGYRRCV  470 (539)
T ss_pred             hHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--chhHH---HHHHHHHHH
Confidence            9998877               5555666666778899999999888754  55554   445555544

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

Probab=98.92  E-value=8.1e-07  Score=74.90  Aligned_cols=250  Identities=10%  Similarity=0.031  Sum_probs=161.9

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcc
Q 044084           29 MEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASI  108 (343)
Q Consensus        29 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  108 (343)
                      ...+.+.|++.+|.-.|+...+++    |....+|..|.......++-..|+..+++..+.... |....-.|.-.|...
T Consensus       292 G~~lm~nG~L~~A~LafEAAVkqd----P~haeAW~~LG~~qaENE~E~~ai~AL~rcl~LdP~-NleaLmaLAVSytNe  366 (579)
T KOG1125|consen  292 GCNLMKNGDLSEAALAFEAAVKQD----PQHAEAWQKLGITQAENENEQNAISALRRCLELDPT-NLEALMALAVSYTNE  366 (579)
T ss_pred             HHHHHhcCCchHHHHHHHHHHhhC----hHHHHHHHHhhhHhhhccchHHHHHHHHHHHhcCCc-cHHHHHHHHHHHhhh
Confidence            345667788888888888776665    445688888888888888888888888888776422 566666777777777


Q ss_pred             cCHHHHHHHHHHHHHcCCCC--------CHHHHHHHHHHHHhcCcHhHHHHHHHHHH-hcCCCCchhhHHHHHHHHhcCC
Q 044084          109 AEVKVAEELFKEAEEKGMLR--------DLEVFLKLVLMYIEEGMVEKTLEVVESMK-NAELNISDCISCVIVNGFSKRR  179 (343)
Q Consensus       109 ~~~~~a~~~~~~~~~~~~~~--------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~  179 (343)
                      |.-..|...++.-+...++-        +...-..  ..+.....+....++|-.+. +.+..+|......|--.|...|
T Consensus       367 g~q~~Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~~--~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~  444 (579)
T KOG1125|consen  367 GLQNQALKMLDKWIRNKPKYVHLVSAGENEDFENT--KSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSG  444 (579)
T ss_pred             hhHHHHHHHHHHHHHhCccchhccccCccccccCC--cCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcch
Confidence            87777877777765533210        0000000  12222233444455555543 3443466667777777777888


Q ss_pred             cHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcC-hhhHHHHHHHHHccCChHHHHHHH
Q 044084          180 AYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKC-VVAYSSMVAMYGKTGRIRDAMRLV  258 (343)
Q Consensus       180 ~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~  258 (343)
                      ++++|.+-|+...... +-|...||.|...++...+.++|...|.+.++..  |+ +.+...|.-+|...|.+++|...|
T Consensus       445 efdraiDcf~~AL~v~-Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqLq--P~yVR~RyNlgIS~mNlG~ykEA~~hl  521 (579)
T KOG1125|consen  445 EFDRAVDCFEAALQVK-PNDYLLWNRLGATLANGNRSEEAISAYNRALQLQ--PGYVRVRYNLGISCMNLGAYKEAVKHL  521 (579)
T ss_pred             HHHHHHHHHHHHHhcC-CchHHHHHHhhHHhcCCcccHHHHHHHHHHHhcC--CCeeeeehhhhhhhhhhhhHHHHHHHH
Confidence            8888888888877763 3456678888888888888888888888887753  43 456666777778888888887777


Q ss_pred             HHHhhC---------CCCchHHHHHHHHHHHhcccChhH
Q 044084          259 AKMKPK---------GCEPNVWIYNSLMDMHGRAKNLRQ  288 (343)
Q Consensus       259 ~~m~~~---------~~~p~~~~~~~l~~~~~~~~~~~~  288 (343)
                      -..+..         +..++...|..|=.++.-.++.+.
T Consensus       522 L~AL~mq~ks~~~~~~~~~se~iw~tLR~als~~~~~D~  560 (579)
T KOG1125|consen  522 LEALSMQRKSRNHNKAPMASENIWQTLRLALSAMNRSDL  560 (579)
T ss_pred             HHHHHhhhcccccccCCcchHHHHHHHHHHHHHcCCchH
Confidence            655421         122344556555555555555553

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.92  E-value=1.5e-05  Score=76.02  Aligned_cols=294  Identities=10%  Similarity=-0.018  Sum_probs=170.9

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCC----CCc-hHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCCh----H
Q 044084           26 CQIMEAFYKIGDSEKVAALFLECESRKLDL----TPS-STHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDP----S   96 (343)
Q Consensus        26 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~----~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~   96 (343)
                      ......+...|+++++...+......-...    ++. .......+...+...|++++|...+++....-...+.    .
T Consensus       413 ~~~a~~~~~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  492 (903)
T PRK04841        413 LLQAWLAQSQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQVAINDGDPEEAERLAELALAELPLTWYYSRIV  492 (903)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCccHHHHHH
Confidence            344455567788888888887765431110    100 1122223344556788899998888887653111121    2


Q ss_pred             hHHHHHHHHhcccCHHHHHHHHHHHHHcCCC---C--CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhc----CCC--C-c
Q 044084           97 VYASLICSFASIAEVKVAEELFKEAEEKGML---R--DLEVFLKLVLMYIEEGMVEKTLEVVESMKNA----ELN--I-S  164 (343)
Q Consensus        97 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~--~-~  164 (343)
                      ..+.+...+...|+++.|...+.+.......   +  ...+...+...+...|+++.|...+++....    +..  + .
T Consensus       493 a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~  572 (903)
T PRK04841        493 ATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMH  572 (903)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHH
Confidence            3344555667788898888888777642111   1  1234556667778889999988888775432    211  1 1


Q ss_pred             hhhHHHHHHHHhcCCcHHHHHHHHHHHHHc--CCCC--CHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCc-ChhhH-
Q 044084          165 DCISCVIVNGFSKRRAYWAAVKVYEQLISQ--GCIP--GQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDK-CVVAY-  238 (343)
Q Consensus       165 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~p--~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~-  238 (343)
                      ...+..+...+...|++++|...+++....  ...+  ....+..+...+...|++++|...+.......-.. ....+ 
T Consensus       573 ~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~  652 (903)
T PRK04841        573 EFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISLARGDLDNARRYLNRLENLLGNGRYHSDWI  652 (903)
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccHhHh
Confidence            223444555666778999988888876543  1112  12334445566777888888888887775431000 01111 


Q ss_pred             ----HHHHHHHHccCChHHHHHHHHHHhhCCCCch---HHHHHHHHHHHhcccChhHHHh--------------------
Q 044084          239 ----SSMVAMYGKTGRIRDAMRLVAKMKPKGCEPN---VWIYNSLMDMHGRAKNLRQLEK--------------------  291 (343)
Q Consensus       239 ----~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~---~~~~~~l~~~~~~~~~~~~a~~--------------------  291 (343)
                          ...+..+...|+.+.|..++...........   ...+..+..++...|+.++|..                    
T Consensus       653 ~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~l~~al~~~~~~g~~~~~a~  732 (903)
T PRK04841        653 ANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIARAQILLGQFDEAEIILEELNENARSLRLMSDLNR  732 (903)
T ss_pred             hHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCchHHHHH
Confidence                1122344557788888888766554211111   1113445556777777777655                    


Q ss_pred             -HHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 044084          292 -YTTVISAYNMAREFDMCVKFYNEFRMNG  319 (343)
Q Consensus       292 -~~~l~~~~~~~g~~~~a~~~~~~m~~~~  319 (343)
                       ...+..++.+.|+.++|...+.+..+..
T Consensus       733 ~~~~la~a~~~~G~~~~A~~~L~~Al~la  761 (903)
T PRK04841        733 NLILLNQLYWQQGRKSEAQRVLLEALKLA  761 (903)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence             3444566778888888888888876643

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.90  E-value=1.1e-06  Score=69.46  Aligned_cols=188  Identities=17%  Similarity=0.061  Sum_probs=110.8

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCCh--HhHH
Q 044084           22 SGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDP--SVYA   99 (343)
Q Consensus        22 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~   99 (343)
                      ...+..+...+.+.|++++|...|+++....... +....++..+..++...|++++|+..++++.+.......  .++.
T Consensus        33 ~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~-~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~  111 (235)
T TIGR03302        33 AEELYEEAKEALDSGDYTEAIKYFEALESRYPFS-PYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAYY  111 (235)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCc-hhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHHH
Confidence            3455666667777777777777777776544221 112245666777777777777777777777665321111  1233


Q ss_pred             HHHHHHhcc--------cCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHH
Q 044084          100 SLICSFASI--------AEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVI  171 (343)
Q Consensus       100 ~l~~~~~~~--------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  171 (343)
                      .+..++...        |+.+.|.+.++.+.+..+. +...+..+.....    ...      ...        .....+
T Consensus       112 ~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~a~~~~~~----~~~------~~~--------~~~~~~  172 (235)
T TIGR03302       112 LRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYPN-SEYAPDAKKRMDY----LRN------RLA--------GKELYV  172 (235)
T ss_pred             HHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHCCC-ChhHHHHHHHHHH----HHH------HHH--------HHHHHH
Confidence            333344333        5667777777777665432 2222221111100    000      000        011245


Q ss_pred             HHHHhcCCcHHHHHHHHHHHHHcCC--CCCHhhHHHHHHHHHccCChhHHHHHHHHHHHc
Q 044084          172 VNGFSKRRAYWAAVKVYEQLISQGC--IPGQVTYASIINAYCRIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       172 ~~~~~~~~~~~~a~~~~~~~~~~~~--~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  229 (343)
                      ...+...|++.+|...++...+...  +.....+..+..++...|++++|..+++.+...
T Consensus       173 a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       173 ARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             HHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            5667888999999999998887621  123467778888899999999999988887765

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).

>PF12854 PPR_1: PPR repeat

Probab=98.90  E-value=2.5e-09  Score=55.29  Aligned_cols=32  Identities=34%  Similarity=0.672  Sum_probs=16.2

Q ss_pred             CCCcChhhHHHHHHHHHccCChHHHHHHHHHH
Q 044084          230 GFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKM  261 (343)
Q Consensus       230 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m  261 (343)
                      |+.||..+|++||.+|++.|++++|.++|++|
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M   33 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEM   33 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence            34455555555555555555555555555444

>PF12854 PPR_1: PPR repeat

Probab=98.89  E-value=2.4e-09  Score=55.39  Aligned_cols=34  Identities=24%  Similarity=0.393  Sum_probs=29.0

Q ss_pred             CCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 044084           16 AGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECE   49 (343)
Q Consensus        16 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~   49 (343)
                      +|+.||..+|++||++|++.|++++|.++|++|+
T Consensus         1 ~G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    1 RGCEPDVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            4778888899999999999999999988888873

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

Probab=98.88  E-value=1.4e-06  Score=73.52  Aligned_cols=217  Identities=13%  Similarity=0.101  Sum_probs=146.7

Q ss_pred             HHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHh
Q 044084           68 DSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVE  147 (343)
Q Consensus        68 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  147 (343)
                      .-+.+.|++.+|.-.|+.....++. +...|..|.......++-..|+..+.+..+..+. +..+.-.|.-.|...|.-.
T Consensus       293 ~~lm~nG~L~~A~LafEAAVkqdP~-haeAW~~LG~~qaENE~E~~ai~AL~rcl~LdP~-NleaLmaLAVSytNeg~q~  370 (579)
T KOG1125|consen  293 CNLMKNGDLSEAALAFEAAVKQDPQ-HAEAWQKLGITQAENENEQNAISALRRCLELDPT-NLEALMALAVSYTNEGLQN  370 (579)
T ss_pred             HHHHhcCCchHHHHHHHHHHhhChH-HHHHHHHhhhHhhhccchHHHHHHHHHHHhcCCc-cHHHHHHHHHHHhhhhhHH
Confidence            3455777788888888877776433 5677888877777888888888888888876543 6777778888888888888


Q ss_pred             HHHHHHHHHHhcCCC--------CchhhHHHHHHHHhcCCcHHHHHHHHHHHHH-cCCCCCHhhHHHHHHHHHccCChhH
Q 044084          148 KTLEVVESMKNAELN--------ISDCISCVIVNGFSKRRAYWAAVKVYEQLIS-QGCIPGQVTYASIINAYCRIGLYSK  218 (343)
Q Consensus       148 ~a~~~~~~~~~~~~~--------~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-~~~~p~~~~~~~ll~~~~~~~~~~~  218 (343)
                      .|...++......++        ++...-..  ..+.....+....++|-++.. .+..+|......|--.|--.|++++
T Consensus       371 ~Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~~--~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdr  448 (579)
T KOG1125|consen  371 QALKMLDKWIRNKPKYVHLVSAGENEDFENT--KSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDR  448 (579)
T ss_pred             HHHHHHHHHHHhCccchhccccCccccccCC--cCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHH
Confidence            888888776443210        01110000  222333344455555555443 3434666666666666777788888


Q ss_pred             HHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchH-HHHHHHHHHHhcccChhHHHh
Q 044084          219 AEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNV-WIYNSLMDMHGRAKNLRQLEK  291 (343)
Q Consensus       219 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~~~~~l~~~~~~~~~~~~a~~  291 (343)
                      |..-|+..+... |-|..+||.|...++...+.++|+..|++.++.  +|+- .+...|.-+|...|.+++|..
T Consensus       449 aiDcf~~AL~v~-Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqL--qP~yVR~RyNlgIS~mNlG~ykEA~~  519 (579)
T KOG1125|consen  449 AVDCFEAALQVK-PNDYLLWNRLGATLANGNRSEEAISAYNRALQL--QPGYVRVRYNLGISCMNLGAYKEAVK  519 (579)
T ss_pred             HHHHHHHHHhcC-CchHHHHHHhhHHhcCCcccHHHHHHHHHHHhc--CCCeeeeehhhhhhhhhhhhHHHHHH
Confidence            888888888765 456778888888888888888888888888875  5553 345556667788888888776

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.87  E-value=1.2e-06  Score=69.34  Aligned_cols=186  Identities=13%  Similarity=0.016  Sum_probs=121.2

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCC-CC-hHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCH--HHHHH
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEKGIL-ED-PSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDL--EVFLK  135 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~-~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~  135 (343)
                      ...+..+...+...|+++.|...|+++...... |. ..++..+..++...|++++|...++++.+..+....  .++..
T Consensus        33 ~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~  112 (235)
T TIGR03302        33 AEELYEEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAYYL  112 (235)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHHHH
Confidence            567777888888888898888888888775321 11 135566777888888888888888888876543111  24555


Q ss_pred             HHHHHHhc--------CcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHH
Q 044084          136 LVLMYIEE--------GMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASII  207 (343)
Q Consensus       136 l~~~~~~~--------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll  207 (343)
                      +..++...        |++++|.+.|+.+....+. +...+..+.....    ..      ....        .....+.
T Consensus       113 ~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~a~~~~~~----~~------~~~~--------~~~~~~a  173 (235)
T TIGR03302       113 RGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYPN-SEYAPDAKKRMDY----LR------NRLA--------GKELYVA  173 (235)
T ss_pred             HHHHHHHhcccccCCHHHHHHHHHHHHHHHHHCCC-ChhHHHHHHHHHH----HH------HHHH--------HHHHHHH
Confidence            55666554        6677788888877765532 2222222211100    00      0000        0112455


Q ss_pred             HHHHccCChhHHHHHHHHHHHcCC--CcChhhHHHHHHHHHccCChHHHHHHHHHHhhC
Q 044084          208 NAYCRIGLYSKAEKVFIEMQQKGF--DKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       208 ~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                      ..+.+.|++++|...++...+...  +.....+..+..++...|++++|...++.+...
T Consensus       174 ~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       174 RFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             HHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            668888999999999999887631  223567888899999999999999988887754

Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).

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

Probab=98.84  E-value=7.4e-06  Score=76.13  Aligned_cols=246  Identities=11%  Similarity=0.053  Sum_probs=187.6

Q ss_pred             HHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhC-CCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHh
Q 044084           10 YEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESR-KLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKE   88 (343)
Q Consensus        10 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~   88 (343)
                      |+++.... |-+...|...|....+.++.++|.++++++... ++.-...-...|.++++.-...|.-+...++|++..+
T Consensus      1447 ferlvrss-PNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcq 1525 (1710)
T KOG1070|consen 1447 FERLVRSS-PNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQ 1525 (1710)
T ss_pred             HHHHHhcC-CCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHH
Confidence            44444432 235567999999999999999999999998654 2222222246788888888888888899999999987


Q ss_pred             cCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCC-chhh
Q 044084           89 KGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNI-SDCI  167 (343)
Q Consensus        89 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~  167 (343)
                      .. . ....|..|...|.+..++++|.++++.|.+.-- -...+|...+..+.+.++-+.|..++.+..+.-++- ....
T Consensus      1526 yc-d-~~~V~~~L~~iy~k~ek~~~A~ell~~m~KKF~-q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv~~ 1602 (1710)
T KOG1070|consen 1526 YC-D-AYTVHLKLLGIYEKSEKNDEADELLRLMLKKFG-QTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVEF 1602 (1710)
T ss_pred             hc-c-hHHHHHHHHHHHHHhhcchhHHHHHHHHHHHhc-chhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHHH
Confidence            53 1 234588899999999999999999999998533 478899999999999999999999999987653321 1223


Q ss_pred             HHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcC--hhhHHHHHHHH
Q 044084          168 SCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKC--VVAYSSMVAMY  245 (343)
Q Consensus       168 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~  245 (343)
                      ..-.+..-.+.|+.+++..+|+.....- +--...|+..+..=.+.|+.+.++.+|+++...++.|-  -..|...+..-
T Consensus      1603 IskfAqLEFk~GDaeRGRtlfEgll~ay-PKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~kkmKfffKkwLeyE 1681 (1710)
T KOG1070|consen 1603 ISKFAQLEFKYGDAERGRTLFEGLLSAY-PKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSIKKMKFFFKKWLEYE 1681 (1710)
T ss_pred             HHHHHHHHhhcCCchhhHHHHHHHHhhC-ccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCChhHhHHHHHHHHHHH
Confidence            4455666678999999999999998773 33557899999999999999999999999999887664  34566666666


Q ss_pred             HccCChHHHHHHHHH
Q 044084          246 GKTGRIRDAMRLVAK  260 (343)
Q Consensus       246 ~~~~~~~~a~~~~~~  260 (343)
                      -..|+-..+..+=.+
T Consensus      1682 k~~Gde~~vE~VKar 1696 (1710)
T KOG1070|consen 1682 KSHGDEKNVEYVKAR 1696 (1710)
T ss_pred             HhcCchhhHHHHHHH
Confidence            666765555444333

>PLN02789 farnesyltranstransferase

Probab=98.82  E-value=1.4e-05  Score=65.33  Aligned_cols=258  Identities=8%  Similarity=0.058  Sum_probs=174.3

Q ss_pred             HHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhccc-CHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 044084           61 HMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIA-EVKVAEELFKEAEEKGMLRDLEVFLKLVLM  139 (343)
Q Consensus        61 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  139 (343)
                      .++..+-..+...++.++|+.+.+++++.... +..+|+..-.++...| ++++++..++++.+..++ +..+|+.....
T Consensus        38 ~a~~~~ra~l~~~e~serAL~lt~~aI~lnP~-~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~npk-nyqaW~~R~~~  115 (320)
T PLN02789         38 EAMDYFRAVYASDERSPRALDLTADVIRLNPG-NYTVWHFRRLCLEALDADLEEELDFAEDVAEDNPK-NYQIWHHRRWL  115 (320)
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHHHHCch-hHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCCc-chHHhHHHHHH
Confidence            44555555566677899999999999886322 3445666656666666 579999999999987765 67788877766


Q ss_pred             HHhcCcH--hHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHcc---C
Q 044084          140 YIEEGMV--EKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRI---G  214 (343)
Q Consensus       140 ~~~~~~~--~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~---~  214 (343)
                      +.+.|+.  ++++.+++++.+.+. -+..+|+.....+...|+++++++.++++.+.+ +-+...|+.....+.+.   |
T Consensus       116 l~~l~~~~~~~el~~~~kal~~dp-kNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d-~~N~sAW~~R~~vl~~~~~l~  193 (320)
T PLN02789        116 AEKLGPDAANKELEFTRKILSLDA-KNYHAWSHRQWVLRTLGGWEDELEYCHQLLEED-VRNNSAWNQRYFVITRSPLLG  193 (320)
T ss_pred             HHHcCchhhHHHHHHHHHHHHhCc-ccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHC-CCchhHHHHHHHHHHhccccc
Confidence            7777763  678999999988876 577889988888889999999999999999886 34556666655555443   2


Q ss_pred             Ch----hHHHHHHHHHHHcCCCcChhhHHHHHHHHHcc----CChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccCh
Q 044084          215 LY----SKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKT----GRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNL  286 (343)
Q Consensus       215 ~~----~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~  286 (343)
                      ..    ++............ +-|...|+-+...+...    ++..+|...+.+..+.+ ..+......|++.|+.....
T Consensus       194 ~~~~~~e~el~y~~~aI~~~-P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~-~~s~~al~~l~d~~~~~~~~  271 (320)
T PLN02789        194 GLEAMRDSELKYTIDAILAN-PRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKD-SNHVFALSDLLDLLCEGLQP  271 (320)
T ss_pred             cccccHHHHHHHHHHHHHhC-CCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhccc-CCcHHHHHHHHHHHHhhhcc
Confidence            22    45666666666654 55778888888888773    34566888888877653 23566777888887753211


Q ss_pred             hHHHhHHHHHHHH-HhcCCHHHHHHHHHHHHhCCCCccHHHHH
Q 044084          287 RQLEKYTTVISAY-NMAREFDMCVKFYNEFRMNGGVIDRAMAG  328 (343)
Q Consensus       287 ~~a~~~~~l~~~~-~~~g~~~~a~~~~~~m~~~~~~p~~~~~~  328 (343)
                      .  ......+.+. ......++|.++++.+.  ...|=..-|.
T Consensus       272 ~--~~~~~~~~~~~~~~~~~~~a~~~~~~l~--~~d~ir~~yw  310 (320)
T PLN02789        272 T--AEFRDTVDTLAEELSDSTLAQAVCSELE--VADPMRRNYW  310 (320)
T ss_pred             c--hhhhhhhhccccccccHHHHHHHHHHHH--hhCcHHHHHH
Confidence            0  0011111111 11224577888888883  3455444443

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.81  E-value=2.2e-06  Score=66.64  Aligned_cols=248  Identities=16%  Similarity=0.161  Sum_probs=148.4

Q ss_pred             HHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHH-HHHHHHH
Q 044084           63 YKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFL-KLVLMYI  141 (343)
Q Consensus        63 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~l~~~~~  141 (343)
                      +.+.+..+.+..++..|++++..-.+...+ +....+.|..+|....++..|-..++++....  |...-|. --...+.
T Consensus        13 ftaviy~lI~d~ry~DaI~~l~s~~Er~p~-~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql~--P~~~qYrlY~AQSLY   89 (459)
T KOG4340|consen   13 FTAVVYRLIRDARYADAIQLLGSELERSPR-SRAGLSLLGYCYYRLQEFALAAECYEQLGQLH--PELEQYRLYQAQSLY   89 (459)
T ss_pred             hHHHHHHHHHHhhHHHHHHHHHHHHhcCcc-chHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC--hHHHHHHHHHHHHHH
Confidence            666777778889999999999988776422 67778889999999999999999999998765  3333332 2245666


Q ss_pred             hcCcHhHHHHHHHHHHhcC-------------------C---------CC---chhhHHHHHHHHhcCCcHHHHHHHHHH
Q 044084          142 EEGMVEKTLEVVESMKNAE-------------------L---------NI---SDCISCVIVNGFSKRRAYWAAVKVYEQ  190 (343)
Q Consensus       142 ~~~~~~~a~~~~~~~~~~~-------------------~---------~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~  190 (343)
                      +.+.+.+|+++...|....                   +         .|   +..+.+.......+.|+++.|.+-|+.
T Consensus        90 ~A~i~ADALrV~~~~~D~~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en~Ad~~in~gCllykegqyEaAvqkFqa  169 (459)
T KOG4340|consen   90 KACIYADALRVAFLLLDNPALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSENEADGQINLGCLLYKEGQYEAAVQKFQA  169 (459)
T ss_pred             HhcccHHHHHHHHHhcCCHHHHHHHHHHHHHHhcccccCcchHHHHHhccCCCccchhccchheeeccccHHHHHHHHHH
Confidence            7788888888877765420                   0         01   111111222223456777777777777


Q ss_pred             HHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCC-------------cCh---------------hhHHHHH
Q 044084          191 LISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFD-------------KCV---------------VAYSSMV  242 (343)
Q Consensus       191 ~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-------------~~~---------------~~~~~l~  242 (343)
                      ..+-+---....|+..+..| +.|+.+.|.+...++.++|++             ||+               ..+|.-.
T Consensus       170 AlqvsGyqpllAYniALaHy-~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsvgNt~~lh~Sal~eAfNLKa  248 (459)
T KOG4340|consen  170 ALQVSGYQPLLAYNLALAHY-SSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSVGNTLVLHQSALVEAFNLKA  248 (459)
T ss_pred             HHhhcCCCchhHHHHHHHHH-hhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcccchHHHHHHHHHHHhhhhh
Confidence            66653333345566555443 456777777777777776543             111               1222223


Q ss_pred             HHHHccCChHHHHHHHHHHhhC-CCCchHHHHHHHHHHHhcccChhHHHh--------------HHHHHHHHHhcCCHHH
Q 044084          243 AMYGKTGRIRDAMRLVAKMKPK-GCEPNVWIYNSLMDMHGRAKNLRQLEK--------------YTTVISAYNMAREFDM  307 (343)
Q Consensus       243 ~~~~~~~~~~~a~~~~~~m~~~-~~~p~~~~~~~l~~~~~~~~~~~~a~~--------------~~~l~~~~~~~g~~~~  307 (343)
                      ..+.+.|+++.|.+.+..|... ....|++|...+.-.-....-.+...+              |..++-.||+..-++.
T Consensus       249 AIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n~~~~p~~g~~KLqFLL~~nPfP~ETFANlLllyCKNeyf~l  328 (459)
T KOG4340|consen  249 AIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMNMDARPTEGFEKLQFLLQQNPFPPETFANLLLLYCKNEYFDL  328 (459)
T ss_pred             hhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhcccCCccccHHHHHHHHhcCCCChHHHHHHHHHHhhhHHHhH
Confidence            3445667777777777776533 234456665544322111111111111              6666666777766666


Q ss_pred             HHHHHHH
Q 044084          308 CVKFYNE  314 (343)
Q Consensus       308 a~~~~~~  314 (343)
                      |-.++-+
T Consensus       329 AADvLAE  335 (459)
T KOG4340|consen  329 AADVLAE  335 (459)
T ss_pred             HHHHHhh
Confidence            6666654

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

Probab=98.80  E-value=2.1e-06  Score=65.34  Aligned_cols=120  Identities=5%  Similarity=-0.020  Sum_probs=68.5

Q ss_pred             ccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHH-hcCCc--HHHH
Q 044084          108 IAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGF-SKRRA--YWAA  184 (343)
Q Consensus       108 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~--~~~a  184 (343)
                      .++.+++...++...+..+. +...|..+...|...|++++|...|++..+..+ .+...+..+..++ ...|+  .++|
T Consensus        52 ~~~~~~~i~~l~~~L~~~P~-~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~P-~~~~~~~~lA~aL~~~~g~~~~~~A  129 (198)
T PRK10370         52 QQTPEAQLQALQDKIRANPQ-NSEQWALLGEYYLWRNDYDNALLAYRQALQLRG-ENAELYAALATVLYYQAGQHMTPQT  129 (198)
T ss_pred             chhHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhcCCCCcHHH
Confidence            44555555555555555432 566666666666666666666666666665554 3444555555542 44444  3666


Q ss_pred             HHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcC
Q 044084          185 VKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKG  230 (343)
Q Consensus       185 ~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  230 (343)
                      .+++++..+.. +-+...+..+...+.+.|++++|...|+.+.+..
T Consensus       130 ~~~l~~al~~d-P~~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l~  174 (198)
T PRK10370        130 REMIDKALALD-ANEVTALMLLASDAFMQADYAQAIELWQKVLDLN  174 (198)
T ss_pred             HHHHHHHHHhC-CCChhHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            66666666553 2244455555555666666666666666666553

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

Probab=98.80  E-value=9.2e-07  Score=76.63  Aligned_cols=216  Identities=14%  Similarity=0.097  Sum_probs=158.8

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHH
Q 044084           24 CYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLIC  103 (343)
Q Consensus        24 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  103 (343)
                      .-..+...+...|-...|..+|++.            ..|..+|.+|...|+..+|..+..+..+.  +||+..|..+.+
T Consensus       400 ~q~~laell~slGitksAl~I~Erl------------emw~~vi~CY~~lg~~~kaeei~~q~lek--~~d~~lyc~LGD  465 (777)
T KOG1128|consen  400 LQRLLAELLLSLGITKSALVIFERL------------EMWDPVILCYLLLGQHGKAEEINRQELEK--DPDPRLYCLLGD  465 (777)
T ss_pred             HHHHHHHHHHHcchHHHHHHHHHhH------------HHHHHHHHHHHHhcccchHHHHHHHHhcC--CCcchhHHHhhh
Confidence            3455677788889999999998774            56888889999999999999888887773  678888888877


Q ss_pred             HHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHH
Q 044084          104 SFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWA  183 (343)
Q Consensus       104 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  183 (343)
                      .....--++.|.++.+.....       .-..+.....+.++++++.+.|+.-...++ ....+|-.+-.+..+.+++..
T Consensus       466 v~~d~s~yEkawElsn~~sar-------A~r~~~~~~~~~~~fs~~~~hle~sl~~np-lq~~~wf~~G~~ALqlek~q~  537 (777)
T KOG1128|consen  466 VLHDPSLYEKAWELSNYISAR-------AQRSLALLILSNKDFSEADKHLERSLEINP-LQLGTWFGLGCAALQLEKEQA  537 (777)
T ss_pred             hccChHHHHHHHHHhhhhhHH-------HHHhhccccccchhHHHHHHHHHHHhhcCc-cchhHHHhccHHHHHHhhhHH
Confidence            766665667777776654322       222233333446788888888887665554 445567777777778888888


Q ss_pred             HHHHHHHHHHcCCCCC-HhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHh
Q 044084          184 AVKVYEQLISQGCIPG-QVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMK  262 (343)
Q Consensus       184 a~~~~~~~~~~~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~  262 (343)
                      |.+.|..-...  .|| ...||.+-.+|.+.++-.+|...+.+..+.+ .-+...|...+....+.|.+++|.+.+.++.
T Consensus       538 av~aF~rcvtL--~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn-~~~w~iWENymlvsvdvge~eda~~A~~rll  614 (777)
T KOG1128|consen  538 AVKAFHRCVTL--EPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCN-YQHWQIWENYMLVSVDVGEFEDAIKAYHRLL  614 (777)
T ss_pred             HHHHHHHHhhc--CCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcC-CCCCeeeechhhhhhhcccHHHHHHHHHHHH
Confidence            88888887765  454 4678888888888888888888888888776 4456677777777788888888888888776


Q ss_pred             hC
Q 044084          263 PK  264 (343)
Q Consensus       263 ~~  264 (343)
                      +.
T Consensus       615 ~~  616 (777)
T KOG1128|consen  615 DL  616 (777)
T ss_pred             Hh
Confidence            53

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

Probab=98.80  E-value=7.8e-06  Score=74.69  Aligned_cols=239  Identities=8%  Similarity=0.020  Sum_probs=142.3

Q ss_pred             CchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChH-hHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHH
Q 044084           57 PSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPS-VYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLK  135 (343)
Q Consensus        57 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  135 (343)
                      |.+...|..|+..+...+++++|.++.+...+.  .|+.. .|-.+...+.+.++.+.+..+                 .
T Consensus        28 p~n~~a~~~Li~~~~~~~~~deai~i~~~~l~~--~P~~i~~yy~~G~l~~q~~~~~~~~lv-----------------~   88 (906)
T PRK14720         28 LSKFKELDDLIDAYKSENLTDEAKDICEEHLKE--HKKSISALYISGILSLSRRPLNDSNLL-----------------N   88 (906)
T ss_pred             cchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh--CCcceehHHHHHHHHHhhcchhhhhhh-----------------h
Confidence            344677788888888888888888888766654  34433 233333344444443333222                 3


Q ss_pred             HHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCC
Q 044084          136 LVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGL  215 (343)
Q Consensus       136 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~  215 (343)
                      ++.......++..+..+...+...+  -+...+-.+..+|-+.|+.+++..+|+++.+.. +-|..+.|.+...|... +
T Consensus        89 ~l~~~~~~~~~~~ve~~~~~i~~~~--~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-d  164 (906)
T PRK14720         89 LIDSFSQNLKWAIVEHICDKILLYG--ENKLALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-D  164 (906)
T ss_pred             hhhhcccccchhHHHHHHHHHHhhh--hhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-h
Confidence            3334444444433344444444432  233356667777777788888888888877775 45566777777777777 7


Q ss_pred             hhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh-HHH
Q 044084          216 YSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK-YTT  294 (343)
Q Consensus       216 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~-~~~  294 (343)
                      +++|.+++......               +...+++..+.++|.++..... -|...+..+.+.....-....+.. +..
T Consensus       165 L~KA~~m~~KAV~~---------------~i~~kq~~~~~e~W~k~~~~~~-~d~d~f~~i~~ki~~~~~~~~~~~~~~~  228 (906)
T PRK14720        165 KEKAITYLKKAIYR---------------FIKKKQYVGIEEIWSKLVHYNS-DDFDFFLRIERKVLGHREFTRLVGLLED  228 (906)
T ss_pred             HHHHHHHHHHHHHH---------------HHhhhcchHHHHHHHHHHhcCc-ccchHHHHHHHHHHhhhccchhHHHHHH
Confidence            77777777666553               4555677777777777776521 133333444443333211222222 666


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHh
Q 044084          295 VISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFS  335 (343)
Q Consensus       295 l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~  335 (343)
                      +...|...+++++++.+++...+...+ |.....-++.+|.
T Consensus       229 l~~~y~~~~~~~~~i~iLK~iL~~~~~-n~~a~~~l~~~y~  268 (906)
T PRK14720        229 LYEPYKALEDWDEVIYILKKILEHDNK-NNKAREELIRFYK  268 (906)
T ss_pred             HHHHHhhhhhhhHHHHHHHHHHhcCCc-chhhHHHHHHHHH
Confidence            667777888888899999888876543 4444555666665

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

Probab=98.79  E-value=4.2e-06  Score=63.71  Aligned_cols=119  Identities=12%  Similarity=0.136  Sum_probs=71.3

Q ss_pred             cCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH-HHhcCc--HhHH
Q 044084           73 SGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLM-YIEEGM--VEKT  149 (343)
Q Consensus        73 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~--~~~a  149 (343)
                      .++.+++...++...+.+ +.|...|..+...|...|+++.|...+++..+..+. +...+..+..+ +...|+  .++|
T Consensus        52 ~~~~~~~i~~l~~~L~~~-P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~P~-~~~~~~~lA~aL~~~~g~~~~~~A  129 (198)
T PRK10370         52 QQTPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWRNDYDNALLAYRQALQLRGE-NAELYAALATVLYYQAGQHMTPQT  129 (198)
T ss_pred             chhHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhcCCCCcHHH
Confidence            445555665565555543 235556666666666666666666666666665543 55566666554 345555  3666


Q ss_pred             HHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHc
Q 044084          150 LEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       150 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  194 (343)
                      .+++++..+.++ -+..++..+...+...|++++|...|+++.+.
T Consensus       130 ~~~l~~al~~dP-~~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l  173 (198)
T PRK10370        130 REMIDKALALDA-NEVTALMLLASDAFMQADYAQAIELWQKVLDL  173 (198)
T ss_pred             HHHHHHHHHhCC-CChhHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            666666666554 34455666666666666666666666666655

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=98.79  E-value=1.6e-05  Score=69.69  Aligned_cols=82  Identities=12%  Similarity=0.035  Sum_probs=65.7

Q ss_pred             hhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHH
Q 044084            4 QSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFF   83 (343)
Q Consensus         4 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~   83 (343)
                      .++++.+++..+.+. -|....-.+.--|+..++++.|.+...+..+.+...+   ...|..|.-.+...+++.+|+.+.
T Consensus       461 ~kslqale~av~~d~-~dp~~if~lalq~A~~R~l~sAl~~~~eaL~l~~~~~---~~~whLLALvlSa~kr~~~Al~vv  536 (799)
T KOG4162|consen  461 KKSLQALEEAVQFDP-TDPLVIFYLALQYAEQRQLTSALDYAREALALNRGDS---AKAWHLLALVLSAQKRLKEALDVV  536 (799)
T ss_pred             HHHHHHHHHHHhcCC-CCchHHHHHHHHHHHHHhHHHHHHHHHHHHHhcCCcc---HHHHHHHHHHHhhhhhhHHHHHHH
Confidence            578899999988764 2444444455568889999999999999988765555   688999999999999999999999


Q ss_pred             HHHHhc
Q 044084           84 RDMKEK   89 (343)
Q Consensus        84 ~~~~~~   89 (343)
                      +.....
T Consensus       537 d~al~E  542 (799)
T KOG4162|consen  537 DAALEE  542 (799)
T ss_pred             HHHHHH
Confidence            887654

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.79  E-value=3.4e-05  Score=73.69  Aligned_cols=309  Identities=10%  Similarity=-0.004  Sum_probs=187.0

Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCC------CCCh--HhHHHHHH
Q 044084           32 FYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGI------LEDP--SVYASLIC  103 (343)
Q Consensus        32 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~------~~~~--~~~~~l~~  103 (343)
                      ....|+++.+...++.+.......++   .........+...|+++++..++......--      .+..  .....+..
T Consensus       384 l~~~g~~~~l~~~l~~lp~~~~~~~~---~l~~~~a~~~~~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~  460 (903)
T PRK04841        384 LFNQGELSLLEECLNALPWEVLLENP---RLVLLQAWLAQSQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQ  460 (903)
T ss_pred             HHhcCChHHHHHHHHhCCHHHHhcCc---chHHHHHHHHHHCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHH
Confidence            33445555555555544221111111   1223344555677899999998887754310      1111  11222334


Q ss_pred             HHhcccCHHHHHHHHHHHHHcCCCCC----HHHHHHHHHHHHhcCcHhHHHHHHHHHHhc----CCC-CchhhHHHHHHH
Q 044084          104 SFASIAEVKVAEELFKEAEEKGMLRD----LEVFLKLVLMYIEEGMVEKTLEVVESMKNA----ELN-ISDCISCVIVNG  174 (343)
Q Consensus       104 ~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~-~~~~~~~~l~~~  174 (343)
                      .+...|+++.|...+++..+.-...+    ....+.+...+...|++++|...+++....    +.. ....++..+...
T Consensus       461 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~  540 (903)
T PRK04841        461 VAINDGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEI  540 (903)
T ss_pred             HHHhCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHH
Confidence            45678999999999998876322222    234556677788899999999999887642    110 112244556677


Q ss_pred             HhcCCcHHHHHHHHHHHHHc----CCC--C-CHhhHHHHHHHHHccCChhHHHHHHHHHHHcC--CCc--ChhhHHHHHH
Q 044084          175 FSKRRAYWAAVKVYEQLISQ----GCI--P-GQVTYASIINAYCRIGLYSKAEKVFIEMQQKG--FDK--CVVAYSSMVA  243 (343)
Q Consensus       175 ~~~~~~~~~a~~~~~~~~~~----~~~--p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~--~~~--~~~~~~~l~~  243 (343)
                      +...|+++.|...+++....    +..  + ....+..+...+...|++++|...+.......  ..+  ....+..+..
T Consensus       541 ~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~  620 (903)
T PRK04841        541 LFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAK  620 (903)
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHH
Confidence            88899999999998886653    211  1 12234445566777899999999988875531  112  2344555667


Q ss_pred             HHHccCChHHHHHHHHHHhhC----CCCchHHHH--HHHHHHHhcccChhHHHh-------------------HHHHHHH
Q 044084          244 MYGKTGRIRDAMRLVAKMKPK----GCEPNVWIY--NSLMDMHGRAKNLRQLEK-------------------YTTVISA  298 (343)
Q Consensus       244 ~~~~~~~~~~a~~~~~~m~~~----~~~p~~~~~--~~l~~~~~~~~~~~~a~~-------------------~~~l~~~  298 (343)
                      .+...|+.+.|.+.+.+....    +..+.....  ...+..+...|+.+.|..                   +..+..+
T Consensus       621 ~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~  700 (903)
T PRK04841        621 ISLARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIARA  700 (903)
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHHH
Confidence            888899999999998887542    111111010  111233344666666554                   2356677


Q ss_pred             HHhcCCHHHHHHHHHHHHhC----CCCccH-HHHHHHHHHHhcccccccC
Q 044084          299 YNMAREFDMCVKFYNEFRMN----GGVIDR-AMAGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       299 ~~~~g~~~~a~~~~~~m~~~----~~~p~~-~~~~~l~~~~~~~g~~~~a  343 (343)
                      +...|++++|...+++....    |..++. .+...+..++.+.|+.++|
T Consensus       701 ~~~~g~~~~A~~~l~~al~~~~~~g~~~~~a~~~~~la~a~~~~G~~~~A  750 (903)
T PRK04841        701 QILLGQFDEAEIILEELNENARSLRLMSDLNRNLILLNQLYWQQGRKSEA  750 (903)
T ss_pred             HHHcCCHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHcCCHHHH
Confidence            88899999999999987553    333332 3566777888888887653

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

Probab=98.75  E-value=1.9e-05  Score=65.74  Aligned_cols=139  Identities=11%  Similarity=0.088  Sum_probs=89.7

Q ss_pred             HhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHH
Q 044084          105 FASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAA  184 (343)
Q Consensus       105 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  184 (343)
                      +...|+.+.|+..++.+...-+. |+..+......+.+.++.++|.+.++++....+ -.....-.+..++.+.|++.+|
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 TYLAGQYDEALKLLQPLIAAQPD-NPYYLELAGDILLEANKAKEAIERLKKALALDP-NSPLLQLNLAQALLKGGKPQEA  393 (484)
T ss_pred             HHHhcccchHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCChHHHHHHHHHHHhcCC-CccHHHHHHHHHHHhcCChHHH
Confidence            33556777777777776665432 566666667777777777777777777766553 1244455666777777777777


Q ss_pred             HHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhC
Q 044084          185 VKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       185 ~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                      +.+++...... +-|...|..|..+|...|+..++..-.                  ...|...|+++.|...+....+.
T Consensus       394 i~~L~~~~~~~-p~dp~~w~~LAqay~~~g~~~~a~~A~------------------AE~~~~~G~~~~A~~~l~~A~~~  454 (484)
T COG4783         394 IRILNRYLFND-PEDPNGWDLLAQAYAELGNRAEALLAR------------------AEGYALAGRLEQAIIFLMRASQQ  454 (484)
T ss_pred             HHHHHHHhhcC-CCCchHHHHHHHHHHHhCchHHHHHHH------------------HHHHHhCCCHHHHHHHHHHHHHh
Confidence            77777766553 456667777777777777766655432                  33445566777777766666654

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=98.75  E-value=5.5e-05  Score=60.29  Aligned_cols=198  Identities=11%  Similarity=0.028  Sum_probs=92.7

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhH-HHH
Q 044084           23 GCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVY-ASL  101 (343)
Q Consensus        23 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~l  101 (343)
                      .-.--+...+...|++..|+.-|....+-+    |.+-.++-.-...|...|+...|+.-+.+.++.  +||-..- ..-
T Consensus        39 ekhlElGk~lla~~Q~sDALt~yHaAve~d----p~~Y~aifrRaT~yLAmGksk~al~Dl~rVlel--KpDF~~ARiQR  112 (504)
T KOG0624|consen   39 EKHLELGKELLARGQLSDALTHYHAAVEGD----PNNYQAIFRRATVYLAMGKSKAALQDLSRVLEL--KPDFMAARIQR  112 (504)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHcCC----chhHHHHHHHHHHHhhhcCCccchhhHHHHHhc--CccHHHHHHHh
Confidence            334445555555666666666665553322    222222223334555555555555555555553  4443211 111


Q ss_pred             HHHHhcccCHHHHHHHHHHHHHcCCCCC--HH------------HHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhh
Q 044084          102 ICSFASIAEVKVAEELFKEAEEKGMLRD--LE------------VFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCI  167 (343)
Q Consensus       102 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  167 (343)
                      ...+.+.|.++.|..-|+.+.++.....  ..            .....+..+...|+...|++....+.+..+ .+...
T Consensus       113 g~vllK~Gele~A~~DF~~vl~~~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi~~-Wda~l  191 (504)
T KOG0624|consen  113 GVVLLKQGELEQAEADFDQVLQHEPSNGLVLEAQSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEIQP-WDASL  191 (504)
T ss_pred             chhhhhcccHHHHHHHHHHHHhcCCCcchhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhcCc-chhHH
Confidence            2334555666666666666555432110  00            111223344445566666666666555443 44445


Q ss_pred             HHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHH
Q 044084          168 SCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQ  228 (343)
Q Consensus       168 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  228 (343)
                      |..-..+|...|++..|+.=++...+.. .-+..++--+-..+...|+.+.++...++..+
T Consensus       192 ~~~Rakc~i~~~e~k~AI~Dlk~askLs-~DnTe~~ykis~L~Y~vgd~~~sL~~iRECLK  251 (504)
T KOG0624|consen  192 RQARAKCYIAEGEPKKAIHDLKQASKLS-QDNTEGHYKISQLLYTVGDAENSLKEIRECLK  251 (504)
T ss_pred             HHHHHHHHHhcCcHHHHHHHHHHHHhcc-ccchHHHHHHHHHHHhhhhHHHHHHHHHHHHc
Confidence            5555556666666665555444444332 12223333333444444555555544444444

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

Probab=98.74  E-value=7.1e-06  Score=62.71  Aligned_cols=160  Identities=11%  Similarity=0.055  Sum_probs=116.4

Q ss_pred             HHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcC
Q 044084           99 ASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKR  178 (343)
Q Consensus        99 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  178 (343)
                      ..+-..+...|+-+....+......... .|......++....+.|++..|+..|.+.....+ +|..+|+.+.-+|.+.
T Consensus        70 ~~~a~a~~~~G~a~~~l~~~~~~~~~~~-~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~p-~d~~~~~~lgaaldq~  147 (257)
T COG5010          70 AKLATALYLRGDADSSLAVLQKSAIAYP-KDRELLAAQGKNQIRNGNFGEAVSVLRKAARLAP-TDWEAWNLLGAALDQL  147 (257)
T ss_pred             HHHHHHHHhcccccchHHHHhhhhccCc-ccHHHHHHHHHHHHHhcchHHHHHHHHHHhccCC-CChhhhhHHHHHHHHc
Confidence            4455566666777777776666544332 3666677788888888888888888888877665 6777888888888888


Q ss_pred             CcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHH
Q 044084          179 RAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLV  258 (343)
Q Consensus       179 ~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  258 (343)
                      |+++.|..-|.+..+.. .-+...++.+.-.+.-.|+.+.|..++......+ +-|..+-..+.......|+++.|..+.
T Consensus       148 Gr~~~Ar~ay~qAl~L~-~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~-~ad~~v~~NLAl~~~~~g~~~~A~~i~  225 (257)
T COG5010         148 GRFDEARRAYRQALELA-PNEPSIANNLGMSLLLRGDLEDAETLLLPAYLSP-AADSRVRQNLALVVGLQGDFREAEDIA  225 (257)
T ss_pred             cChhHHHHHHHHHHHhc-cCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCC-CCchHHHHHHHHHHhhcCChHHHHhhc
Confidence            88888888888877762 2344566777777777888888888888877764 336667777777778888888888776


Q ss_pred             HHHh
Q 044084          259 AKMK  262 (343)
Q Consensus       259 ~~m~  262 (343)
                      ..-.
T Consensus       226 ~~e~  229 (257)
T COG5010         226 VQEL  229 (257)
T ss_pred             cccc
Confidence            5544

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=98.74  E-value=1.6e-05  Score=66.85  Aligned_cols=303  Identities=16%  Similarity=0.144  Sum_probs=187.1

Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCC-hHhHHHHHHHHhcc
Q 044084           30 EAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILED-PSVYASLICSFASI  108 (343)
Q Consensus        30 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~  108 (343)
                      .+....|+++.|...|.+.....    |++...|+.-..+|...|++++|++--.+-.+  +.|+ ...|+....++.-.
T Consensus        10 naa~s~~d~~~ai~~~t~ai~l~----p~nhvlySnrsaa~a~~~~~~~al~da~k~~~--l~p~w~kgy~r~Gaa~~~l   83 (539)
T KOG0548|consen   10 NAAFSSGDFETAIRLFTEAIMLS----PTNHVLYSNRSAAYASLGSYEKALKDATKTRR--LNPDWAKGYSRKGAALFGL   83 (539)
T ss_pred             HhhcccccHHHHHHHHHHHHccC----CCccchhcchHHHHHHHhhHHHHHHHHHHHHh--cCCchhhHHHHhHHHHHhc
Confidence            45668899999999998875433    44578899999999999999999886666555  4565 45788899999999


Q ss_pred             cCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCc-------------------------------------------
Q 044084          109 AEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGM-------------------------------------------  145 (343)
Q Consensus       109 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-------------------------------------------  145 (343)
                      |++++|...|.+-.+.... +...++.+..++.....                                           
T Consensus        84 g~~~eA~~ay~~GL~~d~~-n~~L~~gl~~a~~~~~~~~~~~~~p~~~~~l~~~p~t~~~~~~~~~~~~l~~~~~~p~~l  162 (539)
T KOG0548|consen   84 GDYEEAILAYSEGLEKDPS-NKQLKTGLAQAYLEDYAADQLFTKPYFHEKLANLPLTNYSLSDPAYVKILEIIQKNPTSL  162 (539)
T ss_pred             ccHHHHHHHHHHHhhcCCc-hHHHHHhHHHhhhHHHHhhhhccCcHHHHHhhcChhhhhhhccHHHHHHHHHhhcCcHhh
Confidence            9999999999988776532 56666666666521100                                           


Q ss_pred             --------HhHHHHHHHHHH-----hc-------CCCC---------c-------------hhhHHHHHHHHhcCCcHHH
Q 044084          146 --------VEKTLEVVESMK-----NA-------ELNI---------S-------------DCISCVIVNGFSKRRAYWA  183 (343)
Q Consensus       146 --------~~~a~~~~~~~~-----~~-------~~~~---------~-------------~~~~~~l~~~~~~~~~~~~  183 (343)
                              +..|.-.+....     ..       +..|         .             ..-...+.++..+..+++.
T Consensus       163 ~~~l~d~r~m~a~~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~d~~ee~~~k~~a~~ek~lgnaaykkk~f~~  242 (539)
T KOG0548|consen  163 KLYLNDPRLMKADGQLKGVDELLFYASGIEILASMAEPCKQEHNGFPIIEDNTEERRVKEKAHKEKELGNAAYKKKDFET  242 (539)
T ss_pred             hcccccHHHHHHHHHHhcCccccccccccccCCCCCCcccccCCCCCccchhHHHHHHHHhhhHHHHHHHHHHHhhhHHH
Confidence                    000000000000     00       0000         0             0012234444555556666


Q ss_pred             HHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHH-------HHHHHHccCChHHHHH
Q 044084          184 AVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSS-------MVAMYGKTGRIRDAMR  256 (343)
Q Consensus       184 a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~-------l~~~~~~~~~~~~a~~  256 (343)
                      +.+-+.......  -+..-++....+|...|.+..+...-+...+.|.. ...-|+.       +..+|.+.++++.+..
T Consensus       243 a~q~y~~a~el~--~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gre-~rad~klIak~~~r~g~a~~k~~~~~~ai~  319 (539)
T KOG0548|consen  243 AIQHYAKALELA--TDITYLNNIAAVYLERGKYAECIELCEKAVEVGRE-LRADYKLIAKALARLGNAYTKREDYEGAIK  319 (539)
T ss_pred             HHHHHHHHHhHh--hhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhHH-HHHHHHHHHHHHHHhhhhhhhHHhHHHHHH
Confidence            666666666553  34444555566677777777777666665555421 1222222       3335666677888888


Q ss_pred             HHHHHhhCCCCchHHHHHHHHHHHhcc------cChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHH
Q 044084          257 LVAKMKPKGCEPNVWIYNSLMDMHGRA------KNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIM  330 (343)
Q Consensus       257 ~~~~m~~~~~~p~~~~~~~l~~~~~~~------~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l  330 (343)
                      .|.+.......|+..+=..-..--.+.      -+.+.|.+...-...+.+.|++..|+..|.+++... +-|...|..-
T Consensus       320 ~~~kaLte~Rt~~~ls~lk~~Ek~~k~~e~~a~~~pe~A~e~r~kGne~Fk~gdy~~Av~~YteAIkr~-P~Da~lYsNR  398 (539)
T KOG0548|consen  320 YYQKALTEHRTPDLLSKLKEAEKALKEAERKAYINPEKAEEEREKGNEAFKKGDYPEAVKHYTEAIKRD-PEDARLYSNR  398 (539)
T ss_pred             HHHHHhhhhcCHHHHHHHHHHHHHHHHHHHHHhhChhHHHHHHHHHHHHHhccCHHHHHHHHHHHHhcC-CchhHHHHHH
Confidence            888877654555543322111100000      011222224444778889999999999999999986 3466779999


Q ss_pred             HHHHhcccccccC
Q 044084          331 VGVFSKLSQIEEL  343 (343)
Q Consensus       331 ~~~~~~~g~~~~a  343 (343)
                      .-+|.++|.+.+|
T Consensus       399 Aac~~kL~~~~~a  411 (539)
T KOG0548|consen  399 AACYLKLGEYPEA  411 (539)
T ss_pred             HHHHHHHhhHHHH
Confidence            9999999887653

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

Probab=98.73  E-value=0.00012  Score=63.29  Aligned_cols=145  Identities=14%  Similarity=0.185  Sum_probs=80.3

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHH
Q 044084           24 CYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLIC  103 (343)
Q Consensus        24 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  103 (343)
                      .|-..+....++|++......|+.....- +.+.+ ..+|...+......+-++-++.++++.++.    ++..-+-.+.
T Consensus       104 Iwl~Ylq~l~~Q~~iT~tR~tfdrALraL-pvtqH-~rIW~lyl~Fv~~~~lPets~rvyrRYLk~----~P~~~eeyie  177 (835)
T KOG2047|consen  104 IWLDYLQFLIKQGLITRTRRTFDRALRAL-PVTQH-DRIWDLYLKFVESHGLPETSIRVYRRYLKV----APEAREEYIE  177 (835)
T ss_pred             HHHHHHHHHHhcchHHHHHHHHHHHHHhC-chHhh-ccchHHHHHHHHhCCChHHHHHHHHHHHhc----CHHHHHHHHH
Confidence            34445555666666666666666654432 11111 245666666666666666677777666553    2223444455


Q ss_pred             HHhcccCHHHHHHHHHHHHH----------------------------------------cCCC--CC--HHHHHHHHHH
Q 044084          104 SFASIAEVKVAEELFKEAEE----------------------------------------KGML--RD--LEVFLKLVLM  139 (343)
Q Consensus       104 ~~~~~~~~~~a~~~~~~~~~----------------------------------------~~~~--~~--~~~~~~l~~~  139 (343)
                      .+++.+++++|.+.+.....                                        .|+.  +|  ...|++|.+.
T Consensus       178 ~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw~SLAdY  257 (835)
T KOG2047|consen  178 YLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLWCSLADY  257 (835)
T ss_pred             HHHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhcccCcHHHHHHHHHHHHH
Confidence            55566666666555544331                                        1111  22  3457777777


Q ss_pred             HHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHh
Q 044084          140 YIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFS  176 (343)
Q Consensus       140 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  176 (343)
                      |.+.|.+++|..+|++..+.-.  +..-|+.+.++|+
T Consensus       258 YIr~g~~ekarDvyeeai~~v~--tvrDFt~ifd~Ya  292 (835)
T KOG2047|consen  258 YIRSGLFEKARDVYEEAIQTVM--TVRDFTQIFDAYA  292 (835)
T ss_pred             HHHhhhhHHHHHHHHHHHHhhe--ehhhHHHHHHHHH
Confidence            8888888888888877665432  3333444444443

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

Probab=98.73  E-value=0.00012  Score=63.25  Aligned_cols=284  Identities=10%  Similarity=0.130  Sum_probs=171.1

Q ss_pred             chhhHHHHHHHHHhCCCCCC------hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCc
Q 044084            2 NSQSKLHYYEKMKSAGIVLD------SGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGR   75 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~   75 (343)
                      ++.+-...+.+..+. +.|.      ...|..+.+.|-..|+++.|..+|++..+.+...-..-..+|..-...=.++.+
T Consensus       362 ~~~~~i~tyteAv~~-vdP~ka~Gs~~~Lw~~faklYe~~~~l~~aRvifeka~~V~y~~v~dLa~vw~~waemElrh~~  440 (835)
T KOG2047|consen  362 NAAEQINTYTEAVKT-VDPKKAVGSPGTLWVEFAKLYENNGDLDDARVIFEKATKVPYKTVEDLAEVWCAWAEMELRHEN  440 (835)
T ss_pred             ChHHHHHHHHHHHHc-cCcccCCCChhhHHHHHHHHHHhcCcHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHhhhh
Confidence            345555666666553 2221      235777888888889999999999888766554333334566666667777788


Q ss_pred             HHHHHHHHHHHHhcCCC----------C-------ChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 044084           76 AFEILKFFRDMKEKGIL----------E-------DPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVL  138 (343)
Q Consensus        76 ~~~a~~~~~~~~~~~~~----------~-------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  138 (343)
                      ++.|+++.+........          |       +...|+..+..--..|-++....+++++.+..+. ++...-....
T Consensus       441 ~~~Al~lm~~A~~vP~~~~~~~yd~~~pvQ~rlhrSlkiWs~y~DleEs~gtfestk~vYdriidLria-TPqii~NyAm  519 (835)
T KOG2047|consen  441 FEAALKLMRRATHVPTNPELEYYDNSEPVQARLHRSLKIWSMYADLEESLGTFESTKAVYDRIIDLRIA-TPQIIINYAM  519 (835)
T ss_pred             HHHHHHHHHhhhcCCCchhhhhhcCCCcHHHHHHHhHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhcC-CHHHHHHHHH
Confidence            88888888776432111          1       2233445555555667788888888888887654 5544444444


Q ss_pred             HHHhcCcHhHHHHHHHHHHhcCCCCch-hhHHHHHHHHhc---CCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHH--Hc
Q 044084          139 MYIEEGMVEKTLEVVESMKNAELNISD-CISCVIVNGFSK---RRAYWAAVKVYEQLISQGCIPGQVTYASIINAY--CR  212 (343)
Q Consensus       139 ~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~---~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~--~~  212 (343)
                      .+-...-++++.++|++-...-..|+. ..|+..+.-+.+   ...++.|..+|++..+ |++|...-+--|+-+-  -+
T Consensus       520 fLEeh~yfeesFk~YErgI~LFk~p~v~diW~tYLtkfi~rygg~klEraRdLFEqaL~-~Cpp~~aKtiyLlYA~lEEe  598 (835)
T KOG2047|consen  520 FLEEHKYFEESFKAYERGISLFKWPNVYDIWNTYLTKFIKRYGGTKLERARDLFEQALD-GCPPEHAKTIYLLYAKLEEE  598 (835)
T ss_pred             HHHhhHHHHHHHHHHHcCCccCCCccHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHh-cCCHHHHHHHHHHHHHHHHH
Confidence            455556678888888876554444443 245555544433   4568899999999888 6666543333333221  23


Q ss_pred             cCChhHHHHHHHHHHHcCCCcC--hhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHH---HHHHHhcccChh
Q 044084          213 IGLYSKAEKVFIEMQQKGFDKC--VVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNS---LMDMHGRAKNLR  287 (343)
Q Consensus       213 ~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~---l~~~~~~~~~~~  287 (343)
                      .|-...|..++++.... +++.  ...||..|.--...=-+.....+|++.++.  -||...-..   ..+.=++.|..+
T Consensus       599 ~GLar~amsiyerat~~-v~~a~~l~myni~I~kaae~yGv~~TR~iYekaIe~--Lp~~~~r~mclrFAdlEtklGEid  675 (835)
T KOG2047|consen  599 HGLARHAMSIYERATSA-VKEAQRLDMYNIYIKKAAEIYGVPRTREIYEKAIES--LPDSKAREMCLRFADLETKLGEID  675 (835)
T ss_pred             hhHHHHHHHHHHHHHhc-CCHHHHHHHHHHHHHHHHHHhCCcccHHHHHHHHHh--CChHHHHHHHHHHHHHhhhhhhHH
Confidence            46777788888875543 2332  345666665444433445566777777765  455443322   233445667777


Q ss_pred             HHHh
Q 044084          288 QLEK  291 (343)
Q Consensus       288 ~a~~  291 (343)
                      .|..
T Consensus       676 RARa  679 (835)
T KOG2047|consen  676 RARA  679 (835)
T ss_pred             HHHH
Confidence            7765

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

Probab=98.72  E-value=2.8e-05  Score=71.21  Aligned_cols=268  Identities=12%  Similarity=0.068  Sum_probs=156.4

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHH
Q 044084           21 DSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYAS  100 (343)
Q Consensus        21 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  100 (343)
                      +...+..|+..+...+++++|.++.+...+...    .....|-.+...+.+.++...+..+                 .
T Consensus        30 n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~P----~~i~~yy~~G~l~~q~~~~~~~~lv-----------------~   88 (906)
T PRK14720         30 KFKELDDLIDAYKSENLTDEAKDICEEHLKEHK----KSISALYISGILSLSRRPLNDSNLL-----------------N   88 (906)
T ss_pred             hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCC----cceehHHHHHHHHHhhcchhhhhhh-----------------h
Confidence            566889999999999999999999997665542    2234555555566677765554443                 2


Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCc
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRA  180 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  180 (343)
                      ++.......++..+..+...+.+.+  -+...+..+..+|-+.|+.++|..+|+++.+.++ -+..+.|.+...|... +
T Consensus        89 ~l~~~~~~~~~~~ve~~~~~i~~~~--~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D~-~n~~aLNn~AY~~ae~-d  164 (906)
T PRK14720         89 LIDSFSQNLKWAIVEHICDKILLYG--ENKLALRTLAEAYAKLNENKKLKGVWERLVKADR-DNPEIVKKLATSYEEE-D  164 (906)
T ss_pred             hhhhcccccchhHHHHHHHHHHhhh--hhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcCc-ccHHHHHHHHHHHHHh-h
Confidence            3333334444444444455555533  2445666777777777777777777777777664 5666677777777777 7


Q ss_pred             HHHHHHHHHHHHHcCCCCCHhhHHHHHHHH-----HccCChhHHHHHHHHHHHc-CCCcChhhHHHHHHHHHccCChHHH
Q 044084          181 YWAAVKVYEQLISQGCIPGQVTYASIINAY-----CRIGLYSKAEKVFIEMQQK-GFDKCVVAYSSMVAMYGKTGRIRDA  254 (343)
Q Consensus       181 ~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~-----~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a  254 (343)
                      .++|.+++.+....-  .+..-|+.+...+     ....+++.-.++.+.+... |..--+.++-.+-..|...++++++
T Consensus       165 L~KA~~m~~KAV~~~--i~~kq~~~~~e~W~k~~~~~~~d~d~f~~i~~ki~~~~~~~~~~~~~~~l~~~y~~~~~~~~~  242 (906)
T PRK14720        165 KEKAITYLKKAIYRF--IKKKQYVGIEEIWSKLVHYNSDDFDFFLRIERKVLGHREFTRLVGLLEDLYEPYKALEDWDEV  242 (906)
T ss_pred             HHHHHHHHHHHHHHH--HhhhcchHHHHHHHHHHhcCcccchHHHHHHHHHHhhhccchhHHHHHHHHHHHhhhhhhhHH
Confidence            777777777665541  1111122222111     1122333333444444433 3333455666777888888899999


Q ss_pred             HHHHHHHhhCCCCchHHHHHHHHHHHhcc-cChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 044084          255 MRLVAKMKPKGCEPNVWIYNSLMDMHGRA-KNLRQLEKYTTVISAYNMAREFDMCVKFYNEFR  316 (343)
Q Consensus       255 ~~~~~~m~~~~~~p~~~~~~~l~~~~~~~-~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~  316 (343)
                      ..+++.+.+.... |.....-++.+|... ++....++|-.+...--....+..|+.-|+...
T Consensus       243 i~iLK~iL~~~~~-n~~a~~~l~~~y~~kY~~~~~~ee~l~~s~l~~~~~~~~~~i~~fek~i  304 (906)
T PRK14720        243 IYILKKILEHDNK-NNKAREELIRFYKEKYKDHSLLEDYLKMSDIGNNRKPVKDCIADFEKNI  304 (906)
T ss_pred             HHHHHHHHhcCCc-chhhHHHHHHHHHHHccCcchHHHHHHHhccccCCccHHHHHHHHHHHe
Confidence            9999999876322 556666777766521 222222222222222222245566777776653

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

Probab=98.71  E-value=5.9e-05  Score=62.90  Aligned_cols=198  Identities=11%  Similarity=0.029  Sum_probs=135.2

Q ss_pred             CCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhh-HHHH
Q 044084          128 RDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVT-YASI  206 (343)
Q Consensus       128 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~-~~~l  206 (343)
                      |+...+...+........-..+-.++.+..+.+  -...-|. ..-.+...|+++.|++.++.+...  .|+..- ....
T Consensus       272 ~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~--~~aa~YG-~A~~~~~~~~~d~A~~~l~~L~~~--~P~N~~~~~~~  346 (484)
T COG4783         272 PDFQLARARIRAKYEALPNQQAADLLAKRSKRG--GLAAQYG-RALQTYLAGQYDEALKLLQPLIAA--QPDNPYYLELA  346 (484)
T ss_pred             ccHHHHHHHHHHHhccccccchHHHHHHHhCcc--chHHHHH-HHHHHHHhcccchHHHHHHHHHHh--CCCCHHHHHHH
Confidence            455555555555444433333333333333311  1111233 333445678899999999998877  455544 4455


Q ss_pred             HHHHHccCChhHHHHHHHHHHHcCCCcC-hhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccC
Q 044084          207 INAYCRIGLYSKAEKVFIEMQQKGFDKC-VVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKN  285 (343)
Q Consensus       207 l~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~  285 (343)
                      ...+.+.++.++|.+.++.+....  |+ ....-.+..+|.+.|++.+|..++++.... .+-|+..|..|.++|...|+
T Consensus       347 ~~i~~~~nk~~~A~e~~~kal~l~--P~~~~l~~~~a~all~~g~~~eai~~L~~~~~~-~p~dp~~w~~LAqay~~~g~  423 (484)
T COG4783         347 GDILLEANKAKEAIERLKKALALD--PNSPLLQLNLAQALLKGGKPQEAIRILNRYLFN-DPEDPNGWDLLAQAYAELGN  423 (484)
T ss_pred             HHHHHHcCChHHHHHHHHHHHhcC--CCccHHHHHHHHHHHhcCChHHHHHHHHHHhhc-CCCCchHHHHHHHHHHHhCc
Confidence            677888999999999999988864  44 566777888999999999999999888776 35578889999999999998


Q ss_pred             hhHHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCC--CCccHHHHHHHHHHHh
Q 044084          286 LRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNG--GVIDRAMAGIMVGVFS  335 (343)
Q Consensus       286 ~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~--~~p~~~~~~~l~~~~~  335 (343)
                      ..++.  ......|...|+++.|+..+....+..  ..|+..-+...+....
T Consensus       424 ~~~a~--~A~AE~~~~~G~~~~A~~~l~~A~~~~~~~~~~~aR~dari~~~~  473 (484)
T COG4783         424 RAEAL--LARAEGYALAGRLEQAIIFLMRASQQVKLGFPDWARADARIDQLR  473 (484)
T ss_pred             hHHHH--HHHHHHHHhCCCHHHHHHHHHHHHHhccCCcHHHHHHHHHHHHHH
Confidence            87774  445667788999999999999887753  2345444555555443

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

Probab=98.70  E-value=0.00015  Score=65.96  Aligned_cols=267  Identities=13%  Similarity=0.174  Sum_probs=128.6

Q ss_pred             HHHHHHHhCCCC--CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHH
Q 044084            8 HYYEKMKSAGIV--LDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRD   85 (343)
Q Consensus         8 ~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~   85 (343)
                      ++.+...+.+++  .|+......+.++...+-+.+-.++++++.-.+...+ .+...-|.|+-...+ -+..+..+..++
T Consensus       968 qLiDqVv~tal~E~~dPe~vS~tVkAfMtadLp~eLIELLEKIvL~~S~Fs-e~~nLQnLLiLtAik-ad~trVm~YI~r 1045 (1666)
T KOG0985|consen  968 QLIDQVVQTALPETQDPEEVSVTVKAFMTADLPNELIELLEKIVLDNSVFS-ENRNLQNLLILTAIK-ADRTRVMEYINR 1045 (1666)
T ss_pred             HHHHHHHHhcCCccCChHHHHHHHHHHHhcCCcHHHHHHHHHHhcCCcccc-cchhhhhhHHHHHhh-cChHHHHHHHHH
Confidence            444555554432  2444555666666666666677777666543322221 112233333333333 234445555555


Q ss_pred             HHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCch
Q 044084           86 MKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISD  165 (343)
Q Consensus        86 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  165 (343)
                      +...+. |+      +...+...+-+++|..+|+...     .+....+.|+.   ..+..+.|.+.-++..      ..
T Consensus      1046 LdnyDa-~~------ia~iai~~~LyEEAF~ifkkf~-----~n~~A~~VLie---~i~~ldRA~efAe~~n------~p 1104 (1666)
T KOG0985|consen 1046 LDNYDA-PD------IAEIAIENQLYEEAFAIFKKFD-----MNVSAIQVLIE---NIGSLDRAYEFAERCN------EP 1104 (1666)
T ss_pred             hccCCc-hh------HHHHHhhhhHHHHHHHHHHHhc-----ccHHHHHHHHH---HhhhHHHHHHHHHhhC------Ch
Confidence            543321 11      2223334444555555555432     12333333332   1233344443333332      12


Q ss_pred             hhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHH
Q 044084          166 CISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMY  245 (343)
Q Consensus       166 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  245 (343)
                      ..|+.+..+-.+.|...+|.+-|-+      .-|+..|..+++...+.|.+++-.+.+...++..-.|.+.  +.||-+|
T Consensus      1105 ~vWsqlakAQL~~~~v~dAieSyik------adDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id--~eLi~Ay 1176 (1666)
T KOG0985|consen 1105 AVWSQLAKAQLQGGLVKDAIESYIK------ADDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYID--SELIFAY 1176 (1666)
T ss_pred             HHHHHHHHHHHhcCchHHHHHHHHh------cCCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccch--HHHHHHH
Confidence            2455555555555655555554433      1244556666666666666666666665555544333332  3555666


Q ss_pred             HccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh-------HHHHHHHHHhcCCHHHHHHHH
Q 044084          246 GKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK-------YTTVISAYNMAREFDMCVKFY  312 (343)
Q Consensus       246 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~-------~~~l~~~~~~~g~~~~a~~~~  312 (343)
                      ++.+++.+..+++       .-||......+.+-|...|.++.|.-       |..+...+...|+++.|...-
T Consensus      1177 Akt~rl~elE~fi-------~gpN~A~i~~vGdrcf~~~~y~aAkl~y~~vSN~a~La~TLV~LgeyQ~AVD~a 1243 (1666)
T KOG0985|consen 1177 AKTNRLTELEEFI-------AGPNVANIQQVGDRCFEEKMYEAAKLLYSNVSNFAKLASTLVYLGEYQGAVDAA 1243 (1666)
T ss_pred             HHhchHHHHHHHh-------cCCCchhHHHHhHHHhhhhhhHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHh
Confidence            6666655544433       23455555555555555555555543       555555555566665555443

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

Probab=98.69  E-value=3.5e-06  Score=64.36  Aligned_cols=161  Identities=12%  Similarity=-0.003  Sum_probs=129.6

Q ss_pred             HHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Q 044084           64 KILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEE  143 (343)
Q Consensus        64 ~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  143 (343)
                      ..+-..+...|+-+....+....... ..-|.......+....+.|++..|...+.+.....+ +|...|+.+.-+|.+.
T Consensus        70 ~~~a~a~~~~G~a~~~l~~~~~~~~~-~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~p-~d~~~~~~lgaaldq~  147 (257)
T COG5010          70 AKLATALYLRGDADSSLAVLQKSAIA-YPKDRELLAAQGKNQIRNGNFGEAVSVLRKAARLAP-TDWEAWNLLGAALDQL  147 (257)
T ss_pred             HHHHHHHHhcccccchHHHHhhhhcc-CcccHHHHHHHHHHHHHhcchHHHHHHHHHHhccCC-CChhhhhHHHHHHHHc
Confidence            55667777788888887777765443 233555666688899999999999999999988664 5899999999999999


Q ss_pred             CcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHH
Q 044084          144 GMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVF  223 (343)
Q Consensus       144 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~  223 (343)
                      |+++.|..-|.+..+... -+....+.+.-.+.-.|+.+.|..++......+ .-|...-..+..+....|++++|+.+-
T Consensus       148 Gr~~~Ar~ay~qAl~L~~-~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~-~ad~~v~~NLAl~~~~~g~~~~A~~i~  225 (257)
T COG5010         148 GRFDEARRAYRQALELAP-NEPSIANNLGMSLLLRGDLEDAETLLLPAYLSP-AADSRVRQNLALVVGLQGDFREAEDIA  225 (257)
T ss_pred             cChhHHHHHHHHHHHhcc-CCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCC-CCchHHHHHHHHHHhhcCChHHHHhhc
Confidence            999999999999887655 355578888888899999999999999988774 336667777888889999999999887


Q ss_pred             HHHHH
Q 044084          224 IEMQQ  228 (343)
Q Consensus       224 ~~~~~  228 (343)
                      ..-..
T Consensus       226 ~~e~~  230 (257)
T COG5010         226 VQELL  230 (257)
T ss_pred             ccccc
Confidence            65433

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.69  E-value=2.8e-05  Score=70.27  Aligned_cols=131  Identities=13%  Similarity=0.140  Sum_probs=75.1

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCC-hHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEKGILED-PSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVL  138 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  138 (343)
                      ...+-.|.....+.|.+++|..+++...+.  .|+ ......+...+.+.+++++|....++.....+. +......+..
T Consensus        86 ~~~~~~La~i~~~~g~~~ea~~~l~~~~~~--~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~p~-~~~~~~~~a~  162 (694)
T PRK15179         86 ELFQVLVARALEAAHRSDEGLAVWRGIHQR--FPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGGSS-SAREILLEAK  162 (694)
T ss_pred             HHHHHHHHHHHHHcCCcHHHHHHHHHHHhh--CCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcCCC-CHHHHHHHHH
Confidence            445555556666666666666666666554  333 334444555566666666666666666655533 4555555566


Q ss_pred             HHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHc
Q 044084          139 MYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       139 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  194 (343)
                      ++.+.|++++|..+|+++...++ -+..++..+..++...|+.++|...|++..+.
T Consensus       163 ~l~~~g~~~~A~~~y~~~~~~~p-~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~  217 (694)
T PRK15179        163 SWDEIGQSEQADACFERLSRQHP-EFENGYVGWAQSLTRRGALWRARDVLQAGLDA  217 (694)
T ss_pred             HHHHhcchHHHHHHHHHHHhcCC-CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            66666666666666666655332 23445555666666666666666666665554

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=98.68  E-value=1.9e-05  Score=69.15  Aligned_cols=130  Identities=18%  Similarity=0.324  Sum_probs=85.9

Q ss_pred             HHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCCh
Q 044084          172 VNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRI  251 (343)
Q Consensus       172 ~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  251 (343)
                      +.+.....+|.+|+.+++.+...+  .-..-|..+...|+..|+++.|+++|.+.         ..++-.|.+|.+.|++
T Consensus       739 ieaai~akew~kai~ildniqdqk--~~s~yy~~iadhyan~~dfe~ae~lf~e~---------~~~~dai~my~k~~kw  807 (1636)
T KOG3616|consen  739 IEAAIGAKEWKKAISILDNIQDQK--TASGYYGEIADHYANKGDFEIAEELFTEA---------DLFKDAIDMYGKAGKW  807 (1636)
T ss_pred             HHHHhhhhhhhhhHhHHHHhhhhc--cccccchHHHHHhccchhHHHHHHHHHhc---------chhHHHHHHHhccccH
Confidence            445556677788888888777663  23344666777788888888888877542         2355667778888888


Q ss_pred             HHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh-------HHHHHHHHHhcCCHHHHHHHHHH
Q 044084          252 RDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK-------YTTVISAYNMAREFDMCVKFYNE  314 (343)
Q Consensus       252 ~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~-------~~~l~~~~~~~g~~~~a~~~~~~  314 (343)
                      +.|.++-.+...  .......|..-..-+-..|++.+|++       -...|..|-+.|..++.+++..+
T Consensus       808 ~da~kla~e~~~--~e~t~~~yiakaedldehgkf~eaeqlyiti~~p~~aiqmydk~~~~ddmirlv~k  875 (1636)
T KOG3616|consen  808 EDAFKLAEECHG--PEATISLYIAKAEDLDEHGKFAEAEQLYITIGEPDKAIQMYDKHGLDDDMIRLVEK  875 (1636)
T ss_pred             HHHHHHHHHhcC--chhHHHHHHHhHHhHHhhcchhhhhheeEEccCchHHHHHHHhhCcchHHHHHHHH
Confidence            888777665542  23445556555666777777777777       34456666666666666666554

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.68  E-value=2.5e-05  Score=62.46  Aligned_cols=55  Identities=20%  Similarity=0.277  Sum_probs=24.7

Q ss_pred             HHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHH
Q 044084          206 IINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAK  260 (343)
Q Consensus       206 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  260 (343)
                      +..+++..|.+.+|+++|-.+....++.+..-...|.++|.+++++..|++++-+
T Consensus       399 ~AQAk~atgny~eaEelf~~is~~~ikn~~~Y~s~LArCyi~nkkP~lAW~~~lk  453 (557)
T KOG3785|consen  399 LAQAKLATGNYVEAEELFIRISGPEIKNKILYKSMLARCYIRNKKPQLAWDMMLK  453 (557)
T ss_pred             HHHHHHHhcChHHHHHHHhhhcChhhhhhHHHHHHHHHHHHhcCCchHHHHHHHh
Confidence            4444555555555555554444333222222223334455555555555444433

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.67  E-value=4.5e-06  Score=60.11  Aligned_cols=88  Identities=6%  Similarity=-0.156  Sum_probs=34.4

Q ss_pred             HHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHH
Q 044084          104 SFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWA  183 (343)
Q Consensus       104 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  183 (343)
                      .+...|++++|...|+......+. +...|..+...+...|++++|...|+.....++ .+...+..+..++...|++++
T Consensus        33 ~~~~~g~~~~A~~~~~~al~~~P~-~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p-~~~~a~~~lg~~l~~~g~~~e  110 (144)
T PRK15359         33 ASWQEGDYSRAVIDFSWLVMAQPW-SWRAHIALAGTWMMLKEYTTAINFYGHALMLDA-SHPEPVYQTGVCLKMMGEPGL  110 (144)
T ss_pred             HHHHcCCHHHHHHHHHHHHHcCCC-cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCcHHHHHHHHHHHHcCCHHH
Confidence            333344444444444444333221 333344444444444444444444444433332 233333333334444444444


Q ss_pred             HHHHHHHHHH
Q 044084          184 AVKVYEQLIS  193 (343)
Q Consensus       184 a~~~~~~~~~  193 (343)
                      |...|+...+
T Consensus       111 Ai~~~~~Al~  120 (144)
T PRK15359        111 AREAFQTAIK  120 (144)
T ss_pred             HHHHHHHHHH
Confidence            4444444333

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

Probab=98.66  E-value=3.7e-06  Score=73.01  Aligned_cols=214  Identities=15%  Similarity=0.142  Sum_probs=158.7

Q ss_pred             HHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 044084           63 YKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIE  142 (343)
Q Consensus        63 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  142 (343)
                      -..+...+...|-...|..+|+++..         |.-++.+|+..|+.++|..+..+..+  -+||+..|..+++....
T Consensus       401 q~~laell~slGitksAl~I~Erlem---------w~~vi~CY~~lg~~~kaeei~~q~le--k~~d~~lyc~LGDv~~d  469 (777)
T KOG1128|consen  401 QRLLAELLLSLGITKSALVIFERLEM---------WDPVILCYLLLGQHGKAEEINRQELE--KDPDPRLYCLLGDVLHD  469 (777)
T ss_pred             HHHHHHHHHHcchHHHHHHHHHhHHH---------HHHHHHHHHHhcccchHHHHHHHHhc--CCCcchhHHHhhhhccC
Confidence            34566777888889999999987644         66688889999999999999888777  35789999999888877


Q ss_pred             cCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHH
Q 044084          143 EGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKV  222 (343)
Q Consensus       143 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~  222 (343)
                      ..-+++|.++++.....       .-..+.....+.+++.++.+.|+.-.+.+ +.-..+|-..-.+..+.+++..|.+.
T Consensus       470 ~s~yEkawElsn~~sar-------A~r~~~~~~~~~~~fs~~~~hle~sl~~n-plq~~~wf~~G~~ALqlek~q~av~a  541 (777)
T KOG1128|consen  470 PSLYEKAWELSNYISAR-------AQRSLALLILSNKDFSEADKHLERSLEIN-PLQLGTWFGLGCAALQLEKEQAAVKA  541 (777)
T ss_pred             hHHHHHHHHHhhhhhHH-------HHHhhccccccchhHHHHHHHHHHHhhcC-ccchhHHHhccHHHHHHhhhHHHHHH
Confidence            77789999998876433       11112222344789999999999877764 34566788888888899999999999


Q ss_pred             HHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhc
Q 044084          223 FIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMA  302 (343)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~  302 (343)
                      |....... +-+...||.+-.+|.+.++-.+|...+++..+.+.. +...|...+                   ....+.
T Consensus       542 F~rcvtL~-Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn~~-~w~iWENym-------------------lvsvdv  600 (777)
T KOG1128|consen  542 FHRCVTLE-PDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCNYQ-HWQIWENYM-------------------LVSVDV  600 (777)
T ss_pred             HHHHhhcC-CCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcCCC-CCeeeechh-------------------hhhhhc
Confidence            99888764 345678999999999999999999999999887532 333333333                   333455


Q ss_pred             CCHHHHHHHHHHHH
Q 044084          303 REFDMCVKFYNEFR  316 (343)
Q Consensus       303 g~~~~a~~~~~~m~  316 (343)
                      |.+++|++.++++.
T Consensus       601 ge~eda~~A~~rll  614 (777)
T KOG1128|consen  601 GEFEDAIKAYHRLL  614 (777)
T ss_pred             ccHHHHHHHHHHHH
Confidence            66666666666553

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.66  E-value=2.3e-06  Score=61.57  Aligned_cols=94  Identities=15%  Similarity=0.048  Sum_probs=46.9

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHh
Q 044084           27 QIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFA  106 (343)
Q Consensus        27 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  106 (343)
                      .+...+...|++++|...|+......    |.+...|..+..++...|++++|+..|++....+ +.+...+..+..++.
T Consensus        29 ~~g~~~~~~g~~~~A~~~~~~al~~~----P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~-p~~~~a~~~lg~~l~  103 (144)
T PRK15359         29 ASGYASWQEGDYSRAVIDFSWLVMAQ----PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD-ASHPEPVYQTGVCLK  103 (144)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHcC----CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHH
Confidence            34445555555555555555554332    2223455555555555555555555555555432 124444444555555


Q ss_pred             cccCHHHHHHHHHHHHHcC
Q 044084          107 SIAEVKVAEELFKEAEEKG  125 (343)
Q Consensus       107 ~~~~~~~a~~~~~~~~~~~  125 (343)
                      ..|+.++|...|+...+..
T Consensus       104 ~~g~~~eAi~~~~~Al~~~  122 (144)
T PRK15359        104 MMGEPGLAREAFQTAIKMS  122 (144)
T ss_pred             HcCCHHHHHHHHHHHHHhC
Confidence            5555555555555555443

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.66  E-value=6.1e-06  Score=74.39  Aligned_cols=137  Identities=10%  Similarity=0.017  Sum_probs=118.7

Q ss_pred             CCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHh
Q 044084           18 IVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSV   97 (343)
Q Consensus        18 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~   97 (343)
                      .+.++..+..|..+..+.|.+++|..+++.+.+..    |.+...+..+...+.+.+++++|+..+++....... +...
T Consensus        82 ~~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~----Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~p~-~~~~  156 (694)
T PRK15179         82 YPHTELFQVLVARALEAAHRSDEGLAVWRGIHQRF----PDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGGSS-SARE  156 (694)
T ss_pred             ccccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC----CCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcCCC-CHHH
Confidence            44568889999999999999999999999997765    445688999999999999999999999999987533 5667


Q ss_pred             HHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcC
Q 044084           98 YASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus        98 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  160 (343)
                      ...+..++.+.|++++|..+|+++...+.. +..++..+...+.+.|+.++|...|++..+..
T Consensus       157 ~~~~a~~l~~~g~~~~A~~~y~~~~~~~p~-~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~~  218 (694)
T PRK15179        157 ILLEAKSWDEIGQSEQADACFERLSRQHPE-FENGYVGWAQSLTRRGALWRARDVLQAGLDAI  218 (694)
T ss_pred             HHHHHHHHHHhcchHHHHHHHHHHHhcCCC-cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhh
Confidence            777888899999999999999999985532 58999999999999999999999999987643

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

Probab=98.64  E-value=5.7e-05  Score=68.42  Aligned_cols=274  Identities=14%  Similarity=0.126  Sum_probs=149.4

Q ss_pred             hhHHHHHHHHHhCCC--CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            4 QSKLHYYEKMKSAGI--VLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         4 ~~A~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      .+-.++++++.-..-  .-+...-|.|+-...+ -+..+..+..+++...+. |+         +...+..++-+++|..
T Consensus      1001 ~eLIELLEKIvL~~S~Fse~~nLQnLLiLtAik-ad~trVm~YI~rLdnyDa-~~---------ia~iai~~~LyEEAF~ 1069 (1666)
T KOG0985|consen 1001 NELIELLEKIVLDNSVFSENRNLQNLLILTAIK-ADRTRVMEYINRLDNYDA-PD---------IAEIAIENQLYEEAFA 1069 (1666)
T ss_pred             HHHHHHHHHHhcCCcccccchhhhhhHHHHHhh-cChHHHHHHHHHhccCCc-hh---------HHHHHhhhhHHHHHHH
Confidence            445566666654321  1122233344433333 344555566655533221 11         2333445566777777


Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCC
Q 044084           82 FFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAEL  161 (343)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  161 (343)
                      +|+...     .+....+.|+.-   .+..+.|.+.-++.      ..+.+|..+..+-.+.|.+.+|++-|-+.     
T Consensus      1070 ifkkf~-----~n~~A~~VLie~---i~~ldRA~efAe~~------n~p~vWsqlakAQL~~~~v~dAieSyika----- 1130 (1666)
T KOG0985|consen 1070 IFKKFD-----MNVSAIQVLIEN---IGSLDRAYEFAERC------NEPAVWSQLAKAQLQGGLVKDAIESYIKA----- 1130 (1666)
T ss_pred             HHHHhc-----ccHHHHHHHHHH---hhhHHHHHHHHHhh------CChHHHHHHHHHHHhcCchHHHHHHHHhc-----
Confidence            776542     233334444432   23444444333221      13456666666666666666666555433     


Q ss_pred             CCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHH-----HHHcC------
Q 044084          162 NISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIE-----MQQKG------  230 (343)
Q Consensus       162 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~-----~~~~~------  230 (343)
                       .|...|..+++...+.|.+++..+++....+..-.|..  -+.++-+|++.++..+.++++..     +...|      
T Consensus      1131 -dDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~i--d~eLi~AyAkt~rl~elE~fi~gpN~A~i~~vGdrcf~~ 1207 (1666)
T KOG0985|consen 1131 -DDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYI--DSELIFAYAKTNRLTELEEFIAGPNVANIQQVGDRCFEE 1207 (1666)
T ss_pred             -CCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccc--hHHHHHHHHHhchHHHHHHHhcCCCchhHHHHhHHHhhh
Confidence             23335666666666666666666666555555433332  23455556665555554443210     00000      


Q ss_pred             --------CCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh-----------
Q 044084          231 --------FDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK-----------  291 (343)
Q Consensus       231 --------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~-----------  291 (343)
                              +-.++..|..|...+...|++..|..--++.-      +..||..+-.+|...+.+.-|.-           
T Consensus      1208 ~~y~aAkl~y~~vSN~a~La~TLV~LgeyQ~AVD~aRKAn------s~ktWK~VcfaCvd~~EFrlAQiCGL~iivhade 1281 (1666)
T KOG0985|consen 1208 KMYEAAKLLYSNVSNFAKLASTLVYLGEYQGAVDAARKAN------STKTWKEVCFACVDKEEFRLAQICGLNIIVHADE 1281 (1666)
T ss_pred             hhhHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhhhcc------chhHHHHHHHHHhchhhhhHHHhcCceEEEehHh
Confidence                    00124456666666667777766665544432      67789999899998888887765           


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHH
Q 044084          292 YTTVISAYNMAREFDMCVKFYNEFR  316 (343)
Q Consensus       292 ~~~l~~~~~~~g~~~~a~~~~~~m~  316 (343)
                      ...++.-|-..|-+++-+.+++..+
T Consensus      1282 Leeli~~Yq~rGyFeElIsl~Ea~L 1306 (1666)
T KOG0985|consen 1282 LEELIEYYQDRGYFEELISLLEAGL 1306 (1666)
T ss_pred             HHHHHHHHHhcCcHHHHHHHHHhhh
Confidence            8889999999999999988887653

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

Probab=98.63  E-value=7.9e-05  Score=57.27  Aligned_cols=241  Identities=12%  Similarity=0.114  Sum_probs=144.0

Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhccc
Q 044084           30 EAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIA  109 (343)
Q Consensus        30 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  109 (343)
                      +.+.-.|.+..++..-.......  .+   ...-.-+-++|...|.+...+.   +.+... .|.......+......-+
T Consensus        16 Rn~fY~Gnyq~~ine~~~~~~~~--~~---~e~d~y~~raylAlg~~~~~~~---eI~~~~-~~~lqAvr~~a~~~~~e~   86 (299)
T KOG3081|consen   16 RNYFYLGNYQQCINEAEKFSSSK--TD---VELDVYMYRAYLALGQYQIVIS---EIKEGK-ATPLQAVRLLAEYLELES   86 (299)
T ss_pred             HHHHHhhHHHHHHHHHHhhcccc--ch---hHHHHHHHHHHHHccccccccc---cccccc-CChHHHHHHHHHHhhCcc
Confidence            44555677777766555443332  11   2233335566666666544332   222221 233333333333332233


Q ss_pred             CHH-HHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHH
Q 044084          110 EVK-VAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVY  188 (343)
Q Consensus       110 ~~~-~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  188 (343)
                      +.+ ...++.+.+.......+......-...|+..|++++|++......      +......=...+.+..+.+-|.+.+
T Consensus        87 ~~~~~~~~l~E~~a~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~~~------~lE~~Al~VqI~lk~~r~d~A~~~l  160 (299)
T KOG3081|consen   87 NKKSILASLYELVADSTDGSNLIDLLLAAIIYMHDGDFDEALKALHLGE------NLEAAALNVQILLKMHRFDLAEKEL  160 (299)
T ss_pred             hhHHHHHHHHHHHHhhccchhHHHHHHhhHHhhcCCChHHHHHHHhccc------hHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            332 333445555555444444444455567888889999988877632      2222323344556777888888888


Q ss_pred             HHHHHcCCCCCHhhHHHHHHHHHc----cCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhC
Q 044084          189 EQLISQGCIPGQVTYASIINAYCR----IGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       189 ~~~~~~~~~p~~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                      ++|.+.   -+..|.+-|..++.+    .+.+.+|.-+|++|.+. .+|+..+.+-...++...|++++|..++++...+
T Consensus       161 k~mq~i---ded~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~k  236 (299)
T KOG3081|consen  161 KKMQQI---DEDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDK  236 (299)
T ss_pred             HHHHcc---chHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            888875   355677766666653    45688888899888875 4788888888888888899999999999888876


Q ss_pred             CCCchHHHHHHHHHHHhcccChhHHH
Q 044084          265 GCEPNVWIYNSLMDMHGRAKNLRQLE  290 (343)
Q Consensus       265 ~~~p~~~~~~~l~~~~~~~~~~~~a~  290 (343)
                      ... ++.|...++-.-...|...++.
T Consensus       237 d~~-dpetL~Nliv~a~~~Gkd~~~~  261 (299)
T KOG3081|consen  237 DAK-DPETLANLIVLALHLGKDAEVT  261 (299)
T ss_pred             cCC-CHHHHHHHHHHHHHhCCChHHH
Confidence            433 5666666665555555554443

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.62  E-value=9.4e-05  Score=56.45  Aligned_cols=188  Identities=11%  Similarity=0.115  Sum_probs=131.2

Q ss_pred             cCcHHHHHHHHHHHHhc---C-CCCChH-hHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHh
Q 044084           73 SGRAFEILKFFRDMKEK---G-ILEDPS-VYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVE  147 (343)
Q Consensus        73 ~~~~~~a~~~~~~~~~~---~-~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  147 (343)
                      ..++++..+++.++...   | ..++.. .|..++-+....|+.+.|..+++++...-+ -+..+-..-.-.+-..|+++
T Consensus        25 ~rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~fp-~S~RV~~lkam~lEa~~~~~  103 (289)
T KOG3060|consen   25 VRNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRFP-GSKRVGKLKAMLLEATGNYK  103 (289)
T ss_pred             ccCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhCC-CChhHHHHHHHHHHHhhchh
Confidence            34567777777777543   3 445544 355666677788888888888888877642 23333333333355668889


Q ss_pred             HHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHH
Q 044084          148 KTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQ  227 (343)
Q Consensus       148 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  227 (343)
                      +|.++++.+.+.++ .|..++--=+...-..|+.-+|++-+....+. +..|...|.-+...|...|++++|.--++++.
T Consensus       104 ~A~e~y~~lL~ddp-t~~v~~KRKlAilka~GK~l~aIk~ln~YL~~-F~~D~EAW~eLaeiY~~~~~f~kA~fClEE~l  181 (289)
T KOG3060|consen  104 EAIEYYESLLEDDP-TDTVIRKRKLAILKAQGKNLEAIKELNEYLDK-FMNDQEAWHELAEIYLSEGDFEKAAFCLEELL  181 (289)
T ss_pred             hHHHHHHHHhccCc-chhHHHHHHHHHHHHcCCcHHHHHHHHHHHHH-hcCcHHHHHHHHHHHHhHhHHHHHHHHHHHHH
Confidence            99999999888774 56666666566666677777888777777765 56788889999999999999999998888888


Q ss_pred             HcCCCcChhhHHHHHHHHHccC---ChHHHHHHHHHHhhC
Q 044084          228 QKGFDKCVVAYSSMVAMYGKTG---RIRDAMRLVAKMKPK  264 (343)
Q Consensus       228 ~~~~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~m~~~  264 (343)
                      -.. |.++..+..+.+.+.-.|   +...+.+.|.+..+.
T Consensus       182 l~~-P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alkl  220 (289)
T KOG3060|consen  182 LIQ-PFNPLYFQRLAEVLYTQGGAENLELARKYYERALKL  220 (289)
T ss_pred             HcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHh
Confidence            764 445555666666554444   456788888888775

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=98.59  E-value=0.00017  Score=57.61  Aligned_cols=275  Identities=11%  Similarity=0.036  Sum_probs=184.7

Q ss_pred             hhhHHHHHHHHHhCCCCCChhhHHH---HHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHH
Q 044084            3 SQSKLHYYEKMKSAGIVLDSGCYCQ---IMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEI   79 (343)
Q Consensus         3 ~~~A~~~~~~~~~~~~~~~~~~~~~---l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a   79 (343)
                      +..|+.-|...++.    |+..|.+   -...|...|+...|+.-+....+..  |+  -..+...-...+.++|.+++|
T Consensus        54 ~sDALt~yHaAve~----dp~~Y~aifrRaT~yLAmGksk~al~Dl~rVlelK--pD--F~~ARiQRg~vllK~Gele~A  125 (504)
T KOG0624|consen   54 LSDALTHYHAAVEG----DPNNYQAIFRRATVYLAMGKSKAALQDLSRVLELK--PD--FMAARIQRGVVLLKQGELEQA  125 (504)
T ss_pred             HHHHHHHHHHHHcC----CchhHHHHHHHHHHHhhhcCCccchhhHHHHHhcC--cc--HHHHHHHhchhhhhcccHHHH
Confidence            34566666665553    3334443   3457888888888888888887654  22  223444445677899999999


Q ss_pred             HHHHHHHHhcCCCCC--hHhH------------HHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCc
Q 044084           80 LKFFRDMKEKGILED--PSVY------------ASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGM  145 (343)
Q Consensus        80 ~~~~~~~~~~~~~~~--~~~~------------~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  145 (343)
                      ..-|+.++.....-+  ...+            ...+..+...|+...|+.....+.+..+- |...+..-..+|...|+
T Consensus       126 ~~DF~~vl~~~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi~~W-da~l~~~Rakc~i~~~e  204 (504)
T KOG0624|consen  126 EADFDQVLQHEPSNGLVLEAQSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEIQPW-DASLRQARAKCYIAEGE  204 (504)
T ss_pred             HHHHHHHHhcCCCcchhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhcCcc-hhHHHHHHHHHHHhcCc
Confidence            999999988642111  1111            22344556778999999999999886543 88888888999999999


Q ss_pred             HhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhh----HHH---H------HHHHHc
Q 044084          146 VEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVT----YAS---I------INAYCR  212 (343)
Q Consensus       146 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~----~~~---l------l~~~~~  212 (343)
                      +..|+.=++...+... .++.++--+-..+...|+.+.++...++-.+.  .||...    |..   +      +.....
T Consensus       205 ~k~AI~Dlk~askLs~-DnTe~~ykis~L~Y~vgd~~~sL~~iRECLKl--dpdHK~Cf~~YKklkKv~K~les~e~~ie  281 (504)
T KOG0624|consen  205 PKKAIHDLKQASKLSQ-DNTEGHYKISQLLYTVGDAENSLKEIRECLKL--DPDHKLCFPFYKKLKKVVKSLESAEQAIE  281 (504)
T ss_pred             HHHHHHHHHHHHhccc-cchHHHHHHHHHHHhhhhHHHHHHHHHHHHcc--CcchhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence            9999888777765544 34445555667777888888888888887765  455432    111   1      122345


Q ss_pred             cCChhHHHHHHHHHHHcCCCcC---hhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCch-HHHHHHHHHHHhcccChhH
Q 044084          213 IGLYSKAEKVFIEMQQKGFDKC---VVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPN-VWIYNSLMDMHGRAKNLRQ  288 (343)
Q Consensus       213 ~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~~~~~l~~~~~~~~~~~~  288 (343)
                      .+++.++.+..+...+......   ...+..+-.++...+++.+|++.-.+..+.  .|| ..++.--..+|.-...++.
T Consensus       282 ~~~~t~cle~ge~vlk~ep~~~~ir~~~~r~~c~C~~~d~~~~eAiqqC~evL~~--d~~dv~~l~dRAeA~l~dE~YD~  359 (504)
T KOG0624|consen  282 EKHWTECLEAGEKVLKNEPEETMIRYNGFRVLCTCYREDEQFGEAIQQCKEVLDI--DPDDVQVLCDRAEAYLGDEMYDD  359 (504)
T ss_pred             hhhHHHHHHHHHHHHhcCCcccceeeeeeheeeecccccCCHHHHHHHHHHHHhc--CchHHHHHHHHHHHHhhhHHHHH
Confidence            6777788877777777642212   234455667778888999999988888864  454 6676666667776666666


Q ss_pred             HHh
Q 044084          289 LEK  291 (343)
Q Consensus       289 a~~  291 (343)
                      |..
T Consensus       360 AI~  362 (504)
T KOG0624|consen  360 AIH  362 (504)
T ss_pred             HHH
Confidence            655

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.59  E-value=0.00011  Score=56.06  Aligned_cols=85  Identities=20%  Similarity=0.255  Sum_probs=38.9

Q ss_pred             cCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHH
Q 044084           73 SGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEV  152 (343)
Q Consensus        73 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  152 (343)
                      .|.+++|+++++.+++.+ +.|..++-.=+...-..|+.-+|++-+....+.-+ .|...|.-+...|...|++++|.-.
T Consensus        99 ~~~~~~A~e~y~~lL~dd-pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~F~-~D~EAW~eLaeiY~~~~~f~kA~fC  176 (289)
T KOG3060|consen   99 TGNYKEAIEYYESLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDKFM-NDQEAWHELAEIYLSEGDFEKAAFC  176 (289)
T ss_pred             hhchhhHHHHHHHHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHHhc-CcHHHHHHHHHHHHhHhHHHHHHHH
Confidence            344555555555555443 22333443333333333444444444444444322 2555555555555555555555555


Q ss_pred             HHHHHhc
Q 044084          153 VESMKNA  159 (343)
Q Consensus       153 ~~~~~~~  159 (343)
                      ++++.-.
T Consensus       177 lEE~ll~  183 (289)
T KOG3060|consen  177 LEELLLI  183 (289)
T ss_pred             HHHHHHc
Confidence            5554433

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

Probab=98.56  E-value=7.7e-06  Score=58.43  Aligned_cols=89  Identities=10%  Similarity=-0.034  Sum_probs=36.6

Q ss_pred             HHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHH
Q 044084          103 CSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYW  182 (343)
Q Consensus       103 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  182 (343)
                      ..+...|++++|...++.+...+.. +...+..+...+...|++++|..+++.....++ .+...+..+..++...|+++
T Consensus        25 ~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~~la~~~~~~g~~~  102 (135)
T TIGR02552        25 YNLYQQGRYDEALKLFQLLAAYDPY-NSRYWLGLAACCQMLKEYEEAIDAYALAAALDP-DDPRPYFHAAECLLALGEPE  102 (135)
T ss_pred             HHHHHcccHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CChHHHHHHHHHHHHcCCHH
Confidence            3334444444444444444433321 334444444444444444444444444433332 22233333344444444444


Q ss_pred             HHHHHHHHHHH
Q 044084          183 AAVKVYEQLIS  193 (343)
Q Consensus       183 ~a~~~~~~~~~  193 (343)
                      +|...|+...+
T Consensus       103 ~A~~~~~~al~  113 (135)
T TIGR02552       103 SALKALDLAIE  113 (135)
T ss_pred             HHHHHHHHHHH
Confidence            44444444443

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

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

Probab=98.54  E-value=0.00011  Score=65.19  Aligned_cols=211  Identities=14%  Similarity=0.118  Sum_probs=111.2

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhC---------CCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCC
Q 044084           21 DSGCYCQIMEAFYKIGDSEKVAALFLECESR---------KLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGI   91 (343)
Q Consensus        21 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---------~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~   91 (343)
                      +...|..+...|.+..+++-|.-.+-.|...         ...++  ...+-  ..-.....|-.++|..+|++-++   
T Consensus       756 S~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~--e~eak--vAvLAieLgMlEeA~~lYr~ckR---  828 (1416)
T KOG3617|consen  756 SDSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQNGE--EDEAK--VAVLAIELGMLEEALILYRQCKR---  828 (1416)
T ss_pred             hhHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhCCc--chhhH--HHHHHHHHhhHHHHHHHHHHHHH---
Confidence            3345666666666666665555444433211         01110  01111  12222345666666666666554   


Q ss_pred             CCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHh----------cCC
Q 044084           92 LEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKN----------AEL  161 (343)
Q Consensus        92 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~----------~~~  161 (343)
                            |..|=..|-..|.+++|.++-+.--+..+   ..||......+-..++.+.|++.|++...          ..+
T Consensus       829 ------~DLlNKlyQs~g~w~eA~eiAE~~DRiHL---r~Tyy~yA~~Lear~Di~~AleyyEK~~~hafev~rmL~e~p  899 (1416)
T KOG3617|consen  829 ------YDLLNKLYQSQGMWSEAFEIAETKDRIHL---RNTYYNYAKYLEARRDIEAALEYYEKAGVHAFEVFRMLKEYP  899 (1416)
T ss_pred             ------HHHHHHHHHhcccHHHHHHHHhhccceeh---hhhHHHHHHHHHhhccHHHHHHHHHhcCChHHHHHHHHHhCh
Confidence                  33344455556667766666443222221   23444444555555666666666654311          111


Q ss_pred             ---------CCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCC
Q 044084          162 ---------NISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFD  232 (343)
Q Consensus       162 ---------~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  232 (343)
                               ..+...|......+-..|+.+.|+.+|....+         |-.+++..|-.|+.++|-++-++   .   
T Consensus       900 ~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D---------~fs~VrI~C~qGk~~kAa~iA~e---s---  964 (1416)
T KOG3617|consen  900 KQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAKD---------YFSMVRIKCIQGKTDKAARIAEE---S---  964 (1416)
T ss_pred             HHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhhh---------hhhheeeEeeccCchHHHHHHHh---c---
Confidence                     11222344444444455666666666655443         33455555666777777665443   2   


Q ss_pred             cChhhHHHHHHHHHccCChHHHHHHHHHHh
Q 044084          233 KCVVAYSSMVAMYGKTGRIRDAMRLVAKMK  262 (343)
Q Consensus       233 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~  262 (343)
                      -|......+.+.|-..|++.+|..+|.+..
T Consensus       965 gd~AAcYhlaR~YEn~g~v~~Av~FfTrAq  994 (1416)
T KOG3617|consen  965 GDKAACYHLARMYENDGDVVKAVKFFTRAQ  994 (1416)
T ss_pred             ccHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence            356667788889999999999998887765

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

Probab=98.52  E-value=6.6e-06  Score=58.78  Aligned_cols=97  Identities=11%  Similarity=0.077  Sum_probs=49.5

Q ss_pred             HHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHH
Q 044084          131 EVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAY  210 (343)
Q Consensus       131 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~  210 (343)
                      .....+...+...|++++|.+.|+.+...++ .+...+..+..++...|++++|...+++..+.+ +.+...+..+...+
T Consensus        18 ~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~   95 (135)
T TIGR02552        18 EQIYALAYNLYQQGRYDEALKLFQLLAAYDP-YNSRYWLGLAACCQMLKEYEEAIDAYALAAALD-PDDPRPYFHAAECL   95 (135)
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCChHHHHHHHHHH
Confidence            3444455555555555555555555554433 234445555555555555555555555554442 22334444444455


Q ss_pred             HccCChhHHHHHHHHHHHc
Q 044084          211 CRIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       211 ~~~~~~~~a~~~~~~~~~~  229 (343)
                      ...|++++|...|+...+.
T Consensus        96 ~~~g~~~~A~~~~~~al~~  114 (135)
T TIGR02552        96 LALGEPESALKALDLAIEI  114 (135)
T ss_pred             HHcCCHHHHHHHHHHHHHh
Confidence            5555555555555555543

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

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=98.50  E-value=6.7e-05  Score=67.81  Aligned_cols=182  Identities=12%  Similarity=0.038  Sum_probs=128.7

Q ss_pred             hhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHH
Q 044084            3 SQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKF   82 (343)
Q Consensus         3 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~   82 (343)
                      .+.|+..|-+..+..+ -=...|..|...|....+..+|.+.|+...+.+    +.+...+......|++..+++.|..+
T Consensus       474 ~~~al~ali~alrld~-~~apaf~~LG~iYrd~~Dm~RA~kCf~KAFeLD----atdaeaaaa~adtyae~~~we~a~~I  548 (1238)
T KOG1127|consen  474 SALALHALIRALRLDV-SLAPAFAFLGQIYRDSDDMKRAKKCFDKAFELD----ATDAEAAAASADTYAEESTWEEAFEI  548 (1238)
T ss_pred             HHHHHHHHHHHHhccc-chhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC----chhhhhHHHHHHHhhccccHHHHHHH
Confidence            4556666666665432 124579999999999889999999999886544    44568888999999999999999988


Q ss_pred             HHHHHhcCCC-CChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCC
Q 044084           83 FRDMKEKGIL-EDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAEL  161 (343)
Q Consensus        83 ~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  161 (343)
                      .-..-+.... .-...|....-.+...++...+..-|+...+..+. |...|..++.+|.+.|++..|.++|.+....++
T Consensus       549 ~l~~~qka~a~~~k~nW~~rG~yyLea~n~h~aV~~fQsALR~dPk-D~n~W~gLGeAY~~sGry~~AlKvF~kAs~LrP  627 (1238)
T KOG1127|consen  549 CLRAAQKAPAFACKENWVQRGPYYLEAHNLHGAVCEFQSALRTDPK-DYNLWLGLGEAYPESGRYSHALKVFTKASLLRP  627 (1238)
T ss_pred             HHHHhhhchHHHHHhhhhhccccccCccchhhHHHHHHHHhcCCch-hHHHHHHHHHHHHhcCceehHHHhhhhhHhcCc
Confidence            4333322110 01122333444567888899999999998887764 899999999999999999999999998876543


Q ss_pred             CCchhhHHHHH--HHHhcCCcHHHHHHHHHHHHH
Q 044084          162 NISDCISCVIV--NGFSKRRAYWAAVKVYEQLIS  193 (343)
Q Consensus       162 ~~~~~~~~~l~--~~~~~~~~~~~a~~~~~~~~~  193 (343)
                        +. +|....  ..-+..|.+.++...+.....
T Consensus       628 --~s-~y~~fk~A~~ecd~GkYkeald~l~~ii~  658 (1238)
T KOG1127|consen  628 --LS-KYGRFKEAVMECDNGKYKEALDALGLIIY  658 (1238)
T ss_pred             --Hh-HHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence              21 333222  223457788888777776654

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=98.48  E-value=5.2e-05  Score=66.52  Aligned_cols=188  Identities=16%  Similarity=0.195  Sum_probs=117.2

Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCc
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRA  180 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  180 (343)
                      .+.+....+.|.+|..+++.+.....  -...|..+...|...|+++.|.++|.+.-         .++--|..|.+.|+
T Consensus       738 aieaai~akew~kai~ildniqdqk~--~s~yy~~iadhyan~~dfe~ae~lf~e~~---------~~~dai~my~k~~k  806 (1636)
T KOG3616|consen  738 AIEAAIGAKEWKKAISILDNIQDQKT--ASGYYGEIADHYANKGDFEIAEELFTEAD---------LFKDAIDMYGKAGK  806 (1636)
T ss_pred             HHHHHhhhhhhhhhHhHHHHhhhhcc--ccccchHHHHHhccchhHHHHHHHHHhcc---------hhHHHHHHHhcccc
Confidence            34455566777888888777776542  34456677778888888888888775542         24556777888888


Q ss_pred             HHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHH
Q 044084          181 YWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAK  260 (343)
Q Consensus       181 ~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  260 (343)
                      |+.|.++-.+..  |.......|..-..-.-..|++.+|++++-.+..    |+     ..|.+|-+.|..+..+++..+
T Consensus       807 w~da~kla~e~~--~~e~t~~~yiakaedldehgkf~eaeqlyiti~~----p~-----~aiqmydk~~~~ddmirlv~k  875 (1636)
T KOG3616|consen  807 WEDAFKLAEECH--GPEATISLYIAKAEDLDEHGKFAEAEQLYITIGE----PD-----KAIQMYDKHGLDDDMIRLVEK  875 (1636)
T ss_pred             HHHHHHHHHHhc--CchhHHHHHHHhHHhHHhhcchhhhhheeEEccC----ch-----HHHHHHHhhCcchHHHHHHHH
Confidence            888877765543  2233344454444555667777777776643322    22     345667777777777666655


Q ss_pred             HhhCCCCchHHHHHHHHHHHhcccChhHHHh-------HHHHHHHHHhcCCHHHHHHHHH
Q 044084          261 MKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK-------YTTVISAYNMAREFDMCVKFYN  313 (343)
Q Consensus       261 m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~-------~~~l~~~~~~~g~~~~a~~~~~  313 (343)
                      -....   -..|...+..-|...|++..|+.       |...+..|...+.+++|.++-+
T Consensus       876 ~h~d~---l~dt~~~f~~e~e~~g~lkaae~~flea~d~kaavnmyk~s~lw~dayriak  932 (1636)
T KOG3616|consen  876 HHGDH---LHDTHKHFAKELEAEGDLKAAEEHFLEAGDFKAAVNMYKASELWEDAYRIAK  932 (1636)
T ss_pred             hChhh---hhHHHHHHHHHHHhccChhHHHHHHHhhhhHHHHHHHhhhhhhHHHHHHHHh
Confidence            43211   12344556666677777777765       6777777777777777665544

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.42  E-value=4.1e-07  Score=47.75  Aligned_cols=33  Identities=30%  Similarity=0.667  Sum_probs=23.2

Q ss_pred             hHHHHHHHHHccCChHHHHHHHHHHhhCCCCch
Q 044084          237 AYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPN  269 (343)
Q Consensus       237 ~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~  269 (343)
                      +|+++|.+|++.|++++|.++|++|.+.|+.||
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            566777777777777777777777777776665

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.

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

Probab=98.42  E-value=6.3e-05  Score=57.80  Aligned_cols=193  Identities=13%  Similarity=0.133  Sum_probs=129.5

Q ss_pred             HHHHHHHHHhhccCcHHHHH-HHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 044084           61 HMYKILCDSLGKSGRAFEIL-KFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLM  139 (343)
Q Consensus        61 ~~~~~li~~~~~~~~~~~a~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  139 (343)
                      .....+......-++.+.-+ ++.+.+.......+......-...|+..+++++|++......      +......=...
T Consensus        73 qAvr~~a~~~~~e~~~~~~~~~l~E~~a~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~~~------~lE~~Al~VqI  146 (299)
T KOG3081|consen   73 QAVRLLAEYLELESNKKSILASLYELVADSTDGSNLIDLLLAAIIYMHDGDFDEALKALHLGE------NLEAAALNVQI  146 (299)
T ss_pred             HHHHHHHHHhhCcchhHHHHHHHHHHHHhhccchhHHHHHHhhHHhhcCCChHHHHHHHhccc------hHHHHHHHHHH
Confidence            33333333333344444333 444555444444343444444567889999999999887621      33344444566


Q ss_pred             HHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhc----CCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCC
Q 044084          140 YIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSK----RRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGL  215 (343)
Q Consensus       140 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~  215 (343)
                      +.+..+.+-|.+.+++|.+.   .+..|.+-|..++.+    .+....|.-+|++|-++ .+|+..+.+-...++...|+
T Consensus       147 ~lk~~r~d~A~~~lk~mq~i---ded~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~  222 (299)
T KOG3081|consen  147 LLKMHRFDLAEKELKKMQQI---DEDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGR  222 (299)
T ss_pred             HHHHHHHHHHHHHHHHHHcc---chHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcC
Confidence            77888899999999999875   344566656666554    56788999999999875 47899999999999999999


Q ss_pred             hhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChH-HHHHHHHHHhhC
Q 044084          216 YSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIR-DAMRLVAKMKPK  264 (343)
Q Consensus       216 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~-~a~~~~~~m~~~  264 (343)
                      +++|+.+++...... ..++.+...++.+-...|... ...+.+.+++..
T Consensus       223 ~eeAe~lL~eaL~kd-~~dpetL~Nliv~a~~~Gkd~~~~~r~l~QLk~~  271 (299)
T KOG3081|consen  223 YEEAESLLEEALDKD-AKDPETLANLIVLALHLGKDAEVTERNLSQLKLS  271 (299)
T ss_pred             HHHHHHHHHHHHhcc-CCCHHHHHHHHHHHHHhCCChHHHHHHHHHHHhc
Confidence            999999999998875 345666666666555566543 345566666654

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

Probab=98.40  E-value=6.3e-05  Score=63.02  Aligned_cols=119  Identities=13%  Similarity=0.191  Sum_probs=57.0

Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCc
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRA  180 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  180 (343)
                      ++..+...++++.|..+++++.+..  |+  ....+++.+...++-.+|.+++.+..+..+ .+......-...+...++
T Consensus       175 Ll~~l~~t~~~~~ai~lle~L~~~~--pe--v~~~LA~v~l~~~~E~~AI~ll~~aL~~~p-~d~~LL~~Qa~fLl~k~~  249 (395)
T PF09295_consen  175 LLKYLSLTQRYDEAIELLEKLRERD--PE--VAVLLARVYLLMNEEVEAIRLLNEALKENP-QDSELLNLQAEFLLSKKK  249 (395)
T ss_pred             HHHHHhhcccHHHHHHHHHHHHhcC--Cc--HHHHHHHHHHhcCcHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhcCC
Confidence            3334444455555555555555443  22  222344444445555555555555543332 233334444444555555


Q ss_pred             HHHHHHHHHHHHHcCCCCCH-hhHHHHHHHHHccCChhHHHHHHHHH
Q 044084          181 YWAAVKVYEQLISQGCIPGQ-VTYASIINAYCRIGLYSKAEKVFIEM  226 (343)
Q Consensus       181 ~~~a~~~~~~~~~~~~~p~~-~~~~~ll~~~~~~~~~~~a~~~~~~~  226 (343)
                      ++.|.++.+++.+.  .|+. .+|..|..+|.+.|+++.|...++.+
T Consensus       250 ~~lAL~iAk~av~l--sP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~  294 (395)
T PF09295_consen  250 YELALEIAKKAVEL--SPSEFETWYQLAECYIQLGDFENALLALNSC  294 (395)
T ss_pred             HHHHHHHHHHHHHh--CchhHHHHHHHHHHHHhcCCHHHHHHHHhcC
Confidence            55555555555544  2332 35555555555555555555555443

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

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

Probab=98.39  E-value=0.0011  Score=56.97  Aligned_cols=114  Identities=12%  Similarity=0.086  Sum_probs=67.7

Q ss_pred             hHHHHHHHHhcCCcHHHHHHHHH--------HHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHc------CCC
Q 044084          167 ISCVIVNGFSKRRAYWAAVKVYE--------QLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQK------GFD  232 (343)
Q Consensus       167 ~~~~l~~~~~~~~~~~~a~~~~~--------~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~------~~~  232 (343)
                      +...++......|+++.|.+++.        .+.+.+..|  .+...+...+.+.++-+.|..++......      +-.
T Consensus       378 v~L~~aQl~is~gn~~~A~~il~~~~~~~~ss~~~~~~~P--~~V~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~  455 (652)
T KOG2376|consen  378 VLLLRAQLKISQGNPEVALEILSLFLESWKSSILEAKHLP--GTVGAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGSI  455 (652)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhhhhhhhhhhccCh--hHHHHHHHHHHhccCCccHHHHHHHHHHHHHHhcccch
Confidence            33445555666777777777777        444444333  34445555566666666666666655432      101


Q ss_pred             cChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcc
Q 044084          233 KCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRA  283 (343)
Q Consensus       233 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~  283 (343)
                      .-..++..+...-.+.|+-++|..+++++.+.+ .+|..+...++.+|++.
T Consensus       456 ~l~~~~~~aa~f~lr~G~~~ea~s~leel~k~n-~~d~~~l~~lV~a~~~~  505 (652)
T KOG2376|consen  456 ALLSLMREAAEFKLRHGNEEEASSLLEELVKFN-PNDTDLLVQLVTAYARL  505 (652)
T ss_pred             HHHhHHHHHhHHHHhcCchHHHHHHHHHHHHhC-CchHHHHHHHHHHHHhc
Confidence            112234444445556788888888888888752 55777777777777764

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

Probab=98.39  E-value=0.0001  Score=65.53  Aligned_cols=234  Identities=16%  Similarity=0.147  Sum_probs=155.2

Q ss_pred             ChhhHHHHHH--HHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhc-C-------
Q 044084           21 DSGCYCQIME--AFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEK-G-------   90 (343)
Q Consensus        21 ~~~~~~~l~~--~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-~-------   90 (343)
                      |..|-..+++  .|...|+.+.|.+-.+-+++         ...|..+.+.|.+.++++-|.-.+..|... |       
T Consensus       725 d~~TRkaml~FSfyvtiG~MD~AfksI~~IkS---------~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a  795 (1416)
T KOG3617|consen  725 DESTRKAMLDFSFYVTIGSMDAAFKSIQFIKS---------DSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRA  795 (1416)
T ss_pred             CHHHHHhhhceeEEEEeccHHHHHHHHHHHhh---------hHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHH
Confidence            4445555554  46778999999888776644         367999999999999988887666666432 1       


Q ss_pred             -CCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHH
Q 044084           91 -ILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISC  169 (343)
Q Consensus        91 -~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  169 (343)
                       -.|+ .+=..+.......|.+++|+.+|.+-.+..         .|=..|...|.|++|.++-+.--+..+.   .||.
T Consensus       796 ~q~~~-e~eakvAvLAieLgMlEeA~~lYr~ckR~D---------LlNKlyQs~g~w~eA~eiAE~~DRiHLr---~Tyy  862 (1416)
T KOG3617|consen  796 QQNGE-EDEAKVAVLAIELGMLEEALILYRQCKRYD---------LLNKLYQSQGMWSEAFEIAETKDRIHLR---NTYY  862 (1416)
T ss_pred             HhCCc-chhhHHHHHHHHHhhHHHHHHHHHHHHHHH---------HHHHHHHhcccHHHHHHHHhhccceehh---hhHH
Confidence             1122 222223334557788999999998877632         3446677889999999987765443332   2566


Q ss_pred             HHHHHHhcCCcHHHHHHHHHHHH----------HcC---------CCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcC
Q 044084          170 VIVNGFSKRRAYWAAVKVYEQLI----------SQG---------CIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKG  230 (343)
Q Consensus       170 ~l~~~~~~~~~~~~a~~~~~~~~----------~~~---------~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  230 (343)
                      .....+...++.+.|++.|++..          ...         -..|...|......+-..|+.+.|+.++.....  
T Consensus       863 ~yA~~Lear~Di~~AleyyEK~~~hafev~rmL~e~p~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D--  940 (1416)
T KOG3617|consen  863 NYAKYLEARRDIEAALEYYEKAGVHAFEVFRMLKEYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAKD--  940 (1416)
T ss_pred             HHHHHHHhhccHHHHHHHHHhcCChHHHHHHHHHhChHHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhhh--
Confidence            66677777888888888877532          111         012334445555555567777777777765443  


Q ss_pred             CCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh
Q 044084          231 FDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK  291 (343)
Q Consensus       231 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~  291 (343)
                             |-++++..+-.|+.++|-++-++--      |......|.+.|-..|++.+|..
T Consensus       941 -------~fs~VrI~C~qGk~~kAa~iA~esg------d~AAcYhlaR~YEn~g~v~~Av~  988 (1416)
T KOG3617|consen  941 -------YFSMVRIKCIQGKTDKAARIAEESG------DKAACYHLARMYENDGDVVKAVK  988 (1416)
T ss_pred             -------hhhheeeEeeccCchHHHHHHHhcc------cHHHHHHHHHHhhhhHHHHHHHH
Confidence                   5567777788888888887765532      55556667777888888777766

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.38  E-value=6.2e-07  Score=46.68  Aligned_cols=33  Identities=27%  Similarity=0.548  Sum_probs=19.4

Q ss_pred             hhHHHHHHHHHccCChHHHHHHHHHHhhCCCCc
Q 044084          236 VAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEP  268 (343)
Q Consensus       236 ~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p  268 (343)
                      .+|+.++.+|++.|+++.|.++|++|.+.|++|
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            355566666666666666666666666555554

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

Probab=98.37  E-value=3.6e-05  Score=64.40  Aligned_cols=126  Identities=7%  Similarity=0.085  Sum_probs=104.0

Q ss_pred             HHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHH
Q 044084          131 EVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAY  210 (343)
Q Consensus       131 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~  210 (343)
                      .....|+..+...++++.|+++|+++.+..  |+  ....+++.+...++..+|.+++++..+.. +-+......-...+
T Consensus       170 yLv~~Ll~~l~~t~~~~~ai~lle~L~~~~--pe--v~~~LA~v~l~~~~E~~AI~ll~~aL~~~-p~d~~LL~~Qa~fL  244 (395)
T PF09295_consen  170 YLVDTLLKYLSLTQRYDEAIELLEKLRERD--PE--VAVLLARVYLLMNEEVEAIRLLNEALKEN-PQDSELLNLQAEFL  244 (395)
T ss_pred             HHHHHHHHHHhhcccHHHHHHHHHHHHhcC--Cc--HHHHHHHHHHhcCcHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH
Confidence            345566777778899999999999999876  33  45567888888899999999999998763 34556666667778


Q ss_pred             HccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHh
Q 044084          211 CRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMK  262 (343)
Q Consensus       211 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~  262 (343)
                      .+.++++.|..+.+++.+.. |-+..+|..|..+|.+.|+++.|+..++.+.
T Consensus       245 l~k~~~~lAL~iAk~av~ls-P~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  245 LSKKKYELALEIAKKAVELS-PSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             HhcCCHHHHHHHHHHHHHhC-chhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            89999999999999999975 4456799999999999999999999988875

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

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

Probab=98.36  E-value=3.9e-05  Score=55.42  Aligned_cols=118  Identities=10%  Similarity=-0.018  Sum_probs=52.3

Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCCh--HhHHHHHHHHhcccCHH
Q 044084           35 IGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDP--SVYASLICSFASIAEVK  112 (343)
Q Consensus        35 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~~~~~  112 (343)
                      .++...+...++.+.+...... ......-.+...+...|++++|...|+........|+.  .....+...+...|+++
T Consensus        24 ~~~~~~~~~~~~~l~~~~~~s~-ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~~d  102 (145)
T PF09976_consen   24 AGDPAKAEAAAEQLAKDYPSSP-YAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRLARILLQQGQYD  102 (145)
T ss_pred             CCCHHHHHHHHHHHHHHCCCCh-HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHH
Confidence            4555555555555544432211 11122223344555555555555555555554311111  12222344445555555


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHH
Q 044084          113 VAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVES  155 (343)
Q Consensus       113 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  155 (343)
                      +|+..++......  .....+......|.+.|++++|...|+.
T Consensus       103 ~Al~~L~~~~~~~--~~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen  103 EALATLQQIPDEA--FKALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHHHhccCcc--hHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            5555554422211  2233444455555555555555555543

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.36  E-value=8.4e-07  Score=46.51  Aligned_cols=32  Identities=16%  Similarity=0.436  Sum_probs=14.0

Q ss_pred             HHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCC
Q 044084          168 SCVIVNGFSKRRAYWAAVKVYEQLISQGCIPG  199 (343)
Q Consensus       168 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~  199 (343)
                      |+.+|.+|++.|++++|.++|++|.+.|+.||
T Consensus         3 ~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         3 YNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            44444444444444444444444444444443

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.

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

Probab=98.36  E-value=8.9e-06  Score=53.73  Aligned_cols=89  Identities=13%  Similarity=0.116  Sum_probs=69.5

Q ss_pred             HHHHHHHHHccCChHHHHHHHHHHhhCCC-CchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 044084          238 YSSMVAMYGKTGRIRDAMRLVAKMKPKGC-EPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFR  316 (343)
Q Consensus       238 ~~~l~~~~~~~~~~~~a~~~~~~m~~~~~-~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~  316 (343)
                      ....|..+...+++.....+|+.++..|+ .|+..+|+.++++..+..--..+           -.++.-..+.+|++|.
T Consensus        28 ~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~-----------ie~kl~~LLtvYqDiL   96 (120)
T PF08579_consen   28 QIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSED-----------IENKLTNLLTVYQDIL   96 (120)
T ss_pred             HHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchh-----------HHHHHHHHHHHHHHHH
Confidence            34556666677899999999999999998 89999999999887764322111           1234556789999999


Q ss_pred             hCCCCccHHHHHHHHHHHhcc
Q 044084          317 MNGGVIDRAMAGIMVGVFSKL  337 (343)
Q Consensus       317 ~~~~~p~~~~~~~l~~~~~~~  337 (343)
                      ..+++|+..||+.++..+.+.
T Consensus        97 ~~~lKP~~etYnivl~~Llkg  117 (120)
T PF08579_consen   97 SNKLKPNDETYNIVLGSLLKG  117 (120)
T ss_pred             HhccCCcHHHHHHHHHHHHHh
Confidence            999999999999999988764

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 [, , ].

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

Probab=98.35  E-value=1.1e-05  Score=67.77  Aligned_cols=124  Identities=11%  Similarity=0.053  Sum_probs=90.3

Q ss_pred             CCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcC--CCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhh
Q 044084          125 GMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAE--LNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVT  202 (343)
Q Consensus       125 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~  202 (343)
                      +.+.+......++.......+++.+..++.+.....  ...-..|..++++.|...|..+.++.+++.=...|+-||..+
T Consensus        61 ~~~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s  140 (429)
T PF10037_consen   61 KKPVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFS  140 (429)
T ss_pred             CCCCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhh
Confidence            333466677777777777777888888887776542  212233556888888888888888888888888888888888


Q ss_pred             HHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHcc
Q 044084          203 YASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKT  248 (343)
Q Consensus       203 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  248 (343)
                      ++.+|..+.+.|++..|.++...|...+...+..|+..-+.+|.+.
T Consensus       141 ~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  141 FNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            8888888888888888888888877766556666666555555544

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 [].

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

Probab=98.34  E-value=5.8e-05  Score=54.53  Aligned_cols=13  Identities=15%  Similarity=0.256  Sum_probs=4.7

Q ss_pred             cCHHHHHHHHHHH
Q 044084          109 AEVKVAEELFKEA  121 (343)
Q Consensus       109 ~~~~~a~~~~~~~  121 (343)
                      |++++|...|+.+
T Consensus        62 g~~~~A~~~l~~~   74 (145)
T PF09976_consen   62 GDYDEAKAALEKA   74 (145)
T ss_pred             CCHHHHHHHHHHH
Confidence            3333333333333

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.33  E-value=9.4e-07  Score=45.98  Aligned_cols=32  Identities=31%  Similarity=0.539  Sum_probs=15.2

Q ss_pred             HHHHHHHHhhccCcHHHHHHHHHHHHhcCCCC
Q 044084           62 MYKILCDSLGKSGRAFEILKFFRDMKEKGILE   93 (343)
Q Consensus        62 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~   93 (343)
                      +|+.+|.+|++.|+++.|.++|++|.+.|++|
T Consensus         3 ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    3 TYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            34444444444444444444444444444443

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

Probab=98.33  E-value=1.6e-05  Score=66.87  Aligned_cols=119  Identities=14%  Similarity=0.116  Sum_probs=85.0

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhc--CCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEK--GILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLV  137 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  137 (343)
                      ......+++.+....+.+.+..++.+....  ....-+.|..++++.|.+.|..+.+..++..=...|+-||..++|.||
T Consensus        66 ~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~n~Lm  145 (429)
T PF10037_consen   66 SLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSFNLLM  145 (429)
T ss_pred             HHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhHHHHH
Confidence            455666777777777788888887777665  222334455678888888888888888888878888888888888888


Q ss_pred             HHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcC
Q 044084          138 LMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKR  178 (343)
Q Consensus       138 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  178 (343)
                      +.+.+.|++..|.++...|...+...+..|+...+.+|.+-
T Consensus       146 d~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  146 DHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            88888888888888887776655545555555555544443

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 [].

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=98.32  E-value=0.0023  Score=57.72  Aligned_cols=220  Identities=10%  Similarity=0.114  Sum_probs=130.8

Q ss_pred             CchhhHHHHHHHHHhCCCCCChhhHHHHHHH--HHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHH
Q 044084            1 TNSQSKLHYYEKMKSAGIVLDSGCYCQIMEA--FYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFE   78 (343)
Q Consensus         1 ~~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~   78 (343)
                      +++++|++..+.+.+..  |+.. |...+.+  ..+.|+.++|..+++.....+..    +..+...+-.+|...++.++
T Consensus        23 ~qfkkal~~~~kllkk~--Pn~~-~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~----D~~tLq~l~~~y~d~~~~d~   95 (932)
T KOG2053|consen   23 SQFKKALAKLGKLLKKH--PNAL-YAKVLKALSLFRLGKGDEALKLLEALYGLKGT----DDLTLQFLQNVYRDLGKLDE   95 (932)
T ss_pred             HHHHHHHHHHHHHHHHC--CCcH-HHHHHHHHHHHHhcCchhHHHHHhhhccCCCC----chHHHHHHHHHHHHHhhhhH
Confidence            36778888888888763  4443 3444444  46889999999888877655443    36888889999999999999


Q ss_pred             HHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCc----------HhH
Q 044084           79 ILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGM----------VEK  148 (343)
Q Consensus        79 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~  148 (343)
                      |..+|++....  .|+......+..+|.+.+++.+-.++--++.+.-+ ..+..+=++++.+.+.-.          ..-
T Consensus        96 ~~~~Ye~~~~~--~P~eell~~lFmayvR~~~yk~qQkaa~~LyK~~p-k~~yyfWsV~Slilqs~~~~~~~~~~i~l~L  172 (932)
T KOG2053|consen   96 AVHLYERANQK--YPSEELLYHLFMAYVREKSYKKQQKAALQLYKNFP-KRAYYFWSVISLILQSIFSENELLDPILLAL  172 (932)
T ss_pred             HHHHHHHHHhh--CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-cccchHHHHHHHHHHhccCCcccccchhHHH
Confidence            99999988775  56677777788888888877665555444444322 244444444444443211          123


Q ss_pred             HHHHHHHHHhcC-CCCchhhHHHHHHHHhcCCcHHHHHHHHH-HHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHH
Q 044084          149 TLEVVESMKNAE-LNISDCISCVIVNGFSKRRAYWAAVKVYE-QLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEM  226 (343)
Q Consensus       149 a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~-~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~  226 (343)
                      |...++.+.+.+ ..-+..-.......+...|++++|.+++. ...+.-..-+...-+.-+..+...+++.+..++-.++
T Consensus       173 A~~m~~~~l~~~gk~~s~aE~~Lyl~iL~~~~k~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l~~~L  252 (932)
T KOG2053|consen  173 AEKMVQKLLEKKGKIESEAEIILYLLILELQGKYQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFELSSRL  252 (932)
T ss_pred             HHHHHHHHhccCCccchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHHHHHH
Confidence            444455544433 21121112222333445677777777773 3333222222333334455555556666655555555


Q ss_pred             HHcC
Q 044084          227 QQKG  230 (343)
Q Consensus       227 ~~~~  230 (343)
                      ...|
T Consensus       253 l~k~  256 (932)
T KOG2053|consen  253 LEKG  256 (932)
T ss_pred             HHhC
Confidence            5544

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

Probab=98.29  E-value=2.3e-05  Score=51.85  Aligned_cols=79  Identities=13%  Similarity=0.127  Sum_probs=47.7

Q ss_pred             HHHHHHHhhccCcHHHHHHHHHHHHhcCC-CCChHhHHHHHHHHhccc--------CHHHHHHHHHHHHHcCCCCCHHHH
Q 044084           63 YKILCDSLGKSGRAFEILKFFRDMKEKGI-LEDPSVYASLICSFASIA--------EVKVAEELFKEAEEKGMLRDLEVF  133 (343)
Q Consensus        63 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~--------~~~~a~~~~~~~~~~~~~~~~~~~  133 (343)
                      -...|..+...+++.....+|+.+++.|+ .|+..+|+.++.+.++..        ++-..+.+|+.|...+++|+..+|
T Consensus        28 ~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etY  107 (120)
T PF08579_consen   28 QIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETY  107 (120)
T ss_pred             HHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHH
Confidence            33445555556777777777777777777 677777777776655432        233445555566666666666666


Q ss_pred             HHHHHHHH
Q 044084          134 LKLVLMYI  141 (343)
Q Consensus       134 ~~l~~~~~  141 (343)
                      +.++..+.
T Consensus       108 nivl~~Ll  115 (120)
T PF08579_consen  108 NIVLGSLL  115 (120)
T ss_pred             HHHHHHHH
Confidence            66555544

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 [, , ].

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=98.24  E-value=0.0015  Score=58.78  Aligned_cols=224  Identities=13%  Similarity=0.113  Sum_probs=150.8

Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHh--hccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccC
Q 044084           33 YKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSL--GKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAE  110 (343)
Q Consensus        33 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~--~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  110 (343)
                      ...+++.+|......+.++.+..      .|...+.++  .+.|+.++|..+++.....+.. |..|...+-..|-..++
T Consensus        20 ld~~qfkkal~~~~kllkk~Pn~------~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~-D~~tLq~l~~~y~d~~~   92 (932)
T KOG2053|consen   20 LDSSQFKKALAKLGKLLKKHPNA------LYAKVLKALSLFRLGKGDEALKLLEALYGLKGT-DDLTLQFLQNVYRDLGK   92 (932)
T ss_pred             hhhHHHHHHHHHHHHHHHHCCCc------HHHHHHHHHHHHHhcCchhHHHHHhhhccCCCC-chHHHHHHHHHHHHHhh
Confidence            46688999999999988776432      355555554  5789999999999888776544 88899999999999999


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcC-C---------c
Q 044084          111 VKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKR-R---------A  180 (343)
Q Consensus       111 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~---------~  180 (343)
                      .+++..+|++.....  |+......+..+|.+.+.+.+-.++--++-+.-+ -+...+=++++..... .         -
T Consensus        93 ~d~~~~~Ye~~~~~~--P~eell~~lFmayvR~~~yk~qQkaa~~LyK~~p-k~~yyfWsV~Slilqs~~~~~~~~~~i~  169 (932)
T KOG2053|consen   93 LDEAVHLYERANQKY--PSEELLYHLFMAYVREKSYKKQQKAALQLYKNFP-KRAYYFWSVISLILQSIFSENELLDPIL  169 (932)
T ss_pred             hhHHHHHHHHHHhhC--CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-cccchHHHHHHHHHHhccCCcccccchh
Confidence            999999999998764  6677888888889988877654444333333211 2222333333333321 1         1


Q ss_pred             HHHHHHHHHHHHHcCCCC-CHhhHHHHHHHHHccCChhHHHHHHHH-HHHcCCCcChhhHHHHHHHHHccCChHHHHHHH
Q 044084          181 YWAAVKVYEQLISQGCIP-GQVTYASIINAYCRIGLYSKAEKVFIE-MQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLV  258 (343)
Q Consensus       181 ~~~a~~~~~~~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  258 (343)
                      ..-|.++++.+.+.+-+. +..-...-...+...|++++|..++.. ..+.-.+.+...-+.-+..+...+++.+..++-
T Consensus       170 l~LA~~m~~~~l~~~gk~~s~aE~~Lyl~iL~~~~k~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l~  249 (932)
T KOG2053|consen  170 LALAEKMVQKLLEKKGKIESEAEIILYLLILELQGKYQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFELS  249 (932)
T ss_pred             HHHHHHHHHHHhccCCccchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHHH
Confidence            234666777776654111 111222223445678899999999944 444433445555566778888899999999988


Q ss_pred             HHHhhCCC
Q 044084          259 AKMKPKGC  266 (343)
Q Consensus       259 ~~m~~~~~  266 (343)
                      .++...|.
T Consensus       250 ~~Ll~k~~  257 (932)
T KOG2053|consen  250 SRLLEKGN  257 (932)
T ss_pred             HHHHHhCC
Confidence            88888753

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=98.20  E-value=0.0032  Score=57.62  Aligned_cols=181  Identities=17%  Similarity=0.138  Sum_probs=127.8

Q ss_pred             HHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHH
Q 044084           76 AFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVES  155 (343)
Q Consensus        76 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  155 (343)
                      ...++..|-+..+.... -...|..|...|....+...|.+.|+...+.... +...+......|.+..+++.|..+.-.
T Consensus       474 ~~~al~ali~alrld~~-~apaf~~LG~iYrd~~Dm~RA~kCf~KAFeLDat-daeaaaa~adtyae~~~we~a~~I~l~  551 (1238)
T KOG1127|consen  474 SALALHALIRALRLDVS-LAPAFAFLGQIYRDSDDMKRAKKCFDKAFELDAT-DAEAAAASADTYAEESTWEEAFEICLR  551 (1238)
T ss_pred             HHHHHHHHHHHHhcccc-hhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCch-hhhhHHHHHHHhhccccHHHHHHHHHH
Confidence            56666666555554322 2457888888888888899999999998886543 678888899999999999999998444


Q ss_pred             HHhcCCCCchhh--HHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCc
Q 044084          156 MKNAELNISDCI--SCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDK  233 (343)
Q Consensus       156 ~~~~~~~~~~~~--~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~  233 (343)
                      ..+... .-...  |...--.|...++...+..-|+...+.. +-|...|..+..+|.++|++..|.++|.+.....  |
T Consensus       552 ~~qka~-a~~~k~nW~~rG~yyLea~n~h~aV~~fQsALR~d-PkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~Lr--P  627 (1238)
T KOG1127|consen  552 AAQKAP-AFACKENWVQRGPYYLEAHNLHGAVCEFQSALRTD-PKDYNLWLGLGEAYPESGRYSHALKVFTKASLLR--P  627 (1238)
T ss_pred             Hhhhch-HHHHHhhhhhccccccCccchhhHHHHHHHHhcCC-chhHHHHHHHHHHHHhcCceehHHHhhhhhHhcC--c
Confidence            433322 11112  2233345667788888888888877764 4567888999999999999999999998887754  4


Q ss_pred             ChhhHHHH--HHHHHccCChHHHHHHHHHHhh
Q 044084          234 CVVAYSSM--VAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       234 ~~~~~~~l--~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                      + ..|...  ....+..|.+.+|...+.....
T Consensus       628 ~-s~y~~fk~A~~ecd~GkYkeald~l~~ii~  658 (1238)
T KOG1127|consen  628 L-SKYGRFKEAVMECDNGKYKEALDALGLIIY  658 (1238)
T ss_pred             H-hHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            2 233322  2334567888888888877764

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=98.15  E-value=0.00017  Score=50.07  Aligned_cols=22  Identities=14%  Similarity=0.312  Sum_probs=8.9

Q ss_pred             HHHHHhcCCcHHHHHHHHHHHH
Q 044084          171 IVNGFSKRRAYWAAVKVYEQLI  192 (343)
Q Consensus       171 l~~~~~~~~~~~~a~~~~~~~~  192 (343)
                      +..++...|+++.|.+.|+.+.
T Consensus        45 l~~~~~~~~~~~~A~~~~~~~~   66 (119)
T TIGR02795        45 LGEAYYAQGKYADAAKAFLAVV   66 (119)
T ss_pred             HHHHHHhhccHHHHHHHHHHHH
Confidence            3333444444444444444433

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.

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=98.15  E-value=0.00018  Score=49.90  Aligned_cols=59  Identities=19%  Similarity=0.111  Sum_probs=23.9

Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhc
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGMLR--DLEVFLKLVLMYIEEGMVEKTLEVVESMKNA  159 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  159 (343)
                      +..++.+.|+++.|...++.+....+..  ....+..+..++.+.|+.++|...++++.+.
T Consensus        45 l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~  105 (119)
T TIGR02795        45 LGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLGMSLQELGDKEKAKATLQQVIKR  105 (119)
T ss_pred             HHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHHHHHHHhCChHHHHHHHHHHHHH
Confidence            3444444444444444444444322110  1233334444444444444444444444433

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.

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

Probab=98.11  E-value=0.00025  Score=57.32  Aligned_cols=143  Identities=13%  Similarity=0.089  Sum_probs=93.6

Q ss_pred             HHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHH-HhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 044084           61 HMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICS-FASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLM  139 (343)
Q Consensus        61 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  139 (343)
                      .+|..+++..-+.+..+.|..+|.+.++.+ ..+...|...... +...++.+.|..+|+...+.- ..+...|...+..
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~-~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~f-~~~~~~~~~Y~~~   79 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDK-RCTYHVYVAYALMEYYCNKDPKRARKIFERGLKKF-PSDPDFWLEYLDF   79 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHHH-TT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHH
Confidence            467778888888888888888888887542 2234444444444 233466677888888877753 3477788888888


Q ss_pred             HHhcCcHhHHHHHHHHHHhcCCCCc---hhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHH
Q 044084          140 YIEEGMVEKTLEVVESMKNAELNIS---DCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIIN  208 (343)
Q Consensus       140 ~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~  208 (343)
                      +...++.+.|..+|++.... +.+.   ...|...+..-.+.|+.+.+.++.+++.+.  .|+...+..+++
T Consensus        80 l~~~~d~~~aR~lfer~i~~-l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~--~~~~~~~~~f~~  148 (280)
T PF05843_consen   80 LIKLNDINNARALFERAISS-LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL--FPEDNSLELFSD  148 (280)
T ss_dssp             HHHTT-HHHHHHHHHHHCCT-SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH--TTTS-HHHHHHC
T ss_pred             HHHhCcHHHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--hhhhhHHHHHHH
Confidence            88888888888888887755 3222   236778888778888888888888887775  344344444443

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.

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

Probab=98.10  E-value=0.00011  Score=59.35  Aligned_cols=130  Identities=15%  Similarity=0.123  Sum_probs=68.3

Q ss_pred             hHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH-HHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHH
Q 044084           97 VYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLM-YIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGF  175 (343)
Q Consensus        97 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  175 (343)
                      +|..+++..-+.+..+.|..+|.+..+.+. .+..+|...... |...++.+.|..+|+...+.-. .+...|...+..+
T Consensus         3 v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~-~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~f~-~~~~~~~~Y~~~l   80 (280)
T PF05843_consen    3 VWIQYMRFMRRTEGIEAARKVFKRARKDKR-CTYHVYVAYALMEYYCNKDPKRARKIFERGLKKFP-SDPDFWLEYLDFL   80 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-S-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHHHT-T-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCChHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHH
Confidence            455666666666666666666666654322 233444433333 2223445556666666554422 4445566666666


Q ss_pred             hcCCcHHHHHHHHHHHHHcCCCCCH---hhHHHHHHHHHccCChhHHHHHHHHHHHc
Q 044084          176 SKRRAYWAAVKVYEQLISQGCIPGQ---VTYASIINAYCRIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       176 ~~~~~~~~a~~~~~~~~~~~~~p~~---~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  229 (343)
                      ...++.+.|..+|++.... +.++.   ..|...+..=.+.|+.+.+.++..++.+.
T Consensus        81 ~~~~d~~~aR~lfer~i~~-l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~  136 (280)
T PF05843_consen   81 IKLNDINNARALFERAISS-LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL  136 (280)
T ss_dssp             HHTT-HHHHHHHHHHHCCT-SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH
T ss_pred             HHhCcHHHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            6666666666666666554 22211   25555555555566666666666665554

The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.

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

Probab=98.10  E-value=4.5e-06  Score=42.25  Aligned_cols=29  Identities=28%  Similarity=0.688  Sum_probs=16.5

Q ss_pred             hHHHHHHHHHccCChHHHHHHHHHHhhCC
Q 044084          237 AYSSMVAMYGKTGRIRDAMRLVAKMKPKG  265 (343)
Q Consensus       237 ~~~~l~~~~~~~~~~~~a~~~~~~m~~~~  265 (343)
                      +|+.++++|++.|++++|.++|++|.+.|
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g   30 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERG   30 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCc
Confidence            45555555555555555555555555544

Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.

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

Probab=98.08  E-value=0.00013  Score=48.01  Aligned_cols=89  Identities=22%  Similarity=0.283  Sum_probs=36.5

Q ss_pred             HHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCc
Q 044084           66 LCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGM  145 (343)
Q Consensus        66 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  145 (343)
                      +...+...|++++|...+++..+... .+...+..+...+...++++.|.+.++...+.... +..++..+...+...|+
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~   83 (100)
T cd00189           6 LGNLYYKLGDYDEALEYYEKALELDP-DNADAYYNLAAAYYKLGKYEEALEDYEKALELDPD-NAKAYYNLGLAYYKLGK   83 (100)
T ss_pred             HHHHHHHHhcHHHHHHHHHHHHhcCC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc-chhHHHHHHHHHHHHHh
Confidence            33334444444444444444433311 11233333344444444444444444444443221 22344444444444444


Q ss_pred             HhHHHHHHHHH
Q 044084          146 VEKTLEVVESM  156 (343)
Q Consensus       146 ~~~a~~~~~~~  156 (343)
                      +++|...+...
T Consensus        84 ~~~a~~~~~~~   94 (100)
T cd00189          84 YEEALEAYEKA   94 (100)
T ss_pred             HHHHHHHHHHH
Confidence            44444444443

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

Probab=98.06  E-value=0.0021  Score=54.79  Aligned_cols=178  Identities=13%  Similarity=0.138  Sum_probs=123.8

Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc---CcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHH
Q 044084          112 KVAEELFKEAEEKGMLRDLEVFLKLVLMYIEE---GMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVY  188 (343)
Q Consensus       112 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  188 (343)
                      +++.++++.....-...+..+|..+...--..   +..+...++++++......--..+|..++....+..-+..|..+|
T Consensus       310 ~e~~~~yEr~I~~l~~~~~~Ly~~~a~~eE~~~~~n~~~~~~~~~~~ll~~~~~~~tLv~~~~mn~irR~eGlkaaR~iF  389 (656)
T KOG1914|consen  310 DEAASIYERAIEGLLKENKLLYFALADYEESRYDDNKEKKVHEIYNKLLKIEDIDLTLVYCQYMNFIRRAEGLKAARKIF  389 (656)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHhcccchhhhhHHHHHHHHhhhccCCceehhHHHHHHHHhhhHHHHHHHH
Confidence            45555666555433333444444433321111   135667777777765443333447888999999999999999999


Q ss_pred             HHHHHcCCCC-CHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCC
Q 044084          189 EQLISQGCIP-GQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCE  267 (343)
Q Consensus       189 ~~~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~  267 (343)
                      .+..+.+..+ ++...++++..|| .++.+-|.++|+.=.+. +.-++.--...++.+...|+-..+..+|++....++.
T Consensus       390 ~kaR~~~r~~hhVfVa~A~mEy~c-skD~~~AfrIFeLGLkk-f~d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~  467 (656)
T KOG1914|consen  390 KKAREDKRTRHHVFVAAALMEYYC-SKDKETAFRIFELGLKK-FGDSPEYVLKYLDFLSHLNDDNNARALFERVLTSVLS  467 (656)
T ss_pred             HHHhhccCCcchhhHHHHHHHHHh-cCChhHHHHHHHHHHHh-cCCChHHHHHHHHHHHHhCcchhHHHHHHHHHhccCC
Confidence            9999988777 7778888888776 47899999999975544 1234445567888888999999999999999988666


Q ss_pred             chH--HHHHHHHHHHhcccChhHHHh
Q 044084          268 PNV--WIYNSLMDMHGRAKNLRQLEK  291 (343)
Q Consensus       268 p~~--~~~~~l~~~~~~~~~~~~a~~  291 (343)
                      ||.  ..|..+++-=..-|++..+.+
T Consensus       468 ~~ks~~Iw~r~l~yES~vGdL~si~~  493 (656)
T KOG1914|consen  468 ADKSKEIWDRMLEYESNVGDLNSILK  493 (656)
T ss_pred             hhhhHHHHHHHHHHHHhcccHHHHHH
Confidence            554  678888777676676665544

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=98.06  E-value=0.0019  Score=51.04  Aligned_cols=177  Identities=10%  Similarity=0.039  Sum_probs=95.9

Q ss_pred             HHHHhhccCcHHHHHHHHHHHHhcCCCCChHhH---HHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 044084           66 LCDSLGKSGRAFEILKFFRDMKEKGILEDPSVY---ASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIE  142 (343)
Q Consensus        66 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~---~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  142 (343)
                      ....+...|++++|.+.|+++......+ ....   -.+..++.+.++++.|...+++..+..+.....-+...+.+.+.
T Consensus        38 ~A~~~~~~g~y~~Ai~~f~~l~~~yP~s-~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~~g~~~  116 (243)
T PRK10866         38 TAQQKLQDGNWKQAITQLEALDNRYPFG-PYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLYMRGLTN  116 (243)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCCCC-hHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHHHHHHhh
Confidence            4445566788888888888887753322 2221   33556777888888888888888776543222223333333221


Q ss_pred             --cC---------------c---HhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhh
Q 044084          143 --EG---------------M---VEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVT  202 (343)
Q Consensus       143 --~~---------------~---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~  202 (343)
                        .+               +   ..+|++.|+.+.+.-               -...-..+|...+..+...   .-..-
T Consensus       117 ~~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~~y---------------P~S~ya~~A~~rl~~l~~~---la~~e  178 (243)
T PRK10866        117 MALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVRGY---------------PNSQYTTDATKRLVFLKDR---LAKYE  178 (243)
T ss_pred             hhcchhhhhhccCCCccccCHHHHHHHHHHHHHHHHHC---------------cCChhHHHHHHHHHHHHHH---HHHHH
Confidence              11               1   233445555554432               2222234444433333322   00111


Q ss_pred             HHHHHHHHHccCChhHHHHHHHHHHHc--CCCcChhhHHHHHHHHHccCChHHHHHHHHHHh
Q 044084          203 YASIINAYCRIGLYSKAEKVFIEMQQK--GFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMK  262 (343)
Q Consensus       203 ~~~ll~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~  262 (343)
                       -.+.+-|.+.|.+..|..-++.+.+.  +.+........++.+|...|..++|..+...+.
T Consensus       179 -~~ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l~  239 (243)
T PRK10866        179 -LSVAEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKIIA  239 (243)
T ss_pred             -HHHHHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHHh
Confidence             13455677777777777777777765  222334455666777777777777776665543

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

Probab=98.03  E-value=0.00016  Score=47.55  Aligned_cols=90  Identities=19%  Similarity=0.191  Sum_probs=43.6

Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCc
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRA  180 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  180 (343)
                      +...+...|++++|...+++..+.... +...+..+...+...+++++|.+.++....... .+..++..+...+...|+
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~   83 (100)
T cd00189           6 LGNLYYKLGDYDEALEYYEKALELDPD-NADAYYNLAAAYYKLGKYEEALEDYEKALELDP-DNAKAYYNLGLAYYKLGK   83 (100)
T ss_pred             HHHHHHHHhcHHHHHHHHHHHHhcCCc-cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-cchhHHHHHHHHHHHHHh
Confidence            344444555555555555555543321 334444455555555555555555555544332 222344444445555555


Q ss_pred             HHHHHHHHHHHH
Q 044084          181 YWAAVKVYEQLI  192 (343)
Q Consensus       181 ~~~a~~~~~~~~  192 (343)
                      ++.|...+....
T Consensus        84 ~~~a~~~~~~~~   95 (100)
T cd00189          84 YEEALEAYEKAL   95 (100)
T ss_pred             HHHHHHHHHHHH
Confidence            555555554443

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

Probab=98.03  E-value=9.6e-06  Score=41.00  Aligned_cols=26  Identities=15%  Similarity=0.436  Sum_probs=10.7

Q ss_pred             HHHHHHHHhcCCcHHHHHHHHHHHHH
Q 044084          168 SCVIVNGFSKRRAYWAAVKVYEQLIS  193 (343)
Q Consensus       168 ~~~l~~~~~~~~~~~~a~~~~~~~~~  193 (343)
                      |+.++++|++.|++++|.++|++|.+
T Consensus         3 y~~li~~~~~~~~~~~a~~~~~~M~~   28 (31)
T PF01535_consen    3 YNSLISGYCKMGQFEEALEVFDEMRE   28 (31)
T ss_pred             HHHHHHHHHccchHHHHHHHHHHHhH
Confidence            34444444444444444444444433

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.

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

Probab=98.02  E-value=0.0067  Score=51.83  Aligned_cols=121  Identities=9%  Similarity=0.160  Sum_probs=77.6

Q ss_pred             HHHHHHHHHHHc-CCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHhcccChhHHHh----
Q 044084          218 KAEKVFIEMQQK-GFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEP-NVWIYNSLMDMHGRAKNLRQLEK----  291 (343)
Q Consensus       218 ~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~~~~~l~~~~~~~~~~~~a~~----  291 (343)
                      ....+++++... ...| ..+|-.++..-.+..-+..|..+|.+..+.+..+ +..+.++++.-|+.. +..-|.+    
T Consensus       349 ~~~~~~~~ll~~~~~~~-tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~csk-D~~~AfrIFeL  426 (656)
T KOG1914|consen  349 KVHEIYNKLLKIEDIDL-TLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCSK-DKETAFRIFEL  426 (656)
T ss_pred             hhHHHHHHHHhhhccCC-ceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhcC-ChhHHHHHHHH
Confidence            333444444432 2223 3456677777777777888888998888887766 677777888776643 4444433    


Q ss_pred             -----------HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccH--HHHHHHHHHHhccccc
Q 044084          292 -----------YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDR--AMAGIMVGVFSKLSQI  340 (343)
Q Consensus       292 -----------~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~--~~~~~l~~~~~~~g~~  340 (343)
                                 -...+.-+...++-..|..+|++....++.||.  ..|..+++-=..-|++
T Consensus       427 GLkkf~d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL  488 (656)
T KOG1914|consen  427 GLKKFGDSPEYVLKYLDFLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDL  488 (656)
T ss_pred             HHHhcCCChHHHHHHHHHHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccH
Confidence                       344455556677777888888888887666665  3477777655555543

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

Probab=98.01  E-value=1.8e-05  Score=51.15  Aligned_cols=19  Identities=16%  Similarity=0.176  Sum_probs=7.7

Q ss_pred             HHHHhcccCHHHHHHHHHH
Q 044084          102 ICSFASIAEVKVAEELFKE  120 (343)
Q Consensus       102 ~~~~~~~~~~~~a~~~~~~  120 (343)
                      ..++.+.|++++|..+++.
T Consensus        32 a~~~~~~~~y~~A~~~~~~   50 (84)
T PF12895_consen   32 AQCYFQQGKYEEAIELLQK   50 (84)
T ss_dssp             HHHHHHTTHHHHHHHHHHC
T ss_pred             HHHHHHCCCHHHHHHHHHH
Confidence            3334444444444444433

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

Probab=97.99  E-value=2.8e-05  Score=50.23  Aligned_cols=80  Identities=16%  Similarity=0.226  Sum_probs=36.0

Q ss_pred             cCHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHH
Q 044084          109 AEVKVAEELFKEAEEKGML-RDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKV  187 (343)
Q Consensus       109 ~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  187 (343)
                      |+++.|..+++++.+.... ++...+..+..+|.+.|++++|..+++. .+.+. .+....-.+..++.+.|++++|+++
T Consensus         3 ~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~~-~~~~~~~l~a~~~~~l~~y~eAi~~   80 (84)
T PF12895_consen    3 GNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LKLDP-SNPDIHYLLARCLLKLGKYEEAIKA   80 (84)
T ss_dssp             T-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHHH-CHHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCCC-CCHHHHHHHHHHHHHhCCHHHHHHH
Confidence            4555555555555554331 1233344455555555555555555555 22211 1112222334555555555555555


Q ss_pred             HHH
Q 044084          188 YEQ  190 (343)
Q Consensus       188 ~~~  190 (343)
                      |++
T Consensus        81 l~~   83 (84)
T PF12895_consen   81 LEK   83 (84)
T ss_dssp             HHH
T ss_pred             Hhc
Confidence            543

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.98  E-value=0.00038  Score=49.76  Aligned_cols=90  Identities=8%  Similarity=-0.054  Sum_probs=45.2

Q ss_pred             HHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCc
Q 044084           66 LCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGM  145 (343)
Q Consensus        66 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  145 (343)
                      +...+...|++++|.++|+-+...+.. +..-|-.|..++-..|++++|...|.......+. |+..+..+..++...|+
T Consensus        41 ~A~~ly~~G~l~~A~~~f~~L~~~Dp~-~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~d-dp~~~~~ag~c~L~lG~  118 (157)
T PRK15363         41 YAMQLMEVKEFAGAARLFQLLTIYDAW-SFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKID-APQAPWAAAECYLACDN  118 (157)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC-CchHHHHHHHHHHHcCC
Confidence            344444555555555555555443221 3333444444444555555555555555554432 45555555555555555


Q ss_pred             HhHHHHHHHHHH
Q 044084          146 VEKTLEVVESMK  157 (343)
Q Consensus       146 ~~~a~~~~~~~~  157 (343)
                      .+.|++.|+...
T Consensus       119 ~~~A~~aF~~Ai  130 (157)
T PRK15363        119 VCYAIKALKAVV  130 (157)
T ss_pred             HHHHHHHHHHHH
Confidence            555555555544

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.97  E-value=0.00078  Score=50.29  Aligned_cols=92  Identities=15%  Similarity=0.111  Sum_probs=60.7

Q ss_pred             chHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCC--hHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHH
Q 044084           58 SSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILED--PSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLK  135 (343)
Q Consensus        58 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  135 (343)
                      .....+..+...+...|++++|...|++.......+.  ...+..+...+.+.|+++.|...+.+..+.... +...+..
T Consensus        33 ~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~  111 (172)
T PRK02603         33 KEAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELNPK-QPSALNN  111 (172)
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcc-cHHHHHH
Confidence            3345667777777777888888888887766433222  345666777777778888888888777775432 4566666


Q ss_pred             HHHHHHhcCcHhHHH
Q 044084          136 LVLMYIEEGMVEKTL  150 (343)
Q Consensus       136 l~~~~~~~~~~~~a~  150 (343)
                      +...+...|+...+.
T Consensus       112 lg~~~~~~g~~~~a~  126 (172)
T PRK02603        112 IAVIYHKRGEKAEEA  126 (172)
T ss_pred             HHHHHHHcCChHhHh
Confidence            666776666644433

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=97.96  E-value=0.0049  Score=48.70  Aligned_cols=171  Identities=12%  Similarity=0.083  Sum_probs=99.5

Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCCCCHHH---HHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhc
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGMLRDLEV---FLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSK  177 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  177 (343)
                      ....+...|+++.|...|+.+...-+.+ ...   .-.++.+|.+.+++++|...+++..+..+.-...-|...+.+.+.
T Consensus        38 ~A~~~~~~g~y~~Ai~~f~~l~~~yP~s-~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~~g~~~  116 (243)
T PRK10866         38 TAQQKLQDGNWKQAITQLEALDNRYPFG-PYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLYMRGLTN  116 (243)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCCCC-hHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHHHHHHhh
Confidence            4445567889999999999988865432 222   245667788899999999999988876553333344444444331


Q ss_pred             --C---------------CcH---HHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhh
Q 044084          178 --R---------------RAY---WAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVA  237 (343)
Q Consensus       178 --~---------------~~~---~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  237 (343)
                        .               .+.   ..|.+.|+++.               +-|-...-.++|...+..+...=    ...
T Consensus       117 ~~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li---------------~~yP~S~ya~~A~~rl~~l~~~l----a~~  177 (243)
T PRK10866        117 MALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLV---------------RGYPNSQYTTDATKRLVFLKDRL----AKY  177 (243)
T ss_pred             hhcchhhhhhccCCCccccCHHHHHHHHHHHHHHH---------------HHCcCChhHHHHHHHHHHHHHHH----HHH
Confidence              1               011   22333333333               33333344455555444443320    111


Q ss_pred             HHHHHHHHHccCChHHHHHHHHHHhhC--CCCchHHHHHHHHHHHhcccChhHHHh
Q 044084          238 YSSMVAMYGKTGRIRDAMRLVAKMKPK--GCEPNVWIYNSLMDMHGRAKNLRQLEK  291 (343)
Q Consensus       238 ~~~l~~~~~~~~~~~~a~~~~~~m~~~--~~~p~~~~~~~l~~~~~~~~~~~~a~~  291 (343)
                      --.+.+.|.+.|.+..|..-++.+++.  +..........++.+|...|..++|..
T Consensus       178 e~~ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~  233 (243)
T PRK10866        178 ELSVAEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADK  233 (243)
T ss_pred             HHHHHHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHH
Confidence            125667788899999999989888875  223333444555556665555555443

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

Probab=97.95  E-value=0.0072  Score=49.65  Aligned_cols=103  Identities=11%  Similarity=0.076  Sum_probs=60.0

Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHh
Q 044084          202 TYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHG  281 (343)
Q Consensus       202 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~  281 (343)
                      +.+..+.-+...|+...|.++-.+.   . .|+-.-|...+.+++..++|++...+...   .   -++.-|..++.+|.
T Consensus       179 Sl~~Ti~~li~~~~~k~A~kl~k~F---k-v~dkrfw~lki~aLa~~~~w~eL~~fa~s---k---KsPIGyepFv~~~~  248 (319)
T PF04840_consen  179 SLNDTIRKLIEMGQEKQAEKLKKEF---K-VPDKRFWWLKIKALAENKDWDELEKFAKS---K---KSPIGYEPFVEACL  248 (319)
T ss_pred             CHHHHHHHHHHCCCHHHHHHHHHHc---C-CcHHHHHHHHHHHHHhcCCHHHHHHHHhC---C---CCCCChHHHHHHHH
Confidence            4444455555666666655554333   2 25666666777777777777666554332   1   12345566666666


Q ss_pred             cccChhHHHh------HHHHHHHHHhcCCHHHHHHHHHH
Q 044084          282 RAKNLRQLEK------YTTVISAYNMAREFDMCVKFYNE  314 (343)
Q Consensus       282 ~~~~~~~a~~------~~~l~~~~~~~g~~~~a~~~~~~  314 (343)
                      +.|+..+|..      +..-+..|.+.|++.+|.+.--+
T Consensus       249 ~~~~~~eA~~yI~k~~~~~rv~~y~~~~~~~~A~~~A~~  287 (319)
T PF04840_consen  249 KYGNKKEASKYIPKIPDEERVEMYLKCGDYKEAAQEAFK  287 (319)
T ss_pred             HCCCHHHHHHHHHhCChHHHHHHHHHCCCHHHHHHHHHH
Confidence            6666666665      45556666667777666655433

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

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.94  E-value=0.0014  Score=46.94  Aligned_cols=91  Identities=8%  Similarity=0.048  Sum_probs=51.0

Q ss_pred             HHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcH
Q 044084          102 ICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAY  181 (343)
Q Consensus       102 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  181 (343)
                      ...+...|++++|..+|+.+....+. +...|-.|.-++-..|++++|+..|......++ -+...+-.+..++...|+.
T Consensus        42 A~~ly~~G~l~~A~~~f~~L~~~Dp~-~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~-ddp~~~~~ag~c~L~lG~~  119 (157)
T PRK15363         42 AMQLMEVKEFAGAARLFQLLTIYDAW-SFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKI-DAPQAPWAAAECYLACDNV  119 (157)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCchHHHHHHHHHHHcCCH
Confidence            33444556666666666665554432 455555555566666666666666666555543 3444555555556666666


Q ss_pred             HHHHHHHHHHHHc
Q 044084          182 WAAVKVYEQLISQ  194 (343)
Q Consensus       182 ~~a~~~~~~~~~~  194 (343)
                      +.|.+-|+.....
T Consensus       120 ~~A~~aF~~Ai~~  132 (157)
T PRK15363        120 CYAIKALKAVVRI  132 (157)
T ss_pred             HHHHHHHHHHHHH
Confidence            6666666655543

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.94  E-value=0.00039  Score=51.66  Aligned_cols=62  Identities=19%  Similarity=0.039  Sum_probs=30.9

Q ss_pred             HHHHHHHHhcccCHHHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhc
Q 044084           98 YASLICSFASIAEVKVAEELFKEAEEKGMLR--DLEVFLKLVLMYIEEGMVEKTLEVVESMKNA  159 (343)
Q Consensus        98 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  159 (343)
                      |..+...+...|++++|...+++.......+  ...++..+...+...|++++|+..+++....
T Consensus        38 ~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~  101 (168)
T CHL00033         38 YYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALER  101 (168)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            3444444445555555555555554432221  1234555555555555555555555555443

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

Probab=97.93  E-value=0.00053  Score=57.56  Aligned_cols=95  Identities=7%  Similarity=-0.065  Sum_probs=76.1

Q ss_pred             HHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC
Q 044084           65 ILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEG  144 (343)
Q Consensus        65 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  144 (343)
                      .-...+...|+++.|++.|++.++.... +...|..+..++.+.|++++|...++++.+.... +...|..+..+|...|
T Consensus         7 ~~a~~a~~~~~~~~Ai~~~~~Al~~~P~-~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~-~~~a~~~lg~~~~~lg   84 (356)
T PLN03088          7 DKAKEAFVDDDFALAVDLYTQAIDLDPN-NAELYADRAQANIKLGNFTEAVADANKAIELDPS-LAKAYLRKGTACMKLE   84 (356)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcC-CHHHHHHHHHHHHHhC
Confidence            3455667788999999999998886432 5667777888888889999999999988887643 6778888888899999


Q ss_pred             cHhHHHHHHHHHHhcCC
Q 044084          145 MVEKTLEVVESMKNAEL  161 (343)
Q Consensus       145 ~~~~a~~~~~~~~~~~~  161 (343)
                      ++++|+..|++..+.++
T Consensus        85 ~~~eA~~~~~~al~l~P  101 (356)
T PLN03088         85 EYQTAKAALEKGASLAP  101 (356)
T ss_pred             CHHHHHHHHHHHHHhCC
Confidence            99999999998887653

>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=97.90  E-value=0.00027  Score=52.99  Aligned_cols=105  Identities=14%  Similarity=0.209  Sum_probs=61.4

Q ss_pred             CchhhHHHHHHHHhc-----CCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhh
Q 044084          163 ISDCISCVIVNGFSK-----RRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVA  237 (343)
Q Consensus       163 ~~~~~~~~l~~~~~~-----~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  237 (343)
                      .+..+|..+++.|.+     .|+.+=....++.|.+-|+.-|..+|+.|++.+-+ |.+-               |. ..
T Consensus        45 k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPK-g~fv---------------p~-n~  107 (228)
T PF06239_consen   45 KDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPK-GKFV---------------PR-NF  107 (228)
T ss_pred             ccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCC-CCcc---------------cc-cH
Confidence            344455555555543     34555555555555555655566666666555543 2211               10 01


Q ss_pred             HHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccCh
Q 044084          238 YSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNL  286 (343)
Q Consensus       238 ~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~  286 (343)
                      +.++...|  -.+-+-|++++++|...|+-||..|+..+++.+.+.+..
T Consensus       108 fQ~~F~hy--p~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~p  154 (228)
T PF06239_consen  108 FQAEFMHY--PRQQECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSHP  154 (228)
T ss_pred             HHHHhccC--cHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccHH
Confidence            11111111  123466889999999999999999999999998876643

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=97.88  E-value=0.00052  Score=51.00  Aligned_cols=62  Identities=19%  Similarity=0.045  Sum_probs=26.9

Q ss_pred             HHHHHHHHhhccCcHHHHHHHHHHHHhcCCCC--ChHhHHHHHHHHhcccCHHHHHHHHHHHHH
Q 044084           62 MYKILCDSLGKSGRAFEILKFFRDMKEKGILE--DPSVYASLICSFASIAEVKVAEELFKEAEE  123 (343)
Q Consensus        62 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  123 (343)
                      .|..+...+...|++++|+..|++.......|  ...++..+...+...|++++|...+++..+
T Consensus        37 ~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~  100 (168)
T CHL00033         37 TYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALE  100 (168)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            34444444444444555554444444332111  112344444444444555555555444444

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

Probab=97.87  E-value=0.00043  Score=58.08  Aligned_cols=92  Identities=9%  Similarity=-0.033  Sum_probs=67.0

Q ss_pred             HHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCCh
Q 044084          137 VLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLY  216 (343)
Q Consensus       137 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~  216 (343)
                      ...+...|++++|++.|++..+.+. .+...|..+..+|...|++++|+..++++.... +.+...|..+..+|...|++
T Consensus         9 a~~a~~~~~~~~Ai~~~~~Al~~~P-~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~-P~~~~a~~~lg~~~~~lg~~   86 (356)
T PLN03088          9 AKEAFVDDDFALAVDLYTQAIDLDP-NNAELYADRAQANIKLGNFTEAVADANKAIELD-PSLAKAYLRKGTACMKLEEY   86 (356)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhCCH
Confidence            4556677888888888888777665 355567777777788888888888888877763 23455677777777788888


Q ss_pred             hHHHHHHHHHHHcC
Q 044084          217 SKAEKVFIEMQQKG  230 (343)
Q Consensus       217 ~~a~~~~~~~~~~~  230 (343)
                      ++|...|+...+.+
T Consensus        87 ~eA~~~~~~al~l~  100 (356)
T PLN03088         87 QTAKAALEKGASLA  100 (356)
T ss_pred             HHHHHHHHHHHHhC
Confidence            88888888777754

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.86  E-value=0.0014  Score=48.85  Aligned_cols=89  Identities=18%  Similarity=0.064  Sum_probs=63.8

Q ss_pred             hHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHH
Q 044084           95 PSVYASLICSFASIAEVKVAEELFKEAEEKGMLRD--LEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIV  172 (343)
Q Consensus        95 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  172 (343)
                      ...+..+...+...|++++|...|++..+....+.  ...+..+...+.+.|++++|...+++..+..+ -+...+..+.
T Consensus        35 a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg  113 (172)
T PRK02603         35 AFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELNP-KQPSALNNIA  113 (172)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-ccHHHHHHHH
Confidence            34566677778888999999999998887543332  46788888888899999999999888877654 2444566666


Q ss_pred             HHHhcCCcHHHH
Q 044084          173 NGFSKRRAYWAA  184 (343)
Q Consensus       173 ~~~~~~~~~~~a  184 (343)
                      ..+...|+...+
T Consensus       114 ~~~~~~g~~~~a  125 (172)
T PRK02603        114 VIYHKRGEKAEE  125 (172)
T ss_pred             HHHHHcCChHhH
Confidence            667666664433

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

Probab=97.86  E-value=0.0033  Score=51.11  Aligned_cols=130  Identities=15%  Similarity=0.181  Sum_probs=54.2

Q ss_pred             HHHHHHHHHhc-CcHhHHHHHHHHHHh----cCCC-CchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCC-----CCHh
Q 044084          133 FLKLVLMYIEE-GMVEKTLEVVESMKN----AELN-ISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCI-----PGQV  201 (343)
Q Consensus       133 ~~~l~~~~~~~-~~~~~a~~~~~~~~~----~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-----p~~~  201 (343)
                      +..+...|-.. |++++|++.|++..+    .+.+ .-..++..+...+.+.|++++|.++|++.......     .+..
T Consensus       117 ~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~  196 (282)
T PF14938_consen  117 LKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAK  196 (282)
T ss_dssp             HHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHH
Confidence            33344444444 555555555555432    1210 01123444555566666666666666665543211     1111


Q ss_pred             -hHHHHHHHHHccCChhHHHHHHHHHHHcC--CCcC--hhhHHHHHHHHHcc--CChHHHHHHHHHHh
Q 044084          202 -TYASIINAYCRIGLYSKAEKVFIEMQQKG--FDKC--VVAYSSMVAMYGKT--GRIRDAMRLVAKMK  262 (343)
Q Consensus       202 -~~~~ll~~~~~~~~~~~a~~~~~~~~~~~--~~~~--~~~~~~l~~~~~~~--~~~~~a~~~~~~m~  262 (343)
                       .+...+-++...||+-.|...++......  +..+  ......|+.++-..  ..+..+..-|+.+.
T Consensus       197 ~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~~~~D~e~f~~av~~~d~~~  264 (282)
T PF14938_consen  197 EYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSREYKFLEDLLEAYEEGDVEAFTEAVAEYDSIS  264 (282)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHHHHHHTT-CCCHHHHCHHHTTSS
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHhCCHHHHHHHHHHHcccC
Confidence             11122223344566666666666655432  1111  23344455554321  23444444444444

>PF06239 ECSIT: Evolutionarily conserved signalling intermediate in Toll pathway; InterPro: IPR010418 Activation of NF-kappaB as a consequence of signalling through the Toll and IL-1 receptors is a major element of innate immune responses

Probab=97.85  E-value=0.0004  Score=52.13  Aligned_cols=105  Identities=20%  Similarity=0.273  Sum_probs=74.4

Q ss_pred             CCChHhHHHHHHHHhcc-----cCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchh
Q 044084           92 LEDPSVYASLICSFASI-----AEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDC  166 (343)
Q Consensus        92 ~~~~~~~~~l~~~~~~~-----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  166 (343)
                      ..+-.+|..++..+.+.     |..+-....+..|.+.|+..|..+|+.|++.+=+ |.+-               |.. 
T Consensus        44 ~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPK-g~fv---------------p~n-  106 (228)
T PF06239_consen   44 AKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPK-GKFV---------------PRN-  106 (228)
T ss_pred             cccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCC-CCcc---------------ccc-
Confidence            44777888888877643     6677777788888888888888888888877654 3221               111 


Q ss_pred             hHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCC
Q 044084          167 ISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGL  215 (343)
Q Consensus       167 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~  215 (343)
                      .+.++..-  .-.+-+-|++++++|...|+.||..++..+++.+++.+.
T Consensus       107 ~fQ~~F~h--yp~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~  153 (228)
T PF06239_consen  107 FFQAEFMH--YPRQQECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSH  153 (228)
T ss_pred             HHHHHhcc--CcHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccH
Confidence            11111111  123567789999999999999999999999999987765

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

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.79  E-value=0.0042  Score=54.74  Aligned_cols=63  Identities=10%  Similarity=0.141  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHc
Q 044084          130 LEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       130 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  194 (343)
                      +..|..+.-.+...|++++|...+++....+  |+...|..+...+...|++++|.+.+++....
T Consensus       420 ~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L  482 (517)
T PRK10153        420 PRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTAFNL  482 (517)
T ss_pred             hHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            3444444444444555555555555555444  24445555555555555555555555555444

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

Probab=97.79  E-value=0.0046  Score=50.24  Aligned_cols=134  Identities=14%  Similarity=0.269  Sum_probs=82.7

Q ss_pred             HHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcC-CcHHHHHHHHHHHHHc----CCCCC--HhhHHH
Q 044084          133 FLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKR-RAYWAAVKVYEQLISQ----GCIPG--QVTYAS  205 (343)
Q Consensus       133 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~a~~~~~~~~~~----~~~p~--~~~~~~  205 (343)
                      |...+..|...|++..|-+++..               +...|... |+++.|.+.|++..+.    + .+.  ...+..
T Consensus        97 ~~~A~~~y~~~G~~~~aA~~~~~---------------lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~-~~~~a~~~~~~  160 (282)
T PF14938_consen   97 YEKAIEIYREAGRFSQAAKCLKE---------------LAEIYEEQLGDYEKAIEYYQKAAELYEQEG-SPHSAAECLLK  160 (282)
T ss_dssp             HHHHHHHHHHCT-HHHHHHHHHH---------------HHHHHCCTT--HHHHHHHHHHHHHHHHHTT--HHHHHHHHHH
T ss_pred             HHHHHHHHHhcCcHHHHHHHHHH---------------HHHHHHHHcCCHHHHHHHHHHHHHHHHHCC-ChhhHHHHHHH
Confidence            33444555666666665554444               44556666 8999999999887653    2 222  345667


Q ss_pred             HHHHHHccCChhHHHHHHHHHHHcCCC-----cChh-hHHHHHHHHHccCChHHHHHHHHHHhhC--CCCc--hHHHHHH
Q 044084          206 IINAYCRIGLYSKAEKVFIEMQQKGFD-----KCVV-AYSSMVAMYGKTGRIRDAMRLVAKMKPK--GCEP--NVWIYNS  275 (343)
Q Consensus       206 ll~~~~~~~~~~~a~~~~~~~~~~~~~-----~~~~-~~~~l~~~~~~~~~~~~a~~~~~~m~~~--~~~p--~~~~~~~  275 (343)
                      +...+.+.|++++|.++|+++......     .+.. .+-..+-++...|+...|.+.+++....  ++..  .......
T Consensus       161 ~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~  240 (282)
T PF14938_consen  161 AADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSREYKFLED  240 (282)
T ss_dssp             HHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHH
Confidence            788899999999999999998875322     2222 2334455677789999999999998865  2222  2345555


Q ss_pred             HHHHHhc
Q 044084          276 LMDMHGR  282 (343)
Q Consensus       276 l~~~~~~  282 (343)
                      |+.++-.
T Consensus       241 l~~A~~~  247 (282)
T PF14938_consen  241 LLEAYEE  247 (282)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHHh
Confidence            6666554

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

Probab=97.76  E-value=0.00014  Score=44.65  Aligned_cols=61  Identities=20%  Similarity=0.279  Sum_probs=39.3

Q ss_pred             ccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHH
Q 044084          212 RIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNS  275 (343)
Q Consensus       212 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~  275 (343)
                      ..|++++|..+|+.+.... |-+...+..+..+|.+.|++++|.++++++...  .|+...|..
T Consensus         3 ~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~--~~~~~~~~~   63 (68)
T PF14559_consen    3 KQGDYDEAIELLEKALQRN-PDNPEARLLLAQCYLKQGQYDEAEELLERLLKQ--DPDNPEYQQ   63 (68)
T ss_dssp             HTTHHHHHHHHHHHHHHHT-TTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG--GTTHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CcCHHHHHH
Confidence            4577777777777777664 335666667777777777777777777777765  445444333

...

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=97.75  E-value=0.011  Score=45.50  Aligned_cols=62  Identities=19%  Similarity=0.157  Sum_probs=38.9

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhc
Q 044084           27 QIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEK   89 (343)
Q Consensus        27 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~   89 (343)
                      .....+.+.|++.+|.+.|+.+....+.. +-...+.-.++.++.+.|+++.|...++++.+.
T Consensus        10 ~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s-~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~   71 (203)
T PF13525_consen   10 QKALEALQQGDYEEAIKLFEKLIDRYPNS-PYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKL   71 (203)
T ss_dssp             HHHHHHHHCT-HHHHHHHHHHHHHH-TTS-TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHCCCC-hHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            34445667777777777777776654332 333455666677777777777777777777665

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.74  E-value=0.0052  Score=54.17  Aligned_cols=63  Identities=13%  Similarity=0.007  Sum_probs=36.6

Q ss_pred             HhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhC
Q 044084          200 QVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       200 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                      ...|..+.-.....|++++|...+++....+  |+...|..+...+...|+.++|.+.+++....
T Consensus       420 ~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L  482 (517)
T PRK10153        420 PRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTAFNL  482 (517)
T ss_pred             hHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            3444444333444566666666666666654  45556666666666666666666666666544

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=97.70  E-value=0.021  Score=47.35  Aligned_cols=223  Identities=15%  Similarity=0.055  Sum_probs=102.8

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCC-hHhHHHHHHHHhc
Q 044084           29 MEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILED-PSVYASLICSFAS  107 (343)
Q Consensus        29 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~  107 (343)
                      ...+.+..++..|+..+....+..+.    +...|..-...+...+++++++--.+.-.+.  +|. .....-.-+++..
T Consensus        56 gn~~yk~k~Y~nal~~yt~Ai~~~pd----~a~yy~nRAa~~m~~~~~~~a~~dar~~~r~--kd~~~k~~~r~~~c~~a  129 (486)
T KOG0550|consen   56 GNAFYKQKTYGNALKNYTFAIDMCPD----NASYYSNRAATLMMLGRFEEALGDARQSVRL--KDGFSKGQLREGQCHLA  129 (486)
T ss_pred             cchHHHHhhHHHHHHHHHHHHHhCcc----chhhhchhHHHHHHHHhHhhcccchhhheec--CCCccccccchhhhhhh
Confidence            33455666777777777777665532    2455666666666666676666555443332  111 1122222223333


Q ss_pred             ccCHHHHHHHHH------------H---HHHcCC-CCCHHHHHHH-HHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHH
Q 044084          108 IAEVKVAEELFK------------E---AEEKGM-LRDLEVFLKL-VLMYIEEGMVEKTLEVVESMKNAELNISDCISCV  170 (343)
Q Consensus       108 ~~~~~~a~~~~~------------~---~~~~~~-~~~~~~~~~l-~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  170 (343)
                      .++..+|...++            .   ...... +|.-..+..+ ..++.-.|++++|..+--.+.+.+. .+  .+..
T Consensus       130 ~~~~i~A~~~~~~~~~~~~anal~~~~~~~~s~s~~pac~~a~~lka~cl~~~~~~~~a~~ea~~ilkld~-~n--~~al  206 (486)
T KOG0550|consen  130 LSDLIEAEEKLKSKQAYKAANALPTLEKLAPSHSREPACFKAKLLKAECLAFLGDYDEAQSEAIDILKLDA-TN--AEAL  206 (486)
T ss_pred             hHHHHHHHHHhhhhhhhHHhhhhhhhhcccccccCCchhhHHHHhhhhhhhhcccchhHHHHHHHHHhccc-ch--hHHH
Confidence            333333332222            1   111111 1111222222 2334455666666666665555443 12  2223


Q ss_pred             HHH--HHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHH---H----------HHHHccCChhHHHHHHHHHHHc---CCC
Q 044084          171 IVN--GFSKRRAYWAAVKVYEQLISQGCIPGQVTYASI---I----------NAYCRIGLYSKAEKVFIEMQQK---GFD  232 (343)
Q Consensus       171 l~~--~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l---l----------~~~~~~~~~~~a~~~~~~~~~~---~~~  232 (343)
                      .++  ++.-.++.+.+...|++....+  |+...-..+   .          +-..+.|++..|.+.+.+.+..   +..
T Consensus       207 ~vrg~~~yy~~~~~ka~~hf~qal~ld--pdh~~sk~~~~~~k~le~~k~~gN~~fk~G~y~~A~E~Yteal~idP~n~~  284 (486)
T KOG0550|consen  207 YVRGLCLYYNDNADKAINHFQQALRLD--PDHQKSKSASMMPKKLEVKKERGNDAFKNGNYRKAYECYTEALNIDPSNKK  284 (486)
T ss_pred             HhcccccccccchHHHHHHHhhhhccC--hhhhhHHhHhhhHHHHHHHHhhhhhHhhccchhHHHHHHHHhhcCCccccc
Confidence            333  2333566666776666666542  443322111   1          1123455566666666555543   223


Q ss_pred             cChhhHHHHHHHHHccCChHHHHHHHHHHh
Q 044084          233 KCVVAYSSMVAMYGKTGRIRDAMRLVAKMK  262 (343)
Q Consensus       233 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~  262 (343)
                      |+...|.....+..+.|+..+|+.--+...
T Consensus       285 ~naklY~nra~v~~rLgrl~eaisdc~~Al  314 (486)
T KOG0550|consen  285 TNAKLYGNRALVNIRLGRLREAISDCNEAL  314 (486)
T ss_pred             hhHHHHHHhHhhhcccCCchhhhhhhhhhh
Confidence            344445555555555566665555554444

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

Probab=97.68  E-value=0.00022  Score=43.80  Aligned_cols=50  Identities=22%  Similarity=0.296  Sum_probs=21.3

Q ss_pred             ccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHh
Q 044084          108 IAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKN  158 (343)
Q Consensus       108 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  158 (343)
                      .|++++|.++|+.+....+. +..++..+..+|.+.|++++|.++++++..
T Consensus         4 ~~~~~~A~~~~~~~l~~~p~-~~~~~~~la~~~~~~g~~~~A~~~l~~~~~   53 (68)
T PF14559_consen    4 QGDYDEAIELLEKALQRNPD-NPEARLLLAQCYLKQGQYDEAEELLERLLK   53 (68)
T ss_dssp             TTHHHHHHHHHHHHHHHTTT-SHHHHHHHHHHHHHTT-HHHHHHHHHCCHG
T ss_pred             ccCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            34444444444444443322 344444444444444444444444444443

...

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=97.67  E-value=0.015  Score=44.71  Aligned_cols=45  Identities=13%  Similarity=0.126  Sum_probs=24.4

Q ss_pred             HHHHHHccCChHHHHHHHHHHhhCCCCchH----HHHHHHHHHHhcccChh
Q 044084          241 MVAMYGKTGRIRDAMRLVAKMKPKGCEPNV----WIYNSLMDMHGRAKNLR  287 (343)
Q Consensus       241 l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~----~~~~~l~~~~~~~~~~~  287 (343)
                      +...|.+.|.+..|..-++.+++.  -|+.    .....++.+|.+.|..+
T Consensus       147 ia~~Y~~~~~y~aA~~r~~~v~~~--yp~t~~~~~al~~l~~~y~~l~~~~  195 (203)
T PF13525_consen  147 IARFYYKRGKYKAAIIRFQYVIEN--YPDTPAAEEALARLAEAYYKLGLKQ  195 (203)
T ss_dssp             HHHHHHCTT-HHHHHHHHHHHHHH--STTSHHHHHHHHHHHHHHHHTT-HH
T ss_pred             HHHHHHHcccHHHHHHHHHHHHHH--CCCCchHHHHHHHHHHHHHHhCChH
Confidence            455667777777777777777664  2222    23344555555555444

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

Probab=97.64  E-value=0.00054  Score=42.21  Aligned_cols=56  Identities=25%  Similarity=0.261  Sum_probs=21.2

Q ss_pred             HHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC-cHhHHHHHHHH
Q 044084           99 ASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEG-MVEKTLEVVES  155 (343)
Q Consensus        99 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~  155 (343)
                      ..+...+...|++++|+..|++..+.... +...|..+..+|...| ++++|++.+++
T Consensus         7 ~~~g~~~~~~~~~~~A~~~~~~ai~~~p~-~~~~~~~~g~~~~~~~~~~~~A~~~~~~   63 (69)
T PF13414_consen    7 YNLGQIYFQQGDYEEAIEYFEKAIELDPN-NAEAYYNLGLAYMKLGKDYEEAIEDFEK   63 (69)
T ss_dssp             HHHHHHHHHTTHHHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHTTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHhCccHHHHHHHHHH
Confidence            33333333334444444444433333221 2333333333344433 33444443333

...

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=97.63  E-value=0.027  Score=46.68  Aligned_cols=254  Identities=10%  Similarity=-0.038  Sum_probs=145.6

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      ++..|+..+...++..+ .+...|..-...+...|++++|.--.+.-.+..    +.........-+++...++..+|.+
T Consensus        64 ~Y~nal~~yt~Ai~~~p-d~a~yy~nRAa~~m~~~~~~~a~~dar~~~r~k----d~~~k~~~r~~~c~~a~~~~i~A~~  138 (486)
T KOG0550|consen   64 TYGNALKNYTFAIDMCP-DNASYYSNRAATLMMLGRFEEALGDARQSVRLK----DGFSKGQLREGQCHLALSDLIEAEE  138 (486)
T ss_pred             hHHHHHHHHHHHHHhCc-cchhhhchhHHHHHHHHhHhhcccchhhheecC----CCccccccchhhhhhhhHHHHHHHH
Confidence            35677888888887754 345566666667777777777765554432221    1111223333333333344444433


Q ss_pred             HHH---------------HHHhcCC-CCChHhHHHHH-HHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC
Q 044084           82 FFR---------------DMKEKGI-LEDPSVYASLI-CSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEG  144 (343)
Q Consensus        82 ~~~---------------~~~~~~~-~~~~~~~~~l~-~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  144 (343)
                      .++               ....... +|.-.++..+- .++.-.++.++|.++--...+.... +......-..++.-.+
T Consensus       139 ~~~~~~~~~~anal~~~~~~~~s~s~~pac~~a~~lka~cl~~~~~~~~a~~ea~~ilkld~~-n~~al~vrg~~~yy~~  217 (486)
T KOG0550|consen  139 KLKSKQAYKAANALPTLEKLAPSHSREPACFKAKLLKAECLAFLGDYDEAQSEAIDILKLDAT-NAEALYVRGLCLYYND  217 (486)
T ss_pred             HhhhhhhhHHhhhhhhhhcccccccCCchhhHHHHhhhhhhhhcccchhHHHHHHHHHhcccc-hhHHHHhccccccccc
Confidence            332               1111111 12223343332 3455678888888877666664322 3322222233444567


Q ss_pred             cHhHHHHHHHHHHhcCCCCchhh-------------HHHHHHHHhcCCcHHHHHHHHHHHHHc---CCCCCHhhHHHHHH
Q 044084          145 MVEKTLEVVESMKNAELNISDCI-------------SCVIVNGFSKRRAYWAAVKVYEQLISQ---GCIPGQVTYASIIN  208 (343)
Q Consensus       145 ~~~~a~~~~~~~~~~~~~~~~~~-------------~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~p~~~~~~~ll~  208 (343)
                      +.+.|...|++....++  +...             +..-..-..+.|.+..|.+.|.+.+..   +..|+...|.....
T Consensus       218 ~~~ka~~hf~qal~ldp--dh~~sk~~~~~~k~le~~k~~gN~~fk~G~y~~A~E~Yteal~idP~n~~~naklY~nra~  295 (486)
T KOG0550|consen  218 NADKAINHFQQALRLDP--DHQKSKSASMMPKKLEVKKERGNDAFKNGNYRKAYECYTEALNIDPSNKKTNAKLYGNRAL  295 (486)
T ss_pred             chHHHHHHHhhhhccCh--hhhhHHhHhhhHHHHHHHHhhhhhHhhccchhHHHHHHHHhhcCCccccchhHHHHHHhHh
Confidence            78888888888776553  2111             111123345678899999999988764   34555666777777


Q ss_pred             HHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhC
Q 044084          209 AYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       209 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                      +..+.|+.++|+.--++..+.+ +.-...+..-..++...++|++|.+-|++..+.
T Consensus       296 v~~rLgrl~eaisdc~~Al~iD-~syikall~ra~c~l~le~~e~AV~d~~~a~q~  350 (486)
T KOG0550|consen  296 VNIRLGRLREAISDCNEALKID-SSYIKALLRRANCHLALEKWEEAVEDYEKAMQL  350 (486)
T ss_pred             hhcccCCchhhhhhhhhhhhcC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            7788899999988887777653 111223333345566677888888888877654

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

Probab=97.59  E-value=0.0013  Score=51.71  Aligned_cols=99  Identities=15%  Similarity=0.130  Sum_probs=53.9

Q ss_pred             hcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHH
Q 044084          106 ASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAV  185 (343)
Q Consensus       106 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  185 (343)
                      .+.+++.+|+..|.+.++..+. |.+.|..-..+|++.|.++.|++--+.....+. -...+|..|-.+|...|++++|.
T Consensus        92 m~~~~Y~eAv~kY~~AI~l~P~-nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iDp-~yskay~RLG~A~~~~gk~~~A~  169 (304)
T KOG0553|consen   92 MKNKDYQEAVDKYTEAIELDPT-NAVYYCNRAAAYSKLGEYEDAVKDCESALSIDP-HYSKAYGRLGLAYLALGKYEEAI  169 (304)
T ss_pred             HHhhhHHHHHHHHHHHHhcCCC-cchHHHHHHHHHHHhcchHHHHHHHHHHHhcCh-HHHHHHHHHHHHHHccCcHHHHH
Confidence            3455566666666665554432 555555555566666666666555555554443 23345555556666666666666


Q ss_pred             HHHHHHHHcCCCCCHhhHHHHHH
Q 044084          186 KVYEQLISQGCIPGQVTYASIIN  208 (343)
Q Consensus       186 ~~~~~~~~~~~~p~~~~~~~ll~  208 (343)
                      +.|++..+.  .|+..+|..=++
T Consensus       170 ~aykKaLel--dP~Ne~~K~nL~  190 (304)
T KOG0553|consen  170 EAYKKALEL--DPDNESYKSNLK  190 (304)
T ss_pred             HHHHhhhcc--CCCcHHHHHHHH
Confidence            665555543  455555544443

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

Probab=97.58  E-value=0.00057  Score=41.52  Aligned_cols=57  Identities=25%  Similarity=0.388  Sum_probs=34.6

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhc
Q 044084           29 MEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEK   89 (343)
Q Consensus        29 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~   89 (343)
                      ...+.+.|++++|.+.|+++.+..    |.+...+..+..++...|++++|...|+++.+.
T Consensus         4 a~~~~~~g~~~~A~~~~~~~l~~~----P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~   60 (65)
T PF13432_consen    4 ARALYQQGDYDEAIAAFEQALKQD----PDNPEAWYLLGRILYQQGRYDEALAYYERALEL   60 (65)
T ss_dssp             HHHHHHCTHHHHHHHHHHHHHCCS----TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC----CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            445566666666666666665554    333566666666666666666666666666553

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

Probab=97.58  E-value=0.00061  Score=41.38  Aligned_cols=53  Identities=11%  Similarity=0.135  Sum_probs=21.7

Q ss_pred             HHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHH
Q 044084          139 MYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLI  192 (343)
Q Consensus       139 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  192 (343)
                      .+.+.|++++|.+.|+.+.+..+ -+...+..+..++...|++++|...|+++.
T Consensus         6 ~~~~~g~~~~A~~~~~~~l~~~P-~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~   58 (65)
T PF13432_consen    6 ALYQQGDYDEAIAAFEQALKQDP-DNPEAWYLLGRILYQQGRYDEALAYYERAL   58 (65)
T ss_dssp             HHHHCTHHHHHHHHHHHHHCCST-THHHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            33444444444444444444332 233334444444444444444444444443

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.57  E-value=0.0085  Score=41.28  Aligned_cols=19  Identities=16%  Similarity=0.212  Sum_probs=7.7

Q ss_pred             HHHHhcCcHhHHHHHHHHH
Q 044084          138 LMYIEEGMVEKTLEVVESM  156 (343)
Q Consensus       138 ~~~~~~~~~~~a~~~~~~~  156 (343)
                      ..+...|++++|..++++.
T Consensus        46 stlr~LG~~deA~~~L~~~   64 (120)
T PF12688_consen   46 STLRNLGRYDEALALLEEA   64 (120)
T ss_pred             HHHHHcCCHHHHHHHHHHH
Confidence            3333444444444444433

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.55  E-value=0.011  Score=40.83  Aligned_cols=91  Identities=21%  Similarity=0.177  Sum_probs=45.7

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCC----hHhHHHHHHH
Q 044084           29 MEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILED----PSVYASLICS  104 (343)
Q Consensus        29 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~  104 (343)
                      ..++-..|+.++|..+|++....|.... .-...+..+.+.+...|++++|+.++++.....  |+    ......+..+
T Consensus         8 A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~-~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~--p~~~~~~~l~~f~Al~   84 (120)
T PF12688_consen    8 AWAHDSLGREEEAIPLYRRALAAGLSGA-DRRRALIQLASTLRNLGRYDEALALLEEALEEF--PDDELNAALRVFLALA   84 (120)
T ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCch-HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCccccHHHHHHHHHH
Confidence            3445555666666666666666554432 112445555566666666666666666655431  22    1111122234


Q ss_pred             HhcccCHHHHHHHHHHHH
Q 044084          105 FASIAEVKVAEELFKEAE  122 (343)
Q Consensus       105 ~~~~~~~~~a~~~~~~~~  122 (343)
                      +...|+.++|.+.+-...
T Consensus        85 L~~~gr~~eAl~~~l~~l  102 (120)
T PF12688_consen   85 LYNLGRPKEALEWLLEAL  102 (120)
T ss_pred             HHHCCCHHHHHHHHHHHH
Confidence            445566666655554433

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=97.54  E-value=0.013  Score=46.49  Aligned_cols=120  Identities=12%  Similarity=-0.008  Sum_probs=83.6

Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcC---CcHHHHHHHHHHHHHcC
Q 044084          119 KEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKR---RAYWAAVKVYEQLISQG  195 (343)
Q Consensus       119 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~a~~~~~~~~~~~  195 (343)
                      +.-....+. |...|-.|...|...|+.+.|..-|....+... ++...+..+..++...   ....++..+|+++....
T Consensus       146 e~~L~~nP~-d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g-~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D  223 (287)
T COG4235         146 ETHLQQNPG-DAEGWDLLGRAYMALGRASDALLAYRNALRLAG-DNPEILLGLAEALYYQAGQQMTAKARALLRQALALD  223 (287)
T ss_pred             HHHHHhCCC-CchhHHHHHHHHHHhcchhHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcC
Confidence            333344433 788899999999999999999999988877654 4555666666555443   34567888888888764


Q ss_pred             CCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHH
Q 044084          196 CIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVA  243 (343)
Q Consensus       196 ~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  243 (343)
                       +-+..+...+...+...|++.+|...|+.|.+.. +| ...+..+|.
T Consensus       224 -~~~iral~lLA~~afe~g~~~~A~~~Wq~lL~~l-p~-~~~rr~~ie  268 (287)
T COG4235         224 -PANIRALSLLAFAAFEQGDYAEAAAAWQMLLDLL-PA-DDPRRSLIE  268 (287)
T ss_pred             -CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcC-CC-CCchHHHHH
Confidence             3455566666777888899999999999988875 33 333444444

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.54  E-value=0.059  Score=48.20  Aligned_cols=24  Identities=17%  Similarity=0.130  Sum_probs=13.6

Q ss_pred             HHHHHHHHHhhccCcHHHHHHHHH
Q 044084           61 HMYKILCDSLGKSGRAFEILKFFR   84 (343)
Q Consensus        61 ~~~~~li~~~~~~~~~~~a~~~~~   84 (343)
                      ..|..+.+-....|+++-|..+++
T Consensus       508 iSy~~iA~~Ay~~GR~~LA~kLle  531 (829)
T KOG2280|consen  508 ISYAAIARRAYQEGRFELARKLLE  531 (829)
T ss_pred             eeHHHHHHHHHhcCcHHHHHHHHh
Confidence            345555555555666666655554

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

Probab=97.53  E-value=0.0019  Score=50.91  Aligned_cols=91  Identities=15%  Similarity=0.163  Sum_probs=67.5

Q ss_pred             HHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHh
Q 044084           68 DSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVE  147 (343)
Q Consensus        68 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  147 (343)
                      +-+.+.+++.+|+..|.+.++... -|.+.|..-..+|++.|.++.|.+-.+..+..... ...+|..|..+|...|+++
T Consensus        89 N~~m~~~~Y~eAv~kY~~AI~l~P-~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iDp~-yskay~RLG~A~~~~gk~~  166 (304)
T KOG0553|consen   89 NKLMKNKDYQEAVDKYTEAIELDP-TNAVYYCNRAAAYSKLGEYEDAVKDCESALSIDPH-YSKAYGRLGLAYLALGKYE  166 (304)
T ss_pred             HHHHHhhhHHHHHHHHHHHHhcCC-CcchHHHHHHHHHHHhcchHHHHHHHHHHHhcChH-HHHHHHHHHHHHHccCcHH
Confidence            345567788888888888877642 36667777778888888888888877777765432 4677888888888888888


Q ss_pred             HHHHHHHHHHhcC
Q 044084          148 KTLEVVESMKNAE  160 (343)
Q Consensus       148 ~a~~~~~~~~~~~  160 (343)
                      +|++.|++..+.+
T Consensus       167 ~A~~aykKaLeld  179 (304)
T KOG0553|consen  167 EAIEAYKKALELD  179 (304)
T ss_pred             HHHHHHHhhhccC
Confidence            8888888877655

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

Probab=97.51  E-value=0.0011  Score=40.75  Aligned_cols=65  Identities=17%  Similarity=0.231  Sum_probs=45.1

Q ss_pred             CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCC-cHHHHHHHHHHHHHc
Q 044084          129 DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRR-AYWAAVKVYEQLISQ  194 (343)
Q Consensus       129 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~  194 (343)
                      +..+|..+...+...|++++|+..|++..+.++ .+...|..+..++...| ++++|++.+++..+.
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p-~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~l   67 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELDP-NNAEAYYNLGLAYMKLGKDYEEAIEDFEKALKL   67 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHST-THHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHhCccHHHHHHHHHHHHHc
Confidence            455677777777777777777777777776654 35556677777777777 677777777766553

...

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=97.48  E-value=0.018  Score=50.52  Aligned_cols=260  Identities=14%  Similarity=0.130  Sum_probs=146.0

Q ss_pred             CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCc--------hHHHHHHHHHHhhccCc--HHHHHHHHHHHHhc
Q 044084           20 LDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPS--------STHMYKILCDSLGKSGR--AFEILKFFRDMKEK   89 (343)
Q Consensus        20 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--------~~~~~~~li~~~~~~~~--~~~a~~~~~~~~~~   89 (343)
                      |....+.+-+..|...|.+++|.++--    .|+..+..        ..--++..=.+|.+..+  +-+.+.-+++++++
T Consensus       554 ~~evp~~~~m~q~Ieag~f~ea~~iac----lgVv~~DW~~LA~~ALeAL~f~~ARkAY~rVRdl~~L~li~EL~~~k~r  629 (1081)
T KOG1538|consen  554 AVEVPQSAPMYQYIERGLFKEAYQIAC----LGVTDTDWRELAMEALEALDFETARKAYIRVRDLRYLELISELEERKKR  629 (1081)
T ss_pred             cccccccccchhhhhccchhhhhcccc----cceecchHHHHHHHHHhhhhhHHHHHHHHHHhccHHHHHHHHHHHHHhc
Confidence            344445555667778888887765321    11111000        01123333345555443  33444556677777


Q ss_pred             CCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHH------------HHHH
Q 044084           90 GILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVV------------ESMK  157 (343)
Q Consensus        90 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~------------~~~~  157 (343)
                      |-.|+...   +...|+-.|++.+|.++|.+   .|.+      +..+.+|.....+|.|.+++            ++-.
T Consensus       630 ge~P~~iL---lA~~~Ay~gKF~EAAklFk~---~G~e------nRAlEmyTDlRMFD~aQE~~~~g~~~eKKmL~RKRA  697 (1081)
T KOG1538|consen  630 GETPNDLL---LADVFAYQGKFHEAAKLFKR---SGHE------NRALEMYTDLRMFDYAQEFLGSGDPKEKKMLIRKRA  697 (1081)
T ss_pred             CCCchHHH---HHHHHHhhhhHHHHHHHHHH---cCch------hhHHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHH
Confidence            87787643   34556677888888888764   3433      22334444444444444443            2211


Q ss_pred             h--cCCCCchhhHHHHHHHHhcCCcHHHHHHHHHH------HHHcCC---CCCHhhHHHHHHHHHccCChhHHHHHHHHH
Q 044084          158 N--AELNISDCISCVIVNGFSKRRAYWAAVKVYEQ------LISQGC---IPGQVTYASIINAYCRIGLYSKAEKVFIEM  226 (343)
Q Consensus       158 ~--~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~------~~~~~~---~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~  226 (343)
                      +  .+++..    .+-...+...|+.++|..+.-+      +.+-+-   ..+..+...+...+.+...+.-|.++|..|
T Consensus       698 ~WAr~~keP----kaAAEmLiSaGe~~KAi~i~~d~gW~d~lidI~rkld~~ere~l~~~a~ylk~l~~~gLAaeIF~k~  773 (1081)
T KOG1538|consen  698 DWARNIKEP----KAAAEMLISAGEHVKAIEICGDHGWVDMLIDIARKLDKAEREPLLLCATYLKKLDSPGLAAEIFLKM  773 (1081)
T ss_pred             HHhhhcCCc----HHHHHHhhcccchhhhhhhhhcccHHHHHHHHHhhcchhhhhHHHHHHHHHhhccccchHHHHHHHh
Confidence            1  111111    1233444556666666554321      111111   223445555555556677788888888877


Q ss_pred             HHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHH
Q 044084          227 QQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFD  306 (343)
Q Consensus       227 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~  306 (343)
                      -..         .++++.+...+++++|..+-++..+.  .||.  |....+-++...++++|.      .+|.+.|+-.
T Consensus       774 gD~---------ksiVqlHve~~~W~eAFalAe~hPe~--~~dV--y~pyaqwLAE~DrFeEAq------kAfhkAGr~~  834 (1081)
T KOG1538|consen  774 GDL---------KSLVQLHVETQRWDEAFALAEKHPEF--KDDV--YMPYAQWLAENDRFEEAQ------KAFHKAGRQR  834 (1081)
T ss_pred             ccH---------HHHhhheeecccchHhHhhhhhCccc--cccc--cchHHHHhhhhhhHHHHH------HHHHHhcchH
Confidence            553         36778888999999999998887764  4444  333344455566666654      6888999999


Q ss_pred             HHHHHHHHHHhC
Q 044084          307 MCVKFYNEFRMN  318 (343)
Q Consensus       307 ~a~~~~~~m~~~  318 (343)
                      +|.++++++...
T Consensus       835 EA~~vLeQLtnn  846 (1081)
T KOG1538|consen  835 EAVQVLEQLTNN  846 (1081)
T ss_pred             HHHHHHHHhhhh
Confidence            999999998554

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

Probab=97.40  E-value=0.017  Score=41.77  Aligned_cols=70  Identities=17%  Similarity=0.150  Sum_probs=48.3

Q ss_pred             hHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHH-----hcCCCCchhh
Q 044084           97 VYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMK-----NAELNISDCI  167 (343)
Q Consensus        97 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~-----~~~~~~~~~~  167 (343)
                      +...++..+...|+++.|..+.+.+....+- +...|..+|.+|...|+...|.++|+.+.     +.|+.|+..+
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~-~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~  138 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALDPY-DEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPET  138 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT--HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHH
Confidence            3555667777888888888888888887643 78888888888888888888888888764     3577777654

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

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=97.40  E-value=0.014  Score=46.39  Aligned_cols=125  Identities=10%  Similarity=-0.028  Sum_probs=93.1

Q ss_pred             HHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHcc---CChhHHHHHHHH
Q 044084          149 TLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRI---GLYSKAEKVFIE  225 (343)
Q Consensus       149 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~---~~~~~a~~~~~~  225 (343)
                      ...-++.-.+.++ -|...|-.|...|...|+...|..-|.+..+.. .++...+..+..++...   ..-.++..+|++
T Consensus       141 l~a~Le~~L~~nP-~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~-g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~  218 (287)
T COG4235         141 LIARLETHLQQNP-GDAEGWDLLGRAYMALGRASDALLAYRNALRLA-GDNPEILLGLAEALYYQAGQQMTAKARALLRQ  218 (287)
T ss_pred             HHHHHHHHHHhCC-CCchhHHHHHHHHHHhcchhHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Confidence            3333444444554 577889999999999999999999999998863 34555555555554432   346788999999


Q ss_pred             HHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHH
Q 044084          226 MQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMD  278 (343)
Q Consensus       226 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~  278 (343)
                      +.+.+ +-|+.+...|...+...|++.+|...|+.|.+.  -|....+..+++
T Consensus       219 al~~D-~~~iral~lLA~~afe~g~~~~A~~~Wq~lL~~--lp~~~~rr~~ie  268 (287)
T COG4235         219 ALALD-PANIRALSLLAFAAFEQGDYAEAAAAWQMLLDL--LPADDPRRSLIE  268 (287)
T ss_pred             HHhcC-CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhc--CCCCCchHHHHH
Confidence            99986 557888888999999999999999999999986  333344444444

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=97.40  E-value=0.028  Score=41.31  Aligned_cols=123  Identities=16%  Similarity=0.123  Sum_probs=62.5

Q ss_pred             CCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcC---CCCCHhhHH
Q 044084          128 RDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQG---CIPGQVTYA  204 (343)
Q Consensus       128 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~p~~~~~~  204 (343)
                      |+......|.....+.|+..+|...|++...--..-|......+.++....+++..|...++++.+.+   -.||  +.-
T Consensus        87 pTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd--~~L  164 (251)
T COG4700          87 PTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPD--GHL  164 (251)
T ss_pred             hhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCC--chH
Confidence            45555555556666666666666666655543333444445555555555666666666666555542   1222  233


Q ss_pred             HHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHH
Q 044084          205 SIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDA  254 (343)
Q Consensus       205 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  254 (343)
                      .+.+.+...|++..|+.-|+.....-  |+...-......+.++|+.+++
T Consensus       165 l~aR~laa~g~~a~Aesafe~a~~~y--pg~~ar~~Y~e~La~qgr~~ea  212 (251)
T COG4700         165 LFARTLAAQGKYADAESAFEVAISYY--PGPQARIYYAEMLAKQGRLREA  212 (251)
T ss_pred             HHHHHHHhcCCchhHHHHHHHHHHhC--CCHHHHHHHHHHHHHhcchhHH
Confidence            34455555666666666666555542  3332222223334455544443

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

Probab=97.35  E-value=0.002  Score=46.58  Aligned_cols=72  Identities=17%  Similarity=0.244  Sum_probs=49.0

Q ss_pred             HHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHH-----cCCCCCHhhH
Q 044084          131 EVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLIS-----QGCIPGQVTY  203 (343)
Q Consensus       131 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~p~~~~~  203 (343)
                      .+...++..+...|++++|..+.+.+...++ .+...|..+|.+|...|+...|.++|+++.+     .|+.|+..+-
T Consensus        63 ~~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP-~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~  139 (146)
T PF03704_consen   63 DALERLAEALLEAGDYEEALRLLQRALALDP-YDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETR  139 (146)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST-T-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHH
T ss_pred             HHHHHHHHHHHhccCHHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHH
Confidence            3455667777788888888888888887776 5777888888888888888888888887653     3777776553

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

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.32  E-value=0.049  Score=42.45  Aligned_cols=130  Identities=8%  Similarity=0.086  Sum_probs=65.9

Q ss_pred             HHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHH-----HH
Q 044084           99 ASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVI-----VN  173 (343)
Q Consensus        99 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l-----~~  173 (343)
                      +.++..+.-.|.+.-...++.+.++...+.++.....|++.-.+.|+.+.|...|++..+..-..+..+.+.+     ..
T Consensus       181 y~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~a~  260 (366)
T KOG2796|consen  181 YSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNSAF  260 (366)
T ss_pred             HHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhhhh
Confidence            3344555555555555666666666554555666666666666666666666666655443322333333322     22


Q ss_pred             HHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHc
Q 044084          174 GFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       174 ~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  229 (343)
                      .|.-.+++..|...+++..... ..|....|.=.-+..-.|+...|.+.++.+.+.
T Consensus       261 i~lg~nn~a~a~r~~~~i~~~D-~~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~  315 (366)
T KOG2796|consen  261 LHLGQNNFAEAHRFFTEILRMD-PRNAVANNNKALCLLYLGKLKDALKQLEAMVQQ  315 (366)
T ss_pred             heecccchHHHHHHHhhccccC-CCchhhhchHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            3444556666666666555442 112222222111222235666666666666664

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=97.31  E-value=0.004  Score=51.40  Aligned_cols=116  Identities=16%  Similarity=0.103  Sum_probs=65.5

Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHH--Hhc--CCC-CChHhHHHHHHH
Q 044084           30 EAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDM--KEK--GIL-EDPSVYASLICS  104 (343)
Q Consensus        30 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~--~~~--~~~-~~~~~~~~l~~~  104 (343)
                      .-+++.|+......+|+...+.|-..-..-..+|..|.++|.-.+++++|+++...=  +..  |-+ -...+...|.+.
T Consensus        25 ERLck~gdcraGv~ff~aA~qvGTeDl~tLSAIYsQLGNAyfyL~DY~kAl~yH~hDltlar~lgdklGEAKssgNLGNt  104 (639)
T KOG1130|consen   25 ERLCKMGDCRAGVDFFKAALQVGTEDLSTLSAIYSQLGNAYFYLKDYEKALKYHTHDLTLARLLGDKLGEAKSSGNLGNT  104 (639)
T ss_pred             HHHHhccchhhhHHHHHHHHHhcchHHHHHHHHHHHhcchhhhHhhHHHHHhhhhhhHHHHHHhcchhccccccccccch
Confidence            457888888888899988888775443333466777778888888888887764321  111  100 112223334444


Q ss_pred             HhcccCHHHHHHHHHH----HHHcCCC-CCHHHHHHHHHHHHhcCc
Q 044084          105 FASIAEVKVAEELFKE----AEEKGML-RDLEVFLKLVLMYIEEGM  145 (343)
Q Consensus       105 ~~~~~~~~~a~~~~~~----~~~~~~~-~~~~~~~~l~~~~~~~~~  145 (343)
                      +--.|.+++|.-...+    ..+.|-. .....+..|...|...|+
T Consensus       105 lKv~G~fdeA~~cc~rhLd~areLgDrv~e~RAlYNlgnvYhakGk  150 (639)
T KOG1130|consen  105 LKVKGAFDEALTCCFRHLDFARELGDRVLESRALYNLGNVYHAKGK  150 (639)
T ss_pred             hhhhcccchHHHHHHHHhHHHHHHhHHHhhhHHHhhhhhhhhhccc
Confidence            5555667766654332    2222211 124445556666765553

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=97.31  E-value=0.012  Score=47.04  Aligned_cols=97  Identities=6%  Similarity=-0.004  Sum_probs=48.2

Q ss_pred             HHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCc--hhhHHHHHHHHhcCCcHHHHHHHHHHHHHcC--CCCCHhhHHHHHH
Q 044084          133 FLKLVLMYIEEGMVEKTLEVVESMKNAELNIS--DCISCVIVNGFSKRRAYWAAVKVYEQLISQG--CIPGQVTYASIIN  208 (343)
Q Consensus       133 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~p~~~~~~~ll~  208 (343)
                      |......+.+.|++++|...|+.+.+..+...  ...+-.+..+|...|++++|...|+.+.+.-  -+.....+-.+..
T Consensus       146 Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg~  225 (263)
T PRK10803        146 YNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVGV  225 (263)
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHHH
Confidence            44444444445566666666666555432111  1234455555566666666666666665431  0111223333444


Q ss_pred             HHHccCChhHHHHHHHHHHHc
Q 044084          209 AYCRIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       209 ~~~~~~~~~~a~~~~~~~~~~  229 (343)
                      .+...|+.++|..+|+.+.+.
T Consensus       226 ~~~~~g~~~~A~~~~~~vi~~  246 (263)
T PRK10803        226 IMQDKGDTAKAKAVYQQVIKK  246 (263)
T ss_pred             HHHHcCCHHHHHHHHHHHHHH
Confidence            455566666666666666554

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=97.28  E-value=0.017  Score=46.09  Aligned_cols=98  Identities=13%  Similarity=-0.004  Sum_probs=56.6

Q ss_pred             hHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCC--CchhhHHHHH
Q 044084           97 VYASLICSFASIAEVKVAEELFKEAEEKGMLRD--LEVFLKLVLMYIEEGMVEKTLEVVESMKNAELN--ISDCISCVIV  172 (343)
Q Consensus        97 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~  172 (343)
                      .|...+....+.|++++|...|+.+.+.-+...  +..+..+...|...|++++|...|+.+....+.  .....+-.+.
T Consensus       145 ~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg  224 (263)
T PRK10803        145 DYNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVG  224 (263)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHH
Confidence            344444444555667777777776666543211  345556666777777777777777776643321  1122333445


Q ss_pred             HHHhcCCcHHHHHHHHHHHHHc
Q 044084          173 NGFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       173 ~~~~~~~~~~~a~~~~~~~~~~  194 (343)
                      .++...|+.+.|..+|+.+.+.
T Consensus       225 ~~~~~~g~~~~A~~~~~~vi~~  246 (263)
T PRK10803        225 VIMQDKGDTAKAKAVYQQVIKK  246 (263)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHH
Confidence            5566667777777777776665

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=97.23  E-value=0.095  Score=43.79  Aligned_cols=161  Identities=12%  Similarity=0.108  Sum_probs=75.7

Q ss_pred             HHHHhcccCHHHHHHHHHHHHHcC---CCCCHHHHHHHHHHHHh---cCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHH
Q 044084          102 ICSFASIAEVKVAEELFKEAEEKG---MLRDLEVFLKLVLMYIE---EGMVEKTLEVVESMKNAELNISDCISCVIVNGF  175 (343)
Q Consensus       102 ~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~~l~~~~~~---~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  175 (343)
                      +-+|-...+++...++.+.+....   +.-+..+-....-++.+   .|+.++|++++..+......++..+|..+.+.|
T Consensus       148 llSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~gL~GRIy  227 (374)
T PF13281_consen  148 LLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTLGLLGRIY  227 (374)
T ss_pred             HHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHHHHHHHHH
Confidence            334555555555555555554431   11122222233333444   555555555555543333334444555444433


Q ss_pred             hc---------CCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCC-h---hHHHHHH---H-HHHHcC---CCcCh
Q 044084          176 SK---------RRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGL-Y---SKAEKVF---I-EMQQKG---FDKCV  235 (343)
Q Consensus       176 ~~---------~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~-~---~~a~~~~---~-~~~~~~---~~~~~  235 (343)
                      -.         ....++|...|.+.-+.  .|+.++=-.++..+...|. .   .+..++-   . .+.+.|   -..+-
T Consensus       228 KD~~~~s~~~d~~~ldkAi~~Y~kgFe~--~~~~Y~GIN~AtLL~~~g~~~~~~~el~~i~~~l~~llg~kg~~~~~~dY  305 (374)
T PF13281_consen  228 KDLFLESNFTDRESLDKAIEWYRKGFEI--EPDYYSGINAATLLMLAGHDFETSEELRKIGVKLSSLLGRKGSLEKMQDY  305 (374)
T ss_pred             HHHHHHcCccchHHHHHHHHHHHHHHcC--CccccchHHHHHHHHHcCCcccchHHHHHHHHHHHHHHHhhccccccccH
Confidence            21         12356666666665544  2443332222222222222 1   1222222   1 111222   12344


Q ss_pred             hhHHHHHHHHHccCChHHHHHHHHHHhhC
Q 044084          236 VAYSSMVAMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       236 ~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                      ..+.+++.+..-.|+.++|.+..++|...
T Consensus       306 Wd~ATl~Ea~vL~~d~~ka~~a~e~~~~l  334 (374)
T PF13281_consen  306 WDVATLLEASVLAGDYEKAIQAAEKAFKL  334 (374)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHhhc
Confidence            55667777888888888888888888765

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=97.21  E-value=0.0028  Score=39.47  Aligned_cols=56  Identities=13%  Similarity=0.072  Sum_probs=37.3

Q ss_pred             HHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhC
Q 044084          208 NAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       208 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                      ..|.+.+++++|.++++.+...+ |.++..+.....++.+.|++++|.+.|++..+.
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~   58 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELD-PDDPELWLQRARCLFQLGRYEEALEDLERALEL   58 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC-cccchhhHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            34566677777777777776664 445666666666777777777777777776654

>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=97.14  E-value=0.0075  Score=41.98  Aligned_cols=48  Identities=19%  Similarity=0.226  Sum_probs=37.7

Q ss_pred             CCcChhhHHHHHHHHHccCChHHHHHHHHHHhhC-CCCchHHHHHHHHH
Q 044084          231 FDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK-GCEPNVWIYNSLMD  278 (343)
Q Consensus       231 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~-~~~p~~~~~~~l~~  278 (343)
                      ..|+..+..+++.+|+..|++..|+++++...+. +++.+..+|..|++
T Consensus        48 l~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~   96 (126)
T PF12921_consen   48 LYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLE   96 (126)
T ss_pred             CCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            4577888888888888888888888888887754 66667778887776

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

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=97.11  E-value=0.056  Score=48.05  Aligned_cols=28  Identities=7%  Similarity=-0.043  Sum_probs=18.0

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHH
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMK   87 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~   87 (343)
                      ...|..|.......-.++.|...|-+..
T Consensus       692 prLWrllAe~Al~Kl~l~tAE~AFVrc~  719 (1189)
T KOG2041|consen  692 PRLWRLLAEYALFKLALDTAEHAFVRCG  719 (1189)
T ss_pred             hHHHHHHHHHHHHHHhhhhHhhhhhhhc
Confidence            3677777776666666666666665543

>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=97.11  E-value=0.0095  Score=41.47  Aligned_cols=98  Identities=12%  Similarity=0.084  Sum_probs=59.5

Q ss_pred             CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHH
Q 044084          129 DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIIN  208 (343)
Q Consensus       129 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~  208 (343)
                      |..++..++.++++.|+.+....+++..=  |+.++..         ...+.         --......|+..+..+++.
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~W--gI~~~~~---------~~~~~---------~~~~spl~Pt~~lL~AIv~   60 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVW--GIDVNGK---------KKEGD---------YPPSSPLYPTSRLLIAIVH   60 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhc--CCCCCCc---------cccCc---------cCCCCCCCCCHHHHHHHHH
Confidence            34556666667777777666666665432  1111100         00000         1112245688888888888


Q ss_pred             HHHccCChhHHHHHHHHHHHc-CCCcChhhHHHHHHHHH
Q 044084          209 AYCRIGLYSKAEKVFIEMQQK-GFDKCVVAYSSMVAMYG  246 (343)
Q Consensus       209 ~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~  246 (343)
                      +|+..|++..|.++.+.+.+. +++.+..+|..|+.=..
T Consensus        61 sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W~~   99 (126)
T PF12921_consen   61 SFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEWAY   99 (126)
T ss_pred             HHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            888888888888888887754 56666777877776433

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

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.10  E-value=0.088  Score=41.12  Aligned_cols=145  Identities=10%  Similarity=0.071  Sum_probs=110.7

Q ss_pred             HHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHH---
Q 044084          131 EVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASII---  207 (343)
Q Consensus       131 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll---  207 (343)
                      .+.+.++..+.-.+.+.-....+.+..+.+.+.++.....+.+.-.+.|+.+.|...|++..+..-..+..+++.++   
T Consensus       178 ~Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n  257 (366)
T KOG2796|consen  178 RVMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMN  257 (366)
T ss_pred             HHHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhh
Confidence            34556777777788899999999999988877788888889999999999999999999887654345555554443   


Q ss_pred             --HHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHH
Q 044084          208 --NAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMD  278 (343)
Q Consensus       208 --~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~  278 (343)
                        ..|.-.+++..|...+.++...+ +.|+...|.-.-+..-.|+..+|.+.++.|.+.  .|...+-++++-
T Consensus       258 ~a~i~lg~nn~a~a~r~~~~i~~~D-~~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~--~P~~~l~es~~~  327 (366)
T KOG2796|consen  258 SAFLHLGQNNFAEAHRFFTEILRMD-PRNAVANNNKALCLLYLGKLKDALKQLEAMVQQ--DPRHYLHESVLF  327 (366)
T ss_pred             hhhheecccchHHHHHHHhhccccC-CCchhhhchHHHHHHHHHHHHHHHHHHHHHhcc--CCccchhhhHHH
Confidence              34566788999999998888876 456666666555666688999999999999986  566666555544

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=97.10  E-value=0.0052  Score=38.20  Aligned_cols=55  Identities=22%  Similarity=0.198  Sum_probs=25.4

Q ss_pred             HHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhc
Q 044084          104 SFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNA  159 (343)
Q Consensus       104 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  159 (343)
                      .+.+.++++.|.++++.+...++. ++..+.....++.+.|++++|.+.|+...+.
T Consensus         4 ~~~~~~~~~~A~~~~~~~l~~~p~-~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~   58 (73)
T PF13371_consen    4 IYLQQEDYEEALEVLERALELDPD-DPELWLQRARCLFQLGRYEEALEDLERALEL   58 (73)
T ss_pred             HHHhCCCHHHHHHHHHHHHHhCcc-cchhhHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            344444444444444444444332 3444444444444444444444444444433

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=97.09  E-value=0.066  Score=39.46  Aligned_cols=134  Identities=14%  Similarity=0.123  Sum_probs=93.7

Q ss_pred             CCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCC-CchhhHH
Q 044084           91 ILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELN-ISDCISC  169 (343)
Q Consensus        91 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~  169 (343)
                      ..|+...--.|..+....|+..+|...|++....-+.-|....-.+.++....+++..|...++++.+.++. -+..+..
T Consensus        85 ~ApTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~~L  164 (251)
T COG4700          85 IAPTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDGHL  164 (251)
T ss_pred             hchhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCchH
Confidence            456666666778888888888888888888877555557888888888888888888888888887765421 1222455


Q ss_pred             HHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHH
Q 044084          170 VIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEM  226 (343)
Q Consensus       170 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~  226 (343)
                      .+.+.+...|.+.+|..-|+.....  -|+...-......+.+.|+.+++..-+..+
T Consensus       165 l~aR~laa~g~~a~Aesafe~a~~~--ypg~~ar~~Y~e~La~qgr~~ea~aq~~~v  219 (251)
T COG4700         165 LFARTLAAQGKYADAESAFEVAISY--YPGPQARIYYAEMLAKQGRLREANAQYVAV  219 (251)
T ss_pred             HHHHHHHhcCCchhHHHHHHHHHHh--CCCHHHHHHHHHHHHHhcchhHHHHHHHHH
Confidence            6778888888888888888888876  455444333344456667666655444433

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

Probab=97.09  E-value=0.12  Score=42.55  Aligned_cols=122  Identities=13%  Similarity=0.149  Sum_probs=85.2

Q ss_pred             hHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHH
Q 044084          167 ISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYG  246 (343)
Q Consensus       167 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  246 (343)
                      +.+..|.-+...|+...|.++-.+..    .|+..-|...+.+++..++|++-.++-..      +-.+.-|..++.+|.
T Consensus       179 Sl~~Ti~~li~~~~~k~A~kl~k~Fk----v~dkrfw~lki~aLa~~~~w~eL~~fa~s------kKsPIGyepFv~~~~  248 (319)
T PF04840_consen  179 SLNDTIRKLIEMGQEKQAEKLKKEFK----VPDKRFWWLKIKALAENKDWDELEKFAKS------KKSPIGYEPFVEACL  248 (319)
T ss_pred             CHHHHHHHHHHCCCHHHHHHHHHHcC----CcHHHHHHHHHHHHHhcCCHHHHHHHHhC------CCCCCChHHHHHHHH
Confidence            45556777777888888887766653    47888888889999999998887765432      223578888899999


Q ss_pred             ccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHH
Q 044084          247 KTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNE  314 (343)
Q Consensus       247 ~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~  314 (343)
                      +.|+..+|..++.++.          +..-+..|.+.|++.+|.      ....+.++.+.-..+.+.
T Consensus       249 ~~~~~~eA~~yI~k~~----------~~~rv~~y~~~~~~~~A~------~~A~~~kd~~~L~~i~~~  300 (319)
T PF04840_consen  249 KYGNKKEASKYIPKIP----------DEERVEMYLKCGDYKEAA------QEAFKEKDIDLLKQILKR  300 (319)
T ss_pred             HCCCHHHHHHHHHhCC----------hHHHHHHHHHCCCHHHHH------HHHHHcCCHHHHHHHHHH
Confidence            9999888888877622          134567778888877764      445556665544444443

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

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

Probab=97.05  E-value=0.0026  Score=40.23  Aligned_cols=66  Identities=12%  Similarity=0.282  Sum_probs=45.5

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhCC--CCCC-CchHHHHHHHHHHhhccCcHHHHHHHHHHHHh
Q 044084           23 GCYCQIMEAFYKIGDSEKVAALFLECESRK--LDLT-PSSTHMYKILCDSLGKSGRAFEILKFFRDMKE   88 (343)
Q Consensus        23 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~   88 (343)
                      .+|+.+...|.+.|++++|+..|++..+..  ..++ +....+++.+...+...|++++|++.+++..+
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~   74 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALD   74 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            467788888888888888888888765431  1111 22356777788888888888888888877643

...

>PRK15331 chaperone protein SicA; Provisional

Probab=97.04  E-value=0.058  Score=39.07  Aligned_cols=87  Identities=10%  Similarity=-0.040  Sum_probs=55.9

Q ss_pred             HhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHH
Q 044084          105 FASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAA  184 (343)
Q Consensus       105 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  184 (343)
                      +...|++++|..+|..+.-.++. +...|..|..++-..+++++|+..|......+. -|...+-....++...|+.+.|
T Consensus        47 ~y~~Gk~~eA~~~F~~L~~~d~~-n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~-~dp~p~f~agqC~l~l~~~~~A  124 (165)
T PRK15331         47 FYNQGRLDEAETFFRFLCIYDFY-NPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLK-NDYRPVFFTGQCQLLMRKAAKA  124 (165)
T ss_pred             HHHCCCHHHHHHHHHHHHHhCcC-cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc-CCCCccchHHHHHHHhCCHHHH
Confidence            34567777777777777665543 566667777777777777777777766544332 2223334456667777777777


Q ss_pred             HHHHHHHHH
Q 044084          185 VKVYEQLIS  193 (343)
Q Consensus       185 ~~~~~~~~~  193 (343)
                      ...|.....
T Consensus       125 ~~~f~~a~~  133 (165)
T PRK15331        125 RQCFELVNE  133 (165)
T ss_pred             HHHHHHHHh
Confidence            777776665

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=97.02  E-value=0.16  Score=42.56  Aligned_cols=80  Identities=13%  Similarity=0.191  Sum_probs=41.3

Q ss_pred             HHHHHHHHHHHhcCcHhHHHHHHHHHHhcC---CCCchhhHHHHHHHHhc---CCcHHHHHHHHHHHHHcCCCCCHhhHH
Q 044084          131 EVFLKLVLMYIEEGMVEKTLEVVESMKNAE---LNISDCISCVIVNGFSK---RRAYWAAVKVYEQLISQGCIPGQVTYA  204 (343)
Q Consensus       131 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~~l~~~~~~---~~~~~~a~~~~~~~~~~~~~p~~~~~~  204 (343)
                      .+...++-+|-...+++..+++++.+....   +.-....--...-++.+   .|+.++|.+++..+....-.++..+|.
T Consensus       142 div~~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~g  221 (374)
T PF13281_consen  142 DIVINLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTLG  221 (374)
T ss_pred             hHHHHHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHHH
Confidence            333445555666666666666666665442   11111112223334444   566666666666644444455566666


Q ss_pred             HHHHHH
Q 044084          205 SIINAY  210 (343)
Q Consensus       205 ~ll~~~  210 (343)
                      .+.+.|
T Consensus       222 L~GRIy  227 (374)
T PF13281_consen  222 LLGRIY  227 (374)
T ss_pred             HHHHHH
Confidence            555554

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=96.95  E-value=0.037  Score=45.99  Aligned_cols=40  Identities=23%  Similarity=0.435  Sum_probs=20.7

Q ss_pred             hHHHHHHHHHhCCCCCC----hhhHHHHHHHHHhcCCHHHHHHHH
Q 044084            5 SKLHYYEKMKSAGIVLD----SGCYCQIMEAFYKIGDSEKVAALF   45 (343)
Q Consensus         5 ~A~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~   45 (343)
                      ..+.+|+..++.|.. |    ..+|..|..+|.-.+++++|++..
T Consensus        35 aGv~ff~aA~qvGTe-Dl~tLSAIYsQLGNAyfyL~DY~kAl~yH   78 (639)
T KOG1130|consen   35 AGVDFFKAALQVGTE-DLSTLSAIYSQLGNAYFYLKDYEKALKYH   78 (639)
T ss_pred             hhHHHHHHHHHhcch-HHHHHHHHHHHhcchhhhHhhHHHHHhhh
Confidence            345566666665532 2    223455555555555666665543

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=96.94  E-value=0.074  Score=43.32  Aligned_cols=87  Identities=17%  Similarity=0.225  Sum_probs=39.4

Q ss_pred             hhHHHHHHHHHhCCCCCChhhHHHHHHHHHh--cC----CHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCc--
Q 044084            4 QSKLHYYEKMKSAGIVLDSGCYCQIMEAFYK--IG----DSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGR--   75 (343)
Q Consensus         4 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~----~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~--   75 (343)
                      ++.+.+++.|.+.|..-+..+|-+.......  ..    ...+|..+|+.|++...-.+.+....+..++..  ..++  
T Consensus        79 ~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--~~~~~e  156 (297)
T PF13170_consen   79 KEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--TSEDVE  156 (297)
T ss_pred             HHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc--ccccHH
Confidence            3445566666666665555444432222222  11    134555666666555544443333444444333  2222  


Q ss_pred             --HHHHHHHHHHHHhcCCC
Q 044084           76 --AFEILKFFRDMKEKGIL   92 (343)
Q Consensus        76 --~~~a~~~~~~~~~~~~~   92 (343)
                        .+.+..+|+.+...|..
T Consensus       157 ~l~~~~E~~Y~~L~~~~f~  175 (297)
T PF13170_consen  157 ELAERMEQCYQKLADAGFK  175 (297)
T ss_pred             HHHHHHHHHHHHHHHhCCC
Confidence              23344455555554443

>PRK15331 chaperone protein SicA; Provisional

Probab=96.89  E-value=0.067  Score=38.75  Aligned_cols=90  Identities=16%  Similarity=0.048  Sum_probs=55.7

Q ss_pred             HHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcH
Q 044084           67 CDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMV  146 (343)
Q Consensus        67 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  146 (343)
                      ..-+...|++++|..+|+-+...+.. +..-|..|..++-..++++.|...|......+.. |+..+-....+|...|+.
T Consensus        44 Ay~~y~~Gk~~eA~~~F~~L~~~d~~-n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~~-dp~p~f~agqC~l~l~~~  121 (165)
T PRK15331         44 AYEFYNQGRLDEAETFFRFLCIYDFY-NPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLKN-DYRPVFFTGQCQLLMRKA  121 (165)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCcC-cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccC-CCCccchHHHHHHHhCCH
Confidence            34445667777777777766654422 4444455555555667777777777666554432 444455566777777777


Q ss_pred             hHHHHHHHHHHh
Q 044084          147 EKTLEVVESMKN  158 (343)
Q Consensus       147 ~~a~~~~~~~~~  158 (343)
                      +.|+..|+....
T Consensus       122 ~~A~~~f~~a~~  133 (165)
T PRK15331        122 AKARQCFELVNE  133 (165)
T ss_pred             HHHHHHHHHHHh
Confidence            777777776665

>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []

Probab=96.83  E-value=0.2  Score=40.72  Aligned_cols=166  Identities=16%  Similarity=0.119  Sum_probs=91.7

Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCCch-----HHHHHHHHHHhhccC-cHHHHHHHHHHHHhc--------CCCCCh--
Q 044084           32 FYKIGDSEKVAALFLECESRKLDLTPSS-----THMYKILCDSLGKSG-RAFEILKFFRDMKEK--------GILEDP--   95 (343)
Q Consensus        32 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~-----~~~~~~li~~~~~~~-~~~~a~~~~~~~~~~--------~~~~~~--   95 (343)
                      ..+.|+++.|..++.+........+|..     ...|+. .......+ +++.|..++++..+.        ...|+.  
T Consensus         3 A~~~~~~~~A~~~~~K~~~~~~~~~~~~~~~La~~~yn~-G~~l~~~~~~~~~a~~wL~~a~~~l~~~~~~~~~~~~~~e   81 (278)
T PF08631_consen    3 AWKQGDLDLAEHMYSKAKDLLNSLDPDMAEELARVCYNI-GKSLLSKKDKYEEAVKWLQRAYDILEKPGKMDKLSPDGSE   81 (278)
T ss_pred             chhhCCHHHHHHHHHHhhhHHhcCCcHHHHHHHHHHHHH-HHHHHHcCCChHHHHHHHHHHHHHHHhhhhccccCCcHHH
Confidence            3467899999999988866543333332     122333 33334455 788887777765432        112222  


Q ss_pred             ---HhHHHHHHHHhcccCHH---HHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHH
Q 044084           96 ---SVYASLICSFASIAEVK---VAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISC  169 (343)
Q Consensus        96 ---~~~~~l~~~~~~~~~~~---~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  169 (343)
                         .++..++.++...+..+   +|..+++.+.+.... .+.++..-+..+.+.++.+.+.+++.+|...-. .....+.
T Consensus        82 lr~~iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~~~-~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~~~-~~e~~~~  159 (278)
T PF08631_consen   82 LRLSILRLLANAYLEWDTYESVEKALNALRLLESEYGN-KPEVFLLKLEILLKSFDEEEYEEILMRMIRSVD-HSESNFD  159 (278)
T ss_pred             HHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhCCC-CcHHHHHHHHHHhccCChhHHHHHHHHHHHhcc-cccchHH
Confidence               34555667777666544   445555555443322 345555556666667888888888888876532 1223454


Q ss_pred             HHHHHHhc--CCcHHHHHHHHHHHHHcCCCCCH
Q 044084          170 VIVNGFSK--RRAYWAAVKVYEQLISQGCIPGQ  200 (343)
Q Consensus       170 ~l~~~~~~--~~~~~~a~~~~~~~~~~~~~p~~  200 (343)
                      .++..+..  ......+...++.+....+.|..
T Consensus       160 ~~l~~i~~l~~~~~~~a~~~ld~~l~~r~~~~~  192 (278)
T PF08631_consen  160 SILHHIKQLAEKSPELAAFCLDYLLLNRFKSSE  192 (278)
T ss_pred             HHHHHHHHHHhhCcHHHHHHHHHHHHHHhCCCh
Confidence            44444421  23344556666665555444444

It is also involved in sporulation [].

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=96.74  E-value=0.1  Score=43.39  Aligned_cols=96  Identities=14%  Similarity=0.136  Sum_probs=56.3

Q ss_pred             hHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHh
Q 044084           97 VYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFS  176 (343)
Q Consensus        97 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  176 (343)
                      ++..+.-++.+.+++..|+....+.+..+. +|....-.-..++...|+++.|+..|+++.+..+ .|..+-+.++.+-.
T Consensus       259 ~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~~-~N~KALyRrG~A~l~~~e~~~A~~df~ka~k~~P-~Nka~~~el~~l~~  336 (397)
T KOG0543|consen  259 CHLNLAACYLKLKEYKEAIESCNKVLELDP-NNVKALYRRGQALLALGEYDLARDDFQKALKLEP-SNKAARAELIKLKQ  336 (397)
T ss_pred             HhhHHHHHHHhhhhHHHHHHHHHHHHhcCC-CchhHHHHHHHHHHhhccHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHH
Confidence            345555666677777777777777666654 3566666666777777777777777777766554 23333344444333


Q ss_pred             cCCcH-HHHHHHHHHHHHc
Q 044084          177 KRRAY-WAAVKVYEQLISQ  194 (343)
Q Consensus       177 ~~~~~-~~a~~~~~~~~~~  194 (343)
                      +.... +...++|..|...
T Consensus       337 k~~~~~~kekk~y~~mF~k  355 (397)
T KOG0543|consen  337 KIREYEEKEKKMYANMFAK  355 (397)
T ss_pred             HHHHHHHHHHHHHHHHhhc
Confidence            33332 3345666666543

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

Probab=96.74  E-value=0.0059  Score=38.56  Aligned_cols=61  Identities=15%  Similarity=0.180  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHhcCcHhHHHHHHHHHHhc----CC-CCc-hhhHHHHHHHHhcCCcHHHHHHHHHHH
Q 044084          131 EVFLKLVLMYIEEGMVEKTLEVVESMKNA----EL-NIS-DCISCVIVNGFSKRRAYWAAVKVYEQL  191 (343)
Q Consensus       131 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~-~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~  191 (343)
                      .+++.+...|...|++++|+..|++..+.    |. .|. ..++..+..++...|++++|.+++++.
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~a   72 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKA   72 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            34455555555555555555555554321    10 011 223444455555555555555555543

...

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.65  E-value=0.48  Score=42.76  Aligned_cols=265  Identities=13%  Similarity=0.085  Sum_probs=141.0

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-CchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHH
Q 044084           21 DSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLT-PSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYA   99 (343)
Q Consensus        21 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~   99 (343)
                      +..+|..+.......|+++-|..+++.=...+.... --+..-+...+.-+.+.|+.+-...++-.+...   .+...|.
T Consensus       506 ~~iSy~~iA~~Ay~~GR~~LA~kLle~E~~~~~qV~lLL~m~~~~~AL~kaies~d~~Li~~Vllhlk~~---~~~s~l~  582 (829)
T KOG2280|consen  506 PGISYAAIARRAYQEGRFELARKLLELEPRSGEQVPLLLKMKDSSLALKKAIESGDTDLIIQVLLHLKNK---LNRSSLF  582 (829)
T ss_pred             CceeHHHHHHHHHhcCcHHHHHHHHhcCCCccchhHHHhccchHHHHHHHHHhcCCchhHHHHHHHHHHH---HHHHHHH
Confidence            445688888888899999999988764322221110 000122334445555566666665555555442   1111111


Q ss_pred             HHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHH--HHH----hcCCCCchhhHHHHHH
Q 044084          100 SLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVE--SMK----NAELNISDCISCVIVN  173 (343)
Q Consensus       100 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~--~~~----~~~~~~~~~~~~~l~~  173 (343)
                      .      ...+...|..+|.+..+..-.   .   .+-..|-. ++-.++...|.  ...    ..+..|+   ......
T Consensus       583 ~------~l~~~p~a~~lY~~~~r~~~~---~---~l~d~y~q-~dn~~~~a~~~~q~~~~~~~~~~r~~~---lk~~a~  646 (829)
T KOG2280|consen  583 M------TLRNQPLALSLYRQFMRHQDR---A---TLYDFYNQ-DDNHQALASFHLQASYAAETIEGRIPA---LKTAAN  646 (829)
T ss_pred             H------HHHhchhhhHHHHHHHHhhch---h---hhhhhhhc-ccchhhhhhhhhhhhhhhhhhcccchh---HHHHHH
Confidence            1      122345556666655543211   1   11122222 22222222211  100    1122222   222333


Q ss_pred             HHhcCCc----------HHHHHHHHHHHHHc-CCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHH
Q 044084          174 GFSKRRA----------YWAAVKVYEQLISQ-GCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMV  242 (343)
Q Consensus       174 ~~~~~~~----------~~~a~~~~~~~~~~-~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  242 (343)
                      .+.+...          ..+-+++.+.+... |......+.+--+.-+...|+..+|.++-.+.+    -||-..|-.=+
T Consensus       647 ~~a~sk~~s~e~ka~ed~~kLl~lQ~~Le~q~~~~f~dlSl~dTv~~li~~g~~k~a~ql~~~Fk----ipdKr~~wLk~  722 (829)
T KOG2280|consen  647 AFAKSKEKSFEAKALEDQMKLLKLQRTLEDQFGGSFVDLSLHDTVTTLILIGQNKRAEQLKSDFK----IPDKRLWWLKL  722 (829)
T ss_pred             HHhhhhhhhhHHHHHHHHHHHHHHHHHHHHHhccccccCcHHHHHHHHHHccchHHHHHHHHhcC----CcchhhHHHHH
Confidence            3333322          11222223333322 333444555656666777788888887765543    36777888888


Q ss_pred             HHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh-------HHHHHHHHHhcCCHHHHHHHHHH
Q 044084          243 AMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK-------YTTVISAYNMAREFDMCVKFYNE  314 (343)
Q Consensus       243 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~-------~~~l~~~~~~~g~~~~a~~~~~~  314 (343)
                      .+++..+++++.+++-+.++.      +.-|.-++.+|.+.|+.++|.+       +...+.+|.+.|++.+|.++--+
T Consensus       723 ~aLa~~~kweeLekfAkskks------PIGy~PFVe~c~~~~n~~EA~KYiprv~~l~ekv~ay~~~~~~~eAad~A~~  795 (829)
T KOG2280|consen  723 TALADIKKWEELEKFAKSKKS------PIGYLPFVEACLKQGNKDEAKKYIPRVGGLQEKVKAYLRVGDVKEAADLAAE  795 (829)
T ss_pred             HHHHhhhhHHHHHHHHhccCC------CCCchhHHHHHHhcccHHHHhhhhhccCChHHHHHHHHHhccHHHHHHHHHH
Confidence            888888888887777666552      3334557788888888888888       44577888888888888776444

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=96.61  E-value=0.33  Score=40.38  Aligned_cols=59  Identities=14%  Similarity=0.081  Sum_probs=27.9

Q ss_pred             HHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHcc-CChHHHHHHHHHHhh
Q 044084          203 YASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKT-GRIRDAMRLVAKMKP  263 (343)
Q Consensus       203 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~a~~~~~~m~~  263 (343)
                      ...+..+....|++..|..--+.....  .|....|..|.+.-... |+-.++...+.+...
T Consensus       332 ~~~va~aAlda~e~~~ARa~Aeaa~r~--~pres~~lLlAdIeeAetGDqg~vR~wlAqav~  391 (531)
T COG3898         332 SLAVAEAALDAGEFSAARAKAEAAARE--APRESAYLLLADIEEAETGDQGKVRQWLAQAVK  391 (531)
T ss_pred             HHHHHHHHHhccchHHHHHHHHHHhhh--CchhhHHHHHHHHHhhccCchHHHHHHHHHHhc
Confidence            333444444455555544443333332  34455555555443333 555555555555544

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=96.59  E-value=0.14  Score=43.62  Aligned_cols=66  Identities=24%  Similarity=0.197  Sum_probs=45.8

Q ss_pred             CchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCCh----HhHHHHHHHHhcccCHHHHHHHHHHHHHc
Q 044084           57 PSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDP----SVYASLICSFASIAEVKVAEELFKEAEEK  124 (343)
Q Consensus        57 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  124 (343)
                      |.....|+.+..+|...|++++|+..|++.++.  .|+.    .+|..+..+|...|+.++|...+++..+.
T Consensus        72 P~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL--~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         72 VKTAEDAVNLGLSLFSKGRVKDALAQFETALEL--NPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            344667777777777777777777777777665  3442    24666777777777777777777777664

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=96.56  E-value=0.095  Score=45.36  Aligned_cols=160  Identities=18%  Similarity=0.126  Sum_probs=102.9

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcc
Q 044084           29 MEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASI  108 (343)
Q Consensus        29 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  108 (343)
                      .+...-.++++++.++...-   .+.|.-+ ....+.+++.+-+.|.++.|+++.+.-.            .-.....+.
T Consensus       268 fk~av~~~d~~~v~~~i~~~---~ll~~i~-~~~~~~i~~fL~~~G~~e~AL~~~~D~~------------~rFeLAl~l  331 (443)
T PF04053_consen  268 FKTAVLRGDFEEVLRMIAAS---NLLPNIP-KDQGQSIARFLEKKGYPELALQFVTDPD------------HRFELALQL  331 (443)
T ss_dssp             HHHHHHTT-HHH-----HHH---HTGGG---HHHHHHHHHHHHHTT-HHHHHHHSS-HH------------HHHHHHHHC
T ss_pred             HHHHHHcCChhhhhhhhhhh---hhcccCC-hhHHHHHHHHHHHCCCHHHHHhhcCChH------------HHhHHHHhc
Confidence            34455678888877666411   1111111 3467888888888999999988764321            123455678


Q ss_pred             cCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHH
Q 044084          109 AEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVY  188 (343)
Q Consensus       109 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  188 (343)
                      |+++.|.++.++.      .+...|..|.....+.|+++-|.+.|.+..+         |..++-.|...|+.+...++.
T Consensus       332 g~L~~A~~~a~~~------~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d---------~~~L~lLy~~~g~~~~L~kl~  396 (443)
T PF04053_consen  332 GNLDIALEIAKEL------DDPEKWKQLGDEALRQGNIELAEECYQKAKD---------FSGLLLLYSSTGDREKLSKLA  396 (443)
T ss_dssp             T-HHHHHHHCCCC------STHHHHHHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHCT-HHHHHHHH
T ss_pred             CCHHHHHHHHHhc------CcHHHHHHHHHHHHHcCCHHHHHHHHHhhcC---------ccccHHHHHHhCCHHHHHHHH
Confidence            8888887765432      3788999999999999999999999988753         556777778888888888888


Q ss_pred             HHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHH
Q 044084          189 EQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIE  225 (343)
Q Consensus       189 ~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~  225 (343)
                      +.....|      -++....++.-.|+.+++.+++.+
T Consensus       397 ~~a~~~~------~~n~af~~~~~lgd~~~cv~lL~~  427 (443)
T PF04053_consen  397 KIAEERG------DINIAFQAALLLGDVEECVDLLIE  427 (443)
T ss_dssp             HHHHHTT-------HHHHHHHHHHHT-HHHHHHHHHH
T ss_pred             HHHHHcc------CHHHHHHHHHHcCCHHHHHHHHHH
Confidence            7777665      255556666667888888877754

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.

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=96.52  E-value=0.57  Score=42.10  Aligned_cols=53  Identities=17%  Similarity=0.203  Sum_probs=31.3

Q ss_pred             CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHH
Q 044084          129 DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQ  190 (343)
Q Consensus       129 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  190 (343)
                      +....-.+..++...|.-++|.+.|-+...    |.     +-+..|...++|.+|.++-++
T Consensus       851 ~s~llp~~a~mf~svGMC~qAV~a~Lr~s~----pk-----aAv~tCv~LnQW~~avelaq~  903 (1189)
T KOG2041|consen  851 DSELLPVMADMFTSVGMCDQAVEAYLRRSL----PK-----AAVHTCVELNQWGEAVELAQR  903 (1189)
T ss_pred             ccchHHHHHHHHHhhchHHHHHHHHHhccC----cH-----HHHHHHHHHHHHHHHHHHHHh
Confidence            455556667777777777777766644321    21     234556666667666666554

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=96.48  E-value=0.34  Score=42.58  Aligned_cols=165  Identities=18%  Similarity=0.156  Sum_probs=109.8

Q ss_pred             HHHHHHHHhhccCcHHHHHHHHHHHHhc-CCCCCh-----HhHHHHHHHHhc----ccCHHHHHHHHHHHHHcCCCCCHH
Q 044084           62 MYKILCDSLGKSGRAFEILKFFRDMKEK-GILEDP-----SVYASLICSFAS----IAEVKVAEELFKEAEEKGMLRDLE  131 (343)
Q Consensus        62 ~~~~li~~~~~~~~~~~a~~~~~~~~~~-~~~~~~-----~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~  131 (343)
                      ....++...+-.|+-+.+++.+.+..+. ++.-..     -.|...+..++.    ..+.+.+.++++.+.+.-  |+..
T Consensus       190 ~~~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~y--P~s~  267 (468)
T PF10300_consen  190 KVLKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKRY--PNSA  267 (468)
T ss_pred             HHHHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHhC--CCcH
Confidence            3778888888889999998888887664 333222     235555554443    456788999999888864  4544


Q ss_pred             HHH-HHHHHHHhcCcHhHHHHHHHHHHhcC---CCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHH
Q 044084          132 VFL-KLVLMYIEEGMVEKTLEVVESMKNAE---LNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASII  207 (343)
Q Consensus       132 ~~~-~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll  207 (343)
                      .|. .-.+.+...|++++|++.|++.....   .+.....+--+..++....+|++|.+.|..+.+.+ .-+..+|.-+.
T Consensus       268 lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s-~WSka~Y~Y~~  346 (468)
T PF10300_consen  268 LFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKES-KWSKAFYAYLA  346 (468)
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhcc-ccHHHHHHHHH
Confidence            443 34566777899999999998754311   12223344456677788899999999999998864 33444555443


Q ss_pred             HH-HHccCCh-------hHHHHHHHHHHHc
Q 044084          208 NA-YCRIGLY-------SKAEKVFIEMQQK  229 (343)
Q Consensus       208 ~~-~~~~~~~-------~~a~~~~~~~~~~  229 (343)
                      .+ +...|+.       ++|.++|.++...
T Consensus       347 a~c~~~l~~~~~~~~~~~~a~~l~~~vp~l  376 (468)
T PF10300_consen  347 AACLLMLGREEEAKEHKKEAEELFRKVPKL  376 (468)
T ss_pred             HHHHHhhccchhhhhhHHHHHHHHHHHHHH
Confidence            33 3456666       8888888877643

In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=96.42  E-value=0.26  Score=41.71  Aligned_cols=145  Identities=13%  Similarity=0.084  Sum_probs=72.4

Q ss_pred             HHHHHHHHhhccCcHHHHHHHHHHHHhcC-CCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 044084           62 MYKILCDSLGKSGRAFEILKFFRDMKEKG-ILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMY  140 (343)
Q Consensus        62 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  140 (343)
                      +|...++...+..-.+.|..+|-+..+.+ +.+++..+++++.-++ .|+...|..+|+.-...-. -++..-+..+..+
T Consensus       399 v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl~~f~-d~~~y~~kyl~fL  476 (660)
T COG5107         399 VFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYA-TGDRATAYNIFELGLLKFP-DSTLYKEKYLLFL  476 (660)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHh-cCCcchHHHHHHHHHHhCC-CchHHHHHHHHHH
Confidence            44445555555555666666666666655 4455555666555443 3455566666654333221 1233334445555


Q ss_pred             HhcCcHhHHHHHHHHHHhcCCC-CchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHH
Q 044084          141 IEEGMVEKTLEVVESMKNAELN-ISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAY  210 (343)
Q Consensus       141 ~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~  210 (343)
                      ...++-+.|..+|+.....--. .-...|..+|+.-..-|+...+..+=++|...  .|-..+.....+-|
T Consensus       477 i~inde~naraLFetsv~r~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e~--~pQen~~evF~Sry  545 (660)
T COG5107         477 IRINDEENARALFETSVERLEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFREL--VPQENLIEVFTSRY  545 (660)
T ss_pred             HHhCcHHHHHHHHHHhHHHHHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHHH--cCcHhHHHHHHHHH
Confidence            5666666666666633221000 01224666666666666666665555555543  34444444333333

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=96.41  E-value=0.16  Score=43.25  Aligned_cols=65  Identities=15%  Similarity=-0.017  Sum_probs=47.0

Q ss_pred             ChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCH---HHHHHHHHHHHhcCcHhHHHHHHHHHHhc
Q 044084           94 DPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDL---EVFLKLVLMYIEEGMVEKTLEVVESMKNA  159 (343)
Q Consensus        94 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  159 (343)
                      +...++.+..+|.+.|++++|...|++.++..+. +.   .+|..+..+|...|+.++|++.+++..+.
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd-~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALELNPN-PDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-chHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            4456777777778888888888888887775533 22   35777788888888888888888877764

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=96.38  E-value=0.22  Score=35.62  Aligned_cols=41  Identities=12%  Similarity=0.131  Sum_probs=19.2

Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIE  142 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  142 (343)
                      ++..+...+........++.+...+. .+....+.++..|++
T Consensus        13 vv~~~~~~~~~~~l~~yLe~~~~~~~-~~~~~~~~li~ly~~   53 (140)
T smart00299       13 VVELFEKRNLLEELIPYLESALKLNS-ENPALQTKLIELYAK   53 (140)
T ss_pred             HHHHHHhCCcHHHHHHHHHHHHccCc-cchhHHHHHHHHHHH
Confidence            44444444445555555555444432 344445555555544

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

Probab=96.37  E-value=0.055  Score=42.63  Aligned_cols=88  Identities=18%  Similarity=0.343  Sum_probs=57.4

Q ss_pred             CChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHH
Q 044084          249 GRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAG  328 (343)
Q Consensus       249 ~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~  328 (343)
                      +.++=....++.|.+.|+.-|..+|..|+..+-+..-...-. +....-.|-  .+-+-+++++++|...|+.||..+-.
T Consensus        86 ~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nv-fQ~~F~HYP--~QQ~C~I~vLeqME~hGVmPdkE~e~  162 (406)
T KOG3941|consen   86 THVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNV-FQKVFLHYP--QQQNCAIKVLEQMEWHGVMPDKEIED  162 (406)
T ss_pred             chHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHH-HHHHHhhCc--hhhhHHHHHHHHHHHcCCCCchHHHH
Confidence            344444555666777777777777777777665543322111 112222222  23345899999999999999999999


Q ss_pred             HHHHHHhcccc
Q 044084          329 IMVGVFSKLSQ  339 (343)
Q Consensus       329 ~l~~~~~~~g~  339 (343)
                      .|+.++.+.|-
T Consensus       163 ~lvn~FGr~~~  173 (406)
T KOG3941|consen  163 ILVNAFGRWNF  173 (406)
T ss_pred             HHHHHhccccc
Confidence            99999988763

>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []

Probab=96.36  E-value=0.43  Score=38.80  Aligned_cols=161  Identities=14%  Similarity=0.039  Sum_probs=97.6

Q ss_pred             hccCcHHHHHHHHHHHHhcC--CCCChH------hHHHHHHHHhccc-CHHHHHHHHHHHHHc--------CCCCC----
Q 044084           71 GKSGRAFEILKFFRDMKEKG--ILEDPS------VYASLICSFASIA-EVKVAEELFKEAEEK--------GMLRD----  129 (343)
Q Consensus        71 ~~~~~~~~a~~~~~~~~~~~--~~~~~~------~~~~l~~~~~~~~-~~~~a~~~~~~~~~~--------~~~~~----  129 (343)
                      .+.|+.+.|...+.+.....  ..|+..      .|+.-... ...+ +++.|...+++..+.        ...|+    
T Consensus         4 ~~~~~~~~A~~~~~K~~~~~~~~~~~~~~~La~~~yn~G~~l-~~~~~~~~~a~~wL~~a~~~l~~~~~~~~~~~~~~el   82 (278)
T PF08631_consen    4 WKQGDLDLAEHMYSKAKDLLNSLDPDMAEELARVCYNIGKSL-LSKKDKYEEAVKWLQRAYDILEKPGKMDKLSPDGSEL   82 (278)
T ss_pred             hhhCCHHHHHHHHHHhhhHHhcCCcHHHHHHHHHHHHHHHHH-HHcCCChHHHHHHHHHHHHHHHhhhhccccCCcHHHH
Confidence            46789999999999887643  223221      23333333 3445 888888777765543        12223    


Q ss_pred             -HHHHHHHHHHHHhcCcH---hHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHH
Q 044084          130 -LEVFLKLVLMYIEEGMV---EKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYAS  205 (343)
Q Consensus       130 -~~~~~~l~~~~~~~~~~---~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~  205 (343)
                       ..+...++.+|...+..   ++|.++++.+..... -....+..-+..+.+.++.+.+.+.+.+|...- .-....+..
T Consensus        83 r~~iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~~-~~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~~-~~~e~~~~~  160 (278)
T PF08631_consen   83 RLSILRLLANAYLEWDTYESVEKALNALRLLESEYG-NKPEVFLLKLEILLKSFDEEEYEEILMRMIRSV-DHSESNFDS  160 (278)
T ss_pred             HHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhCC-CCcHHHHHHHHHHhccCChhHHHHHHHHHHHhc-ccccchHHH
Confidence             34566778888887764   456666666654433 223455566777777899999999999999872 223445555


Q ss_pred             HHHHH---HccCChhHHHHHHHHHHHcCCCcCh
Q 044084          206 IINAY---CRIGLYSKAEKVFIEMQQKGFDKCV  235 (343)
Q Consensus       206 ll~~~---~~~~~~~~a~~~~~~~~~~~~~~~~  235 (343)
                      ++..+   .. ...+.+...++.+....+.|..
T Consensus       161 ~l~~i~~l~~-~~~~~a~~~ld~~l~~r~~~~~  192 (278)
T PF08631_consen  161 ILHHIKQLAE-KSPELAAFCLDYLLLNRFKSSE  192 (278)
T ss_pred             HHHHHHHHHh-hCcHHHHHHHHHHHHHHhCCCh
Confidence            55554   33 3345566666666554444444

It is also involved in sporulation [].

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.34  E-value=0.17  Score=41.13  Aligned_cols=156  Identities=11%  Similarity=0.046  Sum_probs=98.3

Q ss_pred             HhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCH--hhHHHHH--HHHHccCCh
Q 044084          141 IEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQ--VTYASII--NAYCRIGLY  216 (343)
Q Consensus       141 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~--~~~~~ll--~~~~~~~~~  216 (343)
                      ...|+..+|-..++++.+.-+ .|...+...=.+|.-.|+.+.-...++++... ..||.  .+|..-+  -++...|-+
T Consensus       114 ~~~g~~h~a~~~wdklL~d~P-tDlla~kfsh~a~fy~G~~~~~k~ai~kIip~-wn~dlp~~sYv~GmyaFgL~E~g~y  191 (491)
T KOG2610|consen  114 WGRGKHHEAAIEWDKLLDDYP-TDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPK-WNADLPCYSYVHGMYAFGLEECGIY  191 (491)
T ss_pred             hccccccHHHHHHHHHHHhCc-hhhhhhhhhhhHHHhccchhhhhhHHHHhccc-cCCCCcHHHHHHHHHHhhHHHhccc
Confidence            356777888888888876544 56666777777888888888888888887755 12333  2333323  334467888


Q ss_pred             hHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHhHHHHH
Q 044084          217 SKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVI  296 (343)
Q Consensus       217 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~  296 (343)
                      ++|++.-++..+.+ +.|...-.+....+--.|++.++.++..+-... .+   .  ..++.+   .       .|-...
T Consensus       192 ~dAEk~A~ralqiN-~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~-Wr---~--s~mlas---H-------NyWH~A  254 (491)
T KOG2610|consen  192 DDAEKQADRALQIN-RFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDD-WR---Q--SWMLAS---H-------NYWHTA  254 (491)
T ss_pred             hhHHHHHHhhccCC-CcchHHHHHHHHHHHhcchhhhHHHHHHhcccc-hh---h--hhHHHh---h-------hhHHHH
Confidence            88888888877765 556667777777777788888887766554322 11   0  001100   0       133334


Q ss_pred             HHHHhcCCHHHHHHHHHHH
Q 044084          297 SAYNMAREFDMCVKFYNEF  315 (343)
Q Consensus       297 ~~~~~~g~~~~a~~~~~~m  315 (343)
                      -.+...+.++.|+++|++-
T Consensus       255 l~~iE~aeye~aleIyD~e  273 (491)
T KOG2610|consen  255 LFHIEGAEYEKALEIYDRE  273 (491)
T ss_pred             HhhhcccchhHHHHHHHHH
Confidence            4455667888888888753

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.30  E-value=0.091  Score=41.34  Aligned_cols=97  Identities=14%  Similarity=0.166  Sum_probs=70.0

Q ss_pred             hHHHHHHHHhcCCcHHHHHHHHHHHHHcC--CCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCC--CcChhhHHHHH
Q 044084          167 ISCVIVNGFSKRRAYWAAVKVYEQLISQG--CIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGF--DKCVVAYSSMV  242 (343)
Q Consensus       167 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~  242 (343)
                      .|+.-+..+ +.|++..|...|....+..  -.-....+-.|..++...|++++|..+|..+.+.-.  +.-+..+-.|.
T Consensus       144 ~Y~~A~~~~-ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKlg  222 (262)
T COG1729         144 LYNAALDLY-KSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLG  222 (262)
T ss_pred             HHHHHHHHH-HcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHHH
Confidence            466655544 5677888888888888762  112234566788888888999988888888877521  11245677777


Q ss_pred             HHHHccCChHHHHHHHHHHhhC
Q 044084          243 AMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       243 ~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                      .+..+.|+.++|...|+++.+.
T Consensus       223 ~~~~~l~~~d~A~atl~qv~k~  244 (262)
T COG1729         223 VSLGRLGNTDEACATLQQVIKR  244 (262)
T ss_pred             HHHHHhcCHHHHHHHHHHHHHH
Confidence            8888888899999998888876

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=96.27  E-value=0.25  Score=35.28  Aligned_cols=127  Identities=11%  Similarity=0.130  Sum_probs=68.1

Q ss_pred             HHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHc
Q 044084          168 SCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGK  247 (343)
Q Consensus       168 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  247 (343)
                      ...++..+...+.+.....+++.+...+ ..+...++.++..|++.+ .++....+..   .   .+......+++.|.+
T Consensus        10 ~~~vv~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~ly~~~~-~~~ll~~l~~---~---~~~yd~~~~~~~c~~   81 (140)
T smart00299       10 VSEVVELFEKRNLLEELIPYLESALKLN-SENPALQTKLIELYAKYD-PQKEIERLDN---K---SNHYDIEKVGKLCEK   81 (140)
T ss_pred             HHHHHHHHHhCCcHHHHHHHHHHHHccC-ccchhHHHHHHHHHHHHC-HHHHHHHHHh---c---cccCCHHHHHHHHHH
Confidence            3456666666667777777777766665 245556666676666543 2222233221   1   123333445555555


Q ss_pred             cCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhc-CCHHHHHHHHHHHHhCCCCccHHH
Q 044084          248 TGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMA-REFDMCVKFYNEFRMNGGVIDRAM  326 (343)
Q Consensus       248 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~-g~~~~a~~~~~~m~~~~~~p~~~~  326 (343)
                      .+.++++..++.++..                            +...+..+... ++++.|++.+++      .-++..
T Consensus        82 ~~l~~~~~~l~~k~~~----------------------------~~~Al~~~l~~~~d~~~a~~~~~~------~~~~~l  127 (140)
T smart00299       82 AKLYEEAVELYKKDGN----------------------------FKDAIVTLIEHLGNYEKAIEYFVK------QNNPEL  127 (140)
T ss_pred             cCcHHHHHHHHHhhcC----------------------------HHHHHHHHHHcccCHHHHHHHHHh------CCCHHH
Confidence            5555555555554432                            22223333333 667777777765      125567


Q ss_pred             HHHHHHHHhc
Q 044084          327 AGIMVGVFSK  336 (343)
Q Consensus       327 ~~~l~~~~~~  336 (343)
                      |..++..+..
T Consensus       128 w~~~~~~~l~  137 (140)
T smart00299      128 WAEVLKALLD  137 (140)
T ss_pred             HHHHHHHHHc
Confidence            7777766543

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=96.16  E-value=0.17  Score=42.15  Aligned_cols=139  Identities=12%  Similarity=0.063  Sum_probs=88.8

Q ss_pred             HHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcH
Q 044084           67 CDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMV  146 (343)
Q Consensus        67 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  146 (343)
                      .+.+.+.|++..|..-|++.... +            -+.+.-+.++......        .-..+++.|.-+|.+.+++
T Consensus       215 Gn~~fK~gk~~~A~~~Yerav~~-l------------~~~~~~~~ee~~~~~~--------~k~~~~lNlA~c~lKl~~~  273 (397)
T KOG0543|consen  215 GNVLFKEGKFKLAKKRYERAVSF-L------------EYRRSFDEEEQKKAEA--------LKLACHLNLAACYLKLKEY  273 (397)
T ss_pred             hhHHHhhchHHHHHHHHHHHHHH-h------------hccccCCHHHHHHHHH--------HHHHHhhHHHHHHHhhhhH
Confidence            44667788888888877776542 0            0111111122111111        2245667788888999999


Q ss_pred             hHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHH-ccCC-hhHHHHHHH
Q 044084          147 EKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYC-RIGL-YSKAEKVFI  224 (343)
Q Consensus       147 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~-~~~~-~~~a~~~~~  224 (343)
                      ..|++.-.+....+. .|.-..---..++...|+++.|+..|+++.+.  .|+....+.=+..|. +..+ .+...++|.
T Consensus       274 ~~Ai~~c~kvLe~~~-~N~KALyRrG~A~l~~~e~~~A~~df~ka~k~--~P~Nka~~~el~~l~~k~~~~~~kekk~y~  350 (397)
T KOG0543|consen  274 KEAIESCNKVLELDP-NNVKALYRRGQALLALGEYDLARDDFQKALKL--EPSNKAARAELIKLKQKIREYEEKEKKMYA  350 (397)
T ss_pred             HHHHHHHHHHHhcCC-CchhHHHHHHHHHHhhccHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999888888776 56555556678888899999999999998886  566665555444443 3333 334467777


Q ss_pred             HHHHc
Q 044084          225 EMQQK  229 (343)
Q Consensus       225 ~~~~~  229 (343)
                      .|-..
T Consensus       351 ~mF~k  355 (397)
T KOG0543|consen  351 NMFAK  355 (397)
T ss_pred             HHhhc
Confidence            77653

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

Probab=96.14  E-value=0.08  Score=41.76  Aligned_cols=105  Identities=20%  Similarity=0.312  Sum_probs=66.7

Q ss_pred             CCChHhHHHHHHHHhcc-----cCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchh
Q 044084           92 LEDPSVYASLICSFASI-----AEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDC  166 (343)
Q Consensus        92 ~~~~~~~~~l~~~~~~~-----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  166 (343)
                      +.|-.+|-..+..+...     +.++-.-..++.|.+.|+..|..+|+.|+..+-+-.                +.|.. 
T Consensus        64 ~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgk----------------fiP~n-  126 (406)
T KOG3941|consen   64 KRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGK----------------FIPQN-  126 (406)
T ss_pred             cccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccc----------------cccHH-
Confidence            44667777777666533     556777777888889999999999988888764321                11211 


Q ss_pred             hHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCC
Q 044084          167 ISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGL  215 (343)
Q Consensus       167 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~  215 (343)
                      .+....-.|-  .+-+-+++++++|...|+.||..+-..+++++.+.+-
T Consensus       127 vfQ~~F~HYP--~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~  173 (406)
T KOG3941|consen  127 VFQKVFLHYP--QQQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNF  173 (406)
T ss_pred             HHHHHHhhCc--hhhhHHHHHHHHHHHcCCCCchHHHHHHHHHhccccc
Confidence            1222222221  2234567777777777777777777777777776654

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=96.02  E-value=0.58  Score=41.66  Aligned_cols=89  Identities=12%  Similarity=0.067  Sum_probs=55.5

Q ss_pred             HHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHh--------
Q 044084          130 LEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQV--------  201 (343)
Q Consensus       130 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~--------  201 (343)
                      ..+...+..-+.+...+.-|-++|.+|-..         ..+++.....++|++|..+-+...+.  .||++        
T Consensus       747 re~l~~~a~ylk~l~~~gLAaeIF~k~gD~---------ksiVqlHve~~~W~eAFalAe~hPe~--~~dVy~pyaqwLA  815 (1081)
T KOG1538|consen  747 REPLLLCATYLKKLDSPGLAAEIFLKMGDL---------KSLVQLHVETQRWDEAFALAEKHPEF--KDDVYMPYAQWLA  815 (1081)
T ss_pred             hhHHHHHHHHHhhccccchHHHHHHHhccH---------HHHhhheeecccchHhHhhhhhCccc--cccccchHHHHhh
Confidence            344444455555666677778888777432         24566677788888888877776553  34432        


Q ss_pred             ---hHHHHHHHHHccCChhHHHHHHHHHHHc
Q 044084          202 ---TYASIINAYCRIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       202 ---~~~~ll~~~~~~~~~~~a~~~~~~~~~~  229 (343)
                         -|...-++|.+.|+-.+|.++++.+...
T Consensus       816 E~DrFeEAqkAfhkAGr~~EA~~vLeQLtnn  846 (1081)
T KOG1538|consen  816 ENDRFEEAQKAFHKAGRQREAVQVLEQLTNN  846 (1081)
T ss_pred             hhhhHHHHHHHHHHhcchHHHHHHHHHhhhh
Confidence               1233445677777777777777776554

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.99  E-value=0.4  Score=35.05  Aligned_cols=140  Identities=11%  Similarity=0.061  Sum_probs=100.1

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHh-HH
Q 044084           21 DSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSV-YA   99 (343)
Q Consensus        21 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~~   99 (343)
                      +...|..-++ +++.+..++|+.-|..+.+.|...-|.  -..........+.|+...|...|++.-.....|-..- ..
T Consensus        58 sgd~flaAL~-lA~~~k~d~Alaaf~~lektg~g~Ypv--LA~mr~at~~a~kgdta~AV~aFdeia~dt~~P~~~rd~A  134 (221)
T COG4649          58 SGDAFLAALK-LAQENKTDDALAAFTDLEKTGYGSYPV--LARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRDLA  134 (221)
T ss_pred             chHHHHHHHH-HHHcCCchHHHHHHHHHHhcCCCcchH--HHHHHHHHHHhhcccHHHHHHHHHHHhccCCCcchhhHHH
Confidence            4445655554 456677899999999999888766543  4455566777889999999999999877654444331 11


Q ss_pred             HH--HHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCC
Q 044084          100 SL--ICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNI  163 (343)
Q Consensus       100 ~l--~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  163 (343)
                      .|  .-.+...|.++.+....+.+-..+-+.-...-..|.-+-.+.|++.+|...|..+....-.|
T Consensus       135 Rlraa~lLvD~gsy~dV~srvepLa~d~n~mR~sArEALglAa~kagd~a~A~~~F~qia~Da~ap  200 (221)
T COG4649         135 RLRAAYLLVDNGSYDDVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIANDAQAP  200 (221)
T ss_pred             HHHHHHHHhccccHHHHHHHhhhccCCCChhHHHHHHHHhHHHHhccchHHHHHHHHHHHccccCc
Confidence            11  12456788999998888887766655456667788888889999999999999987644333

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=95.92  E-value=0.92  Score=38.64  Aligned_cols=79  Identities=13%  Similarity=0.166  Sum_probs=61.1

Q ss_pred             HHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHH
Q 044084            7 LHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDM   86 (343)
Q Consensus         7 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~   86 (343)
                      +++-+++++.  +-|..+|-.|+.-+...+..++..+++++|...-    |--..+|..-|++-...+++.....+|.+.
T Consensus        29 lrLRerIkdN--PtnI~S~fqLiq~~~tq~s~~~~re~yeq~~~pf----p~~~~aw~ly~s~ELA~~df~svE~lf~rC  102 (660)
T COG5107          29 LRLRERIKDN--PTNILSYFQLIQYLETQESMDAEREMYEQLSSPF----PIMEHAWRLYMSGELARKDFRSVESLFGRC  102 (660)
T ss_pred             HHHHHHhhcC--chhHHHHHHHHHHHhhhhhHHHHHHHHHHhcCCC----ccccHHHHHHhcchhhhhhHHHHHHHHHHH
Confidence            3455555543  4578899999999999999999999999995432    333478888888888888899999999888


Q ss_pred             HhcCC
Q 044084           87 KEKGI   91 (343)
Q Consensus        87 ~~~~~   91 (343)
                      +....
T Consensus       103 L~k~l  107 (660)
T COG5107         103 LKKSL  107 (660)
T ss_pred             Hhhhc
Confidence            77543

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=95.91  E-value=0.2  Score=43.37  Aligned_cols=132  Identities=11%  Similarity=0.091  Sum_probs=61.7

Q ss_pred             HhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHH
Q 044084          105 FASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAA  184 (343)
Q Consensus       105 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  184 (343)
                      ..-.++++.+.++.+.-.-. +.......+.++..+.+.|..+.|+++...-.            .-.....+.|+.+.|
T Consensus       271 av~~~d~~~v~~~i~~~~ll-~~i~~~~~~~i~~fL~~~G~~e~AL~~~~D~~------------~rFeLAl~lg~L~~A  337 (443)
T PF04053_consen  271 AVLRGDFEEVLRMIAASNLL-PNIPKDQGQSIARFLEKKGYPELALQFVTDPD------------HRFELALQLGNLDIA  337 (443)
T ss_dssp             HHHTT-HHH-----HHHHTG-GG--HHHHHHHHHHHHHTT-HHHHHHHSS-HH------------HHHHHHHHCT-HHHH
T ss_pred             HHHcCChhhhhhhhhhhhhc-ccCChhHHHHHHHHHHHCCCHHHHHhhcCChH------------HHhHHHHhcCCHHHH
Confidence            33445566555554311100 00124445666666666666666666543321            122334456666666


Q ss_pred             HHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhC
Q 044084          185 VKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       185 ~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                      .++.++      .++...|..|.....+.|+++-|++.|.+...         +..|+-.|.-.|+.+...++.+.....
T Consensus       338 ~~~a~~------~~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d---------~~~L~lLy~~~g~~~~L~kl~~~a~~~  402 (443)
T PF04053_consen  338 LEIAKE------LDDPEKWKQLGDEALRQGNIELAEECYQKAKD---------FSGLLLLYSSTGDREKLSKLAKIAEER  402 (443)
T ss_dssp             HHHCCC------CSTHHHHHHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHCT-HHHHHHHHHHHHHT
T ss_pred             HHHHHh------cCcHHHHHHHHHHHHHcCCHHHHHHHHHhhcC---------ccccHHHHHHhCCHHHHHHHHHHHHHc
Confidence            655433      23455666666666666666666666654322         345555556666666555555554443

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.

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=95.88  E-value=0.39  Score=34.03  Aligned_cols=83  Identities=12%  Similarity=-0.005  Sum_probs=56.7

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHH
Q 044084           26 CQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSF  105 (343)
Q Consensus        26 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  105 (343)
                      -.-.....+.|++++|.+.|+.+..+-... +-...+-..|+.++.+.+++++|...+++..+........-|...+.++
T Consensus        14 y~~a~~~l~~~~Y~~A~~~le~L~~ryP~g-~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~vdYa~Y~~gL   92 (142)
T PF13512_consen   14 YQEAQEALQKGNYEEAIKQLEALDTRYPFG-EYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNVDYAYYMRGL   92 (142)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHhcCCCC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCccHHHHHHHH
Confidence            333445567888888888888887764332 3345677778888888888888888888888865443344566666665


Q ss_pred             hccc
Q 044084          106 ASIA  109 (343)
Q Consensus       106 ~~~~  109 (343)
                      +...
T Consensus        93 ~~~~   96 (142)
T PF13512_consen   93 SYYE   96 (142)
T ss_pred             HHHH
Confidence            5443

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=95.85  E-value=0.37  Score=33.48  Aligned_cols=62  Identities=18%  Similarity=0.287  Sum_probs=31.1

Q ss_pred             HHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCC
Q 044084          204 ASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGC  266 (343)
Q Consensus       204 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~  266 (343)
                      ...+.+....|+-+.-.++...+.+.+ .+++...-.+..+|.+.|+..++.+++.+.-+.|+
T Consensus        90 D~ALd~lv~~~kkDqLdki~~~l~kn~-~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~  151 (161)
T PF09205_consen   90 DLALDILVKQGKKDQLDKIYNELKKNE-EINPEFLVKIANAYKKLGNTREANELLKEACEKGL  151 (161)
T ss_dssp             HHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHhhcc-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhch
Confidence            334455555566666666665555432 44555555666666666666666666666655554

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=95.83  E-value=0.75  Score=36.87  Aligned_cols=122  Identities=14%  Similarity=0.086  Sum_probs=69.1

Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccC
Q 044084           31 AFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAE  110 (343)
Q Consensus        31 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  110 (343)
                      .....|++.+|..+|+.........    ...--.++.+|...|+.+.|..++..+....-.........-|..+.+...
T Consensus       143 ~~~~~e~~~~a~~~~~~al~~~~~~----~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~~~~~~l~a~i~ll~qaa~  218 (304)
T COG3118         143 ELIEAEDFGEAAPLLKQALQAAPEN----SEAKLLLAECLLAAGDVEAAQAILAALPLQAQDKAAHGLQAQIELLEQAAA  218 (304)
T ss_pred             hhhhccchhhHHHHHHHHHHhCccc----chHHHHHHHHHHHcCChHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHhc
Confidence            4556677777777777776654332    255666777777777777777777776544211112222222333444444


Q ss_pred             HHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhc
Q 044084          111 VKVAEELFKEAEEKGMLR-DLEVFLKLVLMYIEEGMVEKTLEVVESMKNA  159 (343)
Q Consensus       111 ~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  159 (343)
                      ..+...+-.+.-..   | |...-..+...+...|+.+.|.+.+-.+...
T Consensus       219 ~~~~~~l~~~~aad---Pdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~  265 (304)
T COG3118         219 TPEIQDLQRRLAAD---PDDVEAALALADQLHLVGRNEAALEHLLALLRR  265 (304)
T ss_pred             CCCHHHHHHHHHhC---CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            33333333333332   3 5666666777777777777777766655543

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.79  E-value=0.27  Score=38.75  Aligned_cols=99  Identities=18%  Similarity=0.130  Sum_probs=55.6

Q ss_pred             HHHHHHHHHhhccCcHHHHHHHHHHHHhcCCC--CChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCC-C-CHHHHHHH
Q 044084           61 HMYKILCDSLGKSGRAFEILKFFRDMKEKGIL--EDPSVYASLICSFASIAEVKVAEELFKEAEEKGML-R-DLEVFLKL  136 (343)
Q Consensus        61 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~-~~~~~~~l  136 (343)
                      ..|+.-+..+ +.|++..|...|....+....  -....+-.|..++...|+++.|..+|..+.+.-++ | -+..+-.|
T Consensus       143 ~~Y~~A~~~~-ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKl  221 (262)
T COG1729         143 KLYNAALDLY-KSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKL  221 (262)
T ss_pred             HHHHHHHHHH-HcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHH
Confidence            3455544443 445566666666666654211  12233444666666666666666666666654322 1 24556666


Q ss_pred             HHHHHhcCcHhHHHHHHHHHHhcC
Q 044084          137 VLMYIEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus       137 ~~~~~~~~~~~~a~~~~~~~~~~~  160 (343)
                      ..+..+.|+.++|..+|+++.+.-
T Consensus       222 g~~~~~l~~~d~A~atl~qv~k~Y  245 (262)
T COG1729         222 GVSLGRLGNTDEACATLQQVIKRY  245 (262)
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHC
Confidence            666666666777777776666543

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

Probab=95.65  E-value=0.19  Score=40.22  Aligned_cols=77  Identities=16%  Similarity=0.170  Sum_probs=55.6

Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhh-----CCCCchHHHHHHH
Q 044084          202 TYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKP-----KGCEPNVWIYNSL  276 (343)
Q Consensus       202 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~-----~~~~p~~~~~~~l  276 (343)
                      ++..++..+...|+.+.+...++++.... +-+...|..++.+|.+.|+...|+..|+.+.+     .|+.|...+....
T Consensus       155 ~l~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~y  233 (280)
T COG3629         155 ALTKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRALY  233 (280)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHHH
Confidence            45566677777777777777777777765 55677777788888888887777777777654     4777777776666


Q ss_pred             HHH
Q 044084          277 MDM  279 (343)
Q Consensus       277 ~~~  279 (343)
                      .++
T Consensus       234 ~~~  236 (280)
T COG3629         234 EEI  236 (280)
T ss_pred             HHH
Confidence            655

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=95.63  E-value=0.056  Score=29.57  Aligned_cols=27  Identities=11%  Similarity=0.349  Sum_probs=13.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhC
Q 044084           25 YCQIMEAFYKIGDSEKVAALFLECESR   51 (343)
Q Consensus        25 ~~~l~~~~~~~~~~~~a~~~~~~~~~~   51 (343)
                      +..+...|.+.|++++|.++|+++.+.
T Consensus         4 ~~~la~~~~~~G~~~~A~~~~~~~l~~   30 (44)
T PF13428_consen    4 WLALARAYRRLGQPDEAERLLRRALAL   30 (44)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            444445555555555555555555443

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=95.55  E-value=0.074  Score=29.08  Aligned_cols=24  Identities=17%  Similarity=0.228  Sum_probs=9.3

Q ss_pred             HHHHHhhccCcHHHHHHHHHHHHh
Q 044084           65 ILCDSLGKSGRAFEILKFFRDMKE   88 (343)
Q Consensus        65 ~li~~~~~~~~~~~a~~~~~~~~~   88 (343)
                      .+...|...|++++|.++|++..+
T Consensus         6 ~la~~~~~~G~~~~A~~~~~~~l~   29 (44)
T PF13428_consen    6 ALARAYRRLGQPDEAERLLRRALA   29 (44)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHH
Confidence            333333333333333333333333

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.54  E-value=0.64  Score=34.06  Aligned_cols=138  Identities=12%  Similarity=0.146  Sum_probs=97.5

Q ss_pred             HHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChH-hHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHH-HH--HH
Q 044084           61 HMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPS-VYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEV-FL--KL  136 (343)
Q Consensus        61 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~~--~l  136 (343)
                      ..|..-++. .+.+..++|+.-|..+...|...-+. .--.........|+...|...|+++-.....|-..- ..  .-
T Consensus        60 d~flaAL~l-A~~~k~d~Alaaf~~lektg~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt~~P~~~rd~ARlra  138 (221)
T COG4649          60 DAFLAALKL-AQENKTDDALAAFTDLEKTGYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRDLARLRA  138 (221)
T ss_pred             HHHHHHHHH-HHcCCchHHHHHHHHHHhcCCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhccCCCcchhhHHHHHHH
Confidence            566665554 46677999999999999887553322 222334556788999999999999988665554331 11  12


Q ss_pred             HHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCC
Q 044084          137 VLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPG  199 (343)
Q Consensus       137 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~  199 (343)
                      .-.+...|.++....-.+-+...+-+.-...-.+|.-+-.+.|++..|.+.|..+......|-
T Consensus       139 a~lLvD~gsy~dV~srvepLa~d~n~mR~sArEALglAa~kagd~a~A~~~F~qia~Da~apr  201 (221)
T COG4649         139 AYLLVDNGSYDDVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIANDAQAPR  201 (221)
T ss_pred             HHHHhccccHHHHHHHhhhccCCCChhHHHHHHHHhHHHHhccchHHHHHHHHHHHccccCcH
Confidence            234567899999998888887665544444566777788899999999999999987644454

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=95.51  E-value=0.91  Score=35.65  Aligned_cols=53  Identities=26%  Similarity=0.365  Sum_probs=23.9

Q ss_pred             HHHHhcCCcHHHHHHHHHHHHHcCCCCC---HhhHHHHHHHHHccCChhHHHHHHHH
Q 044084          172 VNGFSKRRAYWAAVKVYEQLISQGCIPG---QVTYASIINAYCRIGLYSKAEKVFIE  225 (343)
Q Consensus       172 ~~~~~~~~~~~~a~~~~~~~~~~~~~p~---~~~~~~ll~~~~~~~~~~~a~~~~~~  225 (343)
                      .+.|.+.|.+..|..-+++|.+. .+-+   ...+-.+..+|...|-.++|...-.-
T Consensus       174 aryY~kr~~~~AA~nR~~~v~e~-y~~t~~~~eaL~~l~eaY~~lgl~~~a~~~~~v  229 (254)
T COG4105         174 ARYYLKRGAYVAAINRFEEVLEN-YPDTSAVREALARLEEAYYALGLTDEAKKTAKV  229 (254)
T ss_pred             HHHHHHhcChHHHHHHHHHHHhc-cccccchHHHHHHHHHHHHHhCChHHHHHHHHH
Confidence            34445555555555555555544 1111   12233344455555555555444333

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=95.47  E-value=0.52  Score=32.66  Aligned_cols=90  Identities=19%  Similarity=0.200  Sum_probs=48.4

Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhc-CCCCChH---hHHHHHHHHh
Q 044084           31 AFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEK-GILEDPS---VYASLICSFA  106 (343)
Q Consensus        31 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~---~~~~l~~~~~  106 (343)
                      +++..|+++.|++.|.+....-    |.....||.-..++.-+|+.++|++-+++..+. |.+ +..   .|..-...|-
T Consensus        52 alaE~g~Ld~AlE~F~qal~l~----P~raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~-trtacqa~vQRg~lyR  126 (175)
T KOG4555|consen   52 ALAEAGDLDGALELFGQALCLA----PERASAYNNRAQALRLQGDDEEALDDLNKALELAGDQ-TRTACQAFVQRGLLYR  126 (175)
T ss_pred             HHHhccchHHHHHHHHHHHHhc----ccchHhhccHHHHHHHcCChHHHHHHHHHHHHhcCcc-chHHHHHHHHHHHHHH
Confidence            4556666666666666654432    112356666666666666666666666666554 222 111   1222233444


Q ss_pred             cccCHHHHHHHHHHHHHcC
Q 044084          107 SIAEVKVAEELFKEAEEKG  125 (343)
Q Consensus       107 ~~~~~~~a~~~~~~~~~~~  125 (343)
                      ..|+-+.|..-|+...+.|
T Consensus       127 l~g~dd~AR~DFe~AA~LG  145 (175)
T KOG4555|consen  127 LLGNDDAARADFEAAAQLG  145 (175)
T ss_pred             HhCchHHHHHhHHHHHHhC
Confidence            5566666666665555544

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

Probab=95.42  E-value=0.26  Score=39.44  Aligned_cols=77  Identities=16%  Similarity=0.157  Sum_probs=39.2

Q ss_pred             hHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHH-----cCCCcChhhHHHH
Q 044084          167 ISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQ-----KGFDKCVVAYSSM  241 (343)
Q Consensus       167 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~~~~l  241 (343)
                      ++..++..+...|+.+.+...++++.... +-+...|..++.+|.+.|+...|+..++.+.+     .|+.|...+....
T Consensus       155 ~l~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~y  233 (280)
T COG3629         155 ALTKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRALY  233 (280)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHHH
Confidence            34445555555555555555555555442 33445555555555555555555555554443     2555555544444


Q ss_pred             HHH
Q 044084          242 VAM  244 (343)
Q Consensus       242 ~~~  244 (343)
                      ...
T Consensus       234 ~~~  236 (280)
T COG3629         234 EEI  236 (280)
T ss_pred             HHH
Confidence            444

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome

Probab=95.42  E-value=0.32  Score=36.36  Aligned_cols=64  Identities=13%  Similarity=0.013  Sum_probs=44.7

Q ss_pred             HHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCch--hhHHHHHHHHhcCCcHHHHHHHHHHHHHc
Q 044084          131 EVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISD--CISCVIVNGFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       131 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  194 (343)
                      ..+..+...|.+.|+.+.|++.|.++.+....+..  ..+-.+|+.....+++..+...+.+....
T Consensus        37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~  102 (177)
T PF10602_consen   37 MALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESL  102 (177)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            45667778888888888888888887766543332  23556677777778888877777766543

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.

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=95.35  E-value=1.2  Score=35.84  Aligned_cols=51  Identities=20%  Similarity=0.201  Sum_probs=25.9

Q ss_pred             hcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHH
Q 044084          106 ASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMK  157 (343)
Q Consensus       106 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  157 (343)
                      ...|++..|..+|......... +...--.+..+|...|+.+.|..++..+.
T Consensus       145 ~~~e~~~~a~~~~~~al~~~~~-~~~~~~~la~~~l~~g~~e~A~~iL~~lP  195 (304)
T COG3118         145 IEAEDFGEAAPLLKQALQAAPE-NSEAKLLLAECLLAAGDVEAAQAILAALP  195 (304)
T ss_pred             hhccchhhHHHHHHHHHHhCcc-cchHHHHHHHHHHHcCChHHHHHHHHhCc
Confidence            3445555555555555544332 23444445555555555555555555543

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=95.27  E-value=1  Score=37.24  Aligned_cols=223  Identities=13%  Similarity=0.064  Sum_probs=127.9

Q ss_pred             hhhHHHHHHHHHhC--CCCCChhhHHHHHHHHHhcCCHHHHHHHH----HHHHhCCCCCCCchHHHHHHHHHHhhccCcH
Q 044084            3 SQSKLHYYEKMKSA--GIVLDSGCYCQIMEAFYKIGDSEKVAALF----LECESRKLDLTPSSTHMYKILCDSLGKSGRA   76 (343)
Q Consensus         3 ~~~A~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~~~~~~a~~~~----~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~   76 (343)
                      .++|+..+..-..+  +...-..+|..+.++.++.|.+++++..-    +...+..  ....-.++|..+.+++-+.-++
T Consensus        22 ~~~al~~w~~~L~~l~~~~~Rf~~lG~l~~a~s~~g~y~~mL~~a~sqi~~a~~~~--ds~~~~ea~lnlar~~e~l~~f   99 (518)
T KOG1941|consen   22 TEKALQVWTKVLEKLSDLMGRFRVLGCLVTAHSEMGRYKEMLKFAVSQIDTARELE--DSDFLLEAYLNLARSNEKLCEF   99 (518)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhccchhhhhhhHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHh
Confidence            44555555544432  11112345667778888888888766532    1111111  0011135566666666666666


Q ss_pred             HHHHHHHHHHHhc-CCCCC---hHhHHHHHHHHhcccCHHHHHHHHHHHHHcCC-----CCCHHHHHHHHHHHHhcCcHh
Q 044084           77 FEILKFFRDMKEK-GILED---PSVYASLICSFASIAEVKVAEELFKEAEEKGM-----LRDLEVFLKLVLMYIEEGMVE  147 (343)
Q Consensus        77 ~~a~~~~~~~~~~-~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~~~~l~~~~~~~~~~~  147 (343)
                      .+++.+-..-... |..|-   -...-++..++...+.++.+++.|+...+...     .....++..|...|.+..|++
T Consensus       100 ~kt~~y~k~~l~lpgt~~~~~~gq~~l~~~~Ahlgls~fq~~Lesfe~A~~~A~~~~D~~LElqvcv~Lgslf~~l~D~~  179 (518)
T KOG1941|consen  100 HKTISYCKTCLGLPGTRAGQLGGQVSLSMGNAHLGLSVFQKALESFEKALRYAHNNDDAMLELQVCVSLGSLFAQLKDYE  179 (518)
T ss_pred             hhHHHHHHHHhcCCCCCcccccchhhhhHHHHhhhHHHHHHHHHHHHHHHHHhhccCCceeeeehhhhHHHHHHHHHhhh
Confidence            6666665554432 22221   11233455677777888999988888765321     123567889999999999999


Q ss_pred             HHHHHHHHHHh----cCCCCchhhHHH-----HHHHHhcCCcHHHHHHHHHHHHH----cCCCC-CHhhHHHHHHHHHcc
Q 044084          148 KTLEVVESMKN----AELNISDCISCV-----IVNGFSKRRAYWAAVKVYEQLIS----QGCIP-GQVTYASIINAYCRI  213 (343)
Q Consensus       148 ~a~~~~~~~~~----~~~~~~~~~~~~-----l~~~~~~~~~~~~a~~~~~~~~~----~~~~p-~~~~~~~ll~~~~~~  213 (343)
                      +|.-+..+..+    .++..-..-|..     |.-++...|....|.+.-++..+    .|-.| -......+.+.|-..
T Consensus       180 Kal~f~~kA~~lv~s~~l~d~~~kyr~~~lyhmaValR~~G~LgdA~e~C~Ea~klal~~Gdra~~arc~~~~aDIyR~~  259 (518)
T KOG1941|consen  180 KALFFPCKAAELVNSYGLKDWSLKYRAMSLYHMAVALRLLGRLGDAMECCEEAMKLALQHGDRALQARCLLCFADIYRSR  259 (518)
T ss_pred             HHhhhhHhHHHHHHhcCcCchhHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHhCChHHHHHHHHHHHHHHHhc
Confidence            98877655432    233211122332     34456667777777777666543    33222 123344566778888


Q ss_pred             CChhHHHHHHHHHH
Q 044084          214 GLYSKAEKVFIEMQ  227 (343)
Q Consensus       214 ~~~~~a~~~~~~~~  227 (343)
                      |+.+.|+.-++...
T Consensus       260 gd~e~af~rYe~Am  273 (518)
T KOG1941|consen  260 GDLERAFRRYEQAM  273 (518)
T ss_pred             ccHhHHHHHHHHHH
Confidence            99888887776644

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome

Probab=95.23  E-value=0.25  Score=36.88  Aligned_cols=61  Identities=13%  Similarity=0.097  Sum_probs=26.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHH
Q 044084           25 YCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDM   86 (343)
Q Consensus        25 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~   86 (343)
                      +..+...|.+.|+.+.|.+.|.++.+....+. .....+-.+|+.....+++..+...+.+.
T Consensus        39 ~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~-~~id~~l~~irv~i~~~d~~~v~~~i~ka   99 (177)
T PF10602_consen   39 LEDLADHYCKIGDLEEALKAYSRARDYCTSPG-HKIDMCLNVIRVAIFFGDWSHVEKYIEKA   99 (177)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            44444445555555555555544444332222 11233444444444444444444444443

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.

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.22  E-value=0.67  Score=42.48  Aligned_cols=120  Identities=18%  Similarity=0.159  Sum_probs=63.5

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHh
Q 044084           27 QIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFA  106 (343)
Q Consensus        27 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  106 (343)
                      .-+..+.+...++-|..+-+   ..+.+++ ..........+-+.+.|++++|...|-+-... +.|.     .++.-|.
T Consensus       339 ~kL~iL~kK~ly~~Ai~LAk---~~~~d~d-~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~-le~s-----~Vi~kfL  408 (933)
T KOG2114|consen  339 TKLDILFKKNLYKVAINLAK---SQHLDED-TLAEIHRKYGDYLYGKGDFDEATDQYIETIGF-LEPS-----EVIKKFL  408 (933)
T ss_pred             HHHHHHHHhhhHHHHHHHHH---hcCCCHH-HHHHHHHHHHHHHHhcCCHHHHHHHHHHHccc-CChH-----HHHHHhc
Confidence            34444555555555555432   2232222 00122223334455667777777666554432 2221     2445555


Q ss_pred             cccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHH
Q 044084          107 SIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMK  157 (343)
Q Consensus       107 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  157 (343)
                      ........-..++.+.+.|+. +...-..|+.+|.+.++.++-.+..+...
T Consensus       409 daq~IknLt~YLe~L~~~gla-~~dhttlLLncYiKlkd~~kL~efI~~~~  458 (933)
T KOG2114|consen  409 DAQRIKNLTSYLEALHKKGLA-NSDHTTLLLNCYIKLKDVEKLTEFISKCD  458 (933)
T ss_pred             CHHHHHHHHHHHHHHHHcccc-cchhHHHHHHHHHHhcchHHHHHHHhcCC
Confidence            666666666667777777764 55566667777777776666555554443

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=95.22  E-value=0.72  Score=32.72  Aligned_cols=26  Identities=19%  Similarity=0.369  Sum_probs=11.3

Q ss_pred             HHHHHHHHhcCcHhHHHHHHHHHHhc
Q 044084          134 LKLVLMYIEEGMVEKTLEVVESMKNA  159 (343)
Q Consensus       134 ~~l~~~~~~~~~~~~a~~~~~~~~~~  159 (343)
                      -.|+.+|.+.+++++|...+++..+.
T Consensus        51 L~l~yayy~~~~y~~A~a~~~rFirL   76 (142)
T PF13512_consen   51 LDLAYAYYKQGDYEEAIAAYDRFIRL   76 (142)
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            33444444444444444444444433

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.19  E-value=0.75  Score=42.19  Aligned_cols=152  Identities=15%  Similarity=0.116  Sum_probs=91.3

Q ss_pred             HHHHHHHHhcccCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHH
Q 044084           98 YASLICSFASIAEVKVAEELFKEAEEKGMLRD--LEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGF  175 (343)
Q Consensus        98 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  175 (343)
                      ...-+..+.+...++.|..+-+   ..+..++  ..........+.+.|++++|...|-+....- .|     ..+|.-|
T Consensus       337 le~kL~iL~kK~ly~~Ai~LAk---~~~~d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~l-e~-----s~Vi~kf  407 (933)
T KOG2114|consen  337 LETKLDILFKKNLYKVAINLAK---SQHLDEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGFL-EP-----SEVIKKF  407 (933)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHH---hcCCCHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHcccC-Ch-----HHHHHHh
Confidence            4455666666666776666543   3333222  2223333445567888888888776654321 12     2456666


Q ss_pred             hcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHH
Q 044084          176 SKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAM  255 (343)
Q Consensus       176 ~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  255 (343)
                      ........-..+++.+.+.|+. +...-+.|+.+|.+.++.++-.++.+... .|..  ..-....+..+.+.+-.++|.
T Consensus       408 Ldaq~IknLt~YLe~L~~~gla-~~dhttlLLncYiKlkd~~kL~efI~~~~-~g~~--~fd~e~al~Ilr~snyl~~a~  483 (933)
T KOG2114|consen  408 LDAQRIKNLTSYLEALHKKGLA-NSDHTTLLLNCYIKLKDVEKLTEFISKCD-KGEW--FFDVETALEILRKSNYLDEAE  483 (933)
T ss_pred             cCHHHHHHHHHHHHHHHHcccc-cchhHHHHHHHHHHhcchHHHHHHHhcCC-Ccce--eeeHHHHHHHHHHhChHHHHH
Confidence            7777777778888888888753 44445678888888888888766655443 2211  112345566666777777776


Q ss_pred             HHHHHHh
Q 044084          256 RLVAKMK  262 (343)
Q Consensus       256 ~~~~~m~  262 (343)
                      .+-.+..
T Consensus       484 ~LA~k~~  490 (933)
T KOG2114|consen  484 LLATKFK  490 (933)
T ss_pred             HHHHHhc
Confidence            6655543

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=95.19  E-value=1.1  Score=34.66  Aligned_cols=226  Identities=17%  Similarity=0.098  Sum_probs=143.3

Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhc-CCCCChHhHHHHHHHHhcccCHHH
Q 044084           35 IGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEK-GILEDPSVYASLICSFASIAEVKV  113 (343)
Q Consensus        35 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~  113 (343)
                      .+....+...+..........  .....+......+...+.+..+...+...... ........+......+...++...
T Consensus        36 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  113 (291)
T COG0457          36 LGELAEALELLEEALELLPNS--DLAGLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEE  113 (291)
T ss_pred             HhhHHHHHHHHHHHHhcCccc--cchHHHHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHhhHHH
Confidence            456666666666665544331  01345666777777788888887777776642 223345556666667777777888


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHH-HHHhcCcHhHHHHHHHHHHhcCC--CCchhhHHHHHHHHhcCCcHHHHHHHHHH
Q 044084          114 AEELFKEAEEKGMLRDLEVFLKLVL-MYIEEGMVEKTLEVVESMKNAEL--NISDCISCVIVNGFSKRRAYWAAVKVYEQ  190 (343)
Q Consensus       114 a~~~~~~~~~~~~~~~~~~~~~l~~-~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  190 (343)
                      +...+.........+ ......... .+...|+++.|...+.+......  ......+......+...++.+.+...+..
T Consensus       114 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~  192 (291)
T COG0457         114 ALELLEKALALDPDP-DLAEALLALGALYELGDYEEALELYEKALELDPELNELAEALLALGALLEALGRYEEALELLEK  192 (291)
T ss_pred             HHHHHHHHHcCCCCc-chHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCccchHHHHHHhhhHHHHhcCHHHHHHHHHH
Confidence            888888777654433 222222333 67788888888888888755221  11223334444446677888888888888


Q ss_pred             HHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhC
Q 044084          191 LISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       191 ~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                      ............+..+...+...++.+.+...+......... ....+..+...+...+..+.+...+.+....
T Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  265 (291)
T COG0457         193 ALKLNPDDDAEALLNLGLLYLKLGKYEEALEYYEKALELDPD-NAEALYNLALLLLELGRYEEALEALEKALEL  265 (291)
T ss_pred             HHhhCcccchHHHHHhhHHHHHcccHHHHHHHHHHHHhhCcc-cHHHHhhHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            877631113566777777778888888888888887775411 2344444444455666788888888887765

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=95.09  E-value=0.72  Score=32.02  Aligned_cols=92  Identities=16%  Similarity=0.093  Sum_probs=57.0

Q ss_pred             HhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHH---HHHHHHHHHHhcCc
Q 044084           69 SLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLE---VFLKLVLMYIEEGM  145 (343)
Q Consensus        69 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~---~~~~l~~~~~~~~~  145 (343)
                      +....|+.+.|++.|.+.+..- +-....||.-..++--.|+.++|+.-+++..+..-..+..   .|..-...|-..|+
T Consensus        52 alaE~g~Ld~AlE~F~qal~l~-P~raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~trtacqa~vQRg~lyRl~g~  130 (175)
T KOG4555|consen   52 ALAEAGDLDGALELFGQALCLA-PERASAYNNRAQALRLQGDDEEALDDLNKALELAGDQTRTACQAFVQRGLLYRLLGN  130 (175)
T ss_pred             HHHhccchHHHHHHHHHHHHhc-ccchHhhccHHHHHHHcCChHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHhCc
Confidence            4566777777777777776652 2356667777777777777777777777666532222322   23333445666677


Q ss_pred             HhHHHHHHHHHHhcCC
Q 044084          146 VEKTLEVVESMKNAEL  161 (343)
Q Consensus       146 ~~~a~~~~~~~~~~~~  161 (343)
                      -+.|..=|+...+.|.
T Consensus       131 dd~AR~DFe~AA~LGS  146 (175)
T KOG4555|consen  131 DDAARADFEAAAQLGS  146 (175)
T ss_pred             hHHHHHhHHHHHHhCC
Confidence            7777777776665554

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.86  E-value=1.8  Score=35.47  Aligned_cols=152  Identities=8%  Similarity=-0.072  Sum_probs=91.1

Q ss_pred             ccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHhcCcHhH
Q 044084           72 KSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEK---GMLRDLEVFLKLVLMYIEEGMVEK  148 (343)
Q Consensus        72 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~~~~l~~~~~~~~~~~~  148 (343)
                      -.|++.+|-..++++++. .+.|...+...=.+|.-.|+.+.-...++++...   +++....+-..+.-++..+|-+++
T Consensus       115 ~~g~~h~a~~~wdklL~d-~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~wn~dlp~~sYv~GmyaFgL~E~g~y~d  193 (491)
T KOG2610|consen  115 GRGKHHEAAIEWDKLLDD-YPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPKWNADLPCYSYVHGMYAFGLEECGIYDD  193 (491)
T ss_pred             ccccccHHHHHHHHHHHh-CchhhhhhhhhhhHHHhccchhhhhhHHHHhccccCCCCcHHHHHHHHHHhhHHHhccchh
Confidence            356666666677777665 3446666666667777777777777777776643   222123333344455567788888


Q ss_pred             HHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHc---CCCCCHhhHHHHHHHHHccCChhHHHHHHHH
Q 044084          149 TLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQ---GCIPGQVTYASIINAYCRIGLYSKAEKVFIE  225 (343)
Q Consensus       149 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~  225 (343)
                      |.+.-++..+.+. .|...-.+....+-..|++.++.++..+-...   +-..-..-|-...-.+...+.++.|+++|+.
T Consensus       194 AEk~A~ralqiN~-~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~s~mlasHNyWH~Al~~iE~aeye~aleIyD~  272 (491)
T KOG2610|consen  194 AEKQADRALQINR-FDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWMLASHNYWHTALFHIEGAEYEKALEIYDR  272 (491)
T ss_pred             HHHHHHhhccCCC-cchHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHHHhhhhHHHHHhhhcccchhHHHHHHHH
Confidence            8888877777665 45555666667777778888877776553321   1000111122222234455788888888875

>PRK11906 transcriptional regulator; Provisional

Probab=94.74  E-value=2.5  Score=36.47  Aligned_cols=113  Identities=13%  Similarity=0.114  Sum_probs=65.9

Q ss_pred             cHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHH
Q 044084           75 RAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVE  154 (343)
Q Consensus        75 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  154 (343)
                      ...+|.++-++..+.+. -|......+..+..-.++++.+...|++....++. ...+|........-.|+.++|.+.++
T Consensus       319 ~~~~a~~~A~rAveld~-~Da~a~~~~g~~~~~~~~~~~a~~~f~rA~~L~Pn-~A~~~~~~~~~~~~~G~~~~a~~~i~  396 (458)
T PRK11906        319 AAQKALELLDYVSDITT-VDGKILAIMGLITGLSGQAKVSHILFEQAKIHSTD-IASLYYYRALVHFHNEKIEEARICID  396 (458)
T ss_pred             HHHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHhhcchhhHHHHHHHHhhcCCc-cHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            34556666666666543 25666666666666667777788888777775532 45555555556666777888888777


Q ss_pred             HHHhcCC-CCchhhHHHHHHHHhcCCcHHHHHHHHHH
Q 044084          155 SMKNAEL-NISDCISCVIVNGFSKRRAYWAAVKVYEQ  190 (343)
Q Consensus       155 ~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  190 (343)
                      +..+..+ ..-.......++.|+.. ..+.+.++|-+
T Consensus       397 ~alrLsP~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~  432 (458)
T PRK11906        397 KSLQLEPRRRKAVVIKECVDMYVPN-PLKNNIKLYYK  432 (458)
T ss_pred             HHhccCchhhHHHHHHHHHHHHcCC-chhhhHHHHhh
Confidence            7554432 11122233334455543 45555555543

>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=94.38  E-value=1.5  Score=32.29  Aligned_cols=134  Identities=12%  Similarity=0.066  Sum_probs=65.7

Q ss_pred             HHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhc
Q 044084           80 LKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNA  159 (343)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  159 (343)
                      .+.++.+.+.+++|+...+..+++.+.+.|++...    .++...++-+|.......+-.+..  ....+.++=-+|..+
T Consensus        14 lEYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~L----~qllq~~Vi~DSk~lA~~LLs~~~--~~~~~~Ql~lDMLkR   87 (167)
T PF07035_consen   14 LEYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQL----HQLLQYHVIPDSKPLACQLLSLGN--QYPPAYQLGLDMLKR   87 (167)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHHH----HHHHhhcccCCcHHHHHHHHHhHc--cChHHHHHHHHHHHH
Confidence            34555555666777777777777777777765433    333344444444333333322221  222333333333221


Q ss_pred             -CCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHH
Q 044084          160 -ELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQ  228 (343)
Q Consensus       160 -~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  228 (343)
                       +.     .+..+++.+...|++-+|.++.+.....    +......++.+..+.+|...-..+++-..+
T Consensus        88 L~~-----~~~~iievLL~~g~vl~ALr~ar~~~~~----~~~~~~~fLeAA~~~~D~~lf~~V~~ff~~  148 (167)
T PF07035_consen   88 LGT-----AYEEIIEVLLSKGQVLEALRYARQYHKV----DSVPARKFLEAAANSNDDQLFYAVFRFFEE  148 (167)
T ss_pred             hhh-----hHHHHHHHHHhCCCHHHHHHHHHHcCCc----ccCCHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence             11     2445666666677777777666654222    111224455555555555554445444444

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.36  E-value=0.44  Score=38.44  Aligned_cols=107  Identities=11%  Similarity=0.057  Sum_probs=62.8

Q ss_pred             CCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChH
Q 044084           17 GIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPS   96 (343)
Q Consensus        17 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~   96 (343)
                      |.+.+..+...++.......+++.+...+-++....-..-.+ ..+-...++.+. .-++++++.++..=.+.|+-||..
T Consensus        59 g~~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~-~~~~~~~irlll-ky~pq~~i~~l~npIqYGiF~dqf  136 (418)
T KOG4570|consen   59 GLPVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLR-NWTIHTWIRLLL-KYDPQKAIYTLVNPIQYGIFPDQF  136 (418)
T ss_pred             CCCcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhc-cccHHHHHHHHH-ccChHHHHHHHhCcchhccccchh
Confidence            444555566666666666667777777666654332110000 011122233332 234667777777767777778888


Q ss_pred             hHHHHHHHHhcccCHHHHHHHHHHHHHcC
Q 044084           97 VYASLICSFASIAEVKVAEELFKEAEEKG  125 (343)
Q Consensus        97 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  125 (343)
                      +++.+|..+.+.+++..|.++...|....
T Consensus       137 ~~c~l~D~flk~~n~~~aa~vvt~~~~qe  165 (418)
T KOG4570|consen  137 TFCLLMDSFLKKENYKDAASVVTEVMMQE  165 (418)
T ss_pred             hHHHHHHHHHhcccHHHHHHHHHHHHHHH
Confidence            88888888888888777777766665543

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

Probab=94.35  E-value=0.13  Score=26.58  Aligned_cols=24  Identities=29%  Similarity=0.373  Sum_probs=14.9

Q ss_pred             HHHHHHHHHhcCcHhHHHHHHHHH
Q 044084          133 FLKLVLMYIEEGMVEKTLEVVESM  156 (343)
Q Consensus       133 ~~~l~~~~~~~~~~~~a~~~~~~~  156 (343)
                      |..|...|.+.|++++|+++|++.
T Consensus         2 l~~Lg~~~~~~g~~~~Ai~~y~~a   25 (36)
T PF13176_consen    2 LNNLGRIYRQQGDYEKAIEYYEQA   25 (36)
T ss_dssp             HHHHHHHHHHCT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHH
Confidence            556666666666666666666663

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=94.28  E-value=1.2  Score=31.01  Aligned_cols=138  Identities=12%  Similarity=0.110  Sum_probs=59.6

Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHH
Q 044084           34 KIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKV  113 (343)
Q Consensus        34 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  113 (343)
                      -.|..++..++..+......      ..-+|-+|.-....-+-+-..+.++..-+.   .|..          ..|+...
T Consensus        14 ldG~V~qGveii~k~v~Ssn------i~E~NWvICNiiDaa~C~yvv~~LdsIGki---FDis----------~C~NlKr   74 (161)
T PF09205_consen   14 LDGDVKQGVEIIEKTVNSSN------IKEYNWVICNIIDAADCDYVVETLDSIGKI---FDIS----------KCGNLKR   74 (161)
T ss_dssp             HTT-HHHHHHHHHHHHHHS-------HHHHTHHHHHHHHH--HHHHHHHHHHHGGG---S-GG----------G-S-THH
T ss_pred             HhchHHHHHHHHHHHcCcCC------ccccceeeeecchhhchhHHHHHHHHHhhh---cCch----------hhcchHH
Confidence            34677777777776654321      334555555444444444444444443221   1111          1222222


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHH
Q 044084          114 AEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLIS  193 (343)
Q Consensus       114 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  193 (343)
                      ....+..+   +  .+.......+......|+-+.-.+++..+.+.+- +++...-.+..+|.+.|+..++.+++.+.-+
T Consensus        75 Vi~C~~~~---n--~~se~vD~ALd~lv~~~kkDqLdki~~~l~kn~~-~~p~~L~kia~Ay~klg~~r~~~ell~~ACe  148 (161)
T PF09205_consen   75 VIECYAKR---N--KLSEYVDLALDILVKQGKKDQLDKIYNELKKNEE-INPEFLVKIANAYKKLGNTREANELLKEACE  148 (161)
T ss_dssp             HHHHHHHT---T-----HHHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHh---c--chHHHHHHHHHHHHHhccHHHHHHHHHHHhhccC-CCHHHHHHHHHHHHHhcchhhHHHHHHHHHH
Confidence            22222211   1  1333444455555556665655555555543222 4444555555666666666666666666655


Q ss_pred             cCC
Q 044084          194 QGC  196 (343)
Q Consensus       194 ~~~  196 (343)
                      .|+
T Consensus       149 kG~  151 (161)
T PF09205_consen  149 KGL  151 (161)
T ss_dssp             TT-
T ss_pred             hch
Confidence            553

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>PRK11906 transcriptional regulator; Provisional

Probab=94.23  E-value=3.3  Score=35.76  Aligned_cols=114  Identities=11%  Similarity=0.045  Sum_probs=81.8

Q ss_pred             cCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHH
Q 044084          109 AEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVY  188 (343)
Q Consensus       109 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  188 (343)
                      .+..+|.++-++..+.+.. |+.....+..+..-.++++.|..+|++....++ ....+|......+...|+.++|.+.+
T Consensus       318 ~~~~~a~~~A~rAveld~~-Da~a~~~~g~~~~~~~~~~~a~~~f~rA~~L~P-n~A~~~~~~~~~~~~~G~~~~a~~~i  395 (458)
T PRK11906        318 LAAQKALELLDYVSDITTV-DGKILAIMGLITGLSGQAKVSHILFEQAKIHST-DIASLYYYRALVHFHNEKIEEARICI  395 (458)
T ss_pred             HHHHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHhhcchhhHHHHHHHHhhcCC-ccHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            3456777777888887754 888888888888888999999999999987764 34445555556666789999999999


Q ss_pred             HHHHHcCCCCCH---hhHHHHHHHHHccCChhHHHHHHHHHH
Q 044084          189 EQLISQGCIPGQ---VTYASIINAYCRIGLYSKAEKVFIEMQ  227 (343)
Q Consensus       189 ~~~~~~~~~p~~---~~~~~ll~~~~~~~~~~~a~~~~~~~~  227 (343)
                      ++..+.  .|..   ......+..|+. ...+.+..++-+-.
T Consensus       396 ~~alrL--sP~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~  434 (458)
T PRK11906        396 DKSLQL--EPRRRKAVVIKECVDMYVP-NPLKNNIKLYYKET  434 (458)
T ss_pred             HHHhcc--CchhhHHHHHHHHHHHHcC-CchhhhHHHHhhcc
Confidence            997765  3433   233344556665 45677777665433

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=94.23  E-value=0.0016  Score=46.86  Aligned_cols=122  Identities=7%  Similarity=0.079  Sum_probs=67.4

Q ss_pred             HHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccC
Q 044084          206 IINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKN  285 (343)
Q Consensus       206 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~  285 (343)
                      ++..+.+.+.++....+++.+...+...+....+.++..|++.++.++..++++....       .-...+++.|.+.|.
T Consensus        13 vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~~~~-------yd~~~~~~~c~~~~l   85 (143)
T PF00637_consen   13 VISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKTSNN-------YDLDKALRLCEKHGL   85 (143)
T ss_dssp             CHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTSSSS-------S-CTHHHHHHHTTTS
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcccccc-------cCHHHHHHHHHhcch
Confidence            4555566666777777777776655445566677777777777666666666552111       222334455555554


Q ss_pred             hhHHHhHHHHHHHHHhcCCHHHHHHHHHHHHhC-------CCCccHHHHHHHHHHHhccccc
Q 044084          286 LRQLEKYTTVISAYNMAREFDMCVKFYNEFRMN-------GGVIDRAMAGIMVGVFSKLSQI  340 (343)
Q Consensus       286 ~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~~~-------~~~p~~~~~~~l~~~~~~~g~~  340 (343)
                      ++++      +..|.+.|++++|++++..+..-       .-.+++..|..+++.+...++.
T Consensus        86 ~~~a------~~Ly~~~~~~~~al~i~~~~~~~~~a~e~~~~~~~~~l~~~l~~~~l~~~~~  141 (143)
T PF00637_consen   86 YEEA------VYLYSKLGNHDEALEILHKLKDYEEAIEYAKKVDDPELWEQLLKYCLDSKPF  141 (143)
T ss_dssp             HHHH------HHHHHCCTTHTTCSSTSSSTHCSCCCTTTGGGCSSSHHHHHHHHHHCTSTCT
T ss_pred             HHHH------HHHHHHcccHHHHHHHHHHHccHHHHHHHHHhcCcHHHHHHHHHHHHhcCcc
Confidence            4433      33556666666666543222111       1134677788888877766653

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.

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=94.21  E-value=0.083  Score=27.00  Aligned_cols=31  Identities=26%  Similarity=0.388  Sum_probs=18.7

Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHH
Q 044084          119 KEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTL  150 (343)
Q Consensus       119 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  150 (343)
                      ++.++..+. +...|+.+...|...|++++|+
T Consensus         3 ~kAie~~P~-n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen    3 KKAIELNPN-NAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             HHHHHHCCC-CHHHHHHHHHHHHHCcCHHhhc
Confidence            344444432 5666777777777777766664

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=94.19  E-value=0.0011  Score=47.79  Aligned_cols=53  Identities=19%  Similarity=0.237  Sum_probs=22.0

Q ss_pred             HHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHH
Q 044084          102 ICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVE  154 (343)
Q Consensus       102 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  154 (343)
                      +..+.+.+.++.....++.+...+...+....+.++..|++.++.++..++++
T Consensus        14 i~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~   66 (143)
T PF00637_consen   14 ISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLK   66 (143)
T ss_dssp             HHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTT
T ss_pred             HHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcc
Confidence            33344444444444444444443333334444444444444444444444433

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.

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=94.18  E-value=2.7  Score=34.50  Aligned_cols=22  Identities=27%  Similarity=0.603  Sum_probs=10.6

Q ss_pred             HHHHHHHHHHhcCCCCChHhHH
Q 044084           78 EILKFFRDMKEKGILEDPSVYA   99 (343)
Q Consensus        78 ~a~~~~~~~~~~~~~~~~~~~~   99 (343)
                      +.+.+++.|.+.|.+-+..+|-
T Consensus        80 ~~~~~y~~L~~~gFk~~~y~~l  101 (297)
T PF13170_consen   80 EVLDIYEKLKEAGFKRSEYLYL  101 (297)
T ss_pred             HHHHHHHHHHHhccCccChHHH
Confidence            3444555555555554444433

>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=94.05  E-value=0.7  Score=34.87  Aligned_cols=80  Identities=15%  Similarity=0.150  Sum_probs=59.7

Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhc---CCCCChHhHHHHHHHHhc
Q 044084           31 AFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEK---GILEDPSVYASLICSFAS  107 (343)
Q Consensus        31 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~~~~l~~~~~~  107 (343)
                      ...+.|+ +.|.+.|-.+...+...+   ......|...|. ..+.++++.++.+..+.   +-.+|+..+..|.+.+.+
T Consensus       116 ~Wsr~~d-~~A~~~fL~~E~~~~l~t---~elq~aLAtyY~-krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~  190 (203)
T PF11207_consen  116 HWSRFGD-QEALRRFLQLEGTPELET---AELQYALATYYT-KRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQK  190 (203)
T ss_pred             HhhccCc-HHHHHHHHHHcCCCCCCC---HHHHHHHHHHHH-ccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            4566666 678888888877766544   455555555555 67799999999888764   336788999999999999


Q ss_pred             ccCHHHHH
Q 044084          108 IAEVKVAE  115 (343)
Q Consensus       108 ~~~~~~a~  115 (343)
                      .|+.+.|-
T Consensus       191 ~~~~e~AY  198 (203)
T PF11207_consen  191 LKNYEQAY  198 (203)
T ss_pred             hcchhhhh
Confidence            99988774

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

Probab=94.01  E-value=0.13  Score=26.59  Aligned_cols=23  Identities=9%  Similarity=0.215  Sum_probs=12.4

Q ss_pred             HHHHHHHhhccCcHHHHHHHHHH
Q 044084           63 YKILCDSLGKSGRAFEILKFFRD   85 (343)
Q Consensus        63 ~~~li~~~~~~~~~~~a~~~~~~   85 (343)
                      |+.|...|.+.|++++|+++|++
T Consensus         2 l~~Lg~~~~~~g~~~~Ai~~y~~   24 (36)
T PF13176_consen    2 LNNLGRIYRQQGDYEKAIEYYEQ   24 (36)
T ss_dssp             HHHHHHHHHHCT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHH
Confidence            44555555555555555555555

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=93.90  E-value=4.3  Score=35.89  Aligned_cols=231  Identities=12%  Similarity=0.059  Sum_probs=130.3

Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCCCCH------HHHHHHHHHHHh----cCcHhHHHHHHHHHHhcCCCCchhhHHH
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGMLRDL------EVFLKLVLMYIE----EGMVEKTLEVVESMKNAELNISDCISCV  170 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~------~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~  170 (343)
                      ++....-.||-+.+++.+.+..+.+--..+      -.|+..+..++.    ....+.|.++++.+.+.-  |+...|..
T Consensus       194 ll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~y--P~s~lfl~  271 (468)
T PF10300_consen  194 LLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKRY--PNSALFLF  271 (468)
T ss_pred             HHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHhC--CCcHHHHH
Confidence            444555668888888888877664322122      223444443333    346788999999988764  55545543


Q ss_pred             H-HHHHhcCCcHHHHHHHHHHHHHcC---CCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHH-HHHH
Q 044084          171 I-VNGFSKRRAYWAAVKVYEQLISQG---CIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSM-VAMY  245 (343)
Q Consensus       171 l-~~~~~~~~~~~~a~~~~~~~~~~~---~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l-~~~~  245 (343)
                      . .+.+...|++++|.+.|++.....   .+.....+--+.-.+.-..++++|...|..+.+.. .-...+|.-+ ..++
T Consensus       272 ~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s-~WSka~Y~Y~~a~c~  350 (468)
T PF10300_consen  272 FEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKES-KWSKAFYAYLAAACL  350 (468)
T ss_pred             HHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhcc-ccHHHHHHHHHHHHH
Confidence            3 355667899999999999765421   11222334445556777899999999999998864 2233333333 2344


Q ss_pred             HccCCh-------HHHHHHHHHHhhC------CCCchHHHHHHHHHHHhcccC--hhH------HHhHHHHHHHHHhcCC
Q 044084          246 GKTGRI-------RDAMRLVAKMKPK------GCEPNVWIYNSLMDMHGRAKN--LRQ------LEKYTTVISAYNMARE  304 (343)
Q Consensus       246 ~~~~~~-------~~a~~~~~~m~~~------~~~p~~~~~~~l~~~~~~~~~--~~~------a~~~~~l~~~~~~~g~  304 (343)
                      ...|+.       ++|.++|.+....      .-.|-......-++-|...+.  +-+      +.+...+-+++.+.++
T Consensus       351 ~~l~~~~~~~~~~~~a~~l~~~vp~l~~k~~gk~lp~E~Fv~RK~~~~~~~~~~~~~d~~~~~p~~El~y~WNg~~~~~~  430 (468)
T PF10300_consen  351 LMLGREEEAKEHKKEAEELFRKVPKLKQKKAGKSLPLEKFVIRKAQKYEKQAKVDLVDAILVLPALELMYFWNGFPRMPK  430 (468)
T ss_pred             HhhccchhhhhhHHHHHHHHHHHHHHHhhhccCCCChHHHHHHHHHHHHhcCCCcchhhhhcCHHHHHHHHHhccccCCh
Confidence            556777       8888888776532      122322323333344444322  111      1123444455555555


Q ss_pred             HHHHHHHHHHHHhC---CCCccHHHHHHHHHHH
Q 044084          305 FDMCVKFYNEFRMN---GGVIDRAMAGIMVGVF  334 (343)
Q Consensus       305 ~~~a~~~~~~m~~~---~~~p~~~~~~~l~~~~  334 (343)
                      -..-...+......   ...+|......++.+.
T Consensus       431 ~~l~~~~~~~l~~~~~~~~~~De~~l~~lL~g~  463 (468)
T PF10300_consen  431 EELEIKSLLELEESKNSEEDPDERALRHLLKGA  463 (468)
T ss_pred             HHHHHHHHHHHHhcccccCCccHHHHHHHHHHH
Confidence            44433444444332   2456777665566543

In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=93.84  E-value=2.6  Score=33.19  Aligned_cols=54  Identities=13%  Similarity=0.191  Sum_probs=28.9

Q ss_pred             cccCHHHHHHHHHHHHHcCCC--CCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcC
Q 044084          107 SIAEVKVAEELFKEAEEKGML--RDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus       107 ~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  160 (343)
                      +.|++++|.+.|+.+....+-  -...+.-.++-++.+.+++++|+..+++.....
T Consensus        46 ~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~ly  101 (254)
T COG4105          46 QKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLY  101 (254)
T ss_pred             hcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhC
Confidence            456666666666666543221  123444445555566666666666666655443

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.77  E-value=1.2  Score=35.99  Aligned_cols=48  Identities=15%  Similarity=0.257  Sum_probs=24.2

Q ss_pred             HhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHH
Q 044084          146 VEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLIS  193 (343)
Q Consensus       146 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  193 (343)
                      +++++.++..=.+.|+-||..+++.+|+.+.+.+++.+|..+...|..
T Consensus       116 pq~~i~~l~npIqYGiF~dqf~~c~l~D~flk~~n~~~aa~vvt~~~~  163 (418)
T KOG4570|consen  116 PQKAIYTLVNPIQYGIFPDQFTFCLLMDSFLKKENYKDAASVVTEVMM  163 (418)
T ss_pred             hHHHHHHHhCcchhccccchhhHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            344444444444455555555555555555555555555554444443

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=93.66  E-value=2  Score=31.23  Aligned_cols=51  Identities=16%  Similarity=0.076  Sum_probs=21.7

Q ss_pred             cccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHh
Q 044084          107 SIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKN  158 (343)
Q Consensus       107 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  158 (343)
                      +.++.+.+..++..+.-..+. ....-..-...+...|+|.+|+.+|+.+..
T Consensus        22 ~~~~~~D~e~lL~ALrvLRP~-~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~   72 (160)
T PF09613_consen   22 RLGDPDDAEALLDALRVLRPE-FPELDLFDGWLHIVRGDWDDALRLLRELEE   72 (160)
T ss_pred             ccCChHHHHHHHHHHHHhCCC-chHHHHHHHHHHHHhCCHHHHHHHHHHHhc
Confidence            344555555555544443221 111112222334455555555555555443

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=93.64  E-value=4.5  Score=35.25  Aligned_cols=64  Identities=9%  Similarity=0.085  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCC-chhhHHHHHHHHhcCCcHHHHHHHHHHHHHc
Q 044084          131 EVFLKLVLMYIEEGMVEKTLEVVESMKNAELNI-SDCISCVIVNGFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       131 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  194 (343)
                      .+-..+..+.-+.|+.++|++.++++.+..... .......|+.++...+.+.++..++.+-.+.
T Consensus       260 y~KrRLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi  324 (539)
T PF04184_consen  260 YAKRRLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDI  324 (539)
T ss_pred             hhHHHHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccc
Confidence            333455666667788888888888776544322 2335566777888888888888887776543

The molecular function of this protein is uncertain.

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=93.63  E-value=3.7  Score=34.19  Aligned_cols=230  Identities=16%  Similarity=0.135  Sum_probs=113.3

Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhc--CCCC---ChHhHHHHHHHHh
Q 044084           32 FYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEK--GILE---DPSVYASLICSFA  106 (343)
Q Consensus        32 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~--~~~~---~~~~~~~l~~~~~  106 (343)
                      +....+.++|+..|.+...+-...- .-..++..+..+.++.|.+++++..--.....  ...-   --..|..+.+++-
T Consensus        16 Ly~s~~~~~al~~w~~~L~~l~~~~-~Rf~~lG~l~~a~s~~g~y~~mL~~a~sqi~~a~~~~ds~~~~ea~lnlar~~e   94 (518)
T KOG1941|consen   16 LYQSNQTEKALQVWTKVLEKLSDLM-GRFRVLGCLVTAHSEMGRYKEMLKFAVSQIDTARELEDSDFLLEAYLNLARSNE   94 (518)
T ss_pred             HhcCchHHHHHHHHHHHHHHHHHHH-HHHHHhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566677777777766554421111 11345556666777777777665432111110  0000   1122333334444


Q ss_pred             cccCHHHHHHHHHHHHHc-CCCC---CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcC-----CCCchhhHHHHHHHHhc
Q 044084          107 SIAEVKVAEELFKEAEEK-GMLR---DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAE-----LNISDCISCVIVNGFSK  177 (343)
Q Consensus       107 ~~~~~~~a~~~~~~~~~~-~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~  177 (343)
                      +.-++.+++.+-..-... |..|   -.....++..++...+.++++++.|+...+.-     ......++..+-+.|.+
T Consensus        95 ~l~~f~kt~~y~k~~l~lpgt~~~~~~gq~~l~~~~Ahlgls~fq~~Lesfe~A~~~A~~~~D~~LElqvcv~Lgslf~~  174 (518)
T KOG1941|consen   95 KLCEFHKTISYCKTCLGLPGTRAGQLGGQVSLSMGNAHLGLSVFQKALESFEKALRYAHNNDDAMLELQVCVSLGSLFAQ  174 (518)
T ss_pred             HHHHhhhHHHHHHHHhcCCCCCcccccchhhhhHHHHhhhHHHHHHHHHHHHHHHHHhhccCCceeeeehhhhHHHHHHH
Confidence            444444444443332221 1111   12333445566666677777777777654321     11223356667777777


Q ss_pred             CCcHHHHHHHHHHHHHc--CCC-CCH-hhHHH-----HHHHHHccCChhHHHHHHHHHHHc----CCCc-ChhhHHHHHH
Q 044084          178 RRAYWAAVKVYEQLISQ--GCI-PGQ-VTYAS-----IINAYCRIGLYSKAEKVFIEMQQK----GFDK-CVVAYSSMVA  243 (343)
Q Consensus       178 ~~~~~~a~~~~~~~~~~--~~~-p~~-~~~~~-----ll~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~  243 (343)
                      ..++++|.-+..+..+.  .+. -|. ..|..     |.-++-..|+...|.+.-++..+.    |-.+ .....-.+.+
T Consensus       175 l~D~~Kal~f~~kA~~lv~s~~l~d~~~kyr~~~lyhmaValR~~G~LgdA~e~C~Ea~klal~~Gdra~~arc~~~~aD  254 (518)
T KOG1941|consen  175 LKDYEKALFFPCKAAELVNSYGLKDWSLKYRAMSLYHMAVALRLLGRLGDAMECCEEAMKLALQHGDRALQARCLLCFAD  254 (518)
T ss_pred             HHhhhHHhhhhHhHHHHHHhcCcCchhHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHhCChHHHHHHHHHHHH
Confidence            77777777666655432  111 111 11222     223345566666666666654432    3111 1233445666


Q ss_pred             HHHccCChHHHHHHHHHHh
Q 044084          244 MYGKTGRIRDAMRLVAKMK  262 (343)
Q Consensus       244 ~~~~~~~~~~a~~~~~~m~  262 (343)
                      .|...|+.+.|+.-|+...
T Consensus       255 IyR~~gd~e~af~rYe~Am  273 (518)
T KOG1941|consen  255 IYRSRGDLERAFRRYEQAM  273 (518)
T ss_pred             HHHhcccHhHHHHHHHHHH
Confidence            7777777777776665543

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=93.43  E-value=8  Score=37.52  Aligned_cols=20  Identities=30%  Similarity=0.597  Sum_probs=8.8

Q ss_pred             HHHHHccCChHHHHHHHHHH
Q 044084          242 VAMYGKTGRIRDAMRLVAKM  261 (343)
Q Consensus       242 ~~~~~~~~~~~~a~~~~~~m  261 (343)
                      +.+|..+|+|.+|+.+..++
T Consensus       972 l~a~~~~~dWr~~l~~a~ql  991 (1265)
T KOG1920|consen  972 LKAYKECGDWREALSLAAQL  991 (1265)
T ss_pred             HHHHHHhccHHHHHHHHHhh
Confidence            33444444444444444443

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=93.41  E-value=3  Score=32.61  Aligned_cols=26  Identities=23%  Similarity=0.235  Sum_probs=14.6

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHH
Q 044084           24 CYCQIMEAFYKIGDSEKVAALFLECE   49 (343)
Q Consensus        24 ~~~~l~~~~~~~~~~~~a~~~~~~~~   49 (343)
                      .|..-..+|....++++|...+.+..
T Consensus        33 ~yekAAvafRnAk~feKakdcLlkA~   58 (308)
T KOG1585|consen   33 LYEKAAVAFRNAKKFEKAKDCLLKAS   58 (308)
T ss_pred             HHHHHHHHHHhhccHHHHHHHHHHHH
Confidence            34444555666666666666555543

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=93.23  E-value=2.4  Score=30.84  Aligned_cols=18  Identities=17%  Similarity=0.202  Sum_probs=8.6

Q ss_pred             hcCCcHHHHHHHHHHHHH
Q 044084          176 SKRRAYWAAVKVYEQLIS  193 (343)
Q Consensus       176 ~~~~~~~~a~~~~~~~~~  193 (343)
                      ...|++.+|..+|+++..
T Consensus        55 i~r~~w~dA~rlLr~l~~   72 (160)
T PF09613_consen   55 IVRGDWDDALRLLRELEE   72 (160)
T ss_pred             HHhCCHHHHHHHHHHHhc
Confidence            344455555555555443

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=93.23  E-value=3  Score=32.08  Aligned_cols=214  Identities=16%  Similarity=0.145  Sum_probs=105.0

Q ss_pred             CcHHHHHHHHHHHHhcCCC-CChHhHHHHHHHHhcccCHHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHhcCcHhHHHH
Q 044084           74 GRAFEILKFFRDMKEKGIL-EDPSVYASLICSFASIAEVKVAEELFKEAEEK-GMLRDLEVFLKLVLMYIEEGMVEKTLE  151 (343)
Q Consensus        74 ~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~  151 (343)
                      +....+...+......... .....+......+...+++..+...+...... ........+......+...+++..+..
T Consensus        37 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  116 (291)
T COG0457          37 GELAEALELLEEALELLPNSDLAGLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEALE  116 (291)
T ss_pred             hhHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHhhHHHHHH
Confidence            4444444554444443221 12344555555556666666666665555442 122344555555556666666666666


Q ss_pred             HHHHHHhcCCCCchhhHHHHHH-HHhcCCcHHHHHHHHHHHHHcCC--CCCHhhHHHHHHHHHccCChhHHHHHHHHHHH
Q 044084          152 VVESMKNAELNISDCISCVIVN-GFSKRRAYWAAVKVYEQLISQGC--IPGQVTYASIINAYCRIGLYSKAEKVFIEMQQ  228 (343)
Q Consensus       152 ~~~~~~~~~~~~~~~~~~~l~~-~~~~~~~~~~a~~~~~~~~~~~~--~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  228 (343)
                      .+.........+ ......... .+...|+++.+...+.+......  ......+......+...++.+.+...+.....
T Consensus       117 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  195 (291)
T COG0457         117 LLEKALALDPDP-DLAEALLALGALYELGDYEEALELYEKALELDPELNELAEALLALGALLEALGRYEEALELLEKALK  195 (291)
T ss_pred             HHHHHHcCCCCc-chHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCccchHHHHHHhhhHHHHhcCHHHHHHHHHHHHh
Confidence            666665543322 111222222 45566666666666666644210  01222233333334555666666666666665


Q ss_pred             cCCCc-ChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCch-HHHHHHHHHHHhcccChhHHHh
Q 044084          229 KGFDK-CVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPN-VWIYNSLMDMHGRAKNLRQLEK  291 (343)
Q Consensus       229 ~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~~~~~l~~~~~~~~~~~~a~~  291 (343)
                      .. +. ....+..+...+...++++.+...+......  .|+ ...+..+...+...+..+.+..
T Consensus       196 ~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~  257 (291)
T COG0457         196 LN-PDDDAEALLNLGLLYLKLGKYEEALEYYEKALEL--DPDNAEALYNLALLLLELGRYEEALE  257 (291)
T ss_pred             hC-cccchHHHHHhhHHHHHcccHHHHHHHHHHHHhh--CcccHHHHhhHHHHHHHcCCHHHHHH
Confidence            43 22 2455555666666666666666666666554  222 2333333333334444444443

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=93.18  E-value=4.6  Score=34.01  Aligned_cols=280  Identities=13%  Similarity=0.050  Sum_probs=171.6

Q ss_pred             HHHHHHHH--HhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHH--HhhccCcHHHHHHHHHHHHhcCCCCChHhHH-
Q 044084           25 YCQIMEAF--YKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCD--SLGKSGRAFEILKFFRDMKEKGILEDPSVYA-   99 (343)
Q Consensus        25 ~~~l~~~~--~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~--~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-   99 (343)
                      |..|-..+  .-.|+-..|.++-.+..+. +..+   ......|+.  +-.-.|+++.|.+-|+.|..     |+.|-. 
T Consensus        85 yqALStGliAagAGda~lARkmt~~~~~l-lssD---qepLIhlLeAQaal~eG~~~~Ar~kfeAMl~-----dPEtRll  155 (531)
T COG3898          85 YQALSTGLIAAGAGDASLARKMTARASKL-LSSD---QEPLIHLLEAQAALLEGDYEDARKKFEAMLD-----DPETRLL  155 (531)
T ss_pred             HHHHhhhhhhhccCchHHHHHHHHHHHhh-hhcc---chHHHHHHHHHHHHhcCchHHHHHHHHHHhc-----ChHHHHH
Confidence            44444444  3457777887776665422 2222   233444443  44567999999999999986     333332 


Q ss_pred             ---HHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCC-CCchh--hHHHHHH
Q 044084          100 ---SLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAEL-NISDC--ISCVIVN  173 (343)
Q Consensus       100 ---~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~--~~~~l~~  173 (343)
                         -|.-..-+.|+.+.|.+.-+..-..... =...+...+...+..|+|+.|+++++.-....+ .++..  .-..|+.
T Consensus       156 GLRgLyleAqr~GareaAr~yAe~Aa~~Ap~-l~WA~~AtLe~r~~~gdWd~AlkLvd~~~~~~vie~~~aeR~rAvLLt  234 (531)
T COG3898         156 GLRGLYLEAQRLGAREAARHYAERAAEKAPQ-LPWAARATLEARCAAGDWDGALKLVDAQRAAKVIEKDVAERSRAVLLT  234 (531)
T ss_pred             hHHHHHHHHHhcccHHHHHHHHHHHHhhccC-CchHHHHHHHHHHhcCChHHHHHHHHHHHHHHhhchhhHHHHHHHHHH
Confidence               2333345778888888888877765433 467889999999999999999999988665432 22221  1222332


Q ss_pred             HHh---cCCcHHHHHHHHHHHHHcCCCCCHhh-HHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccC
Q 044084          174 GFS---KRRAYWAAVKVYEQLISQGCIPGQVT-YASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTG  249 (343)
Q Consensus       174 ~~~---~~~~~~~a~~~~~~~~~~~~~p~~~~-~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  249 (343)
                      +-.   -.-++..|.+.-.+..+.  .||..- -..-.+++.+.|+..++-.+++.+-+..  |.+..+...+  +.+.|
T Consensus       235 AkA~s~ldadp~~Ar~~A~~a~KL--~pdlvPaav~AAralf~d~~~rKg~~ilE~aWK~e--PHP~ia~lY~--~ar~g  308 (531)
T COG3898         235 AKAMSLLDADPASARDDALEANKL--APDLVPAAVVAARALFRDGNLRKGSKILETAWKAE--PHPDIALLYV--RARSG  308 (531)
T ss_pred             HHHHHHhcCChHHHHHHHHHHhhc--CCccchHHHHHHHHHHhccchhhhhhHHHHHHhcC--CChHHHHHHH--HhcCC
Confidence            221   134566666665555443  565432 2334578899999999999999999875  4444443333  34555


Q ss_pred             ChHHHHHHHHHHhhC-CCCc-hHHHHHHHHHHHhcccChhHHHh--------------HHHHHHHHH-hcCCHHHHHHHH
Q 044084          250 RIRDAMRLVAKMKPK-GCEP-NVWIYNSLMDMHGRAKNLRQLEK--------------YTTVISAYN-MAREFDMCVKFY  312 (343)
Q Consensus       250 ~~~~a~~~~~~m~~~-~~~p-~~~~~~~l~~~~~~~~~~~~a~~--------------~~~l~~~~~-~~g~~~~a~~~~  312 (343)
                      +  .+..-+++.... .++| +......+.++-...|++..|..              |..|.+.-. ..|+-.++..++
T Consensus       309 d--ta~dRlkRa~~L~slk~nnaes~~~va~aAlda~e~~~ARa~Aeaa~r~~pres~~lLlAdIeeAetGDqg~vR~wl  386 (531)
T COG3898         309 D--TALDRLKRAKKLESLKPNNAESSLAVAEAALDAGEFSAARAKAEAAAREAPRESAYLLLADIEEAETGDQGKVRQWL  386 (531)
T ss_pred             C--cHHHHHHHHHHHHhcCccchHHHHHHHHHHHhccchHHHHHHHHHHhhhCchhhHHHHHHHHHhhccCchHHHHHHH
Confidence            4  333333333321 2344 44566667777777888776655              554544433 448888888888


Q ss_pred             HHHHhCCCCc
Q 044084          313 NEFRMNGGVI  322 (343)
Q Consensus       313 ~~m~~~~~~p  322 (343)
                      -+.+..--.|
T Consensus       387 Aqav~APrdP  396 (531)
T COG3898         387 AQAVKAPRDP  396 (531)
T ss_pred             HHHhcCCCCC
Confidence            8877654334

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=92.77  E-value=1.3  Score=28.85  Aligned_cols=49  Identities=12%  Similarity=0.268  Sum_probs=33.4

Q ss_pred             cHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHH
Q 044084          180 AYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQ  228 (343)
Q Consensus       180 ~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  228 (343)
                      +.-++.+-++.+....+.|++....+.+++|-+.+++..|.++|+.++.
T Consensus        22 D~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~   70 (103)
T cd00923          22 DGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKD   70 (103)
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            4445666666666666677777777777777777777777777776663

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.

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=92.38  E-value=7.1  Score=34.12  Aligned_cols=79  Identities=11%  Similarity=0.167  Sum_probs=57.5

Q ss_pred             hhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCC-CCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCc-ChhhHHHHHH
Q 044084          166 CISCVIVNGFSKRRAYWAAVKVYEQLISQGCI-PGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDK-CVVAYSSMVA  243 (343)
Q Consensus       166 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~  243 (343)
                      .+-..+..++.+.|+.++|.+++++|.+.... -.......|+.++...+.+.++..++.+..+...+. -...|+..+-
T Consensus       260 y~KrRLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~lpkSAti~YTaALL  339 (539)
T PF04184_consen  260 YAKRRLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDISLPKSATICYTAALL  339 (539)
T ss_pred             hhHHHHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccccCCchHHHHHHHHHH
Confidence            33445777788899999999999999876321 233466789999999999999999999986544332 2445666553


Q ss_pred             H
Q 044084          244 M  244 (343)
Q Consensus       244 ~  244 (343)
                      -
T Consensus       340 k  340 (539)
T PF04184_consen  340 K  340 (539)
T ss_pred             H
Confidence            3

The molecular function of this protein is uncertain.

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=92.36  E-value=1.3  Score=29.18  Aligned_cols=47  Identities=13%  Similarity=0.222  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHc
Q 044084          183 AAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       183 ~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  229 (343)
                      +..+-++.+....+.|++....+.+++|-+.+++..|.++|+.++..
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K   74 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDK   74 (108)
T ss_dssp             HHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            45555555555556666666666666666666666666666666544

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 ....

>KOG1550 consensus Extracellular protein SEL-1 and related proteins [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=92.28  E-value=8.6  Score=34.91  Aligned_cols=182  Identities=15%  Similarity=0.086  Sum_probs=99.7

Q ss_pred             hhhHHHHHHHHHhCCCCCChhhHHHH--HHH-HHhcCCHHHHHHHHHHHHh-------CCCCCCCchHHHHHHHHHHhhc
Q 044084            3 SQSKLHYYEKMKSAGIVLDSGCYCQI--MEA-FYKIGDSEKVAALFLECES-------RKLDLTPSSTHMYKILCDSLGK   72 (343)
Q Consensus         3 ~~~A~~~~~~~~~~~~~~~~~~~~~l--~~~-~~~~~~~~~a~~~~~~~~~-------~~~~~~~~~~~~~~~li~~~~~   72 (343)
                      ...|.+.++...+.|.. .......+  ... +...++.+.|...|..+.+       ++..+      ....+..+|.+
T Consensus       228 ~~~a~~~~~~~a~~g~~-~a~~~~g~~y~~G~~g~~~d~e~a~~~l~~aa~~~~~~a~~~~~~------a~~~lg~~Y~~  300 (552)
T KOG1550|consen  228 LSEAFKYYREAAKLGHS-EAQYALGICYLAGTYGVTQDLESAIEYLKLAAESFKKAATKGLPP------AQYGLGRLYLQ  300 (552)
T ss_pred             hhHHHHHHHHHHhhcch-HHHHHHHHHHhhccccccccHHHHHHHHHHHHHHHHHHHhhcCCc------cccHHHHHHhc
Confidence            35677777777776631 22222222  222 4466788888888887766       44222      34556666655


Q ss_pred             cC-----cHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhc-ccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH--hcC
Q 044084           73 SG-----RAFEILKFFRDMKEKGILEDPSVYASLICSFAS-IAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYI--EEG  144 (343)
Q Consensus        73 ~~-----~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~--~~~  144 (343)
                      ..     +.+.|..++...-+.|. |+...+-..+..... ..+...|.++|....+.|.. ....+..++-...  ...
T Consensus       301 g~~~~~~d~~~A~~~~~~aA~~g~-~~a~~~lg~~~~~g~~~~d~~~A~~yy~~Aa~~G~~-~A~~~la~~y~~G~gv~r  378 (552)
T KOG1550|consen  301 GLGVEKIDYEKALKLYTKAAELGN-PDAQYLLGVLYETGTKERDYRRAFEYYSLAAKAGHI-LAIYRLALCYELGLGVER  378 (552)
T ss_pred             CCCCccccHHHHHHHHHHHHhcCC-chHHHHHHHHHHcCCccccHHHHHHHHHHHHHcCCh-HHHHHHHHHHHhCCCcCC
Confidence            32     56678888887777653 344333222222222 24567888888888887743 2222222221111  234


Q ss_pred             cHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcC
Q 044084          145 MVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQG  195 (343)
Q Consensus       145 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  195 (343)
                      +...|..++.+..+.+. |...--...+..+.. +.++.+.-.+..+...|
T Consensus       379 ~~~~A~~~~k~aA~~g~-~~A~~~~~~~~~~g~-~~~~~~~~~~~~~a~~g  427 (552)
T KOG1550|consen  379 NLELAFAYYKKAAEKGN-PSAAYLLGAFYEYGV-GRYDTALALYLYLAELG  427 (552)
T ss_pred             CHHHHHHHHHHHHHccC-hhhHHHHHHHHHHcc-ccccHHHHHHHHHHHhh
Confidence            67788888888877774 332222222333333 66666666666666555

>KOG1586 consensus Protein required for fusion of vesicles in vesicular transport, alpha-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=92.12  E-value=4.6  Score=31.42  Aligned_cols=25  Identities=4%  Similarity=0.113  Sum_probs=17.3

Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCcc
Q 044084          299 YNMAREFDMCVKFYNEFRMNGGVID  323 (343)
Q Consensus       299 ~~~~g~~~~a~~~~~~m~~~~~~p~  323 (343)
                      -...+++.+|+++|++.-...+..+
T Consensus       164 aa~leqY~~Ai~iyeqva~~s~~n~  188 (288)
T KOG1586|consen  164 AAQLEQYSKAIDIYEQVARSSLDNN  188 (288)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhccch
Confidence            3456788889999888766544433

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=91.93  E-value=0.74  Score=23.15  Aligned_cols=28  Identities=21%  Similarity=0.268  Sum_probs=14.4

Q ss_pred             HHHHHHHHHHhcCcHhHHHHHHHHHHhc
Q 044084          132 VFLKLVLMYIEEGMVEKTLEVVESMKNA  159 (343)
Q Consensus       132 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~  159 (343)
                      +|..+...|...|++++|+..|++..+.
T Consensus         3 ~~~~~g~~~~~~~~~~~A~~~~~~al~~   30 (34)
T PF00515_consen    3 AYYNLGNAYFQLGDYEEALEYYQRALEL   30 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHHH
Confidence            4445555555555555555555555443

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 ....

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=91.67  E-value=2.6  Score=27.56  Aligned_cols=63  Identities=11%  Similarity=0.102  Sum_probs=47.3

Q ss_pred             ChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHH
Q 044084          215 LYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMD  278 (343)
Q Consensus       215 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~  278 (343)
                      +.-++.+-++.+...++.|++....+.+++|.+.+++..|.++|+-.+.+ +..+...|..+++
T Consensus        22 D~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K-~~~~~~~y~~~lq   84 (103)
T cd00923          22 DGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDK-CGAHKEIYPYILQ   84 (103)
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-ccCchhhHHHHHH
Confidence            45566777777777888899999999999999999999999999887754 2223445555543

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.

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=91.46  E-value=5.3  Score=30.75  Aligned_cols=29  Identities=17%  Similarity=0.185  Sum_probs=15.4

Q ss_pred             hhHHHHHHHHHccCChHHHHHHHHHHhhC
Q 044084          236 VAYSSMVAMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       236 ~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                      .||--+...+...|+.++|..+|+-.+..
T Consensus       238 EtyFYL~K~~l~~G~~~~A~~LfKLaian  266 (297)
T COG4785         238 ETYFYLGKYYLSLGDLDEATALFKLAVAN  266 (297)
T ss_pred             HHHHHHHHHHhccccHHHHHHHHHHHHHH
Confidence            34555555555555555555555555443

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=91.45  E-value=8.6  Score=33.18  Aligned_cols=49  Identities=10%  Similarity=0.123  Sum_probs=31.4

Q ss_pred             ChhHHHHHHHHHHHcCCCc----ChhhHHHHHHHHHccCChHHHHHHHHHHhh
Q 044084          215 LYSKAEKVFIEMQQKGFDK----CVVAYSSMVAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       215 ~~~~a~~~~~~~~~~~~~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                      +.+++..+-+.+....+.+    =..++..++....+.++...|.+.+.-+.-
T Consensus       274 ~~e~~~~~ce~ia~~~i~~Lke~li~~F~~~Ls~~Vk~~~T~~a~q~l~lL~~  326 (549)
T PF07079_consen  274 DPEQVGHFCEAIASSKIEKLKEELIDRFGNLLSFKVKQVQTEEAKQYLALLKI  326 (549)
T ss_pred             ChHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Confidence            5556665555554432211    145677788888888888888887766654

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=91.39  E-value=0.35  Score=24.62  Aligned_cols=21  Identities=24%  Similarity=0.463  Sum_probs=10.7

Q ss_pred             ChhhHHHHHHHHHccCChHHH
Q 044084          234 CVVAYSSMVAMYGKTGRIRDA  254 (343)
Q Consensus       234 ~~~~~~~l~~~~~~~~~~~~a  254 (343)
                      +...|+.+...|...|++++|
T Consensus        12 n~~a~~nla~~~~~~g~~~~A   32 (34)
T PF13431_consen   12 NAEAYNNLANLYLNQGDYEEA   32 (34)
T ss_pred             CHHHHHHHHHHHHHCcCHHhh
Confidence            444555555555555555544

>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=91.10  E-value=4.8  Score=29.65  Aligned_cols=132  Identities=11%  Similarity=0.112  Sum_probs=76.1

Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCC--cHHHHHHHHHHHHH
Q 044084          116 ELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRR--AYWAAVKVYEQLIS  193 (343)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~  193 (343)
                      +.++.+.+.++.|+...+..+++.+.+.|++....    .+.+.++-+|.......+-.+....  -..-+.+++.++..
T Consensus        15 EYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~L~----qllq~~Vi~DSk~lA~~LLs~~~~~~~~~Ql~lDMLkRL~~   90 (167)
T PF07035_consen   15 EYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQLH----QLLQYHVIPDSKPLACQLLSLGNQYPPAYQLGLDMLKRLGT   90 (167)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHHHH----HHHhhcccCCcHHHHHHHHHhHccChHHHHHHHHHHHHhhh
Confidence            44555667788888888888888888888765544    3444444455444333332222211  13344555555442


Q ss_pred             cCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhh
Q 044084          194 QGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       194 ~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                              .+..++..+...|++-+|.++.+......    ......++.+-.+.++...-..+++-..+
T Consensus        91 --------~~~~iievLL~~g~vl~ALr~ar~~~~~~----~~~~~~fLeAA~~~~D~~lf~~V~~ff~~  148 (167)
T PF07035_consen   91 --------AYEEIIEVLLSKGQVLEALRYARQYHKVD----SVPARKFLEAAANSNDDQLFYAVFRFFEE  148 (167)
T ss_pred             --------hHHHHHHHHHhCCCHHHHHHHHHHcCCcc----cCCHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                    24556677788888888888776653321    22234566666666666555555555444

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=91.07  E-value=0.93  Score=22.63  Aligned_cols=28  Identities=21%  Similarity=0.248  Sum_probs=15.7

Q ss_pred             HHHHHHHHHHhcCcHhHHHHHHHHHHhc
Q 044084          132 VFLKLVLMYIEEGMVEKTLEVVESMKNA  159 (343)
Q Consensus       132 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~  159 (343)
                      .+..+...+...|++++|++.|++..+.
T Consensus         3 ~~~~lg~~~~~~~~~~~A~~~~~~al~l   30 (34)
T PF07719_consen    3 AWYYLGQAYYQLGNYEEAIEYFEKALEL   30 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            4455555666666666666666665543

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=91.00  E-value=1.1  Score=29.48  Aligned_cols=61  Identities=11%  Similarity=0.131  Sum_probs=41.5

Q ss_pred             hHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHH
Q 044084          217 SKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMD  278 (343)
Q Consensus       217 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~  278 (343)
                      -+..+-++.+...++.|++....+.+++|.+.+++..|.++|+-++.+ +.+....|..+++
T Consensus        27 we~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K-~~~~~~~Y~~~lq   87 (108)
T PF02284_consen   27 WELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDK-CGNKKEIYPYILQ   87 (108)
T ss_dssp             HHHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TTT-TTHHHHHHH
T ss_pred             HHHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-ccChHHHHHHHHH
Confidence            356666677777788899999999999999999999999999888765 2222225555544

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 ....

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

Probab=90.84  E-value=0.84  Score=24.14  Aligned_cols=27  Identities=26%  Similarity=0.359  Sum_probs=15.3

Q ss_pred             HHHHHHHHHHHhcCcHhHHHHHHHHHH
Q 044084          131 EVFLKLVLMYIEEGMVEKTLEVVESMK  157 (343)
Q Consensus       131 ~~~~~l~~~~~~~~~~~~a~~~~~~~~  157 (343)
                      .+++.|...|...|++++|..++++..
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al   29 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEAL   29 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHH
Confidence            345556666666666666666665543

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=90.55  E-value=4.7  Score=30.59  Aligned_cols=78  Identities=19%  Similarity=0.182  Sum_probs=58.5

Q ss_pred             hcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHh---cCCCCchhhHHHHHHHHhcCCcHH
Q 044084          106 ASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKN---AELNISDCISCVIVNGFSKRRAYW  182 (343)
Q Consensus       106 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~~~~~l~~~~~~~~~~~  182 (343)
                      .+.|+ +.|...|-.+...+.--++.....|...|. ..+.++++.++....+   .+-.+|+..+..|+..+.+.|+++
T Consensus       118 sr~~d-~~A~~~fL~~E~~~~l~t~elq~aLAtyY~-krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~e  195 (203)
T PF11207_consen  118 SRFGD-QEALRRFLQLEGTPELETAELQYALATYYT-KRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNYE  195 (203)
T ss_pred             hccCc-HHHHHHHHHHcCCCCCCCHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcchh
Confidence            34444 677888888877766556776666666665 6778999999888764   233577888999999999999998


Q ss_pred             HHH
Q 044084          183 AAV  185 (343)
Q Consensus       183 ~a~  185 (343)
                      .|.
T Consensus       196 ~AY  198 (203)
T PF11207_consen  196 QAY  198 (203)
T ss_pred             hhh
Confidence            885

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=90.39  E-value=6.4  Score=29.88  Aligned_cols=88  Identities=13%  Similarity=0.081  Sum_probs=39.0

Q ss_pred             hcccCHHHHHHHHHHHHHcCCCCC----HHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcH
Q 044084          106 ASIAEVKVAEELFKEAEEKGMLRD----LEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAY  181 (343)
Q Consensus       106 ~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  181 (343)
                      .+.|++++|..-|...+...+...    ...|..-..++.+.+.++.|++--.+..+.++ ........-..+|.+..++
T Consensus       106 F~ngdyeeA~skY~~Ale~cp~~~~e~rsIly~Nraaa~iKl~k~e~aI~dcsKaiel~p-ty~kAl~RRAeayek~ek~  184 (271)
T KOG4234|consen  106 FKNGDYEEANSKYQEALESCPSTSTEERSILYSNRAAALIKLRKWESAIEDCSKAIELNP-TYEKALERRAEAYEKMEKY  184 (271)
T ss_pred             hhcccHHHHHHHHHHHHHhCccccHHHHHHHHhhhHHHHHHhhhHHHHHHHHHhhHhcCc-hhHHHHHHHHHHHHhhhhH
Confidence            345555555555555554432211    12233333444555555555554444444433 1111111223345555555


Q ss_pred             HHHHHHHHHHHHc
Q 044084          182 WAAVKVYEQLISQ  194 (343)
Q Consensus       182 ~~a~~~~~~~~~~  194 (343)
                      +.|+.=|..+...
T Consensus       185 eealeDyKki~E~  197 (271)
T KOG4234|consen  185 EEALEDYKKILES  197 (271)
T ss_pred             HHHHHHHHHHHHh
Confidence            5555555555544

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=89.66  E-value=8.6  Score=30.25  Aligned_cols=203  Identities=11%  Similarity=0.130  Sum_probs=103.8

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLM  139 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  139 (343)
                      ...|..-..+|...+++++|-..+.+..+. ..-+...|.       ..+.++.|.-+.+++.+..  --+..|+.-...
T Consensus        31 as~yekAAvafRnAk~feKakdcLlkA~~~-yEnnrslfh-------AAKayEqaamLake~~kls--Evvdl~eKAs~l  100 (308)
T KOG1585|consen   31 ASLYEKAAVAFRNAKKFEKAKDCLLKASKG-YENNRSLFH-------AAKAYEQAAMLAKELSKLS--EVVDLYEKASEL  100 (308)
T ss_pred             HHHHHHHHHHHHhhccHHHHHHHHHHHHHH-HHhcccHHH-------HHHHHHHHHHHHHHHHHhH--HHHHHHHHHHHH
Confidence            455666667777778888877766665431 121222222       1233455555555554421  124455666667


Q ss_pred             HHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHc---C--CCCCHhhHHHHHHHHHccC
Q 044084          140 YIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQ---G--CIPGQVTYASIINAYCRIG  214 (343)
Q Consensus       140 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~--~~p~~~~~~~ll~~~~~~~  214 (343)
                      |..+|.++.|-..+++.-+.                ..+.+++.|+++|++...-   +  ..--...+...-+.+.+..
T Consensus       101 Y~E~GspdtAAmaleKAak~----------------lenv~Pd~AlqlYqralavve~~dr~~ma~el~gk~sr~lVrl~  164 (308)
T KOG1585|consen  101 YVECGSPDTAAMALEKAAKA----------------LENVKPDDALQLYQRALAVVEEDDRDQMAFELYGKCSRVLVRLE  164 (308)
T ss_pred             HHHhCCcchHHHHHHHHHHH----------------hhcCCHHHHHHHHHHHHHHHhccchHHHHHHHHHHhhhHhhhhH
Confidence            77777777666666654321                2234455555555554321   0  0001122333445556666


Q ss_pred             ChhHHHHHHHHHHHc----CCCcCh-hhHHHHHHHHHccCChHHHHHHHHHHhhCC---CCchHHHHHHHHHHHhcccCh
Q 044084          215 LYSKAEKVFIEMQQK----GFDKCV-VAYSSMVAMYGKTGRIRDAMRLVAKMKPKG---CEPNVWIYNSLMDMHGRAKNL  286 (343)
Q Consensus       215 ~~~~a~~~~~~~~~~----~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~---~~p~~~~~~~l~~~~~~~~~~  286 (343)
                      ++++|-..|.+-...    .--++. ..|-..|-.|.-..++..|...++.--+.+   -.-+..+...|+.+|- .|+.
T Consensus       165 kf~Eaa~a~lKe~~~~~~~~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~sed~r~lenLL~ayd-~gD~  243 (308)
T KOG1585|consen  165 KFTEAATAFLKEGVAADKCDAYNSQCKAYVAAILVYLYAHDYVQAEKCYRDCSQIPAFLKSEDSRSLENLLTAYD-EGDI  243 (308)
T ss_pred             HhhHHHHHHHHhhhHHHHHhhcccHHHHHHHHHHHHhhHHHHHHHHHHhcchhcCccccChHHHHHHHHHHHHhc-cCCH
Confidence            666665544432211    101111 235555666667778888888887744331   1235566777777665 3444


Q ss_pred             hHH
Q 044084          287 RQL  289 (343)
Q Consensus       287 ~~a  289 (343)
                      +++
T Consensus       244 E~~  246 (308)
T KOG1585|consen  244 EEI  246 (308)
T ss_pred             HHH
Confidence            443

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

Probab=89.65  E-value=0.93  Score=23.96  Aligned_cols=28  Identities=21%  Similarity=0.297  Sum_probs=16.6

Q ss_pred             HHHHHHHHHhhccCcHHHHHHHHHHHHh
Q 044084           61 HMYKILCDSLGKSGRAFEILKFFRDMKE   88 (343)
Q Consensus        61 ~~~~~li~~~~~~~~~~~a~~~~~~~~~   88 (343)
                      .+++.|...|...|++++|..++++...
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            4556666666666666666666666543

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=89.62  E-value=0.99  Score=22.65  Aligned_cols=27  Identities=22%  Similarity=0.274  Sum_probs=13.9

Q ss_pred             HHHHHHHHhhccCcHHHHHHHHHHHHh
Q 044084           62 MYKILCDSLGKSGRAFEILKFFRDMKE   88 (343)
Q Consensus        62 ~~~~li~~~~~~~~~~~a~~~~~~~~~   88 (343)
                      +|..+...+...|++++|+..|++.++
T Consensus         3 ~~~~~g~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF00515_consen    3 AYYNLGNAYFQLGDYEEALEYYQRALE   29 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHH
Confidence            445555555555555555555555544

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 ....

>KOG1550 consensus Extracellular protein SEL-1 and related proteins [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=89.60  E-value=16  Score=33.25  Aligned_cols=182  Identities=15%  Similarity=0.164  Sum_probs=117.1

Q ss_pred             HHHHHHHHHHHHhCCCCCCCchHHHHHHHH--HH-hhccCcHHHHHHHHHHHHh-------cCCCCChHhHHHHHHHHhc
Q 044084           38 SEKVAALFLECESRKLDLTPSSTHMYKILC--DS-LGKSGRAFEILKFFRDMKE-------KGILEDPSVYASLICSFAS  107 (343)
Q Consensus        38 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~li--~~-~~~~~~~~~a~~~~~~~~~-------~~~~~~~~~~~~l~~~~~~  107 (343)
                      ...|.+.++...+.+....    .....++  .+ +....+++.|+.+|+...+       .|   ......-+..+|.+
T Consensus       228 ~~~a~~~~~~~a~~g~~~a----~~~~g~~y~~G~~g~~~d~e~a~~~l~~aa~~~~~~a~~~---~~~a~~~lg~~Y~~  300 (552)
T KOG1550|consen  228 LSEAFKYYREAAKLGHSEA----QYALGICYLAGTYGVTQDLESAIEYLKLAAESFKKAATKG---LPPAQYGLGRLYLQ  300 (552)
T ss_pred             hhHHHHHHHHHHhhcchHH----HHHHHHHHhhccccccccHHHHHHHHHHHHHHHHHHHhhc---CCccccHHHHHHhc
Confidence            4678888888877775322    1122222  22 4566789999999999877       44   33345556666665


Q ss_pred             cc-----CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh-cCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHh--cCC
Q 044084          108 IA-----EVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIE-EGMVEKTLEVVESMKNAELNISDCISCVIVNGFS--KRR  179 (343)
Q Consensus       108 ~~-----~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~--~~~  179 (343)
                      ..     +.+.|..++.+..+.|. |+....-..+..... ..+...|.++|....+.|.. ....+.+++....  ...
T Consensus       301 g~~~~~~d~~~A~~~~~~aA~~g~-~~a~~~lg~~~~~g~~~~d~~~A~~yy~~Aa~~G~~-~A~~~la~~y~~G~gv~r  378 (552)
T KOG1550|consen  301 GLGVEKIDYEKALKLYTKAAELGN-PDAQYLLGVLYETGTKERDYRRAFEYYSLAAKAGHI-LAIYRLALCYELGLGVER  378 (552)
T ss_pred             CCCCccccHHHHHHHHHHHHhcCC-chHHHHHHHHHHcCCccccHHHHHHHHHHHHHcCCh-HHHHHHHHHHHhCCCcCC
Confidence            42     67889999999999885 465554444433333 34678999999999998873 3332322222222  345


Q ss_pred             cHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcC
Q 044084          180 AYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKG  230 (343)
Q Consensus       180 ~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  230 (343)
                      +...|..++.+..+.| .|...--...+..+.. ++++.+.-.+..+.+.|
T Consensus       379 ~~~~A~~~~k~aA~~g-~~~A~~~~~~~~~~g~-~~~~~~~~~~~~~a~~g  427 (552)
T KOG1550|consen  379 NLELAFAYYKKAAEKG-NPSAAYLLGAFYEYGV-GRYDTALALYLYLAELG  427 (552)
T ss_pred             CHHHHHHHHHHHHHcc-ChhhHHHHHHHHHHcc-ccccHHHHHHHHHHHhh
Confidence            7899999999999988 4443333334444555 77777777777776665

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=89.37  E-value=8.4  Score=29.72  Aligned_cols=189  Identities=13%  Similarity=0.072  Sum_probs=100.3

Q ss_pred             ccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHH
Q 044084          108 IAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKV  187 (343)
Q Consensus       108 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  187 (343)
                      .|-+..|.--|.+.....+. -+.+||.|.--+...|+++.|.+.|+...+.++.-+-...|.=| ++.-.|++.-|.+=
T Consensus        78 lGL~~LAR~DftQaLai~P~-m~~vfNyLG~Yl~~a~~fdaa~eaFds~~ELDp~y~Ya~lNRgi-~~YY~gR~~LAq~d  155 (297)
T COG4785          78 LGLRALARNDFSQALAIRPD-MPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGI-ALYYGGRYKLAQDD  155 (297)
T ss_pred             hhHHHHHhhhhhhhhhcCCC-cHHHHHHHHHHHHhcccchHHHHHhhhHhccCCcchHHHhccce-eeeecCchHhhHHH
Confidence            34444454455555543322 47889999999999999999999999998877533222222212 23346888888877


Q ss_pred             HHHHHHcCCCCCHhhHHHH-HHHHHccCChhHHHHHHHH-HHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCC
Q 044084          188 YEQLISQGCIPGQVTYASI-INAYCRIGLYSKAEKVFIE-MQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKG  265 (343)
Q Consensus       188 ~~~~~~~~~~p~~~~~~~l-l~~~~~~~~~~~a~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~  265 (343)
                      +-..-+.. +.|+  |.++ +-.--+.-++.+|..-+.+ ..+    .|..-|...|-.|. .|++. ...+++++... 
T Consensus       156 ~~~fYQ~D-~~DP--fR~LWLYl~E~k~dP~~A~tnL~qR~~~----~d~e~WG~~iV~~y-LgkiS-~e~l~~~~~a~-  225 (297)
T COG4785         156 LLAFYQDD-PNDP--FRSLWLYLNEQKLDPKQAKTNLKQRAEK----SDKEQWGWNIVEFY-LGKIS-EETLMERLKAD-  225 (297)
T ss_pred             HHHHHhcC-CCCh--HHHHHHHHHHhhCCHHHHHHHHHHHHHh----ccHhhhhHHHHHHH-Hhhcc-HHHHHHHHHhh-
Confidence            77666553 1122  2211 1111233456666543332 222    23334433333222 12221 12333444332 


Q ss_pred             CCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCC
Q 044084          266 CEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGG  320 (343)
Q Consensus       266 ~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~  320 (343)
                      -..+...-..|-..            |--+..-+...|+.++|..+|+-....++
T Consensus       226 a~~n~~~Ae~LTEt------------yFYL~K~~l~~G~~~~A~~LfKLaiannV  268 (297)
T COG4785         226 ATDNTSLAEHLTET------------YFYLGKYYLSLGDLDEATALFKLAVANNV  268 (297)
T ss_pred             ccchHHHHHHHHHH------------HHHHHHHHhccccHHHHHHHHHHHHHHhH
Confidence            12122222223233            44456667788899999999988776544

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=89.30  E-value=0.82  Score=22.86  Aligned_cols=27  Identities=19%  Similarity=0.247  Sum_probs=14.6

Q ss_pred             hHHHHHHHHHccCChHHHHHHHHHHhh
Q 044084          237 AYSSMVAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       237 ~~~~l~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                      .|..+...+...|++++|.+.|++..+
T Consensus         3 ~~~~lg~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF07719_consen    3 AWYYLGQAYYQLGNYEEAIEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            344455555566666666666655554

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=88.80  E-value=21  Score=33.68  Aligned_cols=181  Identities=10%  Similarity=0.015  Sum_probs=104.2

Q ss_pred             HHHhcCcHhHHHHHHHHHHhcCCCCchh-------hHHHHHH-HHhcCCcHHHHHHHHHHHHHc----CCCCCHhhHHHH
Q 044084          139 MYIEEGMVEKTLEVVESMKNAELNISDC-------ISCVIVN-GFSKRRAYWAAVKVYEQLISQ----GCIPGQVTYASI  206 (343)
Q Consensus       139 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~-------~~~~l~~-~~~~~~~~~~a~~~~~~~~~~----~~~p~~~~~~~l  206 (343)
                      ......++++|..+..+....-..|+..       .++.+-. .....|+++.+.++-+.....    -..+....+..+
T Consensus       424 ~~~s~~r~~ea~~li~~l~~~l~~~~~~~~~~l~ae~~aL~a~val~~~~~e~a~~lar~al~~L~~~~~~~r~~~~sv~  503 (894)
T COG2909         424 LLASQHRLAEAETLIARLEHFLKAPMHSRQGDLLAEFQALRAQVALNRGDPEEAEDLARLALVQLPEAAYRSRIVALSVL  503 (894)
T ss_pred             HHHHccChHHHHHHHHHHHHHhCcCcccchhhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhcccccchhhhhhhhhh
Confidence            3445678999999988876543322221       2333322 234478899999888877654    223445556667


Q ss_pred             HHHHHccCChhHHHHHHHHHHHcCCCcChhh---HHHHH--HHHHccCChH--HHHHHHHHHhhC-----C-CCchHHHH
Q 044084          207 INAYCRIGLYSKAEKVFIEMQQKGFDKCVVA---YSSMV--AMYGKTGRIR--DAMRLVAKMKPK-----G-CEPNVWIY  273 (343)
Q Consensus       207 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~~~l~--~~~~~~~~~~--~a~~~~~~m~~~-----~-~~p~~~~~  273 (343)
                      ..+..-.|++++|..+.....+..-..++..   |..+.  ..+...|+..  +....|......     . ..+-..+.
T Consensus       504 ~~a~~~~G~~~~Al~~~~~a~~~a~~~~~~~l~~~~~~~~s~il~~qGq~~~a~~~~~~~~~~~q~l~q~~~~~f~~~~r  583 (894)
T COG2909         504 GEAAHIRGELTQALALMQQAEQMARQHDVYHLALWSLLQQSEILEAQGQVARAEQEKAFNLIREQHLEQKPRHEFLVRIR  583 (894)
T ss_pred             hHHHHHhchHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhcccchhHHHHH
Confidence            7777888999999988887665422233333   33332  2345566332  223333333221     1 01233445


Q ss_pred             HHHHHHHhcc-cChhHHHh------------------HHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 044084          274 NSLMDMHGRA-KNLRQLEK------------------YTTVISAYNMAREFDMCVKFYNEFRMNG  319 (343)
Q Consensus       274 ~~l~~~~~~~-~~~~~a~~------------------~~~l~~~~~~~g~~~~a~~~~~~m~~~~  319 (343)
                      ..+..++.+. +...++..                  +..|+......|++++|...++++....
T Consensus       584 ~~ll~~~~r~~~~~~ear~~~~~~~~~~~~~~~~~~~~~~LA~l~~~~Gdl~~A~~~l~~~~~l~  648 (894)
T COG2909         584 AQLLRAWLRLDLAEAEARLGIEVGSVYTPQPLLSRLALSMLAELEFLRGDLDKALAQLDELERLL  648 (894)
T ss_pred             HHHHHHHHHHhhhhHHhhhcchhhhhcccchhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHh
Confidence            5566666551 11111111                  3467788889999999999999886543

>cd08819 CARD_MDA5_2 Caspase activation and recruitment domain found in MDA5, second repeat

Probab=88.52  E-value=3.6  Score=26.34  Aligned_cols=64  Identities=8%  Similarity=0.122  Sum_probs=28.4

Q ss_pred             HHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHH
Q 044084           42 AALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVA  114 (343)
Q Consensus        42 ~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  114 (343)
                      .++++.+.++++-..    .....+-.+-...|+.+.|.+++..+. .|  |+  .|...+.++-..|.-+-|
T Consensus        22 ~~v~d~ll~~~ilT~----~d~e~I~aa~~~~g~~~~ar~LL~~L~-rg--~~--aF~~Fl~aLreT~~~~LA   85 (88)
T cd08819          22 RDVCDKCLEQGLLTE----EDRNRIEAATENHGNESGARELLKRIV-QK--EG--WFSKFLQALRETEHHELA   85 (88)
T ss_pred             HHHHHHHHhcCCCCH----HHHHHHHHhccccCcHHHHHHHHHHhc-cC--Cc--HHHHHHHHHHHcCchhhh
Confidence            345555555553322    222322222234455555566655555 43  22  244455555555444333

Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), second repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protei

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=88.16  E-value=12  Score=30.20  Aligned_cols=61  Identities=8%  Similarity=-0.057  Sum_probs=29.0

Q ss_pred             CCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhc-CCCCchhhHHHHHHHHhcCCcHHHHHHHH
Q 044084          128 RDLEVFLKLVLMYIEEGMVEKTLEVVESMKNA-ELNISDCISCVIVNGFSKRRAYWAAVKVY  188 (343)
Q Consensus       128 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  188 (343)
                      ++..+...++..+++.+++.+-.++++..... ++..|...|..+|......|+..-..++.
T Consensus       200 l~~~vi~~Il~~L~~~~dW~kl~~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~kiI  261 (292)
T PF13929_consen  200 LTRNVIISILEILAESRDWNKLFQFWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRKII  261 (292)
T ss_pred             CChhHHHHHHHHHHhcccHHHHHHHHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHHHh
Confidence            34444445555555555555555555444332 33334444555555555555544444433

>PRK09687 putative lyase; Provisional

Probab=87.89  E-value=13  Score=30.24  Aligned_cols=234  Identities=12%  Similarity=0.043  Sum_probs=121.8

Q ss_pred             CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcH----HHHHHHHHHHHhcCCCCCh
Q 044084           20 LDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRA----FEILKFFRDMKEKGILEDP   95 (343)
Q Consensus        20 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~----~~a~~~~~~~~~~~~~~~~   95 (343)
                      +|.......+..+...|..+ +...+..+....   +   ...-...+.++++.|+.    .++...+..+...  .|+.
T Consensus        35 ~d~~vR~~A~~aL~~~~~~~-~~~~l~~ll~~~---d---~~vR~~A~~aLg~lg~~~~~~~~a~~~L~~l~~~--D~d~  105 (280)
T PRK09687         35 HNSLKRISSIRVLQLRGGQD-VFRLAIELCSSK---N---PIERDIGADILSQLGMAKRCQDNVFNILNNLALE--DKSA  105 (280)
T ss_pred             CCHHHHHHHHHHHHhcCcch-HHHHHHHHHhCC---C---HHHHHHHHHHHHhcCCCccchHHHHHHHHHHHhc--CCCH
Confidence            44555555566666666533 333333332211   1   23444556666666653    4566666666433  3455


Q ss_pred             HhHHHHHHHHhcccCH-----HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHH
Q 044084           96 SVYASLICSFASIAEV-----KVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCV  170 (343)
Q Consensus        96 ~~~~~l~~~~~~~~~~-----~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  170 (343)
                      ..-...+.++...+..     ..+...+.....   .++..+-...+.++.+.++ ++++..+-.+.+.   ++...-..
T Consensus       106 ~VR~~A~~aLG~~~~~~~~~~~~a~~~l~~~~~---D~~~~VR~~a~~aLg~~~~-~~ai~~L~~~L~d---~~~~VR~~  178 (280)
T PRK09687        106 CVRASAINATGHRCKKNPLYSPKIVEQSQITAF---DKSTNVRFAVAFALSVIND-EAAIPLLINLLKD---PNGDVRNW  178 (280)
T ss_pred             HHHHHHHHHHhcccccccccchHHHHHHHHHhh---CCCHHHHHHHHHHHhccCC-HHHHHHHHHHhcC---CCHHHHHH
Confidence            5454555555544321     122233322222   2466666677777777776 4566666665543   23233334


Q ss_pred             HHHHHhcCC-cHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccC
Q 044084          171 IVNGFSKRR-AYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTG  249 (343)
Q Consensus       171 l~~~~~~~~-~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  249 (343)
                      -+.++...+ +...+...+..+..   .++..+-...+.++.+.|+. .+...+-...+.+   +  .....+.++...|
T Consensus       179 A~~aLg~~~~~~~~~~~~L~~~L~---D~~~~VR~~A~~aLg~~~~~-~av~~Li~~L~~~---~--~~~~a~~ALg~ig  249 (280)
T PRK09687        179 AAFALNSNKYDNPDIREAFVAMLQ---DKNEEIRIEAIIGLALRKDK-RVLSVLIKELKKG---T--VGDLIIEAAGELG  249 (280)
T ss_pred             HHHHHhcCCCCCHHHHHHHHHHhc---CCChHHHHHHHHHHHccCCh-hHHHHHHHHHcCC---c--hHHHHHHHHHhcC
Confidence            444444432 23355555555553   35666666777777777774 4444444444433   2  2345667777777


Q ss_pred             ChHHHHHHHHHHhhCCCCchHHHHHHHHHHHh
Q 044084          250 RIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHG  281 (343)
Q Consensus       250 ~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~  281 (343)
                      .. +|...+..+.+.  .||..+-...+.+|.
T Consensus       250 ~~-~a~p~L~~l~~~--~~d~~v~~~a~~a~~  278 (280)
T PRK09687        250 DK-TLLPVLDTLLYK--FDDNEIITKAIDKLK  278 (280)
T ss_pred             CH-hHHHHHHHHHhh--CCChhHHHHHHHHHh
Confidence            74 577777777754  446666555555543

>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A

Probab=87.89  E-value=2.1  Score=21.35  Aligned_cols=27  Identities=26%  Similarity=0.340  Sum_probs=17.5

Q ss_pred             HHHHHHHHHHhcCcHhHHHHHHHHHHh
Q 044084          132 VFLKLVLMYIEEGMVEKTLEVVESMKN  158 (343)
Q Consensus       132 ~~~~l~~~~~~~~~~~~a~~~~~~~~~  158 (343)
                      +|..+...|...|++++|.+.|++..+
T Consensus         3 ~~~~lg~~y~~~~~~~~A~~~~~~a~~   29 (34)
T PF13181_consen    3 AYYNLGKIYEQLGDYEEALEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHTTSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            455666666667777777776666554

...

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=87.68  E-value=7  Score=30.15  Aligned_cols=77  Identities=8%  Similarity=0.009  Sum_probs=52.3

Q ss_pred             hHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcC--CCcChhhHHHHHHH
Q 044084          167 ISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKG--FDKCVVAYSSMVAM  244 (343)
Q Consensus       167 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~  244 (343)
                      |.+..++.+.+.+...+++.+.++-.+.+ +.|..+-..+++.+|-.|++++|..-++-.-+..  ..+-..+|..+|.+
T Consensus         3 Tl~~t~seLL~~~sL~dai~~a~~qVkak-Ptda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l~p~~t~~a~lyr~lir~   81 (273)
T COG4455           3 TLRDTISELLDDNSLQDAIGLARDQVKAK-PTDAGGRHFLFQLLCVAGDWEKALAQLNLAATLSPQDTVGASLYRHLIRC   81 (273)
T ss_pred             chHHHHHHHHHhccHHHHHHHHHHHHhcC-CccccchhHHHHHHhhcchHHHHHHHHHHHhhcCcccchHHHHHHHHHHH
Confidence            44556677778888888888887776663 3455556677888888888888887776665542  22335566666654

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=87.62  E-value=1.9  Score=23.54  Aligned_cols=23  Identities=17%  Similarity=0.323  Sum_probs=11.4

Q ss_pred             HHHHHHccCChHHHHHHHHHHhh
Q 044084          241 MVAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       241 l~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                      +..+|...|+.+.|.+++++...
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~   27 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIE   27 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHH
Confidence            34445555555555555555443

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.

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=87.59  E-value=8.5  Score=27.64  Aligned_cols=20  Identities=10%  Similarity=0.328  Sum_probs=9.2

Q ss_pred             HHhcCcHhHHHHHHHHHHhc
Q 044084          140 YIEEGMVEKTLEVVESMKNA  159 (343)
Q Consensus       140 ~~~~~~~~~a~~~~~~~~~~  159 (343)
                      +...|+|++|.++|+.+.+.
T Consensus        54 ~i~rg~w~eA~rvlr~l~~~   73 (153)
T TIGR02561        54 LIARGNYDEAARILRELLSS   73 (153)
T ss_pred             HHHcCCHHHHHHHHHhhhcc
Confidence            34444444444444444433

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]

Probab=87.55  E-value=1.8  Score=35.55  Aligned_cols=52  Identities=17%  Similarity=0.096  Sum_probs=30.4

Q ss_pred             HHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHH
Q 044084          208 NAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAK  260 (343)
Q Consensus       208 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  260 (343)
                      +-|.++|.+++|+..+..-.... +.|.+++..-..+|.+..++..|..--..
T Consensus       105 N~yFKQgKy~EAIDCYs~~ia~~-P~NpV~~~NRA~AYlk~K~FA~AE~DC~~  156 (536)
T KOG4648|consen  105 NTYFKQGKYEEAIDCYSTAIAVY-PHNPVYHINRALAYLKQKSFAQAEEDCEA  156 (536)
T ss_pred             hhhhhccchhHHHHHhhhhhccC-CCCccchhhHHHHHHHHHHHHHHHHhHHH
Confidence            34666667777766666655542 22666666666666666666655543333

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=87.43  E-value=12  Score=33.64  Aligned_cols=133  Identities=16%  Similarity=0.112  Sum_probs=88.1

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHH
Q 044084           23 GCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLI  102 (343)
Q Consensus        23 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  102 (343)
                      ..-+.+.+.+.+.|-.++|+++-       .+|+    .-|.    ...+.|+++.|.++..+..      +..-|..|.
T Consensus       615 ~~rt~va~Fle~~g~~e~AL~~s-------~D~d----~rFe----lal~lgrl~iA~~la~e~~------s~~Kw~~Lg  673 (794)
T KOG0276|consen  615 EIRTKVAHFLESQGMKEQALELS-------TDPD----QRFE----LALKLGRLDIAFDLAVEAN------SEVKWRQLG  673 (794)
T ss_pred             hhhhhHHhHhhhccchHhhhhcC-------CChh----hhhh----hhhhcCcHHHHHHHHHhhc------chHHHHHHH
Confidence            35667778888888888877642       2222    2232    3346788888887766542      455688888


Q ss_pred             HHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHH
Q 044084          103 CSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYW  182 (343)
Q Consensus       103 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  182 (343)
                      .+....+++..|.+.|.....         |..|+-.+...|+.+....+-....+.|. .|. .    .-+|...|+++
T Consensus       674 ~~al~~~~l~lA~EC~~~a~d---------~~~LlLl~t~~g~~~~l~~la~~~~~~g~-~N~-A----F~~~~l~g~~~  738 (794)
T KOG0276|consen  674 DAALSAGELPLASECFLRARD---------LGSLLLLYTSSGNAEGLAVLASLAKKQGK-NNL-A----FLAYFLSGDYE  738 (794)
T ss_pred             HHHhhcccchhHHHHHHhhcc---------hhhhhhhhhhcCChhHHHHHHHHHHhhcc-cch-H----HHHHHHcCCHH
Confidence            888899999988888876553         34566677777776666666666666654 332 2    23455678888


Q ss_pred             HHHHHHHHH
Q 044084          183 AAVKVYEQL  191 (343)
Q Consensus       183 ~a~~~~~~~  191 (343)
                      ++.+++..-
T Consensus       739 ~C~~lLi~t  747 (794)
T KOG0276|consen  739 ECLELLIST  747 (794)
T ss_pred             HHHHHHHhc
Confidence            888777653

>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

Probab=87.39  E-value=14  Score=29.94  Aligned_cols=70  Identities=13%  Similarity=0.099  Sum_probs=48.7

Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhh-----CCCCchHHH
Q 044084          202 TYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKP-----KGCEPNVWI  272 (343)
Q Consensus       202 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~-----~~~~p~~~~  272 (343)
                      +++...+.|..+|.+.+|.++.+.....+ +.+...+-.++..+...|+--.+..-++++.+     .|+..|...
T Consensus       281 llgkva~~yle~g~~neAi~l~qr~ltld-pL~e~~nk~lm~~la~~gD~is~~khyerya~vleaelgi~vddsi  355 (361)
T COG3947         281 LLGKVARAYLEAGKPNEAIQLHQRALTLD-PLSEQDNKGLMASLATLGDEISAIKHYERYAEVLEAELGIDVDDSI  355 (361)
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHhhcC-hhhhHHHHHHHHHHHHhccchhhhhHHHHHHHHHHHHhCCCcchhH
Confidence            34555677888888888888888877765 56677777888888888887677666666542     355555443

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=87.33  E-value=6.4  Score=30.34  Aligned_cols=75  Identities=11%  Similarity=0.009  Sum_probs=43.7

Q ss_pred             HHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCC--CCHHHHHHHHH
Q 044084           63 YKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGML--RDLEVFLKLVL  138 (343)
Q Consensus        63 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~  138 (343)
                      .+..++.+.+.+...+++...++-.+.. +.|..+-..++..++-.|++++|..-++........  +-..+|..+++
T Consensus         4 l~~t~seLL~~~sL~dai~~a~~qVkak-Ptda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l~p~~t~~a~lyr~lir   80 (273)
T COG4455           4 LRDTISELLDDNSLQDAIGLARDQVKAK-PTDAGGRHFLFQLLCVAGDWEKALAQLNLAATLSPQDTVGASLYRHLIR   80 (273)
T ss_pred             hHHHHHHHHHhccHHHHHHHHHHHHhcC-CccccchhHHHHHHhhcchHHHHHHHHHHHhhcCcccchHHHHHHHHHH
Confidence            3445566666777777777766655542 224555666777777777777777666655543221  22444555554

>PF07163 Pex26: Pex26 protein; InterPro: IPR010797 This family consists of Pex26 and related mammalian proteins

Probab=87.24  E-value=13  Score=29.95  Aligned_cols=56  Identities=13%  Similarity=0.046  Sum_probs=22.3

Q ss_pred             HHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHH
Q 044084          102 ICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMK  157 (343)
Q Consensus       102 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  157 (343)
                      |.+++..++|.++....-+.-+.--+.-+.+...-|-.|.+.+.+..+.++-....
T Consensus        90 IQALAEmnrWreVLsWvlqyYq~pEklPpkIleLCILLysKv~Ep~amlev~~~WL  145 (309)
T PF07163_consen   90 IQALAEMNRWREVLSWVLQYYQVPEKLPPKILELCILLYSKVQEPAAMLEVASAWL  145 (309)
T ss_pred             HHHHHHHhhHHHHHHHHHHHhcCcccCCHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            34444444444444433332221111123333333444445555444444444433

Pex26 is a type II peroxisomal membrane protein that recruits Pex6-Pex1 complexes to peroxisomes []. Mutations in Pex26 can lead to human disorders [].; GO: 0032403 protein complex binding, 0045046 protein import into peroxisome membrane, 0005779 integral to peroxisomal membrane

>PF07163 Pex26: Pex26 protein; InterPro: IPR010797 This family consists of Pex26 and related mammalian proteins

Probab=87.22  E-value=11  Score=30.35  Aligned_cols=123  Identities=13%  Similarity=0.073  Sum_probs=77.2

Q ss_pred             HHHhcCCHHHHHHHHHHHHhCC-----C-CCCCch----HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHH
Q 044084           31 AFYKIGDSEKVAALFLECESRK-----L-DLTPSS----THMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYAS  100 (343)
Q Consensus        31 ~~~~~~~~~~a~~~~~~~~~~~-----~-~~~~~~----~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  100 (343)
                      .+.-..||..|++.-++-.+.-     . .+....    ......=|.+++..+++.+++.+.-+--+.--+..+.....
T Consensus        44 ~LvV~rdF~aal~tCerglqsL~~~a~~ee~~~~~~evK~sLcvvGIQALAEmnrWreVLsWvlqyYq~pEklPpkIleL  123 (309)
T PF07163_consen   44 LLVVHRDFQAALETCERGLQSLASDADAEEPAGSSLEVKCSLCVVGIQALAEMNRWREVLSWVLQYYQVPEKLPPKILEL  123 (309)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcccccccccccchhhhhhhhhhhhHHHHHHHhhHHHHHHHHHHHhcCcccCCHHHHHH
Confidence            3444567777776665543321     0 011000    12233347899999999999887766655422333445666


Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH-----hcCcHhHHHHHH
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYI-----EEGMVEKTLEVV  153 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~-----~~~~~~~a~~~~  153 (343)
                      .|-.|.+.+.+..+.++-..-.+..-.-+..-|..+...|.     -.|.+++|+++.
T Consensus       124 CILLysKv~Ep~amlev~~~WL~~p~Nq~lp~y~~vaELyLl~VLlPLG~~~eAeelv  181 (309)
T PF07163_consen  124 CILLYSKVQEPAAMLEVASAWLQDPSNQSLPEYGTVAELYLLHVLLPLGHFSEAEELV  181 (309)
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHhCcccCCchhhHHHHHHHHHHHHhccccHHHHHHHH
Confidence            67788999999999888877766432234445777766665     469999999887

Pex26 is a type II peroxisomal membrane protein that recruits Pex6-Pex1 complexes to peroxisomes []. Mutations in Pex26 can lead to human disorders [].; GO: 0032403 protein complex binding, 0045046 protein import into peroxisome membrane, 0005779 integral to peroxisomal membrane

>cd08819 CARD_MDA5_2 Caspase activation and recruitment domain found in MDA5, second repeat

Probab=86.90  E-value=6.2  Score=25.29  Aligned_cols=65  Identities=17%  Similarity=0.084  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHH
Q 044084          184 AVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDA  254 (343)
Q Consensus       184 a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  254 (343)
                      +.++++.+.+.|+ .+......+-.+-...|+.+.|.+++..+. .|    +..|..++.++...|.-+-|
T Consensus        21 ~~~v~d~ll~~~i-lT~~d~e~I~aa~~~~g~~~~ar~LL~~L~-rg----~~aF~~Fl~aLreT~~~~LA   85 (88)
T cd08819          21 TRDVCDKCLEQGL-LTEEDRNRIEAATENHGNESGARELLKRIV-QK----EGWFSKFLQALRETEHHELA   85 (88)
T ss_pred             HHHHHHHHHhcCC-CCHHHHHHHHHhccccCcHHHHHHHHHHhc-cC----CcHHHHHHHHHHHcCchhhh
Confidence            3445555555553 222222322222234456666666666666 44    34555666666655554433

Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), second repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protei

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=86.88  E-value=20  Score=31.13  Aligned_cols=77  Identities=16%  Similarity=0.109  Sum_probs=48.7

Q ss_pred             HHhcCCHHHHHHHHHHHHhC--CCCCCC---------chHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCC----CCChH
Q 044084           32 FYKIGDSEKVAALFLECESR--KLDLTP---------SSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGI----LEDPS   96 (343)
Q Consensus        32 ~~~~~~~~~a~~~~~~~~~~--~~~~~~---------~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~----~~~~~   96 (343)
                      +.+.+.+.+|.+.+..-..+  +..+.-         ++...=+..+.++...|++.++..+++++...=.    .-+..
T Consensus        89 ~Y~~k~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d  168 (549)
T PF07079_consen   89 AYKQKEYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSD  168 (549)
T ss_pred             HHHhhhHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHH
Confidence            45778888998888776554  222110         0111223456677889999999999888876532    25777


Q ss_pred             hHHHHHHHHhcc
Q 044084           97 VYASLICSFASI  108 (343)
Q Consensus        97 ~~~~l~~~~~~~  108 (343)
                      +|+.++-.++++
T Consensus       169 ~yd~~vlmlsrS  180 (549)
T PF07079_consen  169 MYDRAVLMLSRS  180 (549)
T ss_pred             HHHHHHHHHhHH
Confidence            888765555443

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>PHA02875 ankyrin repeat protein; Provisional

Probab=86.73  E-value=20  Score=31.09  Aligned_cols=203  Identities=10%  Similarity=0.059  Sum_probs=98.1

Q ss_pred             HHHHHHHHhCCCCCChhh--HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHH
Q 044084            7 LHYYEKMKSAGIVLDSGC--YCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFR   84 (343)
Q Consensus         7 ~~~~~~~~~~~~~~~~~~--~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~   84 (343)
                      .++++.+.+.|..|+...  ..+.+...++.|+.+-+.-+    .+.|..++.......+ .+...+..|+.+.+..+++
T Consensus        15 ~~iv~~Ll~~g~~~n~~~~~g~tpL~~A~~~~~~~~v~~L----l~~ga~~~~~~~~~~t-~L~~A~~~g~~~~v~~Ll~   89 (413)
T PHA02875         15 LDIARRLLDIGINPNFEIYDGISPIKLAMKFRDSEAIKLL----MKHGAIPDVKYPDIES-ELHDAVEEGDVKAVEELLD   89 (413)
T ss_pred             HHHHHHHHHCCCCCCccCCCCCCHHHHHHHcCCHHHHHHH----HhCCCCccccCCCccc-HHHHHHHCCCHHHHHHHHH
Confidence            356677778887766543  34456666778887654443    3445444321111222 3444456777766555543


Q ss_pred             HHHhcCCCCChH---hHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHH--HHHHHHHHHhcCcHhHHHHHHHHHHhc
Q 044084           85 DMKEKGILEDPS---VYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEV--FLKLVLMYIEEGMVEKTLEVVESMKNA  159 (343)
Q Consensus        85 ~~~~~~~~~~~~---~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~--~~~l~~~~~~~~~~~~a~~~~~~~~~~  159 (343)
                          .|...+..   .-.+.+...+..|+.+    +++.+.+.|..|+...  -.+.+...+..|+.+-+..+++    .
T Consensus        90 ----~~~~~~~~~~~~g~tpL~~A~~~~~~~----iv~~Ll~~gad~~~~~~~g~tpLh~A~~~~~~~~v~~Ll~----~  157 (413)
T PHA02875         90 ----LGKFADDVFYKDGMTPLHLATILKKLD----IMKLLIARGADPDIPNTDKFSPLHLAVMMGDIKGIELLID----H  157 (413)
T ss_pred             ----cCCcccccccCCCCCHHHHHHHhCCHH----HHHHHHhCCCCCCCCCCCCCCHHHHHHHcCCHHHHHHHHh----c
Confidence                33211110   0112333445566654    4455556666554221  1234455566777665544443    3


Q ss_pred             CCCC---chhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhh---HHHHHHHHHccCChhHHHHHHHHHHHcCCCc
Q 044084          160 ELNI---SDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVT---YASIINAYCRIGLYSKAEKVFIEMQQKGFDK  233 (343)
Q Consensus       160 ~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~---~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~  233 (343)
                      |..+   +..-.+.+..+ +..|+.+    +.+.+.+.|..|+...   ....+...+..|+.+    +.+.+.+.|..+
T Consensus       158 g~~~~~~d~~g~TpL~~A-~~~g~~e----iv~~Ll~~ga~~n~~~~~~~~t~l~~A~~~~~~~----iv~~Ll~~gad~  228 (413)
T PHA02875        158 KACLDIEDCCGCTPLIIA-MAKGDIA----ICKMLLDSGANIDYFGKNGCVAALCYAIENNKID----IVRLFIKRGADC  228 (413)
T ss_pred             CCCCCCCCCCCCCHHHHH-HHcCCHH----HHHHHHhCCCCCCcCCCCCCchHHHHHHHcCCHH----HHHHHHHCCcCc
Confidence            3322   22223333333 3455554    4455566665555432   123444345556654    444455566555


Q ss_pred             Ch
Q 044084          234 CV  235 (343)
Q Consensus       234 ~~  235 (343)
                      +.
T Consensus       229 n~  230 (413)
T PHA02875        229 NI  230 (413)
T ss_pred             ch
Confidence            53

>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=86.30  E-value=1.4  Score=20.64  Aligned_cols=20  Identities=20%  Similarity=0.240  Sum_probs=10.2

Q ss_pred             HHHHHHHccCChHHHHHHHH
Q 044084          240 SMVAMYGKTGRIRDAMRLVA  259 (343)
Q Consensus       240 ~l~~~~~~~~~~~~a~~~~~  259 (343)
                      .+...+...|++++|..+++
T Consensus         6 ~la~~~~~~G~~~eA~~~l~   25 (26)
T PF07721_consen    6 ALARALLAQGDPDEAERLLR   25 (26)
T ss_pred             HHHHHHHHcCCHHHHHHHHh
Confidence            34445555555555555443

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

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=86.22  E-value=2.2  Score=20.92  Aligned_cols=24  Identities=17%  Similarity=0.297  Sum_probs=12.8

Q ss_pred             HHHHHHhcCcHhHHHHHHHHHHhc
Q 044084          136 LVLMYIEEGMVEKTLEVVESMKNA  159 (343)
Q Consensus       136 l~~~~~~~~~~~~a~~~~~~~~~~  159 (343)
                      +..++.+.|++++|.+.|+++...
T Consensus         6 ~a~~~~~~g~~~~A~~~~~~~~~~   29 (33)
T PF13174_consen    6 LARCYYKLGDYDEAIEYFQRLIKR   29 (33)
T ss_dssp             HHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHH
Confidence            444455555555555555555443

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=85.98  E-value=2.9  Score=22.84  Aligned_cols=27  Identities=15%  Similarity=0.223  Sum_probs=23.0

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCC
Q 044084          294 TVISAYNMAREFDMCVKFYNEFRMNGG  320 (343)
Q Consensus       294 ~l~~~~~~~g~~~~a~~~~~~m~~~~~  320 (343)
                      .+..+|...|+.+.|.+++++....|-
T Consensus         4 dLA~ayie~Gd~e~Ar~lL~evl~~~~   30 (44)
T TIGR03504         4 DLARAYIEMGDLEGARELLEEVIEEGD   30 (44)
T ss_pred             HHHHHHHHcCChHHHHHHHHHHHHcCC
Confidence            367889999999999999999987654

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.

>PF04097 Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic96 is a component of the nuclear pore complex

Probab=85.94  E-value=29  Score=32.11  Aligned_cols=42  Identities=10%  Similarity=0.151  Sum_probs=22.0

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhcc
Q 044084           28 IMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKS   73 (343)
Q Consensus        28 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~   73 (343)
                      +|-.|.|+|++++|.++.......--..    ...+...+..+...
T Consensus       117 ~Iyy~LR~G~~~~A~~~~~~~~~~~~~~----~~~f~~~l~~~~~s  158 (613)
T PF04097_consen  117 LIYYCLRCGDYDEALEVANENRNQFQKI----ERSFPTYLKAYASS  158 (613)
T ss_dssp             HHHHHHTTT-HHHHHHHHHHTGGGS-TT----TTHHHHHHHHCTTT
T ss_pred             HHHHHHhcCCHHHHHHHHHHhhhhhcch----hHHHHHHHHHHHhC
Confidence            4556667777777777764443322111    13455566666554

It is required for the correct assembly of the nuclear pore complex []. In Saccharomyces cerevisiae, Nic96 has been shown to be involved in the distribution and cellular concentration of the GTPase Gsp1 []. The structure of Nic96 has revealed a mostly alpha helical structure [].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 2QX5_B 2RFO_A.

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=85.60  E-value=39  Score=33.28  Aligned_cols=31  Identities=19%  Similarity=0.206  Sum_probs=17.1

Q ss_pred             CCChHhHHHHHHHHhccc--CHHHHHHHHHHHHH
Q 044084           92 LEDPSVYASLICSFASIA--EVKVAEELFKEAEE  123 (343)
Q Consensus        92 ~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~  123 (343)
                      .|+ .....+|.++.+.+  .++.++....+...
T Consensus       788 ~~~-~~~~~ilTs~vk~~~~~ie~aL~kI~~l~~  820 (1265)
T KOG1920|consen  788 APD-KFNLFILTSYVKSNPPEIEEALQKIKELQL  820 (1265)
T ss_pred             Ccc-hhhHHHHHHHHhcCcHHHHHHHHHHHHHHh
Confidence            344 33445666777665  55556555555553

>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A

Probab=85.58  E-value=2.7  Score=20.93  Aligned_cols=27  Identities=19%  Similarity=0.388  Sum_probs=15.0

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 044084           24 CYCQIMEAFYKIGDSEKVAALFLECES   50 (343)
Q Consensus        24 ~~~~l~~~~~~~~~~~~a~~~~~~~~~   50 (343)
                      +|..+...|...|++++|.+.|++..+
T Consensus         3 ~~~~lg~~y~~~~~~~~A~~~~~~a~~   29 (34)
T PF13181_consen    3 AYYNLGKIYEQLGDYEEALEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHTTSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            344555555566666666666555443

...

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=85.44  E-value=21  Score=30.04  Aligned_cols=63  Identities=10%  Similarity=0.087  Sum_probs=33.0

Q ss_pred             hhHHHHHHHHHccCChhHHHHHHHHHHHcCCCc---ChhhHHHHHHHHHccCChHHHHHHHHHHhh
Q 044084          201 VTYASIINAYCRIGLYSKAEKVFIEMQQKGFDK---CVVAYSSMVAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       201 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                      .++..+.+.+.+.|.++.|...+..+...+...   ++...-.-+..+-..|+..+|...++....
T Consensus       147 ~~~l~~a~~aRk~g~~~~A~~~l~~~~~~~~~~~~~~~~v~~e~akllw~~g~~~~Ai~~L~~~~~  212 (352)
T PF02259_consen  147 ETWLKFAKLARKAGNFQLALSALNRLFQLNPSSESLLPRVFLEYAKLLWAQGEQEEAIQKLRELLK  212 (352)
T ss_pred             HHHHHHHHHHHHCCCcHHHHHHHHHHhccCCcccCCCcchHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            445555566666666666666666655532111   223333344455555666666665555554

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>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=85.38  E-value=5.1  Score=27.08  Aligned_cols=26  Identities=8%  Similarity=0.217  Sum_probs=24.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHh
Q 044084          292 YTTVISAYNMAREFDMCVKFYNEFRM  317 (343)
Q Consensus       292 ~~~l~~~~~~~g~~~~a~~~~~~m~~  317 (343)
                      |..++..|...|..++|++++.+..+
T Consensus        42 ~~eL~~lY~~kg~h~~AL~ll~~l~~   67 (108)
T PF10366_consen   42 YQELVDLYQGKGLHRKALELLKKLAD   67 (108)
T ss_pred             HHHHHHHHHccCccHHHHHHHHHHhc
Confidence            78899999999999999999999877

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.

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=84.80  E-value=19  Score=32.42  Aligned_cols=101  Identities=14%  Similarity=0.072  Sum_probs=62.2

Q ss_pred             HhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHH
Q 044084          105 FASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAA  184 (343)
Q Consensus       105 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  184 (343)
                      ..+.|+++.|.++..+.      .+..-|..|.++....+++..|.+.|.....         |..|+-.+...|+-+..
T Consensus       647 al~lgrl~iA~~la~e~------~s~~Kw~~Lg~~al~~~~l~lA~EC~~~a~d---------~~~LlLl~t~~g~~~~l  711 (794)
T KOG0276|consen  647 ALKLGRLDIAFDLAVEA------NSEVKWRQLGDAALSAGELPLASECFLRARD---------LGSLLLLYTSSGNAEGL  711 (794)
T ss_pred             hhhcCcHHHHHHHHHhh------cchHHHHHHHHHHhhcccchhHHHHHHhhcc---------hhhhhhhhhhcCChhHH
Confidence            34566666666654432      2566677777877788888887777776643         44455556666666665


Q ss_pred             HHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHH
Q 044084          185 VKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEM  226 (343)
Q Consensus       185 ~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~  226 (343)
                      ..+-....+.|.      .|...-+|...|+++++.+++..-
T Consensus       712 ~~la~~~~~~g~------~N~AF~~~~l~g~~~~C~~lLi~t  747 (794)
T KOG0276|consen  712 AVLASLAKKQGK------NNLAFLAYFLSGDYEECLELLIST  747 (794)
T ss_pred             HHHHHHHHhhcc------cchHHHHHHHcCCHHHHHHHHHhc
Confidence            555555555542      223334556667777777776543

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=84.44  E-value=13  Score=26.77  Aligned_cols=97  Identities=8%  Similarity=-0.009  Sum_probs=47.2

Q ss_pred             ccCChhHHHHHHHHHHHcCC-CcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHH-HHhcccChhHH
Q 044084          212 RIGLYSKAEKVFIEMQQKGF-DKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMD-MHGRAKNLRQL  289 (343)
Q Consensus       212 ~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~-~~~~~~~~~~a  289 (343)
                      ..+++++++.+++.|.-... .+...++...+  +...|++++|.++|+++.+.+..  ...-..|+. ++.-.|+.+  
T Consensus        22 ~~~d~~D~e~lLdALrvLrP~~~e~d~~dg~l--~i~rg~w~eA~rvlr~l~~~~~~--~p~~kAL~A~CL~al~Dp~--   95 (153)
T TIGR02561        22 RSADPYDAQAMLDALRVLRPNLKELDMFDGWL--LIARGNYDEAARILRELLSSAGA--PPYGKALLALCLNAKGDAE--   95 (153)
T ss_pred             hcCCHHHHHHHHHHHHHhCCCccccchhHHHH--HHHcCCHHHHHHHHHhhhccCCC--chHHHHHHHHHHHhcCChH--
Confidence            35666666666666655321 11222333332  44666777777777766655321  111111221 222233333  


Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 044084          290 EKYTTVISAYNMAREFDMCVKFYNEFR  316 (343)
Q Consensus       290 ~~~~~l~~~~~~~g~~~~a~~~~~~m~  316 (343)
                        |..........|...+++.+.+.+.
T Consensus        96 --Wr~~A~~~le~~~~~~a~~Lv~al~  120 (153)
T TIGR02561        96 --WHVHADEVLARDADADAVALVRALL  120 (153)
T ss_pred             --HHHHHHHHHHhCCCHhHHHHHHHHh
Confidence              5555555555566666666666665

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]

Probab=84.38  E-value=29  Score=30.75  Aligned_cols=177  Identities=12%  Similarity=0.078  Sum_probs=121.8

Q ss_pred             HHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 044084           61 HMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMY  140 (343)
Q Consensus        61 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  140 (343)
                      ....+++..++.+.+..-...+..+|...|  -+-..|..++.+|... ..+....+|+++.+..+. |+..-..|...|
T Consensus        67 ~~l~~~~~~f~~n~k~~~veh~c~~~l~~~--e~kmal~el~q~y~en-~n~~l~~lWer~ve~dfn-Dvv~~ReLa~~y  142 (711)
T COG1747          67 SCLVTLLTIFGDNHKNQIVEHLCTRVLEYG--ESKMALLELLQCYKEN-GNEQLYSLWERLVEYDFN-DVVIGRELADKY  142 (711)
T ss_pred             hHHHHHHHHhccchHHHHHHHHHHHHHHhc--chHHHHHHHHHHHHhc-CchhhHHHHHHHHHhcch-hHHHHHHHHHHH
Confidence            456778888888888999999999998875  3566788888888887 667888999999987764 555555555555


Q ss_pred             HhcCcHhHHHHHHHHHHhcCCCC--c---hhhHHHHHHHHhcCCcHHHHHHHHHHHHHc-CCCCCHhhHHHHHHHHHccC
Q 044084          141 IEEGMVEKTLEVVESMKNAELNI--S---DCISCVIVNGFSKRRAYWAAVKVYEQLISQ-GCIPGQVTYASIINAYCRIG  214 (343)
Q Consensus       141 ~~~~~~~~a~~~~~~~~~~~~~~--~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~p~~~~~~~ll~~~~~~~  214 (343)
                      -+ ++...+...|.++...-++-  +   ...|.-+...-  ..+.+....+..++... |...-...+.-+-.-|....
T Consensus       143 Ek-ik~sk~a~~f~Ka~yrfI~~~q~~~i~evWeKL~~~i--~dD~D~fl~l~~kiqt~lg~~~~~Vl~qdv~~~Ys~~e  219 (711)
T COG1747         143 EK-IKKSKAAEFFGKALYRFIPRRQNAAIKEVWEKLPELI--GDDKDFFLRLQKKIQTKLGEGRGSVLMQDVYKKYSENE  219 (711)
T ss_pred             HH-hchhhHHHHHHHHHHHhcchhhhhhHHHHHHHHHHhc--cccHHHHHHHHHHHHHhhccchHHHHHHHHHHHhcccc
Confidence            55 88888888888887654421  1   12344444321  35666777777666654 33333445555567788889


Q ss_pred             ChhHHHHHHHHHHHcCCCcChhhHHHHHHHH
Q 044084          215 LYSKAEKVFIEMQQKGFDKCVVAYSSMVAMY  245 (343)
Q Consensus       215 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  245 (343)
                      ++++|.+++..+.+++ ..|..+-..++..+
T Consensus       220 N~~eai~Ilk~il~~d-~k~~~ar~~~i~~l  249 (711)
T COG1747         220 NWTEAIRILKHILEHD-EKDVWARKEIIENL  249 (711)
T ss_pred             CHHHHHHHHHHHhhhc-chhhhHHHHHHHHH
Confidence            9999999999888875 44555555555443

>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=83.60  E-value=21  Score=28.61  Aligned_cols=183  Identities=11%  Similarity=0.098  Sum_probs=107.4

Q ss_pred             chhhHHHHHHHHHhCCCCCChh---hHHHHHHHHHhcCCHHHHHHHHHHHHhC---CCCCCCchHHHHHHHHHHhhccCc
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSG---CYCQIMEAFYKIGDSEKVAALFLECESR---KLDLTPSSTHMYKILCDSLGKSGR   75 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~---~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~~~~~~~li~~~~~~~~   75 (343)
                      .|++|+.-|.+..+........   ....++....+.+++++....|.++...   .+.. +-+....|.++.-.+.+.+
T Consensus        42 ~p~~Al~sF~kVlelEgEKgeWGFKALKQmiKI~f~l~~~~eMm~~Y~qlLTYIkSAVTr-NySEKsIN~IlDyiStS~~  120 (440)
T KOG1464|consen   42 EPKEALSSFQKVLELEGEKGEWGFKALKQMIKINFRLGNYKEMMERYKQLLTYIKSAVTR-NYSEKSINSILDYISTSKN  120 (440)
T ss_pred             CHHHHHHHHHHHHhcccccchhHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHhc-cccHHHHHHHHHHHhhhhh
Confidence            5788999998888764333333   3455678888999999888888776421   1111 1124556777766666665


Q ss_pred             HHHHHHHHHHHHhc--CCCCCh----HhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCC-----------CHHHHHHHHH
Q 044084           76 AFEILKFFRDMKEK--GILEDP----SVYASLICSFASIAEVKVAEELFKEAEEKGMLR-----------DLEVFLKLVL  138 (343)
Q Consensus        76 ~~~a~~~~~~~~~~--~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-----------~~~~~~~l~~  138 (343)
                      .+...++|+.-+..  ..+ +.    .|-..|...|...+++....+++.++..+...-           =..+|..-|.
T Consensus       121 m~LLQ~FYeTTL~ALkdAK-NeRLWFKTNtKLgkl~fd~~e~~kl~KIlkqLh~SCq~edGedD~kKGtQLLEiYAlEIQ  199 (440)
T KOG1464|consen  121 MDLLQEFYETTLDALKDAK-NERLWFKTNTKLGKLYFDRGEYTKLQKILKQLHQSCQTEDGEDDQKKGTQLLEIYALEIQ  199 (440)
T ss_pred             hHHHHHHHHHHHHHHHhhh-cceeeeeccchHhhhheeHHHHHHHHHHHHHHHHHhccccCchhhhccchhhhhHhhHhh
Confidence            55555444433221  001 11    123456677778888888888888876532111           1345667778


Q ss_pred             HHHhcCcHhHHHHHHHHHHhcC-CCCchhhHHHHHHHH-----hcCCcHHHHHHH
Q 044084          139 MYIEEGMVEKTLEVVESMKNAE-LNISDCISCVIVNGF-----SKRRAYWAAVKV  187 (343)
Q Consensus       139 ~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~-----~~~~~~~~a~~~  187 (343)
                      +|....+-.+...+|++..... ..|.+... -+|+-|     .+.|++++|..=
T Consensus       200 mYT~qKnNKkLK~lYeqalhiKSAIPHPlIm-GvIRECGGKMHlreg~fe~AhTD  253 (440)
T KOG1464|consen  200 MYTEQKNNKKLKALYEQALHIKSAIPHPLIM-GVIRECGGKMHLREGEFEKAHTD  253 (440)
T ss_pred             hhhhhcccHHHHHHHHHHHHhhccCCchHHH-hHHHHcCCccccccchHHHHHhH
Confidence            8888887777778888765322 11333333 233333     446777776543

>PRK15180 Vi polysaccharide biosynthesis protein TviD; Provisional

Probab=82.79  E-value=32  Score=30.15  Aligned_cols=90  Identities=12%  Similarity=-0.011  Sum_probs=52.3

Q ss_pred             hhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHH
Q 044084           70 LGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKT  149 (343)
Q Consensus        70 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  149 (343)
                      +...|+++.+...+...... +.....+...+++...+.|+++.|..+-+-|....++ ++.+........-..|-++++
T Consensus       333 ~~~lg~ye~~~~~~s~~~~~-~~s~~~~~~~~~r~~~~l~r~~~a~s~a~~~l~~eie-~~ei~~iaa~sa~~l~~~d~~  410 (831)
T PRK15180        333 FSHLGYYEQAYQDISDVEKI-IGTTDSTLRCRLRSLHGLARWREALSTAEMMLSNEIE-DEEVLTVAAGSADALQLFDKS  410 (831)
T ss_pred             HHHhhhHHHHHHHhhchhhh-hcCCchHHHHHHHhhhchhhHHHHHHHHHHHhccccC-ChhheeeecccHHHHhHHHHH
Confidence            34556677666666554332 2234455666666666777777777776666665554 444444444444455566666


Q ss_pred             HHHHHHHHhcCC
Q 044084          150 LEVVESMKNAEL  161 (343)
Q Consensus       150 ~~~~~~~~~~~~  161 (343)
                      ...|+++...+.
T Consensus       411 ~~~wk~~~~~~~  422 (831)
T PRK15180        411 YHYWKRVLLLNP  422 (831)
T ss_pred             HHHHHHHhccCC
Confidence            666666655443

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=82.44  E-value=20  Score=27.42  Aligned_cols=89  Identities=12%  Similarity=0.107  Sum_probs=47.4

Q ss_pred             HHhcCcHhHHHHHHHHHHhcCCCCc----hhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCC
Q 044084          140 YIEEGMVEKTLEVVESMKNAELNIS----DCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGL  215 (343)
Q Consensus       140 ~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~  215 (343)
                      +.+.|++++|..-|......-+..+    ...|..-..++.+.+.++.|++--.+.++.+ +........-..+|.+..+
T Consensus       105 ~F~ngdyeeA~skY~~Ale~cp~~~~e~rsIly~Nraaa~iKl~k~e~aI~dcsKaiel~-pty~kAl~RRAeayek~ek  183 (271)
T KOG4234|consen  105 LFKNGDYEEANSKYQEALESCPSTSTEERSILYSNRAAALIKLRKWESAIEDCSKAIELN-PTYEKALERRAEAYEKMEK  183 (271)
T ss_pred             hhhcccHHHHHHHHHHHHHhCccccHHHHHHHHhhhHHHHHHhhhHHHHHHHHHhhHhcC-chhHHHHHHHHHHHHhhhh
Confidence            4556666666666666555433221    1234444455666666666666666555543 1112222233445666666


Q ss_pred             hhHHHHHHHHHHHc
Q 044084          216 YSKAEKVFIEMQQK  229 (343)
Q Consensus       216 ~~~a~~~~~~~~~~  229 (343)
                      ++.|+.-+..+.+.
T Consensus       184 ~eealeDyKki~E~  197 (271)
T KOG4234|consen  184 YEEALEDYKKILES  197 (271)
T ss_pred             HHHHHHHHHHHHHh
Confidence            66666666666664

>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=82.38  E-value=24  Score=28.33  Aligned_cols=205  Identities=12%  Similarity=0.123  Sum_probs=126.7

Q ss_pred             CCCCCChhhHHHHHHHH-HhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhc---CC
Q 044084           16 AGIVLDSGCYCQIMEAF-YKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEK---GI   91 (343)
Q Consensus        16 ~~~~~~~~~~~~l~~~~-~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---~~   91 (343)
                      .+-.||+..=|..-..- .+...+++|+.-|++..+...........+.-.++....+.+++++..+.|.+++..   .+
T Consensus        20 s~sEpdVDlENQYYnsK~l~e~~p~~Al~sF~kVlelEgEKgeWGFKALKQmiKI~f~l~~~~eMm~~Y~qlLTYIkSAV   99 (440)
T KOG1464|consen   20 SNSEPDVDLENQYYNSKGLKEDEPKEALSSFQKVLELEGEKGEWGFKALKQMIKINFRLGNYKEMMERYKQLLTYIKSAV   99 (440)
T ss_pred             cCCCCCcchHhhhhccccccccCHHHHHHHHHHHHhcccccchhHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHH
Confidence            34567776555433322 244578999999999876543333222445566788999999999999999988642   11


Q ss_pred             --CCChHhHHHHHHHHhcccCHHHHHHHHHHHHH----cCC-CCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCC--
Q 044084           92 --LEDPSVYASLICSFASIAEVKVAEELFKEAEE----KGM-LRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELN--  162 (343)
Q Consensus        92 --~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~----~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--  162 (343)
                        ..+..+.|.++.....+.+.+.....++.-.+    ..- ..--.+-..|...|...+.+.+...++.++.+.--.  
T Consensus       100 TrNySEKsIN~IlDyiStS~~m~LLQ~FYeTTL~ALkdAKNeRLWFKTNtKLgkl~fd~~e~~kl~KIlkqLh~SCq~ed  179 (440)
T KOG1464|consen  100 TRNYSEKSINSILDYISTSKNMDLLQEFYETTLDALKDAKNERLWFKTNTKLGKLYFDRGEYTKLQKILKQLHQSCQTED  179 (440)
T ss_pred             hccccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhhhcceeeeeccchHhhhheeHHHHHHHHHHHHHHHHHhcccc
Confidence              22455677777777777776666555543322    110 001123356778888888888888888887643110  


Q ss_pred             ---------CchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcC-CCCCHhhHHHHHHHH-----HccCChhHHHH
Q 044084          163 ---------ISDCISCVIVNGFSKRRAYWAAVKVYEQLISQG-CIPGQVTYASIINAY-----CRIGLYSKAEK  221 (343)
Q Consensus       163 ---------~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~p~~~~~~~ll~~~-----~~~~~~~~a~~  221 (343)
                               .-...|..=|..|....+-.....+|++...-. -.|.+.. ..+|+-|     .+.|++++|..
T Consensus       180 GedD~kKGtQLLEiYAlEIQmYT~qKnNKkLK~lYeqalhiKSAIPHPlI-mGvIRECGGKMHlreg~fe~AhT  252 (440)
T KOG1464|consen  180 GEDDQKKGTQLLEIYALEIQMYTEQKNNKKLKALYEQALHIKSAIPHPLI-MGVIRECGGKMHLREGEFEKAHT  252 (440)
T ss_pred             CchhhhccchhhhhHhhHhhhhhhhcccHHHHHHHHHHHHhhccCCchHH-HhHHHHcCCccccccchHHHHHh
Confidence                     112357777888888888888888888766542 2344333 3344444     35677777653

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=82.24  E-value=25  Score=28.53  Aligned_cols=131  Identities=9%  Similarity=0.100  Sum_probs=84.5

Q ss_pred             HhHHHHHHHHHHh-cCCCCchhhHHHHHHHHhc--CCcHHHHHHHHHHHHHc-CCCCCHhhHHHHHHHHHccCChhHHHH
Q 044084          146 VEKTLEVVESMKN-AELNISDCISCVIVNGFSK--RRAYWAAVKVYEQLISQ-GCIPGQVTYASIINAYCRIGLYSKAEK  221 (343)
Q Consensus       146 ~~~a~~~~~~~~~-~~~~~~~~~~~~l~~~~~~--~~~~~~a~~~~~~~~~~-~~~p~~~~~~~ll~~~~~~~~~~~a~~  221 (343)
                      +-+|+.+|+.... ..+.-|..+...+++....  ......-.++.+-+... +-.++..+...++..++..+++.+-.+
T Consensus       144 Vv~aL~L~~~~~~~~~Ii~d~evislLL~sMv~~~~~~l~alYEvV~~l~~t~~~~l~~~vi~~Il~~L~~~~dW~kl~~  223 (292)
T PF13929_consen  144 VVEALKLYDGLNPDESIIFDEEVISLLLKSMVIDENTKLNALYEVVDFLVSTFSKSLTRNVIISILEILAESRDWNKLFQ  223 (292)
T ss_pred             HHHHHHHhhccCcccceeeChHHHHHHHHHHHhccccchhhHHHHHHHHHhccccCCChhHHHHHHHHHHhcccHHHHHH
Confidence            4566666663322 2233556666667766655  22333344444444433 346778888889999999999999999


Q ss_pred             HHHHHHHc-CCCcChhhHHHHHHHHHccCChHHHHHHHHHH-----hhCCCCchHHHHHHH
Q 044084          222 VFIEMQQK-GFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKM-----KPKGCEPNVWIYNSL  276 (343)
Q Consensus       222 ~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m-----~~~~~~p~~~~~~~l  276 (343)
                      +++..... +...|...|..+|+.....|+..-...+.++=     +..++..+...-.++
T Consensus       224 fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~kiI~~GhLLwikR~~V~v~~~L~~~L  284 (292)
T PF13929_consen  224 FWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRKIIDDGHLLWIKRNNVDVTDELRSQL  284 (292)
T ss_pred             HHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHHHhhCCCeEEeeecCCcCCHHHHHHH
Confidence            98887765 55678889999999999999977666665542     233444444443333

>KOG1258 consensus mRNA processing protein [RNA processing and modification]

Probab=82.20  E-value=38  Score=30.51  Aligned_cols=185  Identities=10%  Similarity=0.032  Sum_probs=110.0

Q ss_pred             hHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 044084           59 STHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVL  138 (343)
Q Consensus        59 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  138 (343)
                      ....|+.-+..-...|+++.+.-+|++..-.- ..-...|-..+......|+.+.+..++....+...+..+.+--.-..
T Consensus       296 ql~nw~~yLdf~i~~g~~~~~~~l~ercli~c-A~Y~efWiky~~~m~~~~~~~~~~~~~~~~~~i~~k~~~~i~L~~a~  374 (577)
T KOG1258|consen  296 QLKNWRYYLDFEITLGDFSRVFILFERCLIPC-ALYDEFWIKYARWMESSGDVSLANNVLARACKIHVKKTPIIHLLEAR  374 (577)
T ss_pred             HHHHHHHHhhhhhhcccHHHHHHHHHHHHhHH-hhhHHHHHHHHHHHHHcCchhHHHHHHHhhhhhcCCCCcHHHHHHHH
Confidence            36778888888888899999888888875431 11233455555566666888888888877776554433332222222


Q ss_pred             HHHhcCcHhHHHHHHHHHHhcCCCCchh-hHHHHHHHHhcCCcHHHHHH---HHHHHHHcCCCCCHhhHHHHHHH-----
Q 044084          139 MYIEEGMVEKTLEVVESMKNAELNISDC-ISCVIVNGFSKRRAYWAAVK---VYEQLISQGCIPGQVTYASIINA-----  209 (343)
Q Consensus       139 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~---~~~~~~~~~~~p~~~~~~~ll~~-----  209 (343)
                      ..-..|+++.|..+++.+.+.-  |+.. .-..-+....+.|..+.+..   ++......  .-+......+.--     
T Consensus       375 f~e~~~n~~~A~~~lq~i~~e~--pg~v~~~l~~~~~e~r~~~~~~~~~~~~l~s~~~~~--~~~~~i~~~l~~~~~r~~  450 (577)
T KOG1258|consen  375 FEESNGNFDDAKVILQRIESEY--PGLVEVVLRKINWERRKGNLEDANYKNELYSSIYEG--KENNGILEKLYVKFARLR  450 (577)
T ss_pred             HHHhhccHHHHHHHHHHHHhhC--CchhhhHHHHHhHHHHhcchhhhhHHHHHHHHhccc--ccCcchhHHHHHHHHHHH
Confidence            3334578999999999887654  3321 11222344456677776663   22222221  1122222222211     


Q ss_pred             HHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccC
Q 044084          210 YCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTG  249 (343)
Q Consensus       210 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  249 (343)
                      +.-.++.+.|..++..+.+.- +++...|..+++.....+
T Consensus       451 ~~i~~d~~~a~~~l~~~~~~~-~~~k~~~~~~~~~~~~~~  489 (577)
T KOG1258|consen  451 YKIREDADLARIILLEANDIL-PDCKVLYLELIRFELIQP  489 (577)
T ss_pred             HHHhcCHHHHHHHHHHhhhcC-CccHHHHHHHHHHHHhCC
Confidence            233578888888888888863 667777777777665554

>PRK15180 Vi polysaccharide biosynthesis protein TviD; Provisional

Probab=82.16  E-value=34  Score=30.00  Aligned_cols=122  Identities=8%  Similarity=0.025  Sum_probs=81.4

Q ss_pred             hhccCcHHHHHH-HHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhH
Q 044084           70 LGKSGRAFEILK-FFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEK  148 (343)
Q Consensus        70 ~~~~~~~~~a~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  148 (343)
                      ....|+.-.|-+ ++..+....-.|+....  ....+...|+++.+.+.+...... +.....+...+++...+.|++++
T Consensus       299 ~~~~gd~~aas~~~~~~lr~~~~~p~~i~l--~~~i~~~lg~ye~~~~~~s~~~~~-~~s~~~~~~~~~r~~~~l~r~~~  375 (831)
T PRK15180        299 QLADGDIIAASQQLFAALRNQQQDPVLIQL--RSVIFSHLGYYEQAYQDISDVEKI-IGTTDSTLRCRLRSLHGLARWRE  375 (831)
T ss_pred             HhhccCHHHHHHHHHHHHHhCCCCchhhHH--HHHHHHHhhhHHHHHHHhhchhhh-hcCCchHHHHHHHhhhchhhHHH
Confidence            345566665544 44444444334444333  334566789999999888766553 23456788889999999999999


Q ss_pred             HHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcC
Q 044084          149 TLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQG  195 (343)
Q Consensus       149 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  195 (343)
                      |...-+.|....+. +......-.-.....|-++++...|+++...+
T Consensus       376 a~s~a~~~l~~eie-~~ei~~iaa~sa~~l~~~d~~~~~wk~~~~~~  421 (831)
T PRK15180        376 ALSTAEMMLSNEIE-DEEVLTVAAGSADALQLFDKSYHYWKRVLLLN  421 (831)
T ss_pred             HHHHHHHHhccccC-ChhheeeecccHHHHhHHHHHHHHHHHHhccC
Confidence            99999999877663 33333333333345677899999999987764

>cd00280 TRFH Telomeric Repeat binding Factor or TTAGGG Repeat binding Factor, central (dimerization) domain Homology; TRFH

Probab=81.89  E-value=19  Score=26.94  Aligned_cols=93  Identities=12%  Similarity=0.080  Sum_probs=51.7

Q ss_pred             hhHHHHHHHHHHHcCCCcC--hhh-----HHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhH
Q 044084          216 YSKAEKVFIEMQQKGFDKC--VVA-----YSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQ  288 (343)
Q Consensus       216 ~~~a~~~~~~~~~~~~~~~--~~~-----~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~  288 (343)
                      .+.|..+|+.+.+..-.|.  ...     --..+..|.+.|.+++|.+++++...   .|+......-+....+.++.  
T Consensus        85 LESAl~v~~~I~~E~~~~~~lhe~i~~lik~~aV~VCm~~g~Fk~A~eiLkr~~~---d~~~~~~r~kL~~II~~Kd~--  159 (200)
T cd00280          85 LESALMVLESIEKEFSLPETLHEEIRKLIKEQAVAVCMENGEFKKAEEVLKRLFS---DPESQKLRMKLLMIIREKDP--  159 (200)
T ss_pred             HHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHhc---CCCchhHHHHHHHHHHcccc--
Confidence            4566677776665432221  111     12345578899999999999999886   45555556666666665554  


Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 044084          289 LEKYTTVISAYNMAREFDMCVKFYNEFR  316 (343)
Q Consensus       289 a~~~~~l~~~~~~~g~~~~a~~~~~~m~  316 (343)
                         |..++.-+.-..-.+...++++...
T Consensus       160 ---~h~~lqnFSy~~~~~ki~~~ve~~~  184 (200)
T cd00280         160 ---AHPVLQNFSYSHFMQKMKSYVELVL  184 (200)
T ss_pred             ---ccHHHHhccHHHHHHHHHHHHHHHh
Confidence               4444444433222333444444433

Telomeres are protein/DNA complexes that make up the physical ends of eukaryotic linear chromosomes and are essential for chromosome stability, protecting the chromosome ends from degradation and end-to-end fusion. Proteins TRF1, TRF2 and Taz1 bind telomeric DNA and are also involved in recruiting interacting proteins, TIN2, and Rap1, to the telomeres. It has also been demonstrated that PARP1 associates with TRF2 and is capable of poly(ADP-ribosyl)ation of TRF2, which affects binding of TRF2 to telomeric DNA. TRF1, TRF2 and Taz1 proteins contain three functional domains: an N-terminal acidic domain, a central TRF-specific/dimerization domain, and a C-terminal DNA binding domain with a single Myb-like repeat. Homodimerization, a prerequisite to DNA binding, results in the juxtaposition of two Myb DNA binding domains.

>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]

Probab=81.71  E-value=11  Score=31.26  Aligned_cols=53  Identities=11%  Similarity=0.115  Sum_probs=34.4

Q ss_pred             HHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHH
Q 044084          138 LMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQL  191 (343)
Q Consensus       138 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  191 (343)
                      .-|.+.|.+++|+..|.......+ -+.+++..-..+|.+...+..|..=-...
T Consensus       105 N~yFKQgKy~EAIDCYs~~ia~~P-~NpV~~~NRA~AYlk~K~FA~AE~DC~~A  157 (536)
T KOG4648|consen  105 NTYFKQGKYEEAIDCYSTAIAVYP-HNPVYHINRALAYLKQKSFAQAEEDCEAA  157 (536)
T ss_pred             hhhhhccchhHHHHHhhhhhccCC-CCccchhhHHHHHHHHHHHHHHHHhHHHH
Confidence            457777888888888877655442 25666777777777777776555444333

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

Probab=81.68  E-value=7.1  Score=21.77  Aligned_cols=37  Identities=5%  Similarity=-0.037  Sum_probs=30.5

Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHH
Q 044084          297 SAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGV  333 (343)
Q Consensus       297 ~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~  333 (343)
                      ....+.|-..++..++++|.+.|+..++..|..++..
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            3345678888999999999999999999988877653

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

>PRK09687 putative lyase; Provisional

Probab=81.47  E-value=28  Score=28.45  Aligned_cols=232  Identities=11%  Similarity=0.006  Sum_probs=120.3

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCH----HHHHHHHHHHHHcCCCCCHHHHHH
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEV----KVAEELFKEAEEKGMLRDLEVFLK  135 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~----~~a~~~~~~~~~~~~~~~~~~~~~  135 (343)
                      .......+.++...|. +.+...+..+...   +|...-...+.+++..|+.    +++...+..+...  .++..+...
T Consensus        37 ~~vR~~A~~aL~~~~~-~~~~~~l~~ll~~---~d~~vR~~A~~aLg~lg~~~~~~~~a~~~L~~l~~~--D~d~~VR~~  110 (280)
T PRK09687         37 SLKRISSIRVLQLRGG-QDVFRLAIELCSS---KNPIERDIGADILSQLGMAKRCQDNVFNILNNLALE--DKSACVRAS  110 (280)
T ss_pred             HHHHHHHHHHHHhcCc-chHHHHHHHHHhC---CCHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHhc--CCCHHHHHH
Confidence            3455555666666654 3333444444332   3445555556666666653    3455556555332  256666666


Q ss_pred             HHHHHHhcCcH-----hHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHH
Q 044084          136 LVLMYIEEGMV-----EKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAY  210 (343)
Q Consensus       136 l~~~~~~~~~~-----~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~  210 (343)
                      .+.++...+..     ..+.+.+......   ++..+-...+.++.+.++. .+...+-.+.+.   ++..+-...+.++
T Consensus       111 A~~aLG~~~~~~~~~~~~a~~~l~~~~~D---~~~~VR~~a~~aLg~~~~~-~ai~~L~~~L~d---~~~~VR~~A~~aL  183 (280)
T PRK09687        111 AINATGHRCKKNPLYSPKIVEQSQITAFD---KSTNVRFAVAFALSVINDE-AAIPLLINLLKD---PNGDVRNWAAFAL  183 (280)
T ss_pred             HHHHHhcccccccccchHHHHHHHHHhhC---CCHHHHHHHHHHHhccCCH-HHHHHHHHHhcC---CCHHHHHHHHHHH
Confidence            66665554421     2233333332222   2333444556666666653 455555555543   3444444555555


Q ss_pred             HccC-ChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHH
Q 044084          211 CRIG-LYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQL  289 (343)
Q Consensus       211 ~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a  289 (343)
                      .+.+ +.+.+...+..+..   .++..+-...+.++.+.|+. .+...+-+..+.+   +.                   
T Consensus       184 g~~~~~~~~~~~~L~~~L~---D~~~~VR~~A~~aLg~~~~~-~av~~Li~~L~~~---~~-------------------  237 (280)
T PRK09687        184 NSNKYDNPDIREAFVAMLQ---DKNEEIRIEAIIGLALRKDK-RVLSVLIKELKKG---TV-------------------  237 (280)
T ss_pred             hcCCCCCHHHHHHHHHHhc---CCChHHHHHHHHHHHccCCh-hHHHHHHHHHcCC---ch-------------------
Confidence            5542 23345555555553   34566666677777777763 4444444444432   11                   


Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHh
Q 044084          290 EKYTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFS  335 (343)
Q Consensus       290 ~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~  335 (343)
                        ....+.++...|.. +|+..+..+....  ||..+-...+.++.
T Consensus       238 --~~~a~~ALg~ig~~-~a~p~L~~l~~~~--~d~~v~~~a~~a~~  278 (280)
T PRK09687        238 --GDLIIEAAGELGDK-TLLPVLDTLLYKF--DDNEIITKAIDKLK  278 (280)
T ss_pred             --HHHHHHHHHhcCCH-hHHHHHHHHHhhC--CChhHHHHHHHHHh
Confidence              11244556666764 6888888887743  47766555565554

>KOG2063 consensus Vacuolar assembly/sorting proteins VPS39/VAM6/VPS3 [Intracellular trafficking, secretion, and vesicular transport]

Probab=80.97  E-value=55  Score=31.53  Aligned_cols=116  Identities=12%  Similarity=0.106  Sum_probs=68.6

Q ss_pred             HHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCc---hhhHHHHHHHHhcCCcH--HHHHHHHHHHHHcCCCCCHhhHHH-
Q 044084          132 VFLKLVLMYIEEGMVEKTLEVVESMKNAELNIS---DCISCVIVNGFSKRRAY--WAAVKVYEQLISQGCIPGQVTYAS-  205 (343)
Q Consensus       132 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~--~~a~~~~~~~~~~~~~p~~~~~~~-  205 (343)
                      -|..|+..|...|+.++|+++|.+........+   ...+.-+++.+...+..  +-++++-+...+....-....++. 
T Consensus       506 ~y~~Li~LY~~kg~h~~AL~ll~~l~d~~~~~d~~~~~~~e~ii~YL~~l~~~~~~Li~~y~~wvl~~~p~~gi~Ift~~  585 (877)
T KOG2063|consen  506 KYRELIELYATKGMHEKALQLLRDLVDEDSDTDSFQLDGLEKIIEYLKKLGAENLDLILEYADWVLNKNPEAGIQIFTSE  585 (877)
T ss_pred             cHHHHHHHHHhccchHHHHHHHHHHhccccccccchhhhHHHHHHHHHHhcccchhHHHHHhhhhhccCchhheeeeecc
Confidence            477899999999999999999998876431001   11233345544444443  555555555444321111111111 


Q ss_pred             -----------HHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHc
Q 044084          206 -----------IINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGK  247 (343)
Q Consensus       206 -----------ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  247 (343)
                                 -+-.|......+-+..+++.+....-.++....+.++..|++
T Consensus       586 ~~~~~~sis~~~Vl~~l~~~~~~l~I~YLE~li~~~~~~~~~lht~ll~ly~e  638 (877)
T KOG2063|consen  586 DKQEAESISRDDVLNYLKSKEPKLLIPYLEHLISDNRLTSTLLHTVLLKLYLE  638 (877)
T ss_pred             ChhhhccCCHHHHHHHhhhhCcchhHHHHHHHhHhccccchHHHHHHHHHHHH
Confidence                       122355666777888888888776545677777888777764

>TIGR02508 type_III_yscG type III secretion protein, YscG family

Probab=80.57  E-value=14  Score=24.49  Aligned_cols=78  Identities=10%  Similarity=0.037  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHH
Q 044084          181 YWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAK  260 (343)
Q Consensus       181 ~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  260 (343)
                      .++|..+-+.+...+-. ...+--+-+..+.+.|++++|..+.+.+    ..||...|-+|..  .+.|..+++..-+.+
T Consensus        21 HqEA~tIAdwL~~~~~~-~E~v~lIRlsSLmNrG~Yq~Al~l~~~~----~~pdlepw~ALce--~rlGl~s~l~~rl~r   93 (115)
T TIGR02508        21 HQEANTIADWLHLKGES-EEAVQLIRLSSLMNRGDYQSALQLGNKL----CYPDLEPWLALCE--WRLGLGSALESRLNR   93 (115)
T ss_pred             HHHHHHHHHHHhcCCch-HHHHHHHHHHHHHccchHHHHHHhcCCC----CCchHHHHHHHHH--HhhccHHHHHHHHHH
Confidence            45566565555554311 1222222234566677777777665544    3566666665544  356666666666666


Q ss_pred             HhhCC
Q 044084          261 MKPKG  265 (343)
Q Consensus       261 m~~~~  265 (343)
                      |...|
T Consensus        94 la~sg   98 (115)
T TIGR02508        94 LAASG   98 (115)
T ss_pred             HHhCC
Confidence            66554

YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designate Yops (Yersinia outer proteins) in Yersinia. This family consists of YscG of Yersinia, and functionally equivalent type III secretion machinery protein in other species: AscG in Aeromonas, LscG in Photorhabdus luminescens, etc.

>PF10345 Cohesin_load: Cohesin loading factor; InterPro: IPR019440 Cohesin loading factor is a conserved protein that has been characterised in fungi

Probab=80.52  E-value=49  Score=30.67  Aligned_cols=196  Identities=11%  Similarity=0.067  Sum_probs=110.2

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHh-CCCCCCCchHHHHHHHHHHhh-ccCcHHHHHHHHHHHHhcCCCCChH--
Q 044084           21 DSGCYCQIMEAFYKIGDSEKVAALFLECES-RKLDLTPSSTHMYKILCDSLG-KSGRAFEILKFFRDMKEKGILEDPS--   96 (343)
Q Consensus        21 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-~~~~~~~~~~~~~~~li~~~~-~~~~~~~a~~~~~~~~~~~~~~~~~--   96 (343)
                      +...|..||.         .|++.++.+.+ ..++|. ....++-.+...+. ...+++.|...+++.....-.++..  
T Consensus        29 ~l~~Y~kLI~---------~ai~CL~~~~~~~~l~p~-~ea~~~l~la~iL~~eT~n~~~Ae~~L~k~~~l~~~~~~~d~   98 (608)
T PF10345_consen   29 QLKQYYKLIA---------TAIKCLEAVLKQFKLSPR-QEARVRLRLASILLEETENLDLAETYLEKAILLCERHRLTDL   98 (608)
T ss_pred             hHHHHHHHHH---------HHHHHHHHHhccCCCCHH-HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccccchHHH
Confidence            4455666654         34555665553 233322 11345556666666 5678999999999775543222221  


Q ss_pred             ---hHHHHHHHHhcccCHHHHHHHHHHHHHcC----CCCCHHHHHHH-HHHHHhcCcHhHHHHHHHHHHhcC---CCCch
Q 044084           97 ---VYASLICSFASIAEVKVAEELFKEAEEKG----MLRDLEVFLKL-VLMYIEEGMVEKTLEVVESMKNAE---LNISD  165 (343)
Q Consensus        97 ---~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~~~~~~~~l-~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~  165 (343)
                         .-..++..+.+.+... |...+++.++.-    ..+-...+.-+ +..+...+++..|.+.++.+....   ..|..
T Consensus        99 k~~~~~ll~~i~~~~~~~~-a~~~l~~~I~~~~~~~~~~w~~~frll~~~l~~~~~d~~~Al~~L~~~~~~a~~~~d~~~  177 (608)
T PF10345_consen   99 KFRCQFLLARIYFKTNPKA-ALKNLDKAIEDSETYGHSAWYYAFRLLKIQLALQHKDYNAALENLQSIAQLANQRGDPAV  177 (608)
T ss_pred             HHHHHHHHHHHHHhcCHHH-HHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhhhcCCHHH
Confidence               1234556666665555 888888766532    11222333333 333334479999999998876432   22334


Q ss_pred             hhHHHHHHHHh--cCCcHHHHHHHHHHHHHcC---------CCCCHhhHHHHHHHHH--ccCChhHHHHHHHHHH
Q 044084          166 CISCVIVNGFS--KRRAYWAAVKVYEQLISQG---------CIPGQVTYASIINAYC--RIGLYSKAEKVFIEMQ  227 (343)
Q Consensus       166 ~~~~~l~~~~~--~~~~~~~a~~~~~~~~~~~---------~~p~~~~~~~ll~~~~--~~~~~~~a~~~~~~~~  227 (343)
                      .++..++.+..  ..+.++++.+.++++....         ..|-..+|..+++.++  ..|+++.+...++.+.
T Consensus       178 ~v~~~l~~~~l~l~~~~~~d~~~~l~~~~~~~~~~q~~~~~~~~qL~~~~lll~l~~~l~~~~~~~~~~~L~~lq  252 (608)
T PF10345_consen  178 FVLASLSEALLHLRRGSPDDVLELLQRAIAQARSLQLDPSVHIPQLKALFLLLDLCCSLQQGDVKNSKQKLKQLQ  252 (608)
T ss_pred             HHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHhhcccCCCCCcHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            44444554443  3566677777777664321         1345566777776654  5677777766665554

It is associated with the cohesin complex and is required in G1 for cohesin binding to chromosomes, but is dispensable in G2 when cohesion has been established. It is often referred to as Ssl3 in Schizosaccharomyces pombe (Fission yeast), and Scc4 in Saccharomyces cerevisiae (Baker's yeast). It complexes with Mis4 [].

>PF06552 TOM20_plant: Plant specific mitochondrial import receptor subunit TOM20; InterPro: IPR010547 This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins

Probab=80.49  E-value=22  Score=26.63  Aligned_cols=114  Identities=14%  Similarity=0.156  Sum_probs=54.4

Q ss_pred             hhHHHHHHHHHhCCCCCChhhHHHHHHHHH---hcCCHHHHHHHHHHHHhC---CCCCCCchHHHHHHHHHHhhccCc--
Q 044084            4 QSKLHYYEKMKSAGIVLDSGCYCQIMEAFY---KIGDSEKVAALFLECESR---KLDLTPSSTHMYKILCDSLGKSGR--   75 (343)
Q Consensus         4 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~---~~~~~~~a~~~~~~~~~~---~~~~~~~~~~~~~~li~~~~~~~~--   75 (343)
                      +.|.+..+.-...++ .|...++....++.   +..+..++.+++++..++   -+..+|....++..+..++...+.  
T Consensus         8 E~ark~aea~y~~nP-~DadnL~~WG~ALLELAqfk~g~es~~miedAisK~eeAL~I~P~~hdAlw~lGnA~ts~A~l~   86 (186)
T PF06552_consen    8 EHARKKAEAAYAKNP-LDADNLTNWGGALLELAQFKQGPESKKMIEDAISKFEEALKINPNKHDALWCLGNAYTSLAFLT   86 (186)
T ss_dssp             HHHHHHHHHHHHH-T-T-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHhCc-HhHHHHHHHHHHHHHHHhccCcchHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHhhc
Confidence            455566655444443 45555554444443   334434455555444221   111112234566667766655432  


Q ss_pred             ---------HHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCC
Q 044084           76 ---------AFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGM  126 (343)
Q Consensus        76 ---------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  126 (343)
                               +++|.+.|++....  .|+...|+.-+....      .|-+++.++.+.+.
T Consensus        87 ~d~~~A~~~F~kA~~~FqkAv~~--~P~ne~Y~ksLe~~~------kap~lh~e~~~~~~  138 (186)
T PF06552_consen   87 PDTAEAEEYFEKATEYFQKAVDE--DPNNELYRKSLEMAA------KAPELHMEIHKQGL  138 (186)
T ss_dssp             --HHHHHHHHHHHHHHHHHHHHH---TT-HHHHHHHHHHH------THHHHHHHHHHSSS
T ss_pred             CChHHHHHHHHHHHHHHHHHHhc--CCCcHHHHHHHHHHH------hhHHHHHHHHHHHh
Confidence                     44455555555443  677777877766653      34555556655543

Most mitochondrial proteins are encoded by the nuclear genome, and are synthesised in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria [].; GO: 0045040 protein import into mitochondrial outer membrane, 0005742 mitochondrial outer membrane translocase complex; PDB: 1ZU2_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	343
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	2e-10
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	4e-10
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	6e-10
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	2e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	3e-04

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 61.0 bits (146), Expect = 2e-10
 Identities = 17/187 (9%), Positives = 51/187 (27%), Gaps = 33/187 (17%)

Query: 98  YASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMK 157
            A L+        + V +    +  +  +    +  L      +    +     ++    
Sbjct: 95  LARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFKCCLLTDQLPLAHHLLVVHH 154

Query: 158 NAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYS 217
                                               +  +     Y +++  + R G + 
Sbjct: 155 G--------------------------------QRQKRKLLTLDMYNAVMLGWARQGAFK 182

Query: 218 KAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGR-IRDAMRLVAKMKPKGCEPNVWIYNSL 276
           +   V   ++  G    +++Y++ +   G+  +      R + +M  +G +        L
Sbjct: 183 ELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVL 242

Query: 277 MDMHGRA 283
           +    RA
Sbjct: 243 LSEEDRA 249

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 60.2 bits (144), Expect = 4e-10
 Identities = 23/163 (14%), Positives = 55/163 (33%), Gaps = 1/163 (0%)

Query: 67  CDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGM 126
           C    +   A  +L      ++K  L    +Y +++  +A     K    +    ++ G+
Sbjct: 137 CLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGL 196

Query: 127 LRDLEVFLKLVLMYIEEGMVEKTLE-VVESMKNAELNISDCISCVIVNGFSKRRAYWAAV 185
             DL  +   +     +     T+E  +E M    L +    + V+++   +     A  
Sbjct: 197 TPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVH 256

Query: 186 KVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQ 228
           KV         +P  V  + ++             K+ + ++ 
Sbjct: 257 KVKPTFSLPPQLPPPVNTSKLLRDVYAKDGRVSYPKLHLPLKT 299

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 59.8 bits (143), Expect = 6e-10
 Identities = 15/128 (11%), Positives = 45/128 (35%), Gaps = 5/128 (3%)

Query: 200 QVTYASIINAYCRIGLYSKAEKVFI---EMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMR 256
           Q    +             A  + +     +QK     +  Y++++  + + G  ++ + 
Sbjct: 127 QQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVY 186

Query: 257 LVAKMKPKGCEPNVWIYNSLMDMHGRA-KNLRQLEKYTTVISAYNMAREFDMCVKFYNEF 315
           ++  +K  G  P++  Y + +   GR  ++   +E+    +S   +  +  +        
Sbjct: 187 VLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQ-ALFTAVLLSE 245

Query: 316 RMNGGVID 323
                V+ 
Sbjct: 246 EDRATVLK 253

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 51.7 bits (122), Expect = 2e-07
 Identities = 17/181 (9%), Positives = 52/181 (28%), Gaps = 1/181 (0%)

Query: 11  EKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSL 70
            +   A +           +             L +    ++      +  MY  +    
Sbjct: 116 GQHSQAQLSGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGW 175

Query: 71  GKSGRAFEILKFFRDMKEKGILEDPSVYASLI-CSFASIAEVKVAEELFKEAEEKGMLRD 129
            + G   E++     +K+ G+  D   YA+ + C      +    E   ++  ++G+   
Sbjct: 176 ARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQ 235

Query: 130 LEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYE 189
                 L+       +++   +V  +            +  ++     +    +  K++ 
Sbjct: 236 ALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGRVSYPKLHL 295

Query: 190 Q 190
            
Sbjct: 296 P 296

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 52.2 bits (124), Expect = 2e-07
 Identities = 44/322 (13%), Positives = 91/322 (28%), Gaps = 116/322 (36%)

Query: 5   SKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYK 64
            +L   +  ++  +VL +    +   AF    +        L C  + L  T      +K
Sbjct: 235 RRLLKSKPYENCLLVLLNVQNAKAWNAF----N--------LSC--KILLTT-----RFK 275

Query: 65  ILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEK 124
            + D L  +      L    D     +  D     SL        + +  ++L +E    
Sbjct: 276 QVTDFLSAATTTHISL----DHHSMTLTPDEVK--SL---LLKYLDCRP-QDLPREV-LT 324

Query: 125 G----------MLRD----LEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCV 170
                       +RD     + +  +    +   ++E +L V+E    AE          
Sbjct: 325 TNPRRLSIIAESIRDGLATWDNWKHVNCDKLTT-IIESSLNVLEP---AEY--------- 371

Query: 171 IVNGFSKRRAYWA------AVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFI 224
                  R+ +        +            IP  +           I        V +
Sbjct: 372 -------RKMFDRLSVFPPSAH----------IPTIL--------LSLIWFDVIKSDVMV 406

Query: 225 EMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAK 284
            +     +K      S+V    K   I                    I +  +++  + +
Sbjct: 407 VV-----NKLHK--YSLVEKQPKESTIS-------------------IPSIYLELKVKLE 440

Query: 285 NLRQLEKYTTVISAYNMAREFD 306
           N   L +  +++  YN+ + FD
Sbjct: 441 NEYALHR--SIVDHYNIPKTFD 460

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7 Length = 530

 Score = 41.4 bits (96), Expect = 3e-04
 Identities = 23/183 (12%), Positives = 57/183 (31%), Gaps = 5/183 (2%)

Query: 114 AEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVN 173
           A  +++ A    + +++ ++             EK   +   +   E      +    + 
Sbjct: 305 AANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMK 364

Query: 174 GFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDK 233
              +     +   ++++          V   + +  Y      S A K+F    +K  D 
Sbjct: 365 FARRAEGIKSGRMIFKKAREDARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDI 424

Query: 234 C--VVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDM---HGRAKNLRQ 288
              V+AY   ++   +    R     V        E +  I+   +      G   ++ +
Sbjct: 425 PEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILK 484

Query: 289 LEK 291
           +EK
Sbjct: 485 VEK 487

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	343
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.97
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.97
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.95
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.94
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.94
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.91
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.91
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.9
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.89
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.89
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.89
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.88
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.87
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.87
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.86
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.86
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.85
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.85
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.84
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.83
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.83
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.83
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.83
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.81
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.78
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.78
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.78
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.78
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.77
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.77
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.76
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.76
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.74
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.74
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.73
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.73
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.73
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.72
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.72
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.72
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.71
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.71
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.71
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.71
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.71
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.7
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.7
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.69
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.68
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.67
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.67
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.65
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.65
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.64
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.63
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.63
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.63
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.62
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.61
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.6
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.6
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.6
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.59
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.57
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.56
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.56
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.55
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.51
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.51
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.5
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.49
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.48
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.48
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.48
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.47
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.47
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.46
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.45
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.44
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.41
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.31
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	99.29
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.29
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	99.28
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	99.28
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.28
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.28
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	99.25
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	99.25
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	99.25
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	99.24
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	99.24
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	99.23
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	99.19
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.19
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.19
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	99.19
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	99.17
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	99.16
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	99.16
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	99.16
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	99.16
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	99.15
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	99.14
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	99.13
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	99.12
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	99.12
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	99.1
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	99.08
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	99.05
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	99.02
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	99.01
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.99
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.98
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.98
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.98
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.96
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.95
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.91
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.91
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.9
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.89
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.88
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.88
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.88
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.88
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.86
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.86
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.84
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.84
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.84
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.84
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.83
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.83
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.82
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.82
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.81
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.81
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.77
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.76
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.76
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.76
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.74
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.73
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	98.72
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.71
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.71
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.7
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.68
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.67
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.67
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.65
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.65
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.65
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.64
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.64
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.64
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.62
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.61
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.61
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.59
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.57
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.57
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.56
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.55
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.53
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.52
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.51
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.51
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.48
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.46
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.41
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.4
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.39
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.39
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.37
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.36
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.35
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	98.31
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.3
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	98.27
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	98.27
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.27
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	98.26
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	98.25
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.25
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.22
1klx_A	138	Cysteine rich protein B; structural genomics, heli	98.17
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	98.16
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	98.13
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	98.12
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	98.1
1klx_A	138	Cysteine rich protein B; structural genomics, heli	98.09
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	98.06
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.98
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.93
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.91
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.85
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.83
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.81
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.8
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.75
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.63
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.57
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	97.55
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	97.42
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.33
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	97.24
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	97.22
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.22
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	97.13
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	97.05
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	97.05
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	97.03
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.99
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	96.8
1pc2_A	152	Mitochondria fission protein; unknown function; NM	96.74
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	96.7
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	96.61
1pc2_A	152	Mitochondria fission protein; unknown function; NM	96.6
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	96.41
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	96.41
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	96.39
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	96.37
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	96.31
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	96.3
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	96.07
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	96.01
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	95.97
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	95.41
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	95.16
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	94.67
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	94.62
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	94.51
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	94.39
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	94.23
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	94.05
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	94.0
2wpv_A	312	GET4, UPF0363 protein YOR164C; golgi-ER traffickin	93.96
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	93.55
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	93.23
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	92.91
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	91.69
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	91.68
3lpz_A	336	GET4 (YOR164C homolog); protein targeting, tail-an	91.65
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	91.2
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	91.05
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	91.02
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	89.56
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	89.32
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	88.22
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	87.99
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	87.52
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	87.3
3kea_A	285	K1L; tropism, ANK repeat, viral protein; 2.30A {Va	86.76
1wdy_A	285	2-5A-dependent ribonuclease; hydrolase, RNA-bindin	86.39
3lpz_A	336	GET4 (YOR164C homolog); protein targeting, tail-an	85.37
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	85.02
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	85.0
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	84.79
3eiq_C	358	Programmed cell death protein 4; PDCD4, anti-oncog	84.66
2p58_C	116	Putative type III secretion protein YSCG; type III	84.61
1y8m_A	144	FIS1; mitochondria, unknown function; NMR {Sacchar	83.17
2nsz_A	129	Programmed cell death protein 4; PDCD4, tumor supp	80.78
2p58_C	116	Putative type III secretion protein YSCG; type III	80.75
3eu9_A	240	Huntingtin-interacting protein 14; epigenetics, an	80.67

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=100.00  E-value=3.7e-36  Score=259.73  Aligned_cols=209  Identities=12%  Similarity=0.171  Sum_probs=182.2

Q ss_pred             HHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccC--------
Q 044084           39 EKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAE--------  110 (343)
Q Consensus        39 ~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~--------  110 (343)
                      ..+..+.+.+.+++....|  ...++.+|++|++.|++++|+++|++|.+.|+.||..||+.||.+|++.+.        
T Consensus         7 s~~e~L~~~~~~k~~~~sp--e~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~   84 (501)
T 4g26_A            7 SPSENLSRKAKKKAIQQSP--EALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNP   84 (501)
T ss_dssp             -----------------CH--HHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCH
T ss_pred             chHHHHHHHHHHhcccCCC--HHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcc
Confidence            4566677788888776654  357889999999999999999999999999999999999999999987653        


Q ss_pred             -HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHH
Q 044084          111 -VKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYE  189 (343)
Q Consensus       111 -~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  189 (343)
                       ++.|.++|++|.+.|+.||..+|+.||.+|++.|++++|.++|++|.+.|+.||..+|+.+|.+|++.|++++|.++|+
T Consensus        85 ~l~~A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~  164 (501)
T 4g26_A           85 GLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDA  164 (501)
T ss_dssp             HHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHH
Confidence             7899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccC
Q 044084          190 QLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTG  249 (343)
Q Consensus       190 ~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  249 (343)
                      +|.+.|+.||..||+.||.+|++.|++++|.++|++|.+.+..|+..||+.++..|...+
T Consensus       165 ~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s~~  224 (501)
T 4g26_A          165 HMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSEV  224 (501)
T ss_dssp             HHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHSHH
T ss_pred             HHHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhcCc
Confidence            999999999999999999999999999999999999999999999999999999988754

>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=2.7e-35  Score=254.42  Aligned_cols=208  Identities=13%  Similarity=0.111  Sum_probs=180.8

Q ss_pred             hhHHHHHHHHHhCCCCCChh-hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCc-------
Q 044084            4 QSKLHYYEKMKSAGIVLDSG-CYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGR-------   75 (343)
Q Consensus         4 ~~A~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~-------   75 (343)
                      ..+..+.+++.+.+..+++. .++.+|+.|++.|++++|.++|++|.+.|+.|+   ..+||+||.+|++.+.       
T Consensus         7 s~~e~L~~~~~~k~~~~spe~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd---~~tyn~Li~~c~~~~~~~~~~~~   83 (501)
T 4g26_A            7 SPSENLSRKAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLS---QYHYNVLLYVCSLAEAATESSPN   83 (501)
T ss_dssp             -----------------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCC---HHHHHHHHHHHTTCCCCSSSSCC
T ss_pred             chHHHHHHHHHHhcccCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCC---HhHHHHHHHHHHhCCchhhhhhc
Confidence            34666778888887766554 588999999999999999999999999999988   8999999999987654       


Q ss_pred             --HHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHH
Q 044084           76 --AFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVV  153 (343)
Q Consensus        76 --~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  153 (343)
                        .+.|.++|++|...|+.||..||+.+|.+|++.|++++|.++|++|.+.|+.||..+|+.+|.+|++.|++++|.++|
T Consensus        84 ~~l~~A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~  163 (501)
T 4g26_A           84 PGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVD  163 (501)
T ss_dssp             HHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHH
Confidence              788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccC
Q 044084          154 ESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIG  214 (343)
Q Consensus       154 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~  214 (343)
                      ++|.+.|+.||..||++||.+|++.|++++|.+++++|.+.|..|+..||+.++..|+..+
T Consensus       164 ~~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s~~  224 (501)
T 4g26_A          164 AHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSEV  224 (501)
T ss_dssp             HHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHSHH
T ss_pred             HHHHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhcCc
Confidence            9999999999999999999999999999999999999999999999999999999988643

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=100.00  E-value=8.6e-33  Score=247.28  Aligned_cols=231  Identities=10%  Similarity=0.040  Sum_probs=194.4

Q ss_pred             cccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHH
Q 044084          107 SIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVK  186 (343)
Q Consensus       107 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  186 (343)
                      +.|++++|.++|+++.+.  +++..+++.++..|.+.|++++|.++|+++.+.++ .+..++..++.++...|++++|..
T Consensus       284 ~~g~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~  360 (597)
T 2xpi_A          284 HEDELRRAEDYLSSINGL--EKSSDLLLCKADTLFVRSRFIDVLAITTKILEIDP-YNLDVYPLHLASLHESGEKNKLYL  360 (597)
T ss_dssp             THHHHHHHHHHHHTSTTG--GGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCCTTHHHHHHHHHHHTCHHHHHH
T ss_pred             CcchHHHHHHHHHHhhcC--CchHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcCc-ccHHHHHHHHHHHHHhCCHHHHHH
Confidence            344444444444444332  36788888899999999999999999999887765 467788899999999999999999


Q ss_pred             HHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCC
Q 044084          187 VYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGC  266 (343)
Q Consensus       187 ~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~  266 (343)
                      +++++.+.. +.+..+++.++..|.+.|++++|.++|+.+.+.. +.+..+|+.++.+|.+.|++++|.++|+++.+.+ 
T Consensus       361 ~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-  437 (597)
T 2xpi_A          361 ISNDLVDRH-PEKAVTWLAVGIYYLCVNKISEARRYFSKSSTMD-PQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLF-  437 (597)
T ss_dssp             HHHHHHHHC-TTSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-
T ss_pred             HHHHHHhhC-cccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-
Confidence            999988653 5577889999999999999999999999998865 4568899999999999999999999999998763 


Q ss_pred             CchHHHHHHHHHHHhcccChhHHHh---------------HHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCcc--HH
Q 044084          267 EPNVWIYNSLMDMHGRAKNLRQLEK---------------YTTVISAYNMAREFDMCVKFYNEFRMN----GGVID--RA  325 (343)
Q Consensus       267 ~p~~~~~~~l~~~~~~~~~~~~a~~---------------~~~l~~~~~~~g~~~~a~~~~~~m~~~----~~~p~--~~  325 (343)
                      +.+..+|..++.+|.+.|++++|..               |..++..|.+.|++++|+++|+++.+.    +..|+  ..
T Consensus       438 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~  517 (597)
T 2xpi_A          438 QGTHLPYLFLGMQHMQLGNILLANEYLQSSYALFQYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAA  517 (597)
T ss_dssp             TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHH
T ss_pred             ccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHH
Confidence            3477899999999999999999987               889999999999999999999999876    66787  78


Q ss_pred             HHHHHHHHHhcccccccC
Q 044084          326 MAGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       326 ~~~~l~~~~~~~g~~~~a  343 (343)
                      +|..++.+|.+.|++++|
T Consensus       518 ~~~~l~~~~~~~g~~~~A  535 (597)
T 2xpi_A          518 TWANLGHAYRKLKMYDAA  535 (597)
T ss_dssp             HHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHhcCHHHH
Confidence            899999999999998864

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=100.00  E-value=1.2e-31  Score=239.99  Aligned_cols=245  Identities=9%  Similarity=-0.005  Sum_probs=197.2

Q ss_pred             CChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHH
Q 044084           93 EDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIV  172 (343)
Q Consensus        93 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  172 (343)
                      ++..++..++..+.+.|++++|..+|+++.+.++. +..++..++.++.+.|++++|.++++++.+..+ .+..+|+.++
T Consensus       303 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~l~  380 (597)
T 2xpi_A          303 KSSDLLLCKADTLFVRSRFIDVLAITTKILEIDPY-NLDVYPLHLASLHESGEKNKLYLISNDLVDRHP-EKAVTWLAVG  380 (597)
T ss_dssp             GCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TSHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcCcc-cHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhCc-ccHHHHHHHH
Confidence            57778888889999999999999999999887643 677788888888888888888888888876554 5677788888


Q ss_pred             HHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChH
Q 044084          173 NGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIR  252 (343)
Q Consensus       173 ~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  252 (343)
                      ..|.+.|++++|.++|+++.+.. +.+..+|+.++.+|.+.|++++|.++|+++.+.+ +.+..+|+.++.+|.+.|+++
T Consensus       381 ~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~  458 (597)
T 2xpi_A          381 IYYLCVNKISEARRYFSKSSTMD-PQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLF-QGTHLPYLFLGMQHMQLGNIL  458 (597)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-TTCSHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCCHH
Confidence            88888888888888888887753 3456788888888888888888888888888765 457788888888888888888


Q ss_pred             HHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh----------------------HHHHHHHHHhcCCHHHHHH
Q 044084          253 DAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK----------------------YTTVISAYNMAREFDMCVK  310 (343)
Q Consensus       253 ~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~----------------------~~~l~~~~~~~g~~~~a~~  310 (343)
                      +|.++|+++.+.. +.+..+|..++..|.+.|++++|..                      |..++.+|.+.|++++|++
T Consensus       459 ~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~  537 (597)
T 2xpi_A          459 LANEYLQSSYALF-QYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAID  537 (597)
T ss_dssp             HHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHH
Confidence            8888888887653 3367788888888888888887765                      5667778888888888888


Q ss_pred             HHHHHHhCCCCccHHHHHHHHHHHhcccccccC
Q 044084          311 FYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       311 ~~~~m~~~~~~p~~~~~~~l~~~~~~~g~~~~a  343 (343)
                      .|+++.+.+ +.+..+|..+..+|.+.|++++|
T Consensus       538 ~~~~~~~~~-p~~~~~~~~l~~~~~~~g~~~~A  569 (597)
T 2xpi_A          538 ALNQGLLLS-TNDANVHTAIALVYLHKKIPGLA  569 (597)
T ss_dssp             HHHHHHHHS-SCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHH
Confidence            888887765 33677888888888888887764

>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=99.97  E-value=1.6e-27  Score=201.96  Aligned_cols=330  Identities=11%  Similarity=0.081  Sum_probs=259.3

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      ++++|++.++.+.+..+ .+...+..+...+.+.|++++|...++...+..    |.+..+|..+...+.+.|++++|++
T Consensus        14 ~~~~A~~~~~~~~~~~p-~~~~~~~~l~~~~~~~~~~~~a~~~~~~a~~~~----p~~~~~~~~lg~~~~~~g~~~~A~~   88 (388)
T 1w3b_A           14 DFEAAERHCMQLWRQEP-DNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN----PLLAEAYSNLGNVYKERGQLQEAIE   88 (388)
T ss_dssp             CHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC----CCchHHHHHHHHHHHHCCCHHHHHH
Confidence            57888998888887643 355667777788888899999999888877654    3336788889999999999999999


Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCC
Q 044084           82 FFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAEL  161 (343)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  161 (343)
                      .|+++.+.. +.+..+|..+..++.+.|++++|...++++.+..+. +...+..+...+...|++++|.+.|+++....+
T Consensus        89 ~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p  166 (388)
T 1w3b_A           89 HYRHALRLK-PDFIDGYINLAAALVAAGDMEGAVQAYVSALQYNPD-LYCVRSDLGNLLKALGRLEEAKACYLKAIETQP  166 (388)
T ss_dssp             HHHHHHHHC-TTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTT-CTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHcC-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCC
Confidence            999888763 224557888888888899999999999888887643 566777888888888999999999988887654


Q ss_pred             CCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHH
Q 044084          162 NISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSM  241 (343)
Q Consensus       162 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  241 (343)
                       .+..+|..+...+...|++++|...|+++.+.+ +.+...+..+...+...|++++|...++...+.. +.+..++..+
T Consensus       167 -~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l  243 (388)
T 1w3b_A          167 -NFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLS-PNHAVVHGNL  243 (388)
T ss_dssp             -TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             -CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCCHHHHHHH
Confidence             456678888888888999999999998888764 3345677778888888888888888888887764 3456778888


Q ss_pred             HHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh---------------HHHHHHHHHhcCCHH
Q 044084          242 VAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK---------------YTTVISAYNMAREFD  306 (343)
Q Consensus       242 ~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~---------------~~~l~~~~~~~g~~~  306 (343)
                      ...|...|++++|...|+++.+.+ +.+..++..+..++.+.|++++|..               +..+...+...|+++
T Consensus       244 ~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~  322 (388)
T 1w3b_A          244 ACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQGNIE  322 (388)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHcCCHH
Confidence            888888888888888888888753 2246678888888888888888876               677788888888888


Q ss_pred             HHHHHHHHHHhCCCCccHHHHHHHHHHHhcccccccC
Q 044084          307 MCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       307 ~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~g~~~~a  343 (343)
                      +|++.++++.+.. +.+..++..+..+|.+.|++++|
T Consensus       323 ~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A  358 (388)
T 1w3b_A          323 EAVRLYRKALEVF-PEFAAAHSNLASVLQQQGKLQEA  358 (388)
T ss_dssp             HHHHHHHHHTTSC-TTCHHHHHHHHHHHHTTTCCHHH
T ss_pred             HHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHH
Confidence            8888888887753 23466788888888888887764

>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=99.97  E-value=7.8e-27  Score=197.73  Aligned_cols=326  Identities=13%  Similarity=0.096  Sum_probs=282.5

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      ++++|...++...+.. +.+..+|..+...+.+.|++++|...|+++.+..    |....+|..+..++...|++++|.+
T Consensus        48 ~~~~a~~~~~~a~~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~----p~~~~~~~~l~~~~~~~g~~~~A~~  122 (388)
T 1w3b_A           48 RLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLK----PDFIDGYINLAAALVAAGDMEGAVQ  122 (388)
T ss_dssp             CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHHSCSSHHHH
T ss_pred             CHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHcC----cchHHHHHHHHHHHHHcCCHHHHHH
Confidence            5678889998888764 3578899999999999999999999999998754    3336789999999999999999999


Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCC
Q 044084           82 FFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAEL  161 (343)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  161 (343)
                      .|+++.+... .+...+..+...+...|++++|...|+++.+..+. +..+|..+...+...|++++|...|+++.+.++
T Consensus       123 ~~~~al~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p  200 (388)
T 1w3b_A          123 AYVSALQYNP-DLYCVRSDLGNLLKALGRLEEAKACYLKAIETQPN-FAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDP  200 (388)
T ss_dssp             HHHHHHHHCT-TCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHhCC-CcHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC
Confidence            9999988642 24556777888899999999999999999987643 688999999999999999999999999998765


Q ss_pred             CCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHH
Q 044084          162 NISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSM  241 (343)
Q Consensus       162 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  241 (343)
                       .+...|..+...+...|++++|...+++..... +.+..++..+..++.+.|++++|...|+.+.+.+ +.+..+|..+
T Consensus       201 -~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l  277 (388)
T 1w3b_A          201 -NFLDAYINLGNVLKEARIFDRAVAAYLRALSLS-PNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNL  277 (388)
T ss_dssp             -TCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHH
T ss_pred             -CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHH
Confidence             456788899999999999999999999998874 3357788999999999999999999999999875 4467889999


Q ss_pred             HHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh---------------HHHHHHHHHhcCCHH
Q 044084          242 VAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK---------------YTTVISAYNMAREFD  306 (343)
Q Consensus       242 ~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~---------------~~~l~~~~~~~g~~~  306 (343)
                      ...+.+.|++++|...|+++.+. .+.+..++..+...+.+.|++++|..               +..+...+.+.|+++
T Consensus       278 ~~~~~~~g~~~~A~~~~~~al~~-~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~  356 (388)
T 1w3b_A          278 ANALKEKGSVAEAEDCYNTALRL-CPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQ  356 (388)
T ss_dssp             HHHHHHHSCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhh-CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHH
Confidence            99999999999999999999886 34578899999999999999999987               788999999999999


Q ss_pred             HHHHHHHHHHhCCCCccHHHHHHHHHHHhcccc
Q 044084          307 MCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQ  339 (343)
Q Consensus       307 ~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~g~  339 (343)
                      +|++.|+++.+... .+...|..+..++.+.|+
T Consensus       357 ~A~~~~~~a~~~~p-~~~~a~~~lg~~~~~~~~  388 (388)
T 1w3b_A          357 EALMHYKEAIRISP-TFADAYSNMGNTLKEMQD  388 (388)
T ss_dssp             HHHHHHHHHHTTCT-TCHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHhhCC-CCHHHHHhHHHHHHHccC
Confidence            99999999998542 245668888888776653

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A

Probab=99.95  E-value=3.3e-24  Score=185.15  Aligned_cols=316  Identities=11%  Similarity=0.070  Sum_probs=246.5

Q ss_pred             hHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHH
Q 044084            5 SKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFR   84 (343)
Q Consensus         5 ~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~   84 (343)
                      .+...+..+.... +.+...+..+...+.+.|++++|..+|+++.+..    |.+..+|..+..++...|++++|+..|+
T Consensus        10 ~~~~~~~~~~~~~-p~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~----p~~~~~~~~l~~~~~~~g~~~~A~~~~~   84 (450)
T 2y4t_A           10 GVDLGTENLYFQS-MADVEKHLELGKKLLAAGQLADALSQFHAAVDGD----PDNYIAYYRRATVFLAMGKSKAALPDLT   84 (450)
T ss_dssp             --------------CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             ccccccccccccc-HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC----CccHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            3444555555543 2467788999999999999999999999988754    3336889999999999999999999999


Q ss_pred             HHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCH---HHHHHH------------HHHHHhcCcHhHH
Q 044084           85 DMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDL---EVFLKL------------VLMYIEEGMVEKT  149 (343)
Q Consensus        85 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l------------~~~~~~~~~~~~a  149 (343)
                      ++.+.+. .+..++..+..++.+.|++++|...|+++.+..+. +.   ..+..+            ...+...|++++|
T Consensus        85 ~al~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A  162 (450)
T 2y4t_A           85 KVIQLKM-DFTAARLQRGHLLLKQGKLDEAEDDFKKVLKSNPS-ENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAA  162 (450)
T ss_dssp             HHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHhcCC-CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-ChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHH
Confidence            9988753 35778888999999999999999999999886532 34   555555            4448889999999


Q ss_pred             HHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHc
Q 044084          150 LEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       150 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  229 (343)
                      +..|+++.+..+ .+..++..+..+|...|++++|...|+++.+.. +.+..++..+...|...|++++|...|+.+.+.
T Consensus       163 ~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  240 (450)
T 2y4t_A          163 IAFLDKILEVCV-WDAELRELRAECFIKEGEPRKAISDLKAASKLK-NDNTEAFYKISTLYYQLGDHELSLSEVRECLKL  240 (450)
T ss_dssp             HHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHH-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCC-CChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            999999987765 567788899999999999999999999988763 456788899999999999999999999999876


Q ss_pred             CCCcChhhHHHH------------HHHHHccCChHHHHHHHHHHhhCCCCch-----HHHHHHHHHHHhcccChhHHHh-
Q 044084          230 GFDKCVVAYSSM------------VAMYGKTGRIRDAMRLVAKMKPKGCEPN-----VWIYNSLMDMHGRAKNLRQLEK-  291 (343)
Q Consensus       230 ~~~~~~~~~~~l------------~~~~~~~~~~~~a~~~~~~m~~~~~~p~-----~~~~~~l~~~~~~~~~~~~a~~-  291 (343)
                      . +.+...+..+            ...+...|++++|...|+++.+.  .|+     ...+..+..++.+.|++++|.. 
T Consensus       241 ~-p~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  317 (450)
T 2y4t_A          241 D-QDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKT--EPSIAEYTVRSKERICHCFSKDEKPVEAIRV  317 (450)
T ss_dssp             C-TTCHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CCSSHHHHHHHHHHHHHHHHTTTCHHHHHHH
T ss_pred             C-CChHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHHHHCCCHHHHHHH
Confidence            4 3344445444            78889999999999999999875  343     4577888889999999998877 


Q ss_pred             --------------HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHH
Q 044084          292 --------------YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGV  333 (343)
Q Consensus       292 --------------~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~  333 (343)
                                    |..+..+|...|++++|...++++.+.... +...+..+..+
T Consensus       318 ~~~a~~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~~~  372 (450)
T 2y4t_A          318 CSEVLQMEPDNVNALKDRAEAYLIEEMYDEAIQDYETAQEHNEN-DQQIREGLEKA  372 (450)
T ss_dssp             HHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSS-CHHHHHHHHHH
T ss_pred             HHHHHHhCcccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcc-hHHHHHHHHHH
Confidence                          888899999999999999999999885322 34556656533

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.94  E-value=1e-23  Score=184.97  Aligned_cols=330  Identities=11%  Similarity=0.041  Sum_probs=270.0

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      ++++|+..|+++.+.+  |+..+|..+..++.+.|++++|...++++.+.+    |.+..+|..+..++...|++++|..
T Consensus        21 ~~~~A~~~~~~al~~~--p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~----p~~~~~~~~l~~~~~~~g~~~~A~~   94 (514)
T 2gw1_A           21 KYDDAIKYYNWALELK--EDPVFYSNLSACYVSVGDLKKVVEMSTKALELK----PDYSKVLLRRASANEGLGKFADAMF   94 (514)
T ss_dssp             CHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC----SCCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             cHHHHHHHHHHHHhcC--ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC----hHHHHHHHHHHHHHHHHhhHHHHHH
Confidence            6789999999999875  688999999999999999999999999998765    3346889999999999999999999


Q ss_pred             HHHHHHhcCCCCC-------------------------------------------------------------------
Q 044084           82 FFRDMKEKGILED-------------------------------------------------------------------   94 (343)
Q Consensus        82 ~~~~~~~~~~~~~-------------------------------------------------------------------   94 (343)
                      .|+++...+...+                                                                   
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  174 (514)
T 2gw1_A           95 DLSVLSLNGDFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSVTSMASFFGIFKPE  174 (514)
T ss_dssp             HHHHHHHSSSCCGGGTHHHHHHHHHHHHHHHHTTC---------------------------CCCCHHHHHHHHTTSCCC
T ss_pred             HHHHHHhcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchhHHHHHHHhhcCHH
Confidence            9999877642110                                                                   


Q ss_pred             -----------hHhHHHHHHHHh---cccCHHHHHHHHHHHHH-----c--CC------CCCHHHHHHHHHHHHhcCcHh
Q 044084           95 -----------PSVYASLICSFA---SIAEVKVAEELFKEAEE-----K--GM------LRDLEVFLKLVLMYIEEGMVE  147 (343)
Q Consensus        95 -----------~~~~~~l~~~~~---~~~~~~~a~~~~~~~~~-----~--~~------~~~~~~~~~l~~~~~~~~~~~  147 (343)
                                 ...+......+.   +.|+++.|...++++.+     .  .+      +.+..++..+...+...|+++
T Consensus       175 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  254 (514)
T 2gw1_A          175 LTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTGIFKFLKNDPL  254 (514)
T ss_dssp             CCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHHHHHHHSSCHH
T ss_pred             HHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHHHHHHHCCCHH
Confidence                       222222223333   37999999999999888     3  11      124667888899999999999


Q ss_pred             HHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHH
Q 044084          148 KTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQ  227 (343)
Q Consensus       148 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  227 (343)
                      +|...|+++.+..+.  ...+..+...+...|++++|...++++.... +.+...+..+...+...|++++|...++...
T Consensus       255 ~A~~~~~~~l~~~~~--~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~  331 (514)
T 2gw1_A          255 GAHEDIKKAIELFPR--VNSYIYMALIMADRNDSTEYYNYFDKALKLD-SNNSSVYYHRGQMNFILQNYDQAGKDFDKAK  331 (514)
T ss_dssp             HHHHHHHHHHHHCCC--HHHHHHHHHHHHTSSCCTTGGGHHHHHHTTC-TTCTHHHHHHHHHHHHTTCTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhCcc--HHHHHHHHHHHHHCCCHHHHHHHHHHHhhcC-cCCHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            999999999887654  7788889999999999999999999988764 3456788888999999999999999999998


Q ss_pred             HcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh----------------
Q 044084          228 QKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK----------------  291 (343)
Q Consensus       228 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~----------------  291 (343)
                      +.. +.+...+..+...+...|++++|...++++.+.. +.+..++..+...+...|++++|..                
T Consensus       332 ~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~  409 (514)
T 2gw1_A          332 ELD-PENIFPYIQLACLAYRENKFDDCETLFSEAKRKF-PEAPEVPNFFAEILTDKNDFDKALKQYDLAIELENKLDGIY  409 (514)
T ss_dssp             HTC-SSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSSSCS
T ss_pred             HhC-hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHc-ccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccchHH
Confidence            875 4467788899999999999999999999988752 2356778888899999999998876                


Q ss_pred             -----HHHHHHHHHh---cCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHhcccccccC
Q 044084          292 -----YTTVISAYNM---AREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       292 -----~~~l~~~~~~---~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~g~~~~a  343 (343)
                           +..+...+..   .|++++|...++++..... .+...+..+..+|.+.|++++|
T Consensus       410 ~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~la~~~~~~g~~~~A  468 (514)
T 2gw1_A          410 VGIAPLVGKATLLTRNPTVENFIEATNLLEKASKLDP-RSEQAKIGLAQMKLQQEDIDEA  468 (514)
T ss_dssp             SCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhCc-ccHHHHHHHHHHHHHhcCHHHH
Confidence                 5567778888   8999999999999988642 3566788899999999988764

>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=99.94  E-value=1.2e-22  Score=175.33  Aligned_cols=329  Identities=12%  Similarity=0.043  Sum_probs=264.0

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      ++++|+.+|+++.+..+ .+..++..+..++.+.|++++|...|+++.+.+    |....++..+...+...|++++|.+
T Consensus        41 ~~~~A~~~~~~~l~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~----p~~~~~~~~l~~~~~~~g~~~~A~~  115 (450)
T 2y4t_A           41 QLADALSQFHAAVDGDP-DNYIAYYRRATVFLAMGKSKAALPDLTKVIQLK----MDFTAARLQRGHLLLKQGKLDEAED  115 (450)
T ss_dssp             CHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC----CCcHHHHHHHHHHHHHcCCHHHHHH
Confidence            67899999999998643 578899999999999999999999999998875    3336889999999999999999999


Q ss_pred             HHHHHHhcCCCCCh---HhHHHH------------HHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcH
Q 044084           82 FFRDMKEKGILEDP---SVYASL------------ICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMV  146 (343)
Q Consensus        82 ~~~~~~~~~~~~~~---~~~~~l------------~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  146 (343)
                      .|+++.+.... +.   ..+..+            ...+...|++++|...++++.+..+ .+..++..+..+|.+.|++
T Consensus       116 ~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~  193 (450)
T 2y4t_A          116 DFKKVLKSNPS-ENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVCV-WDAELRELRAECFIKEGEP  193 (450)
T ss_dssp             HHHHHHTSCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCG
T ss_pred             HHHHHHhcCCC-ChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CChHHHHHHHHHHHHCCCH
Confidence            99999886422 33   455544            3448899999999999999998764 3789999999999999999


Q ss_pred             hHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHH------------HHHHHccC
Q 044084          147 EKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASI------------INAYCRIG  214 (343)
Q Consensus       147 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l------------l~~~~~~~  214 (343)
                      ++|+++|+++.+..+ .+..++..+...+...|++++|...|+++.... +.+...+..+            ...+...|
T Consensus       194 ~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~~~~~~~~~~~~~~~~~~~~~g  271 (450)
T 2y4t_A          194 RKAISDLKAASKLKN-DNTEAFYKISTLYYQLGDHELSLSEVRECLKLD-QDHKRCFAHYKQVKKLNKLIESAEELIRDG  271 (450)
T ss_dssp             GGGHHHHHHHHHHHC-SCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CChHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            999999999987764 567789999999999999999999999998763 2233444444            78899999


Q ss_pred             ChhHHHHHHHHHHHcCCCcC-----hhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHH
Q 044084          215 LYSKAEKVFIEMQQKGFDKC-----VVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQL  289 (343)
Q Consensus       215 ~~~~a~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a  289 (343)
                      ++++|...|+.+.+..  |+     ...+..+...+.+.|++++|...++++.+.. +.+..+|..+..+|...|++++|
T Consensus       272 ~~~~A~~~~~~~l~~~--p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~~~~~~~~~~A  348 (450)
T 2y4t_A          272 RYTDATSKYESVMKTE--PSIAEYTVRSKERICHCFSKDEKPVEAIRVCSEVLQME-PDNVNALKDRAEAYLIEEMYDEA  348 (450)
T ss_dssp             CHHHHHHHHHHHHHHC--CSSHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             CHHHHHHHHHHHHhcC--CcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhcCHHHH
Confidence            9999999999999864  43     3478889999999999999999999998752 33678999999999999999999


Q ss_pred             Hh---------------HHHHH------------HHHHhcC-----CHHHHHHHHHHH-HhCCC--Ccc-------HHHH
Q 044084          290 EK---------------YTTVI------------SAYNMAR-----EFDMCVKFYNEF-RMNGG--VID-------RAMA  327 (343)
Q Consensus       290 ~~---------------~~~l~------------~~~~~~g-----~~~~a~~~~~~m-~~~~~--~p~-------~~~~  327 (343)
                      ..               +..+.            ..|...|     ..+++.+.|+++ .+...  .|+       ...+
T Consensus       349 ~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~~~~y~~lg~~~~~~~~~~~~~y~~~~l~~~pd~~~~~~~~~~a~~~~  428 (450)
T 2y4t_A          349 IQDYETAQEHNENDQQIREGLEKAQRLLKQSQKRDYYKILGVKRNAKKQEIIKAYRKLALQWHPDNFQNEEEKKKAEKKF  428 (450)
T ss_dssp             HHHHHHHHTTSSSCHHHHHHHHHHHHHHHHHHSCCSGGGSCSSTTCCTTHHHHHHHHHHHHSCGGGCCSHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCcchHHHHHHHHHHHHHhhcccchhHHHHhCCCccCCHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHH
Confidence            87               33333            2233334     566778888863 33211  122       2367


Q ss_pred             HHHHHHHhccccccc
Q 044084          328 GIMVGVFSKLSQIEE  342 (343)
Q Consensus       328 ~~l~~~~~~~g~~~~  342 (343)
                      ..+..+|...|+.+.
T Consensus       429 ~~i~~ay~~L~d~~~  443 (450)
T 2y4t_A          429 IDIAAAKEVLSDPEM  443 (450)
T ss_dssp             HHHHHHHHHSSGGGG
T ss_pred             HHHHHHHHHhCCHHH
Confidence            888888888887654

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.91  E-value=9.1e-21  Score=158.35  Aligned_cols=307  Identities=14%  Similarity=0.100  Sum_probs=152.6

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      ++++|+..|+++.+..+ .+..++..+...+...|++++|...|+++.+..    |.....|..+...+...|++++|..
T Consensus        18 ~~~~A~~~~~~~l~~~p-~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~----~~~~~~~~~l~~~~~~~~~~~~A~~   92 (359)
T 3ieg_A           18 QLADALSQFHAAVDGDP-DNYIAYYRRATVFLAMGKSKAALPDLTKVIALK----MDFTAARLQRGHLLLKQGKLDEAED   92 (359)
T ss_dssp             CHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             CHHHHHHHHHHHHhhCc-ccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC----CCcchHHHHHHHHHHHcCChHHHHH
Confidence            34455555555554432 234455555555555555555555555554432    1123445555555555555555555


Q ss_pred             HHHHHHhcCCC--CChHhHHHH------------HHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHh
Q 044084           82 FFRDMKEKGIL--EDPSVYASL------------ICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVE  147 (343)
Q Consensus        82 ~~~~~~~~~~~--~~~~~~~~l------------~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  147 (343)
                      .|++..+....  .+...+..+            ...+...|++++|...++++.+..+. +..++..+...+...|+++
T Consensus        93 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  171 (359)
T 3ieg_A           93 DFKKVLKSNPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVCVW-DAELRELRAECFIKEGEPR  171 (359)
T ss_dssp             HHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-chHHHHHHHHHHHHCCCHH
Confidence            55555443210  122222222            24444555555555555555544322 4455555555555555555


Q ss_pred             HHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHH------------HHHHHHHccCC
Q 044084          148 KTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYA------------SIINAYCRIGL  215 (343)
Q Consensus       148 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~------------~ll~~~~~~~~  215 (343)
                      +|...++++.+..+ .+..++..+...+...|++++|...+++..+.. +.+...+.            .+...+.+.|+
T Consensus       172 ~A~~~~~~~~~~~~-~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~  249 (359)
T 3ieg_A          172 KAISDLKAASKLKS-DNTEAFYKISTLYYQLGDHELSLSEVRECLKLD-QDHKRCFAHYKQVKKLNKLIESAEELIRDGR  249 (359)
T ss_dssp             HHHHHHHHHHTTCS-CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-ccchHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence            55555555554432 234445555555555555555555555554432 11112111            11333445555


Q ss_pred             hhHHHHHHHHHHHcCCCcCh----hhHHHHHHHHHccCChHHHHHHHHHHhhCCCCc-hHHHHHHHHHHHhcccChhHHH
Q 044084          216 YSKAEKVFIEMQQKGFDKCV----VAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEP-NVWIYNSLMDMHGRAKNLRQLE  290 (343)
Q Consensus       216 ~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~~~~~l~~~~~~~~~~~~a~  290 (343)
                      +++|...++.+.+.. +.+.    ..+..+..++...|++++|...+++..+.  .| +..+                  
T Consensus       250 ~~~A~~~~~~~~~~~-~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~------------------  308 (359)
T 3ieg_A          250 YTDATSKYESVMKTE-PSVAEYTVRSKERICHCFSKDEKPVEAIRICSEVLQM--EPDNVNA------------------  308 (359)
T ss_dssp             HHHHHHHHHHHHHHC-CSSHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHH------------------
T ss_pred             HHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CcccHHH------------------
Confidence            555555555555433 1111    12233444555555555555555555443  12 2222                  


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHhcccc
Q 044084          291 KYTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQ  339 (343)
Q Consensus       291 ~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~g~  339 (343)
                       +..+...+...|++++|.+.|++..+... -+...+..+..+....++
T Consensus       309 -~~~~~~~~~~~g~~~~A~~~~~~a~~~~p-~~~~~~~~l~~~~~~~~~  355 (359)
T 3ieg_A          309 -LKDRAEAYLIEEMYDEAIQDYEAAQEHNE-NDQQIREGLEKAQRLLKQ  355 (359)
T ss_dssp             -HHHHHHHHHHTTCHHHHHHHHHHHHTTCT-TCHHHHHHHHHHHHHHHH
T ss_pred             -HHHHHHHHHHcCCHHHHHHHHHHHHhcCC-CChHHHHHHHHHHHHHHH
Confidence             55666777788999999999999998642 235556666666655443

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=99.91  E-value=1.7e-21  Score=171.88  Aligned_cols=330  Identities=11%  Similarity=0.096  Sum_probs=257.3

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      ++++|+..|+++.+..+ .+..++..+..++.+.|++++|.+.|+++.+.+    |.+..++..+..++...|++++|++
T Consensus        40 ~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~----p~~~~~~~~la~~~~~~g~~~~A~~  114 (537)
T 3fp2_A           40 NFNEAIKYYQYAIELDP-NEPVFYSNISACYISTGDLEKVIEFTTKALEIK----PDHSKALLRRASANESLGNFTDAMF  114 (537)
T ss_dssp             CCC-CHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             cHHHHHHHHHHHHhhCC-CCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC----CchHHHHHHHHHHHHHcCCHHHHHH
Confidence            57889999999998754 578899999999999999999999999998765    3346889999999999999999999


Q ss_pred             HHHHHHhcCC------------------------------------CCChH-----------------------------
Q 044084           82 FFRDMKEKGI------------------------------------LEDPS-----------------------------   96 (343)
Q Consensus        82 ~~~~~~~~~~------------------------------------~~~~~-----------------------------   96 (343)
                      .|+.+....-                                    .|+..                             
T Consensus       115 ~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  194 (537)
T 3fp2_A          115 DLSVLSLNGDFDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLEVSSVNTSSNYDTAYA  194 (537)
T ss_dssp             HHHHHC-----------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSCHHHHHHTSCCCCSSCSSHH
T ss_pred             HHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcChHHHHHHHhhccccccHHH
Confidence            9864421100                                    01110                             


Q ss_pred             -hHHHHHHHHhc--------ccCHHHHHHHHHHHHHcCCCCC-------HHHHHHHHHHHHhcCcHhHHHHHHHHHHhcC
Q 044084           97 -VYASLICSFAS--------IAEVKVAEELFKEAEEKGMLRD-------LEVFLKLVLMYIEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus        97 -~~~~l~~~~~~--------~~~~~~a~~~~~~~~~~~~~~~-------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  160 (343)
                       ....+...+..        .+++++|..+++++.+..+. +       ..++..+...+...|++++|...|++.....
T Consensus       195 ~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~p~-~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~  273 (537)
T 3fp2_A          195 LLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSANTV-DDPLRENAALALCYTGIFHFLKNNLLDAQVLLQESINLH  273 (537)
T ss_dssp             HHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC--CC-CHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHCCC-cchhhHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcC
Confidence             11111111111        14788888888888876533 3       2356777788889999999999999998876


Q ss_pred             CCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHH
Q 044084          161 LNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSS  240 (343)
Q Consensus       161 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  240 (343)
                      +  +...+..+...+...|++++|...++++.+.. +.+..++..+...+...|++++|...++...+.. +.+...+..
T Consensus       274 ~--~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~  349 (537)
T 3fp2_A          274 P--TPNSYIFLALTLADKENSQEFFKFFQKAVDLN-PEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLN-PENVYPYIQ  349 (537)
T ss_dssp             C--CHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCSHHHHH
T ss_pred             C--CchHHHHHHHHHHHhcCHHHHHHHHHHHhccC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC-CCCHHHHHH
Confidence            4  46788889999999999999999999998874 3457788889999999999999999999998875 446788999


Q ss_pred             HHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh---------------------HHHHHHHH
Q 044084          241 MVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK---------------------YTTVISAY  299 (343)
Q Consensus       241 l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~---------------------~~~l~~~~  299 (343)
                      +...+...|++++|...++++.+.. +.+...+..+...+...|++++|..                     +......+
T Consensus       350 la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~a~~~  428 (537)
T 3fp2_A          350 LACLLYKQGKFTESEAFFNETKLKF-PTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKIHVGIGPLIGKATIL  428 (537)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCSSCSSTTHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCcchhhHHHHHHHHHHHHHH
Confidence            9999999999999999999998763 3356688888999999999999987                     22334566


Q ss_pred             Hhc----------CCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHhcccccccC
Q 044084          300 NMA----------REFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       300 ~~~----------g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~g~~~~a  343 (343)
                      .+.          |++++|+..|++..+... .+...+..+..+|.+.|++++|
T Consensus       429 ~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p-~~~~~~~~l~~~~~~~g~~~~A  481 (537)
T 3fp2_A          429 ARQSSQDPTQLDEEKFNAAIKLLTKACELDP-RSEQAKIGLAQLKLQMEKIDEA  481 (537)
T ss_dssp             HHHHTC----CCHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHhhccchhhhHhHHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhccHHHH
Confidence            666          999999999999988643 3567788899999999998764

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.90  E-value=3.9e-21  Score=168.56  Aligned_cols=312  Identities=11%  Similarity=-0.036  Sum_probs=258.6

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHH
Q 044084           22 SGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASL  101 (343)
Q Consensus        22 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  101 (343)
                      ...+......+.+.|++++|...|+++.+.+  |+   ..+|..+..++...|++++|++.++++.+.+ +.+..++..+
T Consensus         6 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~---~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l   79 (514)
T 2gw1_A            6 ALALKDKGNQFFRNKKYDDAIKYYNWALELK--ED---PVFYSNLSACYVSVGDLKKVVEMSTKALELK-PDYSKVLLRR   79 (514)
T ss_dssp             HHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC--CC---HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-SCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhcC--cc---HHHHHhHHHHHHHHhhHHHHHHHHHHHhccC-hHHHHHHHHH
Confidence            4567778889999999999999999998876  33   6789999999999999999999999999875 3356789999


Q ss_pred             HHHHhcccCHHHHHHHHHHHHHcCCCC-----------------------------------------------------
Q 044084          102 ICSFASIAEVKVAEELFKEAEEKGMLR-----------------------------------------------------  128 (343)
Q Consensus       102 ~~~~~~~~~~~~a~~~~~~~~~~~~~~-----------------------------------------------------  128 (343)
                      ..++.+.|++++|...|+++.+.+...                                                     
T Consensus        80 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (514)
T 2gw1_A           80 ASANEGLGKFADAMFDLSVLSLNGDFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLP  159 (514)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHSSSCCGGGTHHHHHHHHHHHHHHHHTTC---------------------------CCC
T ss_pred             HHHHHHHhhHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCc
Confidence            999999999999999999988765310                                                     


Q ss_pred             -------------------------CHHHHHHHHHHHHh---cCcHhHHHHHHHHHHh-----c--CC------CCchhh
Q 044084          129 -------------------------DLEVFLKLVLMYIE---EGMVEKTLEVVESMKN-----A--EL------NISDCI  167 (343)
Q Consensus       129 -------------------------~~~~~~~l~~~~~~---~~~~~~a~~~~~~~~~-----~--~~------~~~~~~  167 (343)
                                               +...+..+...+..   .|++++|...|+++.+     .  .+      +.+..+
T Consensus       160 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  239 (514)
T 2gw1_A          160 SVTSMASFFGIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAIS  239 (514)
T ss_dssp             CHHHHHHHHTTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHH
T ss_pred             hhHHHHHHHhhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHH
Confidence                                     13333444444444   8999999999999887     3  11      123456


Q ss_pred             HHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHc
Q 044084          168 SCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGK  247 (343)
Q Consensus       168 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  247 (343)
                      +..+...+...|++++|...++++.+..  |+...+..+...+...|++++|...++.+.+.. +.+...+..+...+..
T Consensus       240 ~~~~~~~~~~~~~~~~A~~~~~~~l~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~  316 (514)
T 2gw1_A          240 LEHTGIFKFLKNDPLGAHEDIKKAIELF--PRVNSYIYMALIMADRNDSTEYYNYFDKALKLD-SNNSSVYYHRGQMNFI  316 (514)
T ss_dssp             HHHHHHHHHHSSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTC-TTCTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhhC--ccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcC-cCCHHHHHHHHHHHHH
Confidence            7888899999999999999999999875  447888889999999999999999999998875 5577889999999999


Q ss_pred             cCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh---------------HHHHHHHHHhcCCHHHHHHHH
Q 044084          248 TGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK---------------YTTVISAYNMAREFDMCVKFY  312 (343)
Q Consensus       248 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~---------------~~~l~~~~~~~g~~~~a~~~~  312 (343)
                      .|++++|...++++.+.. +.+...+..+...+...|++++|..               +..+...+...|++++|+..+
T Consensus       317 ~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~  395 (514)
T 2gw1_A          317 LQNYDQAGKDFDKAKELD-PENIFPYIQLACLAYRENKFDDCETLFSEAKRKFPEAPEVPNFFAEILTDKNDFDKALKQY  395 (514)
T ss_dssp             TTCTTHHHHHHHHHHHTC-SSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             hCCHHHHHHHHHHHHHhC-hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            999999999999998863 2356788899999999999999987               778889999999999999999


Q ss_pred             HHHHhCCCC-cc----HHHHHHHHHHHhc---ccccccC
Q 044084          313 NEFRMNGGV-ID----RAMAGIMVGVFSK---LSQIEEL  343 (343)
Q Consensus       313 ~~m~~~~~~-p~----~~~~~~l~~~~~~---~g~~~~a  343 (343)
                      +++...... |+    ...+..+..++.+   .|++++|
T Consensus       396 ~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A  434 (514)
T 2gw1_A          396 DLAIELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEA  434 (514)
T ss_dssp             HHHHHHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHH
T ss_pred             HHHHHhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHH
Confidence            999775322 11    2378889999999   8988764

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=99.89  E-value=6e-20  Score=151.67  Aligned_cols=295  Identities=11%  Similarity=0.045  Sum_probs=239.6

Q ss_pred             CCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHh
Q 044084           18 IVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSV   97 (343)
Q Consensus        18 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~   97 (343)
                      .+.+...+..+...+...|++++|.++|+++.+.....    ...+..++..+...|++++|...++++.+... .+...
T Consensus        18 ~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~----~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~   92 (330)
T 3hym_B           18 LQENLDVVVSLAERHYYNCDFKMCYKLTSVVMEKDPFH----ASCLPVHIGTLVELNKANELFYLSHKLVDLYP-SNPVS   92 (330)
T ss_dssp             --CCCTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTC----TTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TSTHH
T ss_pred             chhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCC----hhhHHHHHHHHHHhhhHHHHHHHHHHHHHhCc-CCHHH
Confidence            45677788899999999999999999999998765332    35677788888999999999999999988643 36778


Q ss_pred             HHHHHHHHhccc-CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHh
Q 044084           98 YASLICSFASIA-EVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFS  176 (343)
Q Consensus        98 ~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  176 (343)
                      +..+...+...| ++++|...++++.+.... +...|..+...+...|++++|...|++..+... .+...+..+...+.
T Consensus        93 ~~~l~~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~l~~~~~  170 (330)
T 3hym_B           93 WFAVGCYYLMVGHKNEHARRYLSKATTLEKT-YGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMK-GCHLPMLYIGLEYG  170 (330)
T ss_dssp             HHHHHHHHHHSCSCHHHHHHHHHHHHTTCTT-CTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTT-TCSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhHHHHHHHHHHHHHhCCc-cHHHHHHHHHHHHHccCHHHHHHHHHHHHHhcc-ccHHHHHHHHHHHH
Confidence            888999999999 999999999999987643 678899999999999999999999999988765 34566777999999


Q ss_pred             cCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcC--------CCcChhhHHHHHHHHHcc
Q 044084          177 KRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKG--------FDKCVVAYSSMVAMYGKT  248 (343)
Q Consensus       177 ~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~--------~~~~~~~~~~l~~~~~~~  248 (343)
                      ..|++++|...+++..+.. +.+...+..+...+...|++++|...++...+..        .+.+..++..+...+...
T Consensus       171 ~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~  249 (330)
T 3hym_B          171 LTNNSKLAERFFSQALSIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKL  249 (330)
T ss_dssp             HTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHT
T ss_pred             HHhhHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHh
Confidence            9999999999999998874 4567888899999999999999999999988752        134467899999999999


Q ss_pred             CChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHH
Q 044084          249 GRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAG  328 (343)
Q Consensus       249 ~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~  328 (343)
                      |++++|...+++..+... .+...                   +..+...+...|++++|.+.+++..+... .+...+.
T Consensus       250 g~~~~A~~~~~~a~~~~~-~~~~~-------------------~~~la~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~  308 (330)
T 3hym_B          250 KKYAEALDYHRQALVLIP-QNAST-------------------YSAIGYIHSLMGNFENAVDYFHTALGLRR-DDTFSVT  308 (330)
T ss_dssp             TCHHHHHHHHHHHHHHST-TCSHH-------------------HHHHHHHHHHHTCHHHHHHHHHTTTTTCS-CCHHHHH
T ss_pred             cCHHHHHHHHHHHHhhCc-cchHH-------------------HHHHHHHHHHhccHHHHHHHHHHHHccCC-CchHHHH
Confidence            999999999999987521 12333                   34455666778888999999999887542 3566777


Q ss_pred             HHHHHH-hcccccc
Q 044084          329 IMVGVF-SKLSQIE  341 (343)
Q Consensus       329 ~l~~~~-~~~g~~~  341 (343)
                      .+..++ ...|+.+
T Consensus       309 ~l~~~~~~~~g~~~  322 (330)
T 3hym_B          309 MLGHCIEMYIGDSE  322 (330)
T ss_dssp             HHHHHHHTTTTC--
T ss_pred             HHHHHHHHHhCchh
Confidence            788877 5666543

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=99.89  E-value=1.1e-19  Score=149.98  Aligned_cols=275  Identities=8%  Similarity=-0.048  Sum_probs=232.8

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccC-cHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSG-RAFEIL   80 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~-~~~~a~   80 (343)
                      ++++|+++|+++.+..+ .+...+..++..+.+.|++++|..+++++.+...    .+..+|..+...+...| ++++|.
T Consensus        37 ~~~~A~~~~~~~l~~~p-~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~----~~~~~~~~l~~~~~~~~~~~~~A~  111 (330)
T 3hym_B           37 DFKMCYKLTSVVMEKDP-FHASCLPVHIGTLVELNKANELFYLSHKLVDLYP----SNPVSWFAVGCYYLMVGHKNEHAR  111 (330)
T ss_dssp             CHHHHHHHHHHHHHHCT-TCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCT----TSTHHHHHHHHHHHHSCSCHHHHH
T ss_pred             CHHHHHHHHHHHHHcCC-CChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhCc----CCHHHHHHHHHHHHHhhhhHHHHH
Confidence            67899999999998754 4667788888999999999999999999988653    23578999999999999 999999


Q ss_pred             HHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcC
Q 044084           81 KFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  160 (343)
                      +.|++...... .+...|..+...+...|++++|...++++.+.... +...+..+...|...|++++|.+.+++..+..
T Consensus       112 ~~~~~a~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~  189 (330)
T 3hym_B          112 RYLSKATTLEK-TYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMKG-CHLPMLYIGLEYGLTNNSKLAERFFSQALSIA  189 (330)
T ss_dssp             HHHHHHHTTCT-TCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTT-CSHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhCC-ccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhccc-cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC
Confidence            99999988642 35778899999999999999999999999987654 56777789999999999999999999998876


Q ss_pred             CCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcC--------CCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCC
Q 044084          161 LNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQG--------CIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFD  232 (343)
Q Consensus       161 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--------~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  232 (343)
                      + .+...+..+...+...|++++|...+++..+..        .+....++..+..++...|++++|...++...+.. +
T Consensus       190 ~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~-~  267 (330)
T 3hym_B          190 P-EDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQALVLI-P  267 (330)
T ss_dssp             T-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-T
T ss_pred             C-CChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhhC-c
Confidence            5 567789999999999999999999999988742        13335688899999999999999999999999875 4


Q ss_pred             cChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHH-hcccCh
Q 044084          233 KCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMH-GRAKNL  286 (343)
Q Consensus       233 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~-~~~~~~  286 (343)
                      .+...+..+...+...|++++|...+++..+.. +.+...+..+..++ ...|+.
T Consensus       268 ~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~g~~  321 (330)
T 3hym_B          268 QNASTYSAIGYIHSLMGNFENAVDYFHTALGLR-RDDTFSVTMLGHCIEMYIGDS  321 (330)
T ss_dssp             TCSHHHHHHHHHHHHHTCHHHHHHHHHTTTTTC-SCCHHHHHHHHHHHHTTTTC-
T ss_pred             cchHHHHHHHHHHHHhccHHHHHHHHHHHHccC-CCchHHHHHHHHHHHHHhCch
Confidence            578899999999999999999999999998763 23567777777777 445544

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.89  E-value=2.2e-19  Score=149.93  Aligned_cols=261  Identities=9%  Similarity=0.029  Sum_probs=151.8

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHH
Q 044084           22 SGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASL  101 (343)
Q Consensus        22 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  101 (343)
                      +..+..+...+.+.|++++|...|+++.+..    |.+..++..+...+...|++++|+..++++.+... .+...+..+
T Consensus         3 ~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~----p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l   77 (359)
T 3ieg_A            3 VEKHLELGKKLLAAGQLADALSQFHAAVDGD----PDNYIAYYRRATVFLAMGKSKAALPDLTKVIALKM-DFTAARLQR   77 (359)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC----cccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCC-CcchHHHHH
Confidence            3445556666666666666666666665543    22245666666666666666666666666665431 244556666


Q ss_pred             HHHHhcccCHHHHHHHHHHHHHcCCC--CCHHHHHHH------------HHHHHhcCcHhHHHHHHHHHHhcCCCCchhh
Q 044084          102 ICSFASIAEVKVAEELFKEAEEKGML--RDLEVFLKL------------VLMYIEEGMVEKTLEVVESMKNAELNISDCI  167 (343)
Q Consensus       102 ~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l------------~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  167 (343)
                      ...+...|++++|...++++.+..+.  .+...+..+            ...+...|++++|.+.++++.+..+ .+...
T Consensus        78 ~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~  156 (359)
T 3ieg_A           78 GHLLLKQGKLDEAEDDFKKVLKSNPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVCV-WDAEL  156 (359)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHH
T ss_pred             HHHHHHcCChHHHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCC-CchHH
Confidence            66666666666666666666654320  133333333            4566666666666666666665544 34455


Q ss_pred             HHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHH--------
Q 044084          168 SCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYS--------  239 (343)
Q Consensus       168 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~--------  239 (343)
                      +..+...+...|++++|...++++.+.. +.+..++..+...+...|++++|...++...+.. +.+...+.        
T Consensus       157 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~~~~~~  234 (359)
T 3ieg_A          157 RELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGDHELSLSEVRECLKLD-QDHKRCFAHYKQVKKL  234 (359)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-ccchHHHHHHHHHHHH
Confidence            6666666666666666666666666553 3345566666666666666666666666666543 22222222        


Q ss_pred             ----HHHHHHHccCChHHHHHHHHHHhhCCCCchH----HHHHHHHHHHhcccChhHHHh
Q 044084          240 ----SMVAMYGKTGRIRDAMRLVAKMKPKGCEPNV----WIYNSLMDMHGRAKNLRQLEK  291 (343)
Q Consensus       240 ----~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~----~~~~~l~~~~~~~~~~~~a~~  291 (343)
                          .+...+.+.|++++|...++++.+.... +.    ..+..+..++...|++++|..
T Consensus       235 ~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~la~~~~~~~~~~~A~~  293 (359)
T 3ieg_A          235 NKLIESAEELIRDGRYTDATSKYESVMKTEPS-VAEYTVRSKERICHCFSKDEKPVEAIR  293 (359)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-SHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-chHHHHHHHHHHHHHHHHccCHHHHHH
Confidence                2244566666666666666666654211 11    223345556666666666665

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A

Probab=99.88  E-value=2.6e-20  Score=156.33  Aligned_cols=280  Identities=10%  Similarity=0.044  Sum_probs=209.0

Q ss_pred             hhhHHH-HHHHHHhCCC---CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHH
Q 044084            3 SQSKLH-YYEKMKSAGI---VLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFE   78 (343)
Q Consensus         3 ~~~A~~-~~~~~~~~~~---~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~   78 (343)
                      +++|+. .|++..+...   ..+...+..+...+.+.|++++|...|+++.+..    |.+..+|..+...+...|++++
T Consensus        41 ~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~----p~~~~~~~~l~~~~~~~g~~~~  116 (368)
T 1fch_A           41 YDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQD----PKHMEAWQYLGTTQAENEQELL  116 (368)
T ss_dssp             -----CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSC----TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC----CCCHHHHHHHHHHHHHCcCHHH
Confidence            345555 5554443321   1135668888899999999999999999988765    3336788899999999999999


Q ss_pred             HHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHH---------------HHHHHHhc
Q 044084           79 ILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLK---------------LVLMYIEE  143 (343)
Q Consensus        79 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~---------------l~~~~~~~  143 (343)
                      |++.|+++.+.. +.+..++..+...+...|++++|...++++.+..+. +...+..               .+..+...
T Consensus       117 A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  194 (368)
T 1fch_A          117 AISALRRCLELK-PDNQTALMALAVSFTNESLQRQACEILRDWLRYTPA-YAHLVTPAEEGAGGAGLGPSKRILGSLLSD  194 (368)
T ss_dssp             HHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTT-TGGGCC---------------CTTHHHHHH
T ss_pred             HHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcC-cHHHHHHHHHHhhhhcccHHHHHHHHHhhc
Confidence            999999988874 336778888889999999999999999998886543 2222211               13333488


Q ss_pred             CcHhHHHHHHHHHHhcCCCC-chhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHH
Q 044084          144 GMVEKTLEVVESMKNAELNI-SDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKV  222 (343)
Q Consensus       144 ~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~  222 (343)
                      |++++|...|+++.+..+.. +..++..+...+...|++++|...++++.... +.+..++..+...+...|++++|...
T Consensus       195 ~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~  273 (368)
T 1fch_A          195 SLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAA  273 (368)
T ss_dssp             HHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            99999999999988776432 46778888999999999999999999988763 34567888889999999999999999


Q ss_pred             HHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCc----------hHHHHHHHHHHHhcccChhHHH
Q 044084          223 FIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEP----------NVWIYNSLMDMHGRAKNLRQLE  290 (343)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p----------~~~~~~~l~~~~~~~~~~~~a~  290 (343)
                      ++.+.+.. +.+..++..+..+|.+.|++++|...|+++.+.....          ...+|..+..+|...|+.++|.
T Consensus       274 ~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  350 (368)
T 1fch_A          274 YRRALELQ-PGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYG  350 (368)
T ss_dssp             HHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGHH
T ss_pred             HHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccchhhHHHHHHHHHHHHhCChHhHH
Confidence            99988875 4567788899999999999999999998887641110          1456666666666666665554

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.87  E-value=3.1e-20  Score=155.81  Aligned_cols=237  Identities=9%  Similarity=0.014  Sum_probs=192.0

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHH
Q 044084           21 DSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYAS  100 (343)
Q Consensus        21 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  100 (343)
                      +...+..+...+.+.|++++|...|+++.+..    |.+..+|..+...+...|++++|++.|++..+.. +.+..++..
T Consensus        64 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~----p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~  138 (365)
T 4eqf_A           64 DWPGAFEEGLKRLKEGDLPVTILFMEAAILQD----PGDAEAWQFLGITQAENENEQAAIVALQRCLELQ-PNNLKALMA  138 (365)
T ss_dssp             TCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHH
T ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC----cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHH
Confidence            45568888999999999999999999998765    3336889999999999999999999999998864 235778999


Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCCC---------CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCC-CchhhHHH
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGMLR---------DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELN-ISDCISCV  170 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~~---------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~  170 (343)
                      +...+...|++++|...++++.+..+..         ....+..+...+...|++++|+..|+++.+..+. ++..++..
T Consensus       139 l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~  218 (365)
T 4eqf_A          139 LAVSYTNTSHQQDACEALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTG  218 (365)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCHHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHH
T ss_pred             HHHHHHccccHHHHHHHHHHHHHhCccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHH
Confidence            9999999999999999999998754220         1233445678899999999999999999887652 15678889


Q ss_pred             HHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCC
Q 044084          171 IVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGR  250 (343)
Q Consensus       171 l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  250 (343)
                      +...+...|++++|.+.|+++.+.. +.+..++..+..+|...|++++|...|+...+.. +.+..++..+..+|...|+
T Consensus       219 l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~  296 (365)
T 4eqf_A          219 LGVLFHLSGEFNRAIDAFNAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQ-PGFIRSRYNLGISCINLGA  296 (365)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCC
Confidence            9999999999999999999998874 4567889999999999999999999999998875 4458889999999999999


Q ss_pred             hHHHHHHHHHHhhC
Q 044084          251 IRDAMRLVAKMKPK  264 (343)
Q Consensus       251 ~~~a~~~~~~m~~~  264 (343)
                      +++|...|+++.+.
T Consensus       297 ~~~A~~~~~~al~~  310 (365)
T 4eqf_A          297 YREAVSNFLTALSL  310 (365)
T ss_dssp             CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999998764

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A

Probab=99.87  E-value=5.3e-20  Score=154.48  Aligned_cols=288  Identities=8%  Similarity=-0.001  Sum_probs=216.4

Q ss_pred             HHhcCCHHHHHH-HHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccC
Q 044084           32 FYKIGDSEKVAA-LFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAE  110 (343)
Q Consensus        32 ~~~~~~~~~a~~-~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  110 (343)
                      +.-.|++++|.. .|++...............+..+...+...|++++|+..|+++.+.. +.+..++..+...+...|+
T Consensus        35 ~~~~~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~  113 (368)
T 1fch_A           35 HPWLSDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQ  113 (368)
T ss_dssp             -----------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTC
T ss_pred             hHHHHHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcC
Confidence            445578888888 77765443221111123567888999999999999999999999874 3367788999999999999


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHH---------------HHHHH
Q 044084          111 VKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCV---------------IVNGF  175 (343)
Q Consensus       111 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~---------------l~~~~  175 (343)
                      +++|...++++.+..+. +..++..+...|...|++++|.+.++++....+.. ...+..               .+..+
T Consensus       114 ~~~A~~~~~~al~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~  191 (368)
T 1fch_A          114 ELLAISALRRCLELKPD-NQTALMALAVSFTNESLQRQACEILRDWLRYTPAY-AHLVTPAEEGAGGAGLGPSKRILGSL  191 (368)
T ss_dssp             HHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTT-GGGCC---------------CTTHHH
T ss_pred             HHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCc-HHHHHHHHHHhhhhcccHHHHHHHHH
Confidence            99999999999988643 78999999999999999999999999998876532 222221               23334


Q ss_pred             hcCCcHHHHHHHHHHHHHcCCCC-CHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHH
Q 044084          176 SKRRAYWAAVKVYEQLISQGCIP-GQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDA  254 (343)
Q Consensus       176 ~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  254 (343)
                      ...|++++|...++++.+..... +..++..+...|...|++++|...++.+.+.. +.+..++..+...+...|++++|
T Consensus       192 ~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A  270 (368)
T 1fch_A          192 LSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEA  270 (368)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             hhcccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHcCCHHHH
Confidence            48899999999999998874221 47888999999999999999999999998875 45678999999999999999999


Q ss_pred             HHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCc----------cH
Q 044084          255 MRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGGVI----------DR  324 (343)
Q Consensus       255 ~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p----------~~  324 (343)
                      ...|+++.+.. +.+..++                   ..+...|.+.|++++|...|++..+.....          ..
T Consensus       271 ~~~~~~al~~~-~~~~~~~-------------------~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  330 (368)
T 1fch_A          271 VAAYRRALELQ-PGYIRSR-------------------YNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSE  330 (368)
T ss_dssp             HHHHHHHHHHC-TTCHHHH-------------------HHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCH
T ss_pred             HHHHHHHHHhC-CCcHHHH-------------------HHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccchhh
Confidence            99999998752 2233443                   344555667778888888888886643221          15


Q ss_pred             HHHHHHHHHHhcccccccC
Q 044084          325 AMAGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       325 ~~~~~l~~~~~~~g~~~~a  343 (343)
                      .+|..+..+|.+.|++++|
T Consensus       331 ~~~~~l~~~~~~~g~~~~A  349 (368)
T 1fch_A          331 NIWSTLRLALSMLGQSDAY  349 (368)
T ss_dssp             HHHHHHHHHHHHHTCGGGH
T ss_pred             HHHHHHHHHHHHhCChHhH
Confidence            7799999999999999874

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=99.86  E-value=3.6e-18  Score=150.63  Aligned_cols=312  Identities=9%  Similarity=0.018  Sum_probs=241.8

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCC------------------------
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTP------------------------   57 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~------------------------   57 (343)
                      ++++|++.|+++.+.++ .+..++..+..++...|++++|...|+.+ ........                        
T Consensus        74 ~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~g~~~~A~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l~  151 (537)
T 3fp2_A           74 DLEKVIEFTTKALEIKP-DHSKALLRRASANESLGNFTDAMFDLSVL-SLNGDFDGASIEPMLERNLNKQAMKVLNENLS  151 (537)
T ss_dssp             CHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHH-C-----------CHHHHHHHHHHHHHHHHHCC
T ss_pred             CHHHHHHHHHHHHhcCC-chHHHHHHHHHHHHHcCCHHHHHHHHHHH-hcCCCCChHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67899999999998764 47788999999999999999999999643 21111100                        


Q ss_pred             ----------------------------------------chHHHHHHHHHHhhcc--------CcHHHHHHHHHHHHhc
Q 044084           58 ----------------------------------------SSTHMYKILCDSLGKS--------GRAFEILKFFRDMKEK   89 (343)
Q Consensus        58 ----------------------------------------~~~~~~~~li~~~~~~--------~~~~~a~~~~~~~~~~   89 (343)
                                                              ........+...+...        |++++|+.+++++.+.
T Consensus       152 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~  231 (537)
T 3fp2_A          152 KDEGRGSQVLPSNTSLASFFGIFDSHLEVSSVNTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSA  231 (537)
T ss_dssp             -------CCCCCHHHHHHHHHTSCHHHHHHTSCCCCSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             hCccccccccchHhHHHHHHHhcChHHHHHHHhhccccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHH
Confidence                                                    0000222222222222        4788999999999876


Q ss_pred             CCCCC-------hHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCC
Q 044084           90 GILED-------PSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELN  162 (343)
Q Consensus        90 ~~~~~-------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  162 (343)
                      ... +       ..++..+...+...|++++|...++++.+..  |+...+..+...+...|++++|.+.|+++.+..+ 
T Consensus       232 ~p~-~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-  307 (537)
T 3fp2_A          232 NTV-DDPLRENAALALCYTGIFHFLKNNLLDAQVLLQESINLH--PTPNSYIFLALTLADKENSQEFFKFFQKAVDLNP-  307 (537)
T ss_dssp             -CC-CHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHCT-
T ss_pred             CCC-cchhhHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcC--CCchHHHHHHHHHHHhcCHHHHHHHHHHHhccCC-
Confidence            422 2       2246666778888999999999999999875  5588899999999999999999999999988765 


Q ss_pred             CchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHH
Q 044084          163 ISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMV  242 (343)
Q Consensus       163 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  242 (343)
                      .+..++..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|...++.+.+.. +.+...+..+.
T Consensus       308 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~  385 (537)
T 3fp2_A          308 EYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLN-PENVYPYIQLACLLYKQGKFTESEAFFNETKLKF-PTLPEVPTFFA  385 (537)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHH
Confidence            466789999999999999999999999999874 3346788889999999999999999999999875 55678899999


Q ss_pred             HHHHccCChHHHHHHHHHHhhCC-----CCchHHHHHHHHHHHhcc----------cChhHHHh---------------H
Q 044084          243 AMYGKTGRIRDAMRLVAKMKPKG-----CEPNVWIYNSLMDMHGRA----------KNLRQLEK---------------Y  292 (343)
Q Consensus       243 ~~~~~~~~~~~a~~~~~~m~~~~-----~~p~~~~~~~l~~~~~~~----------~~~~~a~~---------------~  292 (343)
                      ..+...|++++|...|+++.+..     .......+......+...          |++++|..               +
T Consensus       386 ~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~  465 (537)
T 3fp2_A          386 EILTDRGDFDTAIKQYDIAKRLEEVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELDPRSEQAK  465 (537)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHCSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             HHHHHhCCHHHHHHHHHHHHHcCCcchhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhCCCCHHHH
Confidence            99999999999999999987642     111222344455667777          88888877               8


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 044084          293 TTVISAYNMAREFDMCVKFYNEFRMNGGV  321 (343)
Q Consensus       293 ~~l~~~~~~~g~~~~a~~~~~~m~~~~~~  321 (343)
                      ..+...|...|++++|.+.|++..+....
T Consensus       466 ~~l~~~~~~~g~~~~A~~~~~~al~~~~~  494 (537)
T 3fp2_A          466 IGLAQLKLQMEKIDEAIELFEDSAILART  494 (537)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHHhCCC
Confidence            88999999999999999999999886543

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=99.86  E-value=3.5e-19  Score=146.84  Aligned_cols=235  Identities=7%  Similarity=-0.046  Sum_probs=197.9

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHH
Q 044084           21 DSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYAS  100 (343)
Q Consensus        21 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  100 (343)
                      +...+..+...+.+.|++++|..+|+++.+...    .+..+|..+...+...|++++|.+.++++.+.. +.+..++..
T Consensus        20 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~----~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~   94 (327)
T 3cv0_A           20 YHENPMEEGLSMLKLANLAEAALAFEAVCQAAP----EREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAA   94 (327)
T ss_dssp             GSSCHHHHHHHHHHTTCHHHHHHHHHHHHHHCT----TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHH
T ss_pred             hhHHHHHHHHHHHHhccHHHHHHHHHHHHHhCC----CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cCCHHHHHH
Confidence            456678888999999999999999999987653    336889999999999999999999999998874 336778888


Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHH--------------HH-HHHhcCcHhHHHHHHHHHHhcCCCCch
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKL--------------VL-MYIEEGMVEKTLEVVESMKNAELNISD  165 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l--------------~~-~~~~~~~~~~a~~~~~~~~~~~~~~~~  165 (343)
                      +...+...|++++|...++++.+.... +...+..+              .. .+...|++++|...++++.+..+ .+.
T Consensus        95 la~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~-~~~  172 (327)
T 3cv0_A           95 LAVSHTNEHNANAALASLRAWLLSQPQ-YEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMNP-NDA  172 (327)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTSTT-TTTC--------------------CCTTSHHHHHHHHHHHHHHHHHST-TCH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCCc-cHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhCC-CCH
Confidence            999999999999999999999986543 33333333              22 37788999999999999988765 467


Q ss_pred             hhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHH
Q 044084          166 CISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMY  245 (343)
Q Consensus       166 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  245 (343)
                      ..+..+...+...|++++|.+.++++.+.. +.+..++..+...+...|++++|...++...+.. +.+..++..+...|
T Consensus       173 ~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~  250 (327)
T 3cv0_A          173 QLHASLGVLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEALDAYNRALDIN-PGYVRVMYNMAVSY  250 (327)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHH
Confidence            789999999999999999999999998874 4457788999999999999999999999998875 45678899999999


Q ss_pred             HccCChHHHHHHHHHHhhC
Q 044084          246 GKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       246 ~~~~~~~~a~~~~~~m~~~  264 (343)
                      ...|++++|...++++.+.
T Consensus       251 ~~~g~~~~A~~~~~~a~~~  269 (327)
T 3cv0_A          251 SNMSQYDLAAKQLVRAIYM  269 (327)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHh
Confidence            9999999999999998865

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=99.85  E-value=1.2e-18  Score=143.70  Aligned_cols=253  Identities=10%  Similarity=-0.016  Sum_probs=211.9

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      ++++|+.+|+++.+..+ .+...+..+...+.+.|++++|...|+++.+..    |.+..++..+...+...|++++|++
T Consensus        36 ~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~----~~~~~~~~~la~~~~~~~~~~~A~~  110 (327)
T 3cv0_A           36 NLAEAALAFEAVCQAAP-EREEAWRSLGLTQAENEKDGLAIIALNHARMLD----PKDIAVHAALAVSHTNEHNANAALA  110 (327)
T ss_dssp             CHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC----cCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            67899999999988754 477889999999999999999999999998764    3336789999999999999999999


Q ss_pred             HHHHHHhcCCCCChHhHHHH--------------HH-HHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcH
Q 044084           82 FFRDMKEKGILEDPSVYASL--------------IC-SFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMV  146 (343)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~l--------------~~-~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  146 (343)
                      .++++...... +...+..+              .. .+...|++++|...++++.+.... +..++..+...+...|++
T Consensus       111 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~~~~  188 (327)
T 3cv0_A          111 SLRAWLLSQPQ-YEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMNPN-DAQLHASLGVLYNLSNNY  188 (327)
T ss_dssp             HHHHHHHTSTT-TTTC--------------------CCTTSHHHHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHhCCc-cHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhCCC-CHHHHHHHHHHHHHhccH
Confidence            99999886422 33333333              22 377889999999999999987654 789999999999999999


Q ss_pred             hHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHH
Q 044084          147 EKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEM  226 (343)
Q Consensus       147 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~  226 (343)
                      ++|.+.++++.+..+ .+..++..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|...++..
T Consensus       189 ~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a  266 (327)
T 3cv0_A          189 DSAAANLRRAVELRP-DDAQLWNKLGATLANGNRPQEALDAYNRALDIN-PGYVRVMYNMAVSYSNMSQYDLAAKQLVRA  266 (327)
T ss_dssp             HHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHH
Confidence            999999999988765 466789999999999999999999999998874 345778889999999999999999999998


Q ss_pred             HHcCCCc-----------ChhhHHHHHHHHHccCChHHHHHHHHHHhh
Q 044084          227 QQKGFDK-----------CVVAYSSMVAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       227 ~~~~~~~-----------~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                      .+.....           +..+|..+..++...|++++|..++++..+
T Consensus       267 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~  314 (327)
T 3cv0_A          267 IYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNVE  314 (327)
T ss_dssp             HHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTCCSH
T ss_pred             HHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            8764221           477899999999999999999999876553

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.85  E-value=6e-19  Score=147.96  Aligned_cols=252  Identities=9%  Similarity=0.030  Sum_probs=206.2

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      ++++|+..|+++.+..+ .+..++..+...+.+.|++++|...|+++.+..    |.+..+|..+...+...|++++|++
T Consensus        80 ~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~----p~~~~~~~~l~~~~~~~g~~~~A~~  154 (365)
T 4eqf_A           80 DLPVTILFMEAAILQDP-GDAEAWQFLGITQAENENEQAAIVALQRCLELQ----PNNLKALMALAVSYTNTSHQQDACE  154 (365)
T ss_dssp             CHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCc-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC----CCCHHHHHHHHHHHHccccHHHHHH
Confidence            67899999999998754 478899999999999999999999999998765    3336889999999999999999999


Q ss_pred             HHHHHHhcCCCC---------ChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcCcHhHHHH
Q 044084           82 FFRDMKEKGILE---------DPSVYASLICSFASIAEVKVAEELFKEAEEKGMLR-DLEVFLKLVLMYIEEGMVEKTLE  151 (343)
Q Consensus        82 ~~~~~~~~~~~~---------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~  151 (343)
                      .|+++.+.....         ....+..+...+...|++++|...++++.+..+.. +..++..+...|...|++++|+.
T Consensus       155 ~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~  234 (365)
T 4eqf_A          155 ALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLGVLFHLSGEFNRAID  234 (365)
T ss_dssp             HHHHHHHHCHHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHhCccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHHHHHHHCCCHHHHHH
Confidence            999998753110         11223345788899999999999999999876432 68899999999999999999999


Q ss_pred             HHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCC
Q 044084          152 VVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGF  231 (343)
Q Consensus       152 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  231 (343)
                      .|++..+..+ .+..+|..+..+|...|++++|...|+++.+.. +.+..++..+..+|...|++++|...|+...+...
T Consensus       235 ~~~~al~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~  312 (365)
T 4eqf_A          235 AFNAALTVRP-EDYSLWNRLGATLANGDRSEEAVEAYTRALEIQ-PGFIRSRYNLGISCINLGAYREAVSNFLTALSLQR  312 (365)
T ss_dssp             HHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCc
Confidence            9999988765 567789999999999999999999999999874 34578899999999999999999999999887531


Q ss_pred             C-----------cChhhHHHHHHHHHccCChHHHHHHHHH
Q 044084          232 D-----------KCVVAYSSMVAMYGKTGRIRDAMRLVAK  260 (343)
Q Consensus       232 ~-----------~~~~~~~~l~~~~~~~~~~~~a~~~~~~  260 (343)
                      .           .+..+|..+..++...|+.+.+..+..+
T Consensus       313 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  352 (365)
T 4eqf_A          313 KSRNQQQVPHPAISGNIWAALRIALSLMDQPELFQAANLG  352 (365)
T ss_dssp             CC------------CHHHHHHHHHHHHHTCHHHHHHHHTT
T ss_pred             ccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHHHHHHHh
Confidence            1           1367899999999999999988887765

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.84  E-value=3.5e-18  Score=138.24  Aligned_cols=246  Identities=11%  Similarity=0.093  Sum_probs=180.1

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      +++.|+..++......+.+.......+.++|...|+++.|...++.       .+++...++..+...+...++.++|++
T Consensus        14 ~y~~ai~~~~~~~~~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~-------~~~~~~~a~~~la~~~~~~~~~~~A~~   86 (291)
T 3mkr_A           14 SYQQCINEAQRVKPSSPERDVERDVFLYRAYLAQRKYGVVLDEIKP-------SSAPELQAVRMFAEYLASHSRRDAIVA   86 (291)
T ss_dssp             CHHHHHHHHHHSCCCSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCT-------TSCHHHHHHHHHHHHHHCSTTHHHHHH
T ss_pred             HHHHHHHHHHhcccCCchhhHHHHHHHHHHHHHCCCHHHHHHHhcc-------cCChhHHHHHHHHHHHcCCCcHHHHHH
Confidence            4566777776655443222234556677888888888888875533       134456778888888888888888888


Q ss_pred             HHHHHHhcCCCCC-hHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcC
Q 044084           82 FFRDMKEKGILED-PSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus        82 ~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  160 (343)
                      .++++...+..|+ ...+..+...+...|++++|...+++      +.+...+..++..+.+.|++++|.+.|+++.+..
T Consensus        87 ~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~  160 (291)
T 3mkr_A           87 ELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQILLKLDRLDLARKELKKMQDQD  160 (291)
T ss_dssp             HHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC
Confidence            8888887665454 44556666788888888888888877      3577888888888888888889988888888765


Q ss_pred             CCCchhh---HHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhh
Q 044084          161 LNISDCI---SCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVA  237 (343)
Q Consensus       161 ~~~~~~~---~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  237 (343)
                        |+...   ...++..+...|++++|..+|+++.+.. +.+...++.+..++.+.|++++|+..|++..+.. +-+..+
T Consensus       161 --p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~-p~~~~~  236 (291)
T 3mkr_A          161 --EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKC-SPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKD-SGHPET  236 (291)
T ss_dssp             --TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHH
T ss_pred             --cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHH
Confidence              33211   1223344455688888888888888773 5677788888888888888888888888888775 456778


Q ss_pred             HHHHHHHHHccCChHH-HHHHHHHHhhC
Q 044084          238 YSSMVAMYGKTGRIRD-AMRLVAKMKPK  264 (343)
Q Consensus       238 ~~~l~~~~~~~~~~~~-a~~~~~~m~~~  264 (343)
                      +..++..+...|+.++ +.++++++.+.
T Consensus       237 l~~l~~~~~~~g~~~eaa~~~~~~~~~~  264 (291)
T 3mkr_A          237 LINLVVLSQHLGKPPEVTNRYLSQLKDA  264 (291)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence            8888888888888865 56788887765

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.83  E-value=8e-21  Score=169.93  Aligned_cols=151  Identities=13%  Similarity=0.148  Sum_probs=113.1

Q ss_pred             HHHHHHHHHHHHhcCcHhHHHHHHHHHH---hcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHH
Q 044084          130 LEVFLKLVLMYIEEGMVEKTLEVVESMK---NAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASI  206 (343)
Q Consensus       130 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l  206 (343)
                      ..+|++||++|++.|++++|.++|++|.   ..|+.||..|||+||.+|++.|++++|.++|++|.+.|+.||..||+++
T Consensus       127 ~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYntL  206 (1134)
T 3spa_A          127 QQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAA  206 (1134)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHHH
Confidence            5678888888888888888888887765   3467788888888888888888888888888888888888888888888


Q ss_pred             HHHHHccCCh-hHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCch------HHHHHHHHHH
Q 044084          207 INAYCRIGLY-SKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPN------VWIYNSLMDM  279 (343)
Q Consensus       207 l~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~------~~~~~~l~~~  279 (343)
                      |.++++.|+. ++|.++|++|.+.|+.||..+|+.++....+    +.+++..+++ ..++.|+      ..+...|.+.
T Consensus       207 I~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR----~~vL~~Vrkv-~P~f~p~~~~~~~~~t~~LL~dl  281 (1134)
T 3spa_A          207 LQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDR----ATVLKAVHKV-KPTFSLPPQLPPPVNTSKLLRDV  281 (1134)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHH----HHHHHHHGGG-CCCCCCCCCCCCCCCCCTTTHHH
T ss_pred             HHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhH----HHHHHHHHHh-CcccCCCCCCcccccchHHHHHH
Confidence            8888888874 6788888888888888888888888765544    3344444444 3344443      3444455555


Q ss_pred             HhcccC
Q 044084          280 HGRAKN  285 (343)
Q Consensus       280 ~~~~~~  285 (343)
                      |.+.+.
T Consensus       282 ~s~d~~  287 (1134)
T 3spa_A          282 YAKDGR  287 (1134)
T ss_dssp             HCCCSC
T ss_pred             HccCCC
Confidence            655543

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.83  E-value=2.5e-18  Score=139.15  Aligned_cols=253  Identities=11%  Similarity=0.036  Sum_probs=198.0

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCCch-HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhc
Q 044084           29 MEAFYKIGDSEKVAALFLECESRKLDLTPSS-THMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFAS  107 (343)
Q Consensus        29 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  107 (343)
                      ++.....|++..|+..++......    |.+ ......+.++|...|+++.|+..++.    .-+|+..++..+...+..
T Consensus         6 ~~~~~~~g~y~~ai~~~~~~~~~~----p~~~~e~~~~l~r~yi~~g~~~~al~~~~~----~~~~~~~a~~~la~~~~~   77 (291)
T 3mkr_A            6 VKNAFYIGSYQQCINEAQRVKPSS----PERDVERDVFLYRAYLAQRKYGVVLDEIKP----SSAPELQAVRMFAEYLAS   77 (291)
T ss_dssp             HHHHHHTTCHHHHHHHHHHSCCCS----HHHHHHHHHHHHHHHHHTTCHHHHHHHSCT----TSCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHhcccCC----chhhHHHHHHHHHHHHHCCCHHHHHHHhcc----cCChhHHHHHHHHHHHcC
Confidence            455667899999999887653322    222 34556778999999999999987654    235677788889999999


Q ss_pred             ccCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHH
Q 044084          108 IAEVKVAEELFKEAEEKGMLR-DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVK  186 (343)
Q Consensus       108 ~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  186 (343)
                      .++.+.|.+.++++...+..| +...+..+...+...|++++|++.+++      +.+...+..++..+.+.|++++|.+
T Consensus        78 ~~~~~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~~~~~g~~~~A~~  151 (291)
T 3mkr_A           78 HSRRDAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQILLKLDRLDLARK  151 (291)
T ss_dssp             STTHHHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             CCcHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            999999999999999876444 677788888999999999999999988      3667789999999999999999999


Q ss_pred             HHHHHHHcCCCCCHhhH---HHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhh
Q 044084          187 VYEQLISQGCIPGQVTY---ASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       187 ~~~~~~~~~~~p~~~~~---~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                      .|+++.+..  |+....   ...+..+...|++++|..+|+++.+.. +.+...++.+..++.+.|++++|...|++..+
T Consensus       152 ~l~~~~~~~--p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~  228 (291)
T 3mkr_A          152 ELKKMQDQD--EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKC-SPTLLLLNGQAACHMAQGRWEAAEGVLQEALD  228 (291)
T ss_dssp             HHHHHHHHC--TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhhC--cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            999999874  553211   123344455699999999999999884 67889999999999999999999999999987


Q ss_pred             CCCCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHH-HHHHHHHHHhC
Q 044084          264 KGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDM-CVKFYNEFRMN  318 (343)
Q Consensus       264 ~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~-a~~~~~~m~~~  318 (343)
                      .. +-+..++..++..+..                   .|+.++ +.++++++.+.
T Consensus       229 ~~-p~~~~~l~~l~~~~~~-------------------~g~~~eaa~~~~~~~~~~  264 (291)
T 3mkr_A          229 KD-SGHPETLINLVVLSQH-------------------LGKPPEVTNRYLSQLKDA  264 (291)
T ss_dssp             HC-TTCHHHHHHHHHHHHH-------------------TTCCHHHHHHHHHHHHHH
T ss_pred             hC-CCCHHHHHHHHHHHHH-------------------cCCCHHHHHHHHHHHHHh
Confidence            63 2255666666555544                   444443 56777777764

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.83  E-value=9.8e-21  Score=169.35  Aligned_cols=150  Identities=15%  Similarity=0.156  Sum_probs=122.2

Q ss_pred             hHhHHHHHHHHhcccCHHHHHHHHHHHH---HcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHH
Q 044084           95 PSVYASLICSFASIAEVKVAEELFKEAE---EKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVI  171 (343)
Q Consensus        95 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  171 (343)
                      ..||+++|++|++.|++++|.++|.+|.   +.|+.||..+||+||.+|++.|++++|.++|++|.+.|+.||..||+++
T Consensus       127 ~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYntL  206 (1134)
T 3spa_A          127 QQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAA  206 (1134)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHHH
Confidence            4589999999999999999999998876   4588999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcCCc-HHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcC------hhhHHHHHHH
Q 044084          172 VNGFSKRRA-YWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKC------VVAYSSMVAM  244 (343)
Q Consensus       172 ~~~~~~~~~-~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~------~~~~~~l~~~  244 (343)
                      |.++++.|+ .++|.++|++|.+.|+.||..+|+.++..+.+.+-    .+..+++ ..++.|+      +.+...|.+.
T Consensus       207 I~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~~v----L~~Vrkv-~P~f~p~~~~~~~~~t~~LL~dl  281 (1134)
T 3spa_A          207 LQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATV----LKAVHKV-KPTFSLPPQLPPPVNTSKLLRDV  281 (1134)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHHHH----HHHHGGG-CCCCCCCCCCCCCCCCCTTTHHH
T ss_pred             HHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHHHH----HHHHHHh-CcccCCCCCCcccccchHHHHHH
Confidence            999999987 57899999999999999999999998876554322    2222222 2234443      4444555555


Q ss_pred             HHccC
Q 044084          245 YGKTG  249 (343)
Q Consensus       245 ~~~~~  249 (343)
                      |.+.+
T Consensus       282 ~s~d~  286 (1134)
T 3spa_A          282 YAKDG  286 (1134)
T ss_dssp             HCCCS
T ss_pred             HccCC
Confidence            55543

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.83  E-value=7.8e-16  Score=134.17  Aligned_cols=311  Identities=12%  Similarity=0.089  Sum_probs=237.3

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhc----c
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYK----IGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGK----S   73 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~----~   73 (343)
                      ++++|+..|++..+.|   +...+..|...|..    .+++++|.+.|++..+.+.      ...+..|...|..    .
T Consensus        58 ~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~------~~a~~~Lg~~y~~g~g~~  128 (490)
T 2xm6_A           58 DLTQAMDWFRRAAEQG---YTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKGL------PQAQQNLGVMYHEGNGVK  128 (490)
T ss_dssp             CHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC------HHHHHHHHHHHHHTSSSC
T ss_pred             CHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCC------HHHHHHHHHHHHcCCCCC
Confidence            5778889998888764   45677788888888    8899999999998877652      4567778888877    7


Q ss_pred             CcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhc----ccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----cCc
Q 044084           74 GRAFEILKFFRDMKEKGILEDPSVYASLICSFAS----IAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIE----EGM  145 (343)
Q Consensus        74 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~  145 (343)
                      +++++|+++|++..+.|   +...+..+...|..    .++.++|...|++..+.|   +...+..|...|..    .++
T Consensus       129 ~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~  202 (490)
T 2xm6_A          129 VDKAESVKWFRLAAEQG---RDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQG---NVWSCNQLGYMYSRGLGVERN  202 (490)
T ss_dssp             CCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCC
T ss_pred             CCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCCCcC
Confidence            88999999999888765   55667777777776    778999999999888864   67888888888887    788


Q ss_pred             HhHHHHHHHHHHhcCCCCchhhHHHHHHHHhc----CCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHc----cCChh
Q 044084          146 VEKTLEVVESMKNAELNISDCISCVIVNGFSK----RRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCR----IGLYS  217 (343)
Q Consensus       146 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~----~~~~~  217 (343)
                      .++|.+.|++..+.+   +...+..+...|..    .+++++|..+|++..+.|   +...+..+...|..    .++++
T Consensus       203 ~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~~~~~d~~  276 (490)
T 2xm6_A          203 DAISAQWYRKSATSG---DELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQG---NSIAQFRLGYILEQGLAGAKEPL  276 (490)
T ss_dssp             HHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHTTTSSCCHH
T ss_pred             HHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHCCCCCCCCHH
Confidence            999999999888765   33456667777765    788999999999888764   34556666666766    78899


Q ss_pred             HHHHHHHHHHHcCCCcChhhHHHHHHHHHcc-----CChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhccc---ChhHH
Q 044084          218 KAEKVFIEMQQKGFDKCVVAYSSMVAMYGKT-----GRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAK---NLRQL  289 (343)
Q Consensus       218 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~---~~~~a  289 (343)
                      +|...|+...+.+   +...+..+...|...     +++++|...|++..+.|   +...+..+...|...|   +.++|
T Consensus       277 ~A~~~~~~a~~~~---~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~~g~~~~~~~A  350 (490)
T 2xm6_A          277 KALEWYRKSAEQG---NSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQG---DATAQANLGAIYFRLGSEEEHKKA  350 (490)
T ss_dssp             HHHHHHHHHHTTT---CHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHSCCHHHHHHH
T ss_pred             HHHHHHHHHHHcC---CHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhCCCcccHHHH
Confidence            9999999888765   456677777777776     88999999999988864   3455666666666545   55666


Q ss_pred             Hh-------------HHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHhc----cccccc
Q 044084          290 EK-------------YTTVISAYNM----AREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSK----LSQIEE  342 (343)
Q Consensus       290 ~~-------------~~~l~~~~~~----~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~----~g~~~~  342 (343)
                      ..             +..+...|..    .+++++|++.|++..+.|   ++..+..|...|.+    .+++++
T Consensus       351 ~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~~~---~~~a~~~Lg~~y~~g~g~~~d~~~  421 (490)
T 2xm6_A          351 VEWFRKAAAKGEKAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAEQG---LSAAQVQLGEIYYYGLGVERDYVQ  421 (490)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhCC---CHHHHHHHHHHHHcCCCCCCCHHH
Confidence            55             6677777777    789999999999988875   45566667777776    555543

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3

Probab=99.81  E-value=4.8e-19  Score=146.96  Aligned_cols=266  Identities=12%  Similarity=0.173  Sum_probs=125.4

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      +.++|.++++++.      ++.+|..++.++.+.|++++|.+.|.+.      ++   ..+|..++.++...|++++|+.
T Consensus        18 ~ld~A~~fae~~~------~~~vWs~La~A~l~~g~~~eAIdsfika------~D---~~~y~~V~~~ae~~g~~EeAi~   82 (449)
T 1b89_A           18 NLDRAYEFAERCN------EPAVWSQLAKAQLQKGMVKEAIDSYIKA------DD---PSSYMEVVQAANTSGNWEELVK   82 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CHHHHHHHHHhCC------ChHHHHHHHHHHHHcCCHHHHHHHHHcC------CC---HHHHHHHHHHHHhCCCHHHHHH
Confidence            4677888887772      3358999999999999999999999653      22   3579999999999999999999


Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCC
Q 044084           82 FFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAEL  161 (343)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  161 (343)
                      .++..++.  .+++.+.+.++.+|.+.|+++++.++++       .|+..+|+.++..|...|++++|...|..+     
T Consensus        83 yl~~ark~--~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a-----  148 (449)
T 1b89_A           83 YLQMARKK--ARESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV-----  148 (449)
T ss_dssp             ----------------------------CHHHHTTTTT-------CC----------------CTTTHHHHHHHT-----
T ss_pred             HHHHHHHh--CccchhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHh-----
Confidence            88777664  4567889999999999999999998885       267789999999999999999999999977     


Q ss_pred             CCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHH
Q 044084          162 NISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSM  241 (343)
Q Consensus       162 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  241 (343)
                          ..|..++.++.+.|++++|.+.++++      .++.+|..++.+|...|+++.|......+     ..++.-...+
T Consensus       149 ----~n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L-----~~~ad~l~~l  213 (449)
T 1b89_A          149 ----SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLHI-----VVHADELEEL  213 (449)
T ss_dssp             ----TCHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTTT-----TTCHHHHHHH
T ss_pred             ----hhHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHHH-----HhCHhhHHHH
Confidence                26999999999999999999999988      37789999999999999999996655432     2334445578


Q ss_pred             HHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhc--ccChhHHHh--------------------HHHHHHHH
Q 044084          242 VAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGR--AKNLRQLEK--------------------YTTVISAY  299 (343)
Q Consensus       242 ~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~--~~~~~~a~~--------------------~~~l~~~~  299 (343)
                      +..|.+.|++++|..+++...... +-....|+-|.-+|++  -++..+..+                    |..++..|
T Consensus       214 v~~Yek~G~~eEai~lLe~aL~le-~ah~~~ftel~il~~ky~p~k~~ehl~~~~~~ini~k~~~~~~~~~~w~e~~~ly  292 (449)
T 1b89_A          214 INYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKFKPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLY  292 (449)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHTTCHHHHHHHHHHHSTTSCHHHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHhCCc-HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999998653 3345556655555544  333444333                    88899999


Q ss_pred             HhcCCHHHHHHHH
Q 044084          300 NMAREFDMCVKFY  312 (343)
Q Consensus       300 ~~~g~~~~a~~~~  312 (343)
                      ...++++.|....
T Consensus       293 ~~~~e~d~A~~tm  305 (449)
T 1b89_A          293 DKYEEYDNAIITM  305 (449)
T ss_dssp             HHTTCHHHHHHHH
T ss_pred             HhhchHHHHHHHH
Confidence            9999999887643

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.78  E-value=1.4e-14  Score=126.26  Aligned_cols=293  Identities=12%  Similarity=0.096  Sum_probs=243.4

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhc----c
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYK----IGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGK----S   73 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~----~   73 (343)
                      ++++|+..|++..+.|   +...+..|...|..    .+++++|...|++..+.+.      ..++..|...|..    .
T Consensus        94 ~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~------~~a~~~Lg~~y~~g~g~~  164 (490)
T 2xm6_A           94 DYAQAVIWYKKAALKG---LPQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQGR------DSGQQSMGDAYFEGDGVT  164 (490)
T ss_dssp             CHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC------HHHHHHHHHHHHHTSSSC
T ss_pred             CHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCC------HHHHHHHHHHHHcCCCCC
Confidence            6789999999999875   56677788888888    7899999999999988753      4678888888876    7


Q ss_pred             CcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhc----ccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----cCc
Q 044084           74 GRAFEILKFFRDMKEKGILEDPSVYASLICSFAS----IAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIE----EGM  145 (343)
Q Consensus        74 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~  145 (343)
                      +++++|+++|++..+.|   +...+..+...|..    .++.++|...|++..+.|   +...+..+...|..    .++
T Consensus       165 ~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~g~~~~  238 (490)
T 2xm6_A          165 RDYVMAREWYSKAAEQG---NVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATSG---DELGQLHLADMYYFGIGVTQD  238 (490)
T ss_dssp             CCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCC
T ss_pred             CCHHHHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCC
Confidence            89999999999998875   67778888888887    899999999999999875   67788888888886    889


Q ss_pred             HhHHHHHHHHHHhcCCCCchhhHHHHHHHHhc----CCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHcc-----CCh
Q 044084          146 VEKTLEVVESMKNAELNISDCISCVIVNGFSK----RRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRI-----GLY  216 (343)
Q Consensus       146 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~-----~~~  216 (343)
                      +++|..+|++..+.+.   ...+..+...|..    .+++++|...|++..+.|   +...+..+...|...     +++
T Consensus       239 ~~~A~~~~~~a~~~~~---~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~~~~g~~~~~  312 (490)
T 2xm6_A          239 YTQSRVLFSQSAEQGN---SIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQG---NSDGQYYLAHLYDKGAEGVAKNR  312 (490)
T ss_dssp             HHHHHHHHHHHHTTTC---HHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHCBTTBCCCH
T ss_pred             HHHHHHHHHHHHHCCC---HHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHcCCCCCcCCH
Confidence            9999999999987653   3456666667766    899999999999998765   445667777777776     899


Q ss_pred             hHHHHHHHHHHHcCCCcChhhHHHHHHHHHccC---ChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhc----ccChhHH
Q 044084          217 SKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTG---RIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGR----AKNLRQL  289 (343)
Q Consensus       217 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~----~~~~~~a  289 (343)
                      ++|...++...+.+   +...+..+...|...|   +.++|.++|++..+.|   +...+..+...|..    .++.++|
T Consensus       313 ~~A~~~~~~a~~~~---~~~a~~~lg~~y~~~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A  386 (490)
T 2xm6_A          313 EQAISWYTKSAEQG---DATAQANLGAIYFRLGSEEEHKKAVEWFRKAAAKG---EKAAQFNLGNALLQGKGVKKDEQQA  386 (490)
T ss_dssp             HHHHHHHHHHHHTT---CHHHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHH
T ss_pred             HHHHHHHHHHHhcC---CHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHH
Confidence            99999999999876   4567778888887766   7899999999999874   56777888888887    7888888


Q ss_pred             Hh-------------HHHHHHHHHh----cCCHHHHHHHHHHHHhCCCC
Q 044084          290 EK-------------YTTVISAYNM----AREFDMCVKFYNEFRMNGGV  321 (343)
Q Consensus       290 ~~-------------~~~l~~~~~~----~g~~~~a~~~~~~m~~~~~~  321 (343)
                      ..             +..+...|..    .+++++|...|++..+.+..
T Consensus       387 ~~~~~~A~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~  435 (490)
T 2xm6_A          387 AIWMRKAAEQGLSAAQVQLGEIYYYGLGVERDYVQAWAWFDTASTNDMN  435 (490)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCC
Confidence            77             6777888887    89999999999999988754

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.78  E-value=2e-16  Score=125.71  Aligned_cols=226  Identities=13%  Similarity=0.106  Sum_probs=186.9

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCC--CC----h
Q 044084           22 SGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGIL--ED----P   95 (343)
Q Consensus        22 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~--~~----~   95 (343)
                      ...+..+...+...|++++|...|+++.+..  .+   ..+|..+...+...|++++|++.+++..+....  ++    .
T Consensus         5 a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~---~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~   79 (258)
T 3uq3_A            5 ADKEKAEGNKFYKARQFDEAIEHYNKAWELH--KD---ITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVIS   79 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CC---THHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhh--cc---HHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHH
Confidence            4567888889999999999999999988776  33   478889999999999999999999998775311  12    4


Q ss_pred             HhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHH
Q 044084           96 SVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGF  175 (343)
Q Consensus        96 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  175 (343)
                      .++..+...+...|++++|...+++..+..  |+.       ..+...|++++|...++++....+ .+...+..+...+
T Consensus        80 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~--~~~-------~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~~~~  149 (258)
T 3uq3_A           80 KSFARIGNAYHKLGDLKKTIEYYQKSLTEH--RTA-------DILTKLRNAEKELKKAEAEAYVNP-EKAEEARLEGKEY  149 (258)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCH-------HHHHHHHHHHHHHHHHHHHHHCCH-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHhcC--chh-------HHHHHHhHHHHHHHHHHHHHHcCc-chHHHHHHHHHHH
Confidence            678888889999999999999999998865  443       346667889999999999887654 3556788888899


Q ss_pred             hcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHH
Q 044084          176 SKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAM  255 (343)
Q Consensus       176 ~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  255 (343)
                      ...|++++|...+++..+.. +.+...+..+...+...|++++|...++...+.. +.+...+..+..++...|++++|.
T Consensus       150 ~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~  227 (258)
T 3uq3_A          150 FTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQIAVKEYASAL  227 (258)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-HHHHHHHHHHHHHHHHHhhHHHHH
Confidence            99999999999999998874 4467788888999999999999999999998875 456788889999999999999999


Q ss_pred             HHHHHHhhC
Q 044084          256 RLVAKMKPK  264 (343)
Q Consensus       256 ~~~~~m~~~  264 (343)
                      ..+++..+.
T Consensus       228 ~~~~~a~~~  236 (258)
T 3uq3_A          228 ETLDAARTK  236 (258)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            999988765

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.78  E-value=1.6e-15  Score=131.53  Aligned_cols=319  Identities=10%  Similarity=-0.006  Sum_probs=204.7

Q ss_pred             CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhC-----CCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhc-----
Q 044084           20 LDSGCYCQIMEAFYKIGDSEKVAALFLECESR-----KLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEK-----   89 (343)
Q Consensus        20 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-----   89 (343)
                      .....|+.|...+...|++++|++.|++..+.     +...++....+|+.+..+|...|++++|...+++..+.     
T Consensus        49 ~~a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~  128 (472)
T 4g1t_A           49 FKATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFS  128 (472)
T ss_dssp             -CCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSC
T ss_pred             hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhcc
Confidence            34567999999999999999999999886442     22233444688999999999999999999999887652     


Q ss_pred             C-CCC-ChHhHHHHHHHHhc--ccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH---HhcCcHhHHHHHHHHHHhcCCC
Q 044084           90 G-ILE-DPSVYASLICSFAS--IAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMY---IEEGMVEKTLEVVESMKNAELN  162 (343)
Q Consensus        90 ~-~~~-~~~~~~~l~~~~~~--~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~---~~~~~~~~a~~~~~~~~~~~~~  162 (343)
                      + ..+ ...++.....++..  .+++++|...|++..+..+. ++..+..+...+   ...++.++|++.+++..+.++ 
T Consensus       129 ~~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~p~-~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~p-  206 (472)
T 4g1t_A          129 SPYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKKPK-NPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLNP-  206 (472)
T ss_dssp             CSSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHCS-
T ss_pred             cccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcCC-
Confidence            1 111 23455555544444  45789999999999887643 566666655553   345677888888888776654 


Q ss_pred             CchhhHHHHHHHHh----cCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhH
Q 044084          163 ISDCISCVIVNGFS----KRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAY  238 (343)
Q Consensus       163 ~~~~~~~~l~~~~~----~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  238 (343)
                      .+..++..+...+.    ..+++++|.+.+++..... +.+..++..+...|...|++++|...++...+.. |.+..++
T Consensus       207 ~~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~  284 (472)
T 4g1t_A          207 DNQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKA-PGVTDVLRSAAKFYRRKDEPDKAIELLKKALEYI-PNNAYLH  284 (472)
T ss_dssp             SCHHHHHHHHHHHHHCC------CHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHH
T ss_pred             cchHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhC-ccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHhC-CChHHHH
Confidence            34444544444333    3466778888888877664 3455677778888888888888888888877764 3344555


Q ss_pred             HHHHHHHHcc-------------------CChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh--------
Q 044084          239 SSMVAMYGKT-------------------GRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK--------  291 (343)
Q Consensus       239 ~~l~~~~~~~-------------------~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~--------  291 (343)
                      ..+..+|...                   +..+.|...+++..+.. +.+..++..+...|...|++++|..        
T Consensus       285 ~~lg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~  363 (472)
T 4g1t_A          285 CQIGCCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEAN-DNLFRVCSILASLHALADQYEEAEYYFQKEFSK  363 (472)
T ss_dssp             HHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHC-TTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhcC-CchhhhhhhHHHHHHHhccHHHHHHHHHHHHhc
Confidence            5555444321                   12345555565555432 2233455666666777777776665        


Q ss_pred             ----------HHHHHH-HHHhcCCHHHHHHHHHHHHhCCC-----------------------CccHHHHHHHHHHHhcc
Q 044084          292 ----------YTTVIS-AYNMAREFDMCVKFYNEFRMNGG-----------------------VIDRAMAGIMVGVFSKL  337 (343)
Q Consensus       292 ----------~~~l~~-~~~~~g~~~~a~~~~~~m~~~~~-----------------------~p~~~~~~~l~~~~~~~  337 (343)
                                +..+.. ...+.|++++|+..|++..+...                       +.+..+|..+..+|...
T Consensus       364 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~i~~~~~~~~~~~~~l~~~~~~~l~~~p~~~~~~~~LG~~~~~~  443 (472)
T 4g1t_A          364 ELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVKINQKSREKEKMKDKLQKIAKMRLSKNGADSEALHVLAFLQELN  443 (472)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHHHHCC-CTTHHHHHHHHHHHH
T ss_pred             CCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHc
Confidence                      111111 22356777777777766654321                       23456789999999999


Q ss_pred             cccccC
Q 044084          338 SQIEEL  343 (343)
Q Consensus       338 g~~~~a  343 (343)
                      |++++|
T Consensus       444 g~~~~A  449 (472)
T 4g1t_A          444 EKMQQA  449 (472)
T ss_dssp             HHCC--
T ss_pred             CCHHHH
Confidence            999876

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.78  E-value=1.1e-16  Score=123.87  Aligned_cols=209  Identities=12%  Similarity=0.080  Sum_probs=94.4

Q ss_pred             CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHH
Q 044084           20 LDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYA   99 (343)
Q Consensus        20 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~   99 (343)
                      ++...+..+...+.+.|++++|...|++..+..    |.+...|..+...+.+.|++++|+..|++..+... .+...+.
T Consensus         3 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~----p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~P-~~~~a~~   77 (217)
T 2pl2_A            3 TAEQNPLRLGVQLYALGRYDAALTLFERALKEN----PQDPEALYWLARTQLKLGLVNPALENGKTLVARTP-RYLGGYM   77 (217)
T ss_dssp             -CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS----SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC----CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CcHHHHH
Confidence            444455555555555555555555555554433    22234555555555555555555555555554421 1333444


Q ss_pred             HHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCC
Q 044084          100 SLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRR  179 (343)
Q Consensus       100 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  179 (343)
                      .+..++...+             ...  ..         .+...|++++|+..|++..+..+ -+...+..+...+...|
T Consensus        78 ~lg~~~~~~~-------------~~~--~~---------~~~~~g~~~~A~~~~~~al~~~P-~~~~~~~~lg~~~~~~g  132 (217)
T 2pl2_A           78 VLSEAYVALY-------------RQA--ED---------RERGKGYLEQALSVLKDAERVNP-RYAPLHLQRGLVYALLG  132 (217)
T ss_dssp             HHHHHHHHHH-------------HTC--SS---------HHHHHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhh-------------hhh--hh---------hcccccCHHHHHHHHHHHHHhCc-ccHHHHHHHHHHHHHcC
Confidence            4444444440             000  00         00000555555555555554443 23344555555555555


Q ss_pred             cHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHH
Q 044084          180 AYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVA  259 (343)
Q Consensus       180 ~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  259 (343)
                      ++++|...|++..+..  .+...+..+..+|...|++++|...|+...+.. |.+...+..+...+...|++++|...++
T Consensus       133 ~~~~A~~~~~~al~~~--~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~~~~~  209 (217)
T 2pl2_A          133 ERDKAEASLKQALALE--DTPEIRSALAELYLSMGRLDEALAQYAKALEQA-PKDLDLRVRYASALLLKGKAEEAARAAA  209 (217)
T ss_dssp             CHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTC------------
T ss_pred             ChHHHHHHHHHHHhcc--cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHccCHHHHHHHHH
Confidence            5555555555555544  444455555555555555555555555555543 3344555555555555566655555555


Q ss_pred             HH
Q 044084          260 KM  261 (343)
Q Consensus       260 ~m  261 (343)
                      +.
T Consensus       210 ~~  211 (217)
T 2pl2_A          210 LE  211 (217)
T ss_dssp             --
T ss_pred             HH
Confidence            44

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.77  E-value=1.4e-16  Score=123.27  Aligned_cols=182  Identities=13%  Similarity=0.066  Sum_probs=134.8

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhcc--------
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKS--------   73 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~--------   73 (343)
                      ++++|+..|++..+..+ .+...+..+...+.+.|++++|...|++..+.+    |.+...+..+...+...        
T Consensus        20 ~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~----P~~~~a~~~lg~~~~~~~~~~~~~~   94 (217)
T 2pl2_A           20 RYDAALTLFERALKENP-QDPEALYWLARTQLKLGLVNPALENGKTLVART----PRYLGGYMVLSEAYVALYRQAEDRE   94 (217)
T ss_dssp             CHHHHHHHHHHHHTTSS-SCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHHHHTCSSHH
T ss_pred             CHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC----CCcHHHHHHHHHHHHHhhhhhhhhc
Confidence            57899999999998764 478889999999999999999999999998765    33467899999999988        


Q ss_pred             ---CcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHH
Q 044084           74 ---GRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTL  150 (343)
Q Consensus        74 ---~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  150 (343)
                         |++++|+..|++..+.... +...+..+..++...|++++|...|++..+..  .++..+..+...|...|++++|+
T Consensus        95 ~~~g~~~~A~~~~~~al~~~P~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~la~~~~~~g~~~~A~  171 (217)
T 2pl2_A           95 RGKGYLEQALSVLKDAERVNPR-YAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRSALAELYLSMGRLDEAL  171 (217)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             ccccCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHHHHHHHHHHcCCHHHHH
Confidence               8888888888888776322 45677777778888888888888888888776  57778888888888888888888


Q ss_pred             HHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHH
Q 044084          151 EVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLI  192 (343)
Q Consensus       151 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  192 (343)
                      ..|++..+..+ .+...+..+...+...|++++|...+++..
T Consensus       172 ~~~~~al~~~P-~~~~~~~~la~~~~~~g~~~~A~~~~~~~~  212 (217)
T 2pl2_A          172 AQYAKALEQAP-KDLDLRVRYASALLLKGKAEEAARAAALEH  212 (217)
T ss_dssp             HHHHHHHHHST-TCHHHHHHHHHHHTC---------------
T ss_pred             HHHHHHHHhCC-CChHHHHHHHHHHHHccCHHHHHHHHHHHh
Confidence            88888777654 455667777777888888888887777654

>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=99.77  E-value=2.4e-18  Score=142.85  Aligned_cols=187  Identities=13%  Similarity=0.176  Sum_probs=51.1

Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHH
Q 044084           34 KIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKV  113 (343)
Q Consensus        34 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  113 (343)
                      +.|++++|.+.++++      +.   ..+|..|+.++.+.|++++|++.|.+.      +|..+|..++..+...|++++
T Consensus        15 ~~~~ld~A~~fae~~------~~---~~vWs~La~A~l~~g~~~eAIdsfika------~D~~~y~~V~~~ae~~g~~Ee   79 (449)
T 1b89_A           15 HIGNLDRAYEFAERC------NE---PAVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAANTSGNWEE   79 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HccCHHHHHHHHHhC------CC---hHHHHHHHHHHHHcCCHHHHHHHHHcC------CCHHHHHHHHHHHHhCCCHHH
Confidence            566677777777665      21   246777777777777777777777542      355667777777777777777


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHH
Q 044084          114 AEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLIS  193 (343)
Q Consensus       114 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  193 (343)
                      |...++...+.  .+++.+.+.++.+|.+.|+++++.++++       .|+..+|..+...|...|.+++|...|..+  
T Consensus        80 Ai~yl~~ark~--~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a--  148 (449)
T 1b89_A           80 LVKYLQMARKK--ARESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV--  148 (449)
T ss_dssp             -------------------------------CHHHHTTTTT-------CC----------------CTTTHHHHHHHT--
T ss_pred             HHHHHHHHHHh--CccchhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHh--
Confidence            77766655553  2346667777777777777777766663       145556777777777777777777777754  


Q ss_pred             cCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHH
Q 044084          194 QGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVA  259 (343)
Q Consensus       194 ~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  259 (343)
                             ..|..++.++.+.|++++|.+.+..+      .++.+|..++.+|...|+++.|.....
T Consensus       149 -------~n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l  201 (449)
T 1b89_A          149 -------SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGL  201 (449)
T ss_dssp             -------TCHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTT
T ss_pred             -------hhHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHH
Confidence                   35667777777777777777777665      246677777777777777777744433

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.76  E-value=6e-17  Score=130.11  Aligned_cols=226  Identities=11%  Similarity=-0.046  Sum_probs=173.7

Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHH
Q 044084           33 YKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVK  112 (343)
Q Consensus        33 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  112 (343)
                      ...|++++|...|+++.+.....+|....+|..+...+...|++++|+..|++..+... .+..++..+...+...|+++
T Consensus        16 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~-~~~~~~~~la~~~~~~~~~~   94 (275)
T 1xnf_A           16 QPTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRP-DMPEVFNYLGIYLTQAGNFD   94 (275)
T ss_dssp             CCCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHTTCHH
T ss_pred             CccchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcCC-CcHHHHHHHHHHHHHccCHH
Confidence            34578899999999888764433344567888889999999999999999999888642 36778888888999999999


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHH
Q 044084          113 VAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLI  192 (343)
Q Consensus       113 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  192 (343)
                      +|...++++.+..+. +..++..+...|...|++++|...|+++.+..+  +.......+..+...|++++|...+++..
T Consensus        95 ~A~~~~~~al~~~~~-~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~--~~~~~~~~~~~~~~~~~~~~A~~~~~~~~  171 (275)
T 1xnf_A           95 AAYEAFDSVLELDPT-YNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDP--NDPFRSLWLYLAEQKLDEKQAKEVLKQHF  171 (275)
T ss_dssp             HHHHHHHHHHHHCTT-CTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHHCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCcc-ccHHHHHHHHHHHHhccHHHHHHHHHHHHHhCC--CChHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            999999998887543 678888899999999999999999999887653  33333444445566789999999998877


Q ss_pred             HcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCC---cChhhHHHHHHHHHccCChHHHHHHHHHHhhC
Q 044084          193 SQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFD---KCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       193 ~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                      ... +++... ..++..+...++.++|...+....+....   .+..++..+...|...|++++|...|++..+.
T Consensus       172 ~~~-~~~~~~-~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  244 (275)
T 1xnf_A          172 EKS-DKEQWG-WNIVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVAN  244 (275)
T ss_dssp             HHS-CCCSTH-HHHHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             hcC-CcchHH-HHHHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHhC
Confidence            763 333333 34667777888888888888877654311   12577888899999999999999999999876

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.76  E-value=7.2e-16  Score=122.45  Aligned_cols=226  Identities=17%  Similarity=0.100  Sum_probs=186.4

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCC--C----HHHH
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLR--D----LEVF  133 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~----~~~~  133 (343)
                      ...|..+...+...|++++|+..|++..+..  .+...+..+..++...|++++|...+++..+.....  +    ..++
T Consensus         5 a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~   82 (258)
T 3uq3_A            5 ADKEKAEGNKFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSF   82 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHH
Confidence            4678899999999999999999999999887  688899999999999999999999999988754321  2    6889


Q ss_pred             HHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHcc
Q 044084          134 LKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRI  213 (343)
Q Consensus       134 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~  213 (343)
                      ..+...+...|++++|...|++......  +.       ..+...|++++|...++++.... +.+...+..+...+...
T Consensus        83 ~~l~~~~~~~~~~~~A~~~~~~a~~~~~--~~-------~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~  152 (258)
T 3uq3_A           83 ARIGNAYHKLGDLKKTIEYYQKSLTEHR--TA-------DILTKLRNAEKELKKAEAEAYVN-PEKAEEARLEGKEYFTK  152 (258)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCC--CH-------HHHHHHHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcccHHHHHHHHHHHHhcCc--hh-------HHHHHHhHHHHHHHHHHHHHHcC-cchHHHHHHHHHHHHHh
Confidence            9999999999999999999999988653  32       34666789999999999998863 33456788888999999


Q ss_pred             CChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHhHH
Q 044084          214 GLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYT  293 (343)
Q Consensus       214 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~  293 (343)
                      |++++|...++...+.. +.+..++..+...|...|++++|...+++..+.. +.+...+..                  
T Consensus       153 ~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~------------------  212 (258)
T 3uq3_A          153 SDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIR------------------  212 (258)
T ss_dssp             TCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHH------------------
T ss_pred             cCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-HHHHHHHHH------------------
Confidence            99999999999999875 5578889999999999999999999999998753 223444444                  


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhC
Q 044084          294 TVISAYNMAREFDMCVKFYNEFRMN  318 (343)
Q Consensus       294 ~l~~~~~~~g~~~~a~~~~~~m~~~  318 (343)
                       +...+...|++++|...+++..+.
T Consensus       213 -l~~~~~~~g~~~~A~~~~~~a~~~  236 (258)
T 3uq3_A          213 -KATAQIAVKEYASALETLDAARTK  236 (258)
T ss_dssp             -HHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             -HHHHHHHHhhHHHHHHHHHHHHHh
Confidence             444555667777777777777654

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.74  E-value=7.1e-15  Score=127.51  Aligned_cols=320  Identities=10%  Similarity=-0.012  Sum_probs=198.0

Q ss_pred             chhhHHHHHHHHHhC-----C--CCC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCCCCchHHHHHHHHHH
Q 044084            2 NSQSKLHYYEKMKSA-----G--IVL-DSGCYCQIMEAFYKIGDSEKVAALFLECESR----KLDLTPSSTHMYKILCDS   69 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~-----~--~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~~~~~~~~li~~   69 (343)
                      +.++|++.|++..+.     +  ..| ...+|+.+..+|...|++++|...+++..+.    .....+....++..+..+
T Consensus        66 ~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~~~~~~~~~~~~~~g~~  145 (472)
T 4g1t_A           66 QNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSSPYRIESPELDCEEGWT  145 (472)
T ss_dssp             CHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCSSCCCCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhcccccchhhHHHHHHHHHH
Confidence            467788888776541     1  122 3567899999999999999999999887542    111122234667766665


Q ss_pred             hhc--cCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHH---hcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh--
Q 044084           70 LGK--SGRAFEILKFFRDMKEKGILEDPSVYASLICSF---ASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIE--  142 (343)
Q Consensus        70 ~~~--~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~---~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~--  142 (343)
                      +..  .+++++|++.|++..+.... ++..+..+..++   ...++.++|.+.+++..+..+. +..++..+...+..  
T Consensus       146 ~~~~~~~~y~~A~~~~~kal~~~p~-~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~p~-~~~~~~~l~~~~~~~~  223 (472)
T 4g1t_A          146 RLKCGGNQNERAKVCFEKALEKKPK-NPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLNPD-NQYLKVLLALKLHKMR  223 (472)
T ss_dssp             HHHHCTTHHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHCSS-CHHHHHHHHHHHHHCC
T ss_pred             HHHHccccHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcCCc-chHHHHHHHHHHHHHH
Confidence            554  45799999999999886422 344554444443   3446667888888888876543 56666666555544  


Q ss_pred             --cCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHcc-------
Q 044084          143 --EGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRI-------  213 (343)
Q Consensus       143 --~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~-------  213 (343)
                        .+++++|.+.+++.....+ .+..++..+...|...|++++|...+++..+.. +-+..++..+..+|...       
T Consensus       224 ~~~~~~~~a~~~~~~al~~~~-~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~y~~~~~~~~~~  301 (472)
T 4g1t_A          224 EEGEEEGEGEKLVEEALEKAP-GVTDVLRSAAKFYRRKDEPDKAIELLKKALEYI-PNNAYLHCQIGCCYRAKVFQVMNL  301 (472)
T ss_dssp             ------CHHHHHHHHHHHHCS-SCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             hhhhHHHHHHHHHHHHHHhCc-cHHHHHHHHHHHHHHcCchHHHHHHHHHHHHhC-CChHHHHHHHHHHHHHHHHHhhhH
Confidence              4567888888888877665 456678888888899999999999998888763 23344555554444321       


Q ss_pred             ------------CChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHH--HHHHHHH-
Q 044084          214 ------------GLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVW--IYNSLMD-  278 (343)
Q Consensus       214 ------------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~--~~~~l~~-  278 (343)
                                  +..+.|...++...+.. +.+..++..+...|...|++++|...|++..+....|...  .+..+.. 
T Consensus       302 ~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~~~~~~~~~~~~~~~~~~  380 (472)
T 4g1t_A          302 RENGMYGKRKLLELIGHAVAHLKKADEAN-DNLFRVCSILASLHALADQYEEAEYYFQKEFSKELTPVAKQLLHLRYGNF  380 (472)
T ss_dssp             ------CHHHHHHHHHHHHHHHHHHHHHC-TTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHhhcC-CchhhhhhhHHHHHHHhccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHH
Confidence                        23556677777766654 4456677788888888888888888888887764333321  1222222 


Q ss_pred             HHhcccChhHHHh---------------------------------------HHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 044084          279 MHGRAKNLRQLEK---------------------------------------YTTVISAYNMAREFDMCVKFYNEFRMNG  319 (343)
Q Consensus       279 ~~~~~~~~~~a~~---------------------------------------~~~l~~~~~~~g~~~~a~~~~~~m~~~~  319 (343)
                      .....|+.++|..                                       |..+...|...|++++|++.|++.++.|
T Consensus       381 ~~~~~~~~~~Ai~~y~kal~i~~~~~~~~~~~~~l~~~~~~~l~~~p~~~~~~~~LG~~~~~~g~~~~A~~~y~kALe~~  460 (472)
T 4g1t_A          381 QLYQMKCEDKAIHHFIEGVKINQKSREKEKMKDKLQKIAKMRLSKNGADSEALHVLAFLQELNEKMQQADEDSERGLESG  460 (472)
T ss_dssp             HHHTSSCHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHHHHCC-CTTHHHHHHHHHHHHHHCC-------------
T ss_pred             HHHHCCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            2335566665543                                       7788899999999999999999998865


Q ss_pred             C-CccHHH
Q 044084          320 G-VIDRAM  326 (343)
Q Consensus       320 ~-~p~~~~  326 (343)
                      . .|+..+
T Consensus       461 ~~~p~a~~  468 (472)
T 4g1t_A          461 SLIPSASS  468 (472)
T ss_dssp             --------
T ss_pred             CCCCcHhh
Confidence            3 344443

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.74  E-value=2.2e-15  Score=120.79  Aligned_cols=236  Identities=9%  Similarity=0.036  Sum_probs=189.9

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCC--hHhHH
Q 044084           22 SGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILED--PSVYA   99 (343)
Q Consensus        22 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~   99 (343)
                      ...+......+...|++++|...|+++.+....    +...+..+...+...|++++|++.+++..+.+..|+  ...|.
T Consensus         3 ~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~----~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~   78 (272)
T 3u4t_A            3 DDVEFRYADFLFKNNNYAEAIEVFNKLEAKKYN----SPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFE   78 (272)
T ss_dssp             --CHHHHHHHHHTTTCHHHHHHHHHHHHHTTCC----CSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC----cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHH
Confidence            445667788899999999999999999886533    235788899999999999999999999988432222  23478


Q ss_pred             HHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCC
Q 044084          100 SLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRR  179 (343)
Q Consensus       100 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  179 (343)
                      .+...+...|++++|...+++..+..+. +..++..+...|...|++++|+..|++..+..+ .+...+..+...+...+
T Consensus        79 ~lg~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~-~~~~~~~~l~~~~~~~~  156 (272)
T 3u4t_A           79 YYGKILMKKGQDSLAIQQYQAAVDRDTT-RLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPTT-TDPKVFYELGQAYYYNK  156 (272)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHSTT-CTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSSC-CCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcccHHHHHHHHHHHHhcCcc-cHHHHHHHHHHHHHccCHHHHHHHHHHHhhcCC-CcHHHHHHHHHHHHHHH
Confidence            8899999999999999999999997654 678999999999999999999999999987754 45566777773444456


Q ss_pred             cHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCC---hhHHHHHHHHHHHcC-CCcC------hhhHHHHHHHHHccC
Q 044084          180 AYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGL---YSKAEKVFIEMQQKG-FDKC------VVAYSSMVAMYGKTG  249 (343)
Q Consensus       180 ~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~---~~~a~~~~~~~~~~~-~~~~------~~~~~~l~~~~~~~~  249 (343)
                      ++++|.+.|++..+.. +.+...+..+..++...|+   +++|...+++..+.. -.|+      ..+|..+...|...|
T Consensus       157 ~~~~A~~~~~~a~~~~-p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  235 (272)
T 3u4t_A          157 EYVKADSSFVKVLELK-PNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKYKDELIEANEYIAYYYTINR  235 (272)
T ss_dssp             CHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGGHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHcC
Confidence            9999999999999874 3346677778888888888   888999998887642 1133      257888999999999


Q ss_pred             ChHHHHHHHHHHhhC
Q 044084          250 RIRDAMRLVAKMKPK  264 (343)
Q Consensus       250 ~~~~a~~~~~~m~~~  264 (343)
                      ++++|...|++..+.
T Consensus       236 ~~~~A~~~~~~al~~  250 (272)
T 3u4t_A          236 DKVKADAAWKNILAL  250 (272)
T ss_dssp             CHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHhc
Confidence            999999999999876

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A

Probab=99.73  E-value=2.4e-15  Score=119.15  Aligned_cols=201  Identities=12%  Similarity=0.022  Sum_probs=160.0

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLM  139 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  139 (343)
                      ...|..+...+...|++++|++.|+++.+.. +.+...+..+...+...|++++|...++++.+.... +..++..+...
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~la~~  114 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTEMEPKLADEEYRKALASDSR-NARVLNNYGGF  114 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC-cHHHHHHHHHH
Confidence            4667778888888888888888888887764 235677788888888888888998888888877543 67888888888


Q ss_pred             HHhcCcHhHHHHHHHHHHhcCCCC-chhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhH
Q 044084          140 YIEEGMVEKTLEVVESMKNAELNI-SDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSK  218 (343)
Q Consensus       140 ~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~  218 (343)
                      |...|++++|.+.++++...+..| +...+..+...+...|++++|...+++..+.. +.+...+..+...+...|++++
T Consensus       115 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~  193 (252)
T 2ho1_A          115 LYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLLYKEREYVP  193 (252)
T ss_dssp             HHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCCHHH
Confidence            888999999999988887732223 45567778888888899999999998888764 3456777888888888999999


Q ss_pred             HHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhC
Q 044084          219 AEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       219 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                      |...++.+.+.. +.+...+..+...+...|++++|.+.++++.+.
T Consensus       194 A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~  238 (252)
T 2ho1_A          194 ARQYYDLFAQGG-GQNARSLLLGIRLAKVFEDRDTAASYGLQLKRL  238 (252)
T ss_dssp             HHHHHHHHHTTS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-cCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            999998887764 456677888888888899999999999888775

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.73  E-value=5.5e-15  Score=118.58  Aligned_cols=248  Identities=13%  Similarity=0.001  Sum_probs=191.6

Q ss_pred             hhccCcHHHHHHHHHHHHhcCCC---CChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcH
Q 044084           70 LGKSGRAFEILKFFRDMKEKGIL---EDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMV  146 (343)
Q Consensus        70 ~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  146 (343)
                      ....|++++|++.|+++.+....   .+..++..+...+...|++++|...++++.+..+. +..++..+...|...|++
T Consensus        15 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~-~~~~~~~la~~~~~~~~~   93 (275)
T 1xnf_A           15 LQPTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPD-MPEVFNYLGIYLTQAGNF   93 (275)
T ss_dssp             CCCCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHTTCH
T ss_pred             cCccchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcCCC-cHHHHHHHHHHHHHccCH
Confidence            44568999999999999886321   14567888899999999999999999999997653 789999999999999999


Q ss_pred             hHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHH
Q 044084          147 EKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEM  226 (343)
Q Consensus       147 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~  226 (343)
                      ++|...|++..+..+ .+..++..+...+...|++++|...++++.+.  .|+.......+..+...|++++|...+...
T Consensus        94 ~~A~~~~~~al~~~~-~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~  170 (275)
T 1xnf_A           94 DAAYEAFDSVLELDP-TYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD--DPNDPFRSLWLYLAEQKLDEKQAKEVLKQH  170 (275)
T ss_dssp             HHHHHHHHHHHHHCT-TCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCc-cccHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            999999999988765 45678999999999999999999999999987  355555555556667789999999999888


Q ss_pred             HHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHH
Q 044084          227 QQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFD  306 (343)
Q Consensus       227 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~  306 (343)
                      .... +++...+ .++..+...++.++|...+++..+.  .|+...              ..+..+..+...|...|+++
T Consensus       171 ~~~~-~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~--------------~~~~~~~~la~~~~~~g~~~  232 (275)
T 1xnf_A          171 FEKS-DKEQWGW-NIVEFYLGNISEQTLMERLKADATD--NTSLAE--------------HLSETNFYLGKYYLSLGDLD  232 (275)
T ss_dssp             HHHS-CCCSTHH-HHHHHHTTSSCHHHHHHHHHHHCCS--HHHHHH--------------HHHHHHHHHHHHHHHTTCHH
T ss_pred             HhcC-CcchHHH-HHHHHHHHhcCHHHHHHHHHHHhcc--cccccc--------------cccHHHHHHHHHHHHcCCHH
Confidence            8764 4444444 4777788888999999999998865  222110              00111555677788889999


Q ss_pred             HHHHHHHHHHhCCCCccHHHHHHHHHHHhcccccccC
Q 044084          307 MCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       307 ~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~g~~~~a  343 (343)
                      +|...|++..+..  |+.  +.....++...|++++|
T Consensus       233 ~A~~~~~~al~~~--p~~--~~~~~~~~~~l~~~~~a  265 (275)
T 1xnf_A          233 SATALFKLAVANN--VHN--FVEHRYALLELSLLGQD  265 (275)
T ss_dssp             HHHHHHHHHHTTC--CTT--CHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhCC--chh--HHHHHHHHHHHHHHHhh
Confidence            9999999998864  422  22235566667776654

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.73  E-value=5.5e-15  Score=114.75  Aligned_cols=201  Identities=8%  Similarity=-0.042  Sum_probs=120.4

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLM  139 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  139 (343)
                      ...|..+...+...|++++|++.+++..+.. +.+...+..+...+...|++++|...++++.+.... +..++..+...
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~l~~~   85 (225)
T 2vq2_A            8 SNIKTQLAMEYMRGQDYRQATASIEDALKSD-PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIKPD-SAEINNNYGWF   85 (225)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCC-ChHHHHHHHHH
Confidence            4555566666666666666666666665542 223455555666666666666666666666655432 55566666666


Q ss_pred             HHhc-CcHhHHHHHHHHHHhcCCCC-chhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChh
Q 044084          140 YIEE-GMVEKTLEVVESMKNAELNI-SDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYS  217 (343)
Q Consensus       140 ~~~~-~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~  217 (343)
                      +... |++++|...++++.+.+..| +...+..+..++...|++++|...++++.+.. +.+...+..+...+...|+++
T Consensus        86 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~  164 (225)
T 2vq2_A           86 LCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQ-PQFPPAFKELARTKMLAGQLG  164 (225)
T ss_dssp             HHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHH
T ss_pred             HHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCchHHHHHHHHHHHcCCHH
Confidence            6666 66666666666666521112 23455566666666666666666666666553 223555666666666677777


Q ss_pred             HHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhh
Q 044084          218 KAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       218 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                      +|...++...+.....+...+..+...+...|+.+.+..+++.+.+
T Consensus       165 ~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  210 (225)
T 2vq2_A          165 DADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQA  210 (225)
T ss_dssp             HHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHH
Confidence            7777776666653113455566666666667777777776666654

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1

Probab=99.72  E-value=3.1e-14  Score=114.26  Aligned_cols=224  Identities=13%  Similarity=0.004  Sum_probs=190.0

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhc----cCcHHHHHHHHHHHHhcCCCCChH
Q 044084           21 DSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGK----SGRAFEILKFFRDMKEKGILEDPS   96 (343)
Q Consensus        21 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~   96 (343)
                      +..++..+...+...|++++|...|++..+.+    +  ..++..+...+..    .+++++|++.|++..+.+   +..
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~~----~--~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~   75 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK----E--NSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSN   75 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT----C--HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHCC----C--HHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHH
Confidence            56678888889999999999999999988732    1  4678888888888    999999999999998875   677


Q ss_pred             hHHHHHHHHhc----ccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----cCcHhHHHHHHHHHHhcCCCCchhhH
Q 044084           97 VYASLICSFAS----IAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIE----EGMVEKTLEVVESMKNAELNISDCIS  168 (343)
Q Consensus        97 ~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~  168 (343)
                      .+..+...+..    .+++++|...+++..+.+   +...+..+...|..    .+++++|+..|++..+.+   +...+
T Consensus        76 a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~  149 (273)
T 1ouv_A           76 GCHLLGNLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGC  149 (273)
T ss_dssp             HHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHH
T ss_pred             HHHHHHHHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---cHHHH
Confidence            88888888888    999999999999998875   77889999999999    999999999999988875   34567


Q ss_pred             HHHHHHHhc----CCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHc----cCChhHHHHHHHHHHHcCCCcChhhHHH
Q 044084          169 CVIVNGFSK----RRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCR----IGLYSKAEKVFIEMQQKGFDKCVVAYSS  240 (343)
Q Consensus       169 ~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~  240 (343)
                      ..+...|..    .+++++|...|++..+.+   +...+..+...|..    .+++++|...|+...+.+   +...+..
T Consensus       150 ~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~  223 (273)
T 1ouv_A          150 TILGSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGGGCFN  223 (273)
T ss_dssp             HHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHHHHHH
T ss_pred             HHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCC---CHHHHHH
Confidence            777777877    899999999999988874   45677778888888    899999999999988875   2667788


Q ss_pred             HHHHHHc----cCChHHHHHHHHHHhhCC
Q 044084          241 MVAMYGK----TGRIRDAMRLVAKMKPKG  265 (343)
Q Consensus       241 l~~~~~~----~~~~~~a~~~~~~m~~~~  265 (343)
                      +...|..    .+++++|...|++..+.|
T Consensus       224 l~~~~~~g~~~~~~~~~A~~~~~~a~~~~  252 (273)
T 1ouv_A          224 LGAMQYNGEGVTRNEKQAIENFKKGCKLG  252 (273)
T ss_dssp             HHHHHHTTSSSSCCSTTHHHHHHHHHHHT
T ss_pred             HHHHHHcCCCcccCHHHHHHHHHHHHHcC
Confidence            8888888    899999999999988864

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.72  E-value=5e-14  Score=124.02  Aligned_cols=330  Identities=12%  Similarity=0.090  Sum_probs=167.0

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHh-hccCcHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSL-GKSGRAFEIL   80 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~-~~~~~~~~a~   80 (343)
                      ++++|..+|+++.+.. |.+...|..++..+.+.|++++|..+|+++....  |+   ...|...+... ...|+.+.|.
T Consensus        27 ~~~~a~~~~e~al~~~-P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~~--p~---~~lw~~~~~~~~~~~~~~~~a~  100 (530)
T 2ooe_A           27 PIDKARKTYERLVAQF-PSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMKV--LH---IDLWKCYLSYVRETKGKLPSYK  100 (530)
T ss_dssp             CHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTC--CC---HHHHHHHHHHHHHHTTTSTTHH
T ss_pred             CHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC--CC---hHHHHHHHHHHHHHccchhhHH
Confidence            4567777777777753 2456677777777777778888888877776554  22   44666665432 2345555544


Q ss_pred             H----HHHHHHhc-CCCC-ChHhHHHHHHHHhc---------ccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH-----
Q 044084           81 K----FFRDMKEK-GILE-DPSVYASLICSFAS---------IAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMY-----  140 (343)
Q Consensus        81 ~----~~~~~~~~-~~~~-~~~~~~~l~~~~~~---------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~-----  140 (343)
                      +    +|++.... |..| +...|...+....+         .|+++.|..+|++..+.........|.......     
T Consensus       101 ~~~~~~~~~al~~~g~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al~~P~~~~~~~~~~~~~~e~~~~~  180 (530)
T 2ooe_A          101 EKMAQAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVNPMINIEQLWRDYNKYEEGINI  180 (530)
T ss_dssp             HHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHTTSCCTTHHHHHHHHHHHHHHHCH
T ss_pred             HHHHHHHHHHHHHCCCCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHHHHHHhchhhhHHHHHHHHHHHHHhhch
Confidence            4    55555443 4333 34556665555443         577888888888777621111122332221110     


Q ss_pred             --------HhcCcHhHHHHHHH----------------------------------------------------------
Q 044084          141 --------IEEGMVEKTLEVVE----------------------------------------------------------  154 (343)
Q Consensus       141 --------~~~~~~~~a~~~~~----------------------------------------------------------  154 (343)
                              .+.+++..|..++.                                                          
T Consensus       181 ~~~~~~l~~~~~~~~~A~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~~~w~~~~~~e~~~~~~~~~~~~~~~~a~~~  260 (530)
T 2ooe_A          181 HLAKKMIEDRSRDYMNARRVAKEYETVMKGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFA  260 (530)
T ss_dssp             HHHHHHHHTTHHHHHHHHHHHHHHHHHHHHCCSSSCCCCCC--CCHHHHHHHHHHHHHHHHHCSSCCSCSHHHHHHHHHH
T ss_pred             hHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhccccccCCCCCChhHHHHHHHHHHHHHHHHcCCccCCcchhHHHHHHHH
Confidence                    01122333333333                                                          


Q ss_pred             --HHHhcCCCCchhhHHHHHHHHhc-------CCcHH-------HHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhH
Q 044084          155 --SMKNAELNISDCISCVIVNGFSK-------RRAYW-------AAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSK  218 (343)
Q Consensus       155 --~~~~~~~~~~~~~~~~l~~~~~~-------~~~~~-------~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~  218 (343)
                        +.....+ .+...|..++..+..       .|+++       +|..+|++..+.-.+-+...|..++..+.+.|++++
T Consensus       261 y~~al~~~p-~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~g~~~~  339 (530)
T 2ooe_A          261 YEQCLLVLG-HHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEK  339 (530)
T ss_dssp             HHHHHHHHT-TCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHhCC-CCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHH
Confidence              2222211 122333333333332       45544       555566555542112234455555555556666666


Q ss_pred             HHHHHHHHHHcCCCcC-h-hhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHH-HhcccChhHHHh----
Q 044084          219 AEKVFIEMQQKGFDKC-V-VAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDM-HGRAKNLRQLEK----  291 (343)
Q Consensus       219 a~~~~~~~~~~~~~~~-~-~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~-~~~~~~~~~a~~----  291 (343)
                      |..+|+.+.+.  +|+ . ..|..++..+.+.|++++|..+|++..+.. +.+...+...... +...|+.++|..    
T Consensus       340 A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~-~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~  416 (530)
T 2ooe_A          340 VHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-RTRHHVYVTAALMEYYCSKDKSVAFKIFEL  416 (530)
T ss_dssp             HHHHHHHHHHS--SSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCT-TCCTHHHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHhCc--cccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhcc-CCchHHHHHHHHHHHHHcCChhHHHHHHHH
Confidence            66666666553  232 1 355555555555666666666666665531 1111122111111 223555555544    


Q ss_pred             -----------HHHHHHHHHhcCCHHHHHHHHHHHHhCCC-Ccc--HHHHHHHHHHHhcccccc
Q 044084          292 -----------YTTVISAYNMAREFDMCVKFYNEFRMNGG-VID--RAMAGIMVGVFSKLSQIE  341 (343)
Q Consensus       292 -----------~~~l~~~~~~~g~~~~a~~~~~~m~~~~~-~p~--~~~~~~l~~~~~~~g~~~  341 (343)
                                 |..++..+.+.|+.++|..+|++....+. .|+  ...|...+....+.|+.+
T Consensus       417 al~~~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~~~~~~~lw~~~~~~e~~~G~~~  480 (530)
T 2ooe_A          417 GLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLA  480 (530)
T ss_dssp             HHHHHTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSCGGGCHHHHHHHHHHHHHSSCHH
T ss_pred             HHHHCCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHH
Confidence                       55555555666666666666666665432 222  234555555555555544

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=99.72  E-value=6.7e-15  Score=123.07  Aligned_cols=247  Identities=10%  Similarity=0.069  Sum_probs=202.9

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCc-HHHHHHHHHHHHhcCCCCChHhHHH
Q 044084           22 SGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGR-AFEILKFFRDMKEKGILEDPSVYAS  100 (343)
Q Consensus        22 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~  100 (343)
                      ...|..+...+.+.|++++|+..|+++.+.+    |.+..+|+.+...+...|+ +++|+..|++..+.... +...|..
T Consensus        97 ~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~----P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P~-~~~a~~~  171 (382)
T 2h6f_A           97 RDVYDYFRAVLQRDERSERAFKLTRDAIELN----AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPK-NYQVWHH  171 (382)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTT-CHHHHHH
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHhC----ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCCC-CHHHHHH
Confidence            3568888899999999999999999998765    4446899999999999997 99999999999987543 6778999


Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhc-CC
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSK-RR  179 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~  179 (343)
                      +..++...|++++|+..|+++++.... +...|..+..++.+.|++++|+..|+++.+.++ -+...|+.+..++.. .|
T Consensus       172 ~g~~~~~~g~~~eAl~~~~kal~ldP~-~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P-~~~~a~~~lg~~l~~l~~  249 (382)
T 2h6f_A          172 RRVLVEWLRDPSQELEFIADILNQDAK-NYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDV-RNNSVWNQRYFVISNTTG  249 (382)
T ss_dssp             HHHHHHHHTCCTTHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHhCcc-CHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhcC
Confidence            999999999999999999999998764 899999999999999999999999999998876 567789999999888 66


Q ss_pred             cHHHH-----HHHHHHHHHcCCCCCHhhHHHHHHHHHccC--ChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccC---
Q 044084          180 AYWAA-----VKVYEQLISQGCIPGQVTYASIINAYCRIG--LYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTG---  249 (343)
Q Consensus       180 ~~~~a-----~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---  249 (343)
                      ..++|     +..+++..... +-+...|..+...+...|  ++++|.+.+..+ +.. +.+...+..+..+|.+.|   
T Consensus       250 ~~~eA~~~~el~~~~~Al~l~-P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~~~-p~~~~al~~La~~~~~~~~~~  326 (382)
T 2h6f_A          250 YNDRAVLEREVQYTLEMIKLV-PHNESAWNYLKGILQDRGLSKYPNLLNQLLDL-QPS-HSSPYLIAFLVDIYEDMLENQ  326 (382)
T ss_dssp             SCSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-TTT-CCCHHHHHHHHHHHHHHHHTT
T ss_pred             cchHHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHccCccchHHHHHHHHHh-ccC-CCCHHHHHHHHHHHHHHhccc
Confidence            65666     58888888764 335678888888888888  689999999887 433 456778889999998874   


Q ss_pred             ------ChHHHHHHHHHH-hhCCCCch-HHHHHHHHHHH
Q 044084          250 ------RIRDAMRLVAKM-KPKGCEPN-VWIYNSLMDMH  280 (343)
Q Consensus       250 ------~~~~a~~~~~~m-~~~~~~p~-~~~~~~l~~~~  280 (343)
                            ..++|..+++++ .+.  .|. ...|..+...+
T Consensus       327 ~~~~~~~~~~A~~~~~~l~~~~--DP~r~~~w~~~~~~l  363 (382)
T 2h6f_A          327 CDNKEDILNKALELCEILAKEK--DTIRKEYWRYIGRSL  363 (382)
T ss_dssp             CSSHHHHHHHHHHHHHHHHHTT--CGGGHHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHHHHHHh--CchhHHHHHHHHHHH
Confidence                  258999999998 654  443 34455554443

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.71  E-value=1.5e-15  Score=119.59  Aligned_cols=198  Identities=12%  Similarity=0.079  Sum_probs=94.2

Q ss_pred             HHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 044084           62 MYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYI  141 (343)
Q Consensus        62 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  141 (343)
                      .|..+...+...|++++|...|++..+.. +.+...+..+...+...|++++|...++++.+.... +..++..+...+.
T Consensus        25 ~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~  102 (243)
T 2q7f_A           25 TGGQQMGRGSEFGDYEKAAEAFTKAIEEN-KEDAIPYINFANLLSSVNELERALAFYDKALELDSS-AATAYYGAGNVYV  102 (243)
T ss_dssp             -----------------CCTTHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCc-chHHHHHHHHHHH
Confidence            34444444455555555555555544432 113444444445555555555555555555444321 4455555555555


Q ss_pred             hcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHH
Q 044084          142 EEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEK  221 (343)
Q Consensus       142 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~  221 (343)
                      ..|++++|.+.++++.+... .+...+..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|..
T Consensus       103 ~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~  180 (243)
T 2q7f_A          103 VKEMYKEAKDMFEKALRAGM-ENGDLFYMLGTVLVKLEQPKLALPYLQRAVELN-ENDTEARFQFGMCLANEGMLDEALS  180 (243)
T ss_dssp             HTTCHHHHHHHHHHHHHHTC-CSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCHHHHH
T ss_pred             HhccHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHcCCHHHHHH
Confidence            55555555555555554433 233445555555555555555555555555442 2234455555555556666666666


Q ss_pred             HHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhC
Q 044084          222 VFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                      .++.+.+.. +.+..++..+...|...|++++|...++++.+.
T Consensus       181 ~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  222 (243)
T 2q7f_A          181 QFAAVTEQD-PGHADAFYNAGVTYAYKENREKALEMLDKAIDI  222 (243)
T ss_dssp             HHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHH
T ss_pred             HHHHHHHhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHcc
Confidence            666555543 234455555666666666666666666665553

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.71  E-value=1e-13  Score=122.05  Aligned_cols=322  Identities=11%  Similarity=0.082  Sum_probs=231.7

Q ss_pred             HHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhc
Q 044084           10 YEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEK   89 (343)
Q Consensus        10 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~   89 (343)
                      |++.++..+ -+...|..++.. .+.|++++|..+|+++.+..    |.+...|..++..+.+.|++++|..+|++....
T Consensus         2 le~al~~~P-~~~~~w~~l~~~-~~~~~~~~a~~~~e~al~~~----P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~   75 (530)
T 2ooe_A            2 AEKKLEENP-YDLDAWSILIRE-AQNQPIDKARKTYERLVAQF----PSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMK   75 (530)
T ss_dssp             HHHHHHHCT-TCHHHHHHHHHH-HHSSCHHHHHHHHHHHHTTC----TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTT
T ss_pred             hhhHhhhCC-CCHHHHHHHHHH-HHhCCHHHHHHHHHHHHHHC----CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc
Confidence            455555442 477789999984 78899999999999998764    334688999999999999999999999999886


Q ss_pred             CCCCChHhHHHHHHHH-hcccCHHHHHH----HHHHHHHc-CCCC-CHHHHHHHHHHHHh---------cCcHhHHHHHH
Q 044084           90 GILEDPSVYASLICSF-ASIAEVKVAEE----LFKEAEEK-GMLR-DLEVFLKLVLMYIE---------EGMVEKTLEVV  153 (343)
Q Consensus        90 ~~~~~~~~~~~l~~~~-~~~~~~~~a~~----~~~~~~~~-~~~~-~~~~~~~l~~~~~~---------~~~~~~a~~~~  153 (343)
                      .  |+...|...+... ...|+.+.|.+    +|++.... |..| +...|...+....+         .|+++.|..+|
T Consensus        76 ~--p~~~lw~~~~~~~~~~~~~~~~a~~~~~~~~~~al~~~g~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y  153 (530)
T 2ooe_A           76 V--LHIDLWKCYLSYVRETKGKLPSYKEKMAQAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVY  153 (530)
T ss_dssp             C--CCHHHHHHHHHHHHHHTTTSTTHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHH
T ss_pred             C--CChHHHHHHHHHHHHHccchhhHHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHH
Confidence            3  6777777766533 34466665554    77776653 5443 57788888877655         68899999999


Q ss_pred             HHHHhcCCCCchhhHHH---------------------------------------------------------------
Q 044084          154 ESMKNAELNISDCISCV---------------------------------------------------------------  170 (343)
Q Consensus       154 ~~~~~~~~~~~~~~~~~---------------------------------------------------------------  170 (343)
                      ++..+.........|..                                                               
T Consensus       154 ~~al~~P~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~~~~~~~A~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~~~w  233 (530)
T 2ooe_A          154 QRGCVNPMINIEQLWRDYNKYEEGINIHLAKKMIEDRSRDYMNARRVAKEYETVMKGLDRNAPSVPPQNTPQEAQQVDMW  233 (530)
T ss_dssp             HHHTTSCCTTHHHHHHHHHHHHHHHCHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHCCSSSCCCCCC--CCHHHHHHHH
T ss_pred             HHHHhchhhhHHHHHHHHHHHHHhhchhHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhccccccCCCCCChhHHHHHHHH
Confidence            98876311111112221                                                               


Q ss_pred             --HHHHHhc----CCc----HHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHc-------cCChh-------HHHHHHHHH
Q 044084          171 --IVNGFSK----RRA----YWAAVKVYEQLISQGCIPGQVTYASIINAYCR-------IGLYS-------KAEKVFIEM  226 (343)
Q Consensus       171 --l~~~~~~----~~~----~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~-------~~~~~-------~a~~~~~~~  226 (343)
                        .+.....    .++    ...+..+|++..... +-+...|......+.+       .|+++       +|..+++..
T Consensus       234 ~~~~~~e~~~~~~~~~~~~~~~~a~~~y~~al~~~-p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~A  312 (530)
T 2ooe_A          234 KKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERA  312 (530)
T ss_dssp             HHHHHHHHHCSSCCSCSHHHHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCccCCcchhHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHH
Confidence              1100000    011    136778899888763 4466778777777765       68887       899999998


Q ss_pred             HHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCch--HHHHHHHHHHHhcccChhHHHh-------------
Q 044084          227 QQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPN--VWIYNSLMDMHGRAKNLRQLEK-------------  291 (343)
Q Consensus       227 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~--~~~~~~l~~~~~~~~~~~~a~~-------------  291 (343)
                      .+.-.+.+...|..++..+.+.|++++|..+|+++.+.  .|+  ...|..++..+.+.|+.++|..             
T Consensus       313 l~~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~~~~~  390 (530)
T 2ooe_A          313 ISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRH  390 (530)
T ss_dssp             TTTTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--SSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCCT
T ss_pred             HHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCc--cccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhccCCch
Confidence            86323456888999999999999999999999999985  453  3578888888889999988877             


Q ss_pred             --HHHHH-HHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHhcccccccC
Q 044084          292 --YTTVI-SAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       292 --~~~l~-~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~g~~~~a  343 (343)
                        |.... ..+...|++++|..+|++..+... -+...|..++..+.+.|+.++|
T Consensus       391 ~~~~~~a~~~~~~~~~~~~A~~~~e~al~~~p-~~~~~~~~~~~~~~~~g~~~~A  444 (530)
T 2ooe_A          391 HVYVTAALMEYYCSKDKSVAFKIFELGLKKYG-DIPEYVLAYIDYLSHLNEDNNT  444 (530)
T ss_dssp             HHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHTTTTCHHHH
T ss_pred             HHHHHHHHHHHHHcCChhHHHHHHHHHHHHCC-CCHHHHHHHHHHHHhCCCHhhH
Confidence              11111 113368999999999999887632 3567889999999999887653

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.71  E-value=1.6e-14  Score=112.07  Aligned_cols=211  Identities=8%  Similarity=-0.094  Sum_probs=177.2

Q ss_pred             CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHH
Q 044084           20 LDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYA   99 (343)
Q Consensus        20 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~   99 (343)
                      .+...+..+...+...|++++|.+.|+.+.+...    .+...|..+...+...|++++|.+.+++..... +.+..++.
T Consensus         6 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~----~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~   80 (225)
T 2vq2_A            6 QVSNIKTQLAMEYMRGQDYRQATASIEDALKSDP----KNELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINN   80 (225)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT----TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             ccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCc----cchHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHH
Confidence            3566788899999999999999999999887652    235789999999999999999999999998864 33677888


Q ss_pred             HHHHHHhcc-cCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhc
Q 044084          100 SLICSFASI-AEVKVAEELFKEAEEKGMLR-DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSK  177 (343)
Q Consensus       100 ~l~~~~~~~-~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  177 (343)
                      .+...+... |++++|...++++.+.+..| +...+..+...+...|++++|...++++.+..+ .+...+..+...+..
T Consensus        81 ~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~la~~~~~  159 (225)
T 2vq2_A           81 NYGWFLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQP-QFPPAFKELARTKML  159 (225)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCchHHHHHHHHHHH
Confidence            899999999 99999999999998833233 367889999999999999999999999988765 456788899999999


Q ss_pred             CCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhH
Q 044084          178 RRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAY  238 (343)
Q Consensus       178 ~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  238 (343)
                      .|++++|...++++.+.....+...+..+...+...|+.+.+..+++.+.+..  |+....
T Consensus       160 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~--p~~~~~  218 (225)
T 2vq2_A          160 AGQLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQANF--PYSEEL  218 (225)
T ss_dssp             HTCHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHH
T ss_pred             cCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHhC--CCCHHH
Confidence            99999999999999887421466777778888899999999999999988764  444333

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A

Probab=99.71  E-value=1e-14  Score=115.50  Aligned_cols=202  Identities=13%  Similarity=0.068  Sum_probs=175.0

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHH
Q 044084           22 SGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASL  101 (343)
Q Consensus        22 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  101 (343)
                      ...+..+...+...|++++|.+.|+++.+..    |....++..+...+...|++++|.+.++++.+... .+...+..+
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~----~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~l  111 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEID----PSSADAHAALAVVFQTEMEPKLADEEYRKALASDS-RNARVLNNY  111 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHC----TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcC----CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCc-CcHHHHHHH
Confidence            5678888999999999999999999998764    22367899999999999999999999999988743 367788889


Q ss_pred             HHHHhcccCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCc
Q 044084          102 ICSFASIAEVKVAEELFKEAEEKGMLR-DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRA  180 (343)
Q Consensus       102 ~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  180 (343)
                      ...+...|++++|...++++.+.+..| +...+..+...+...|++++|...|++..+... .+...+..+...+...|+
T Consensus       112 a~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~la~~~~~~g~  190 (252)
T 2ho1_A          112 GGFLYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLNR-NQPSVALEMADLLYKERE  190 (252)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCS-CCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCc-ccHHHHHHHHHHHHHcCC
Confidence            999999999999999999998833334 577888999999999999999999999988765 456788899999999999


Q ss_pred             HHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcC
Q 044084          181 YWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKG  230 (343)
Q Consensus       181 ~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  230 (343)
                      +++|...++++.+.. +.+...+..+...+...|++++|.+.++.+.+..
T Consensus       191 ~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~  239 (252)
T 2ho1_A          191 YVPARQYYDLFAQGG-GQNARSLLLGIRLAKVFEDRDTAASYGLQLKRLY  239 (252)
T ss_dssp             HHHHHHHHHHHHTTS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC
Confidence            999999999998764 4566778888899999999999999999998874

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.71  E-value=2.8e-15  Score=118.01  Aligned_cols=213  Identities=14%  Similarity=0.080  Sum_probs=163.6

Q ss_pred             CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHH
Q 044084           20 LDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYA   99 (343)
Q Consensus        20 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~   99 (343)
                      .....|..+...+.+.|++++|...|+++.+..    |.+...+..+...+...|++++|++.+++..+.. +.+...+.
T Consensus        21 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~----~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~   95 (243)
T 2q7f_A           21 MASMTGGQQMGRGSEFGDYEKAAEAFTKAIEEN----KEDAIPYINFANLLSSVNELERALAFYDKALELD-SSAATAYY   95 (243)
T ss_dssp             ---------------------CCTTHHHHHTTC----TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             hHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHhC----cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CcchHHHH
Confidence            456678888999999999999999999998754    3336889999999999999999999999998874 33677888


Q ss_pred             HHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCC
Q 044084          100 SLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRR  179 (343)
Q Consensus       100 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  179 (343)
                      .+...+...|++++|...++++.+.... +...+..+...+...|++++|...++++.+... .+...+..+...+...|
T Consensus        96 ~la~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~  173 (243)
T 2q7f_A           96 GAGNVYVVKEMYKEAKDMFEKALRAGME-NGDLFYMLGTVLVKLEQPKLALPYLQRAVELNE-NDTEARFQFGMCLANEG  173 (243)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHTCC-SHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHcC
Confidence            8999999999999999999999987643 788899999999999999999999999987765 46678888999999999


Q ss_pred             cHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHH
Q 044084          180 AYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSM  241 (343)
Q Consensus       180 ~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  241 (343)
                      ++++|...++++.+.. +.+..++..+..+|...|++++|...++.+.+.. +.+...+..+
T Consensus       174 ~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~~  233 (243)
T 2q7f_A          174 MLDEALSQFAAVTEQD-PGHADAFYNAGVTYAYKENREKALEMLDKAIDIQ-PDHMLALHAK  233 (243)
T ss_dssp             CCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHccC-cchHHHHHHH
Confidence            9999999999998874 3457788899999999999999999999998875 3344444433

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.70  E-value=2e-14  Score=115.17  Aligned_cols=256  Identities=12%  Similarity=0.082  Sum_probs=193.9

Q ss_pred             HHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCC--CHHHHHHHHHH
Q 044084           62 MYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLR--DLEVFLKLVLM  139 (343)
Q Consensus        62 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~  139 (343)
                      .+......+...|++++|+..|++..+... .+...+..+...+...|++++|...+++..+.+..+  ....|..+...
T Consensus         5 ~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~   83 (272)
T 3u4t_A            5 VEFRYADFLFKNNNYAEAIEVFNKLEAKKY-NSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKI   83 (272)
T ss_dssp             CHHHHHHHHHTTTCHHHHHHHHHHHHHTTC-CCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHH
Confidence            456678889999999999999999988743 255588889999999999999999999999843222  24568999999


Q ss_pred             HHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHH
Q 044084          140 YIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKA  219 (343)
Q Consensus       140 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a  219 (343)
                      +...|++++|+..|++..+..+ .+..++..+...+...|++++|...+++..+.. +.+...+..+...+...+++++|
T Consensus        84 ~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A  161 (272)
T 3u4t_A           84 LMKKGQDSLAIQQYQAAVDRDT-TRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPT-TTDPKVFYELGQAYYYNKEYVKA  161 (272)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHST-TCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSS-CCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHcccHHHHHHHHHHHHhcCc-ccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcC-CCcHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999988765 456789999999999999999999999988763 34556666666244445699999


Q ss_pred             HHHHHHHHHcCCCcChhhHHHHHHHHHccCC---hHHHHHHHHHHhhCC-CCchHHHHHHHHHHHhcccChhHHHhHHHH
Q 044084          220 EKVFIEMQQKGFDKCVVAYSSMVAMYGKTGR---IRDAMRLVAKMKPKG-CEPNVWIYNSLMDMHGRAKNLRQLEKYTTV  295 (343)
Q Consensus       220 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~m~~~~-~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l  295 (343)
                      ...|+...+.. +.+...+..+..++...|+   +++|...+++..+.. -.|+.. -..+..+            |..+
T Consensus       162 ~~~~~~a~~~~-p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~-~~~~~~~------------~~~l  227 (272)
T 3u4t_A          162 DSSFVKVLELK-PNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKY-KDELIEA------------NEYI  227 (272)
T ss_dssp             HHHHHHHHHHS-TTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGG-HHHHHHH------------HHHH
T ss_pred             HHHHHHHHHhC-ccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccc-hHHHHHH------------HHHH
Confidence            99999999875 4457788888888888888   888998888887541 123321 1111111            5556


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHh
Q 044084          296 ISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFS  335 (343)
Q Consensus       296 ~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~  335 (343)
                      ...|...|++++|.+.|++..+... -+...+..+.....
T Consensus       228 ~~~~~~~~~~~~A~~~~~~al~~~p-~~~~a~~~l~~~~~  266 (272)
T 3u4t_A          228 AYYYTINRDKVKADAAWKNILALDP-TNKKAIDGLKMKLE  266 (272)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHC----
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhcCc-cHHHHHHHhhhhhc
Confidence            6778889999999999999988642 23444544444433

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=99.70  E-value=2e-14  Score=120.17  Aligned_cols=259  Identities=10%  Similarity=0.086  Sum_probs=206.1

Q ss_pred             CchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccC-HHHHHHHHHHHHHcCCCCCHHHHHH
Q 044084           57 PSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAE-VKVAEELFKEAEEKGMLRDLEVFLK  135 (343)
Q Consensus        57 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~  135 (343)
                      |....+|+.+...+...|++++|++.+++.+..... +...|+.+..++...|+ +++|+..++++.+..+. +...|..
T Consensus        94 p~~~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~P~-~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P~-~~~a~~~  171 (382)
T 2h6f_A           94 DKFRDVYDYFRAVLQRDERSERAFKLTRDAIELNAA-NYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPK-NYQVWHH  171 (382)
T ss_dssp             HHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTT-CHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCcc-CHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCCC-CHHHHHH
Confidence            445688999999999999999999999999987432 57788999999999996 99999999999998765 8999999


Q ss_pred             HHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHc-cC
Q 044084          136 LVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCR-IG  214 (343)
Q Consensus       136 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~-~~  214 (343)
                      +..++...|++++|+..|+++.+.++ -+...|..+..++...|++++|+..++++.+.. +-+...|+.+..++.. .|
T Consensus       172 ~g~~~~~~g~~~eAl~~~~kal~ldP-~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~-P~~~~a~~~lg~~l~~l~~  249 (382)
T 2h6f_A          172 RRVLVEWLRDPSQELEFIADILNQDA-KNYHAWQHRQWVIQEFKLWDNELQYVDQLLKED-VRNNSVWNQRYFVISNTTG  249 (382)
T ss_dssp             HHHHHHHHTCCTTHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHhCc-cCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcC
Confidence            99999999999999999999998876 577889999999999999999999999999885 3467888999999988 66


Q ss_pred             ChhHH-----HHHHHHHHHcCCCcChhhHHHHHHHHHccC--ChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChh
Q 044084          215 LYSKA-----EKVFIEMQQKGFDKCVVAYSSMVAMYGKTG--RIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLR  287 (343)
Q Consensus       215 ~~~~a-----~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~  287 (343)
                      ..++|     ...++...+.. +-+...|+.+...+...|  ++++|.+.+.++ +. ...+...+..+...|.+.|+..
T Consensus       250 ~~~eA~~~~el~~~~~Al~l~-P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~~-~p~~~~al~~La~~~~~~~~~~  326 (382)
T 2h6f_A          250 YNDRAVLEREVQYTLEMIKLV-PHNESAWNYLKGILQDRGLSKYPNLLNQLLDL-QP-SHSSPYLIAFLVDIYEDMLENQ  326 (382)
T ss_dssp             SCSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-TT-TCCCHHHHHHHHHHHHHHHHTT
T ss_pred             cchHHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHccCccchHHHHHHHHHh-cc-CCCCHHHHHHHHHHHHHHhccc
Confidence            65777     48888888875 446788999999999888  689999999888 33 2345667777777666543110


Q ss_pred             HHHhHHHHHHHHHhcCC-HHHHHHHHHHH-HhCCCCccHH-HHHHHHHHHh
Q 044084          288 QLEKYTTVISAYNMARE-FDMCVKFYNEF-RMNGGVIDRA-MAGIMVGVFS  335 (343)
Q Consensus       288 ~a~~~~~l~~~~~~~g~-~~~a~~~~~~m-~~~~~~p~~~-~~~~l~~~~~  335 (343)
                      .           ...++ +++|+++|+++ .+.  .|... .|..+...+.
T Consensus       327 ~-----------~~~~~~~~~A~~~~~~l~~~~--DP~r~~~w~~~~~~l~  364 (382)
T 2h6f_A          327 C-----------DNKEDILNKALELCEILAKEK--DTIRKEYWRYIGRSLQ  364 (382)
T ss_dssp             C-----------SSHHHHHHHHHHHHHHHHHTT--CGGGHHHHHHHHHHHH
T ss_pred             c-----------cchHHHHHHHHHHHHHHHHHh--CchhHHHHHHHHHHHH
Confidence            0           00122 47899999998 553  45544 4555555544

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=99.69  E-value=1.8e-13  Score=127.08  Aligned_cols=260  Identities=13%  Similarity=0.141  Sum_probs=195.2

Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhccc
Q 044084           30 EAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIA  109 (343)
Q Consensus        30 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  109 (343)
                      ..+...|.+++|..+|++..    ..    ....+.++.   ..+++++|.++.++.      -++.+|..+..++.+.|
T Consensus      1057 ~Iai~lglyEEAf~IYkKa~----~~----~~A~~VLie---~i~nldrAiE~Aerv------n~p~vWsqLAKAql~~G 1119 (1630)
T 1xi4_A         1057 NIAISNELFEEAFAIFRKFD----VN----TSAVQVLIE---HIGNLDRAYEFAERC------NEPAVWSQLAKAQLQKG 1119 (1630)
T ss_pred             HHHHhCCCHHHHHHHHHHcC----CH----HHHHHHHHH---HHhhHHHHHHHHHhc------CCHHHHHHHHHHHHhCC
Confidence            34556677777777777652    11    233344433   556777777777754      24667888999999999


Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHH
Q 044084          110 EVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYE  189 (343)
Q Consensus       110 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  189 (343)
                      ++++|...|.+.      -|...|..++..+.+.|++++|.+.|....+...  +....+.++.+|++.++++....+. 
T Consensus      1120 ~~kEAIdsYiKA------dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~~--e~~Idt~LafaYAKl~rleele~fI- 1190 (1630)
T 1xi4_A         1120 MVKEAIDSYIKA------DDPSSYMEVVQAANTSGNWEELVKYLQMARKKAR--ESYVETELIFALAKTNRLAELEEFI- 1190 (1630)
T ss_pred             CHHHHHHHHHhc------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhcc--cccccHHHHHHHHhhcCHHHHHHHH-
Confidence            999999988653      3778888899999999999999999988776553  2223445888888888887544442 


Q ss_pred             HHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCch
Q 044084          190 QLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPN  269 (343)
Q Consensus       190 ~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~  269 (343)
                         +   .|+...|..+...|...|++++|..+|...         ..|..+..+|.+.|++++|.+.+++..      +
T Consensus      1191 ---~---~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEaarKA~------n 1249 (1630)
T 1xi4_A         1191 ---N---GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKAN------S 1249 (1630)
T ss_pred             ---h---CCCHHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHHHHHhC------C
Confidence               2   356667778888999999999999999874         478999999999999999999998873      6


Q ss_pred             HHHHHHHHHHHhcccChhHHHh-----------HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHhcc
Q 044084          270 VWIYNSLMDMHGRAKNLRQLEK-----------YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKL  337 (343)
Q Consensus       270 ~~~~~~l~~~~~~~~~~~~a~~-----------~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~  337 (343)
                      ..+|..+..+|...|+++.|..           +..++..|.+.|.+++|+.+++..+... +-....|.-|..+|++.
T Consensus      1250 ~~aWkev~~acve~~Ef~LA~~cgl~Iiv~~deLeeli~yYe~~G~feEAI~LlE~aL~Le-raH~gmftELaiLyaKy 1327 (1630)
T 1xi4_A         1250 TRTWKEVCFACVDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKF 1327 (1630)
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHhhhcCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccC-hhHhHHHHHHHHHHHhC
Confidence            6889999999999999888877           6788899999999999999998876543 22223465666666553

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1

Probab=99.68  E-value=2.8e-13  Score=108.65  Aligned_cols=228  Identities=12%  Similarity=-0.002  Sum_probs=188.1

Q ss_pred             hHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhc----ccCHHHHHHHHHHHHHcCCCCCHHHHH
Q 044084           59 STHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFAS----IAEVKVAEELFKEAEEKGMLRDLEVFL  134 (343)
Q Consensus        59 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~  134 (343)
                      +..++..+...+...|++++|++.|++..+.+   +...+..+...+..    .+++++|...|++..+.+   +...+.
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~   78 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCH   78 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHHHHH
Confidence            35788889999999999999999999998843   56678888888998    999999999999999875   788999


Q ss_pred             HHHHHHHh----cCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhc----CCcHHHHHHHHHHHHHcCCCCCHhhHHHH
Q 044084          135 KLVLMYIE----EGMVEKTLEVVESMKNAELNISDCISCVIVNGFSK----RRAYWAAVKVYEQLISQGCIPGQVTYASI  206 (343)
Q Consensus       135 ~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~p~~~~~~~l  206 (343)
                      .+...|..    .+++++|+..|++..+.+   +...+..+...|..    .+++++|...|++..+.+   +...+..+
T Consensus        79 ~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~l  152 (273)
T 1ouv_A           79 LLGNLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGCTIL  152 (273)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHH
T ss_pred             HHHHHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---cHHHHHHH
Confidence            99999999    999999999999998875   55678888888988    999999999999999875   55677778


Q ss_pred             HHHHHc----cCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHc----cCChHHHHHHHHHHhhCCCCchHHHHHHHHH
Q 044084          207 INAYCR----IGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGK----TGRIRDAMRLVAKMKPKGCEPNVWIYNSLMD  278 (343)
Q Consensus       207 l~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~  278 (343)
                      ...|..    .+++++|...|+...+.+   +...+..+...|..    .+++++|...|++..+.+.   ...+..+..
T Consensus       153 g~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~---~~a~~~l~~  226 (273)
T 1ouv_A          153 GSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELEN---GGGCFNLGA  226 (273)
T ss_dssp             HHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTTC---HHHHHHHHH
T ss_pred             HHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCCC---HHHHHHHHH
Confidence            888887    899999999999998875   46778889999999    9999999999999988742   344444444


Q ss_pred             HHhcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 044084          279 MHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNG  319 (343)
Q Consensus       279 ~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~  319 (343)
                      .|...               ....+++++|++.|++..+.|
T Consensus       227 ~~~~g---------------~~~~~~~~~A~~~~~~a~~~~  252 (273)
T 1ouv_A          227 MQYNG---------------EGVTRNEKQAIENFKKGCKLG  252 (273)
T ss_dssp             HHHTT---------------SSSSCCSTTHHHHHHHHHHHT
T ss_pred             HHHcC---------------CCcccCHHHHHHHHHHHHHcC
Confidence            44330               001667777888888877765

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.67  E-value=8.6e-15  Score=124.20  Aligned_cols=307  Identities=12%  Similarity=0.026  Sum_probs=213.8

Q ss_pred             CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhc----CCCC-
Q 044084           19 VLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEK----GILE-   93 (343)
Q Consensus        19 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~----~~~~-   93 (343)
                      .+....+......+...|++++|...|+++.+...........+|..+...+...|++++|...+++....    +..| 
T Consensus         6 ~~~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~   85 (406)
T 3sf4_A            6 EASCLELALEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLG   85 (406)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHHHHhccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHH
Confidence            34555677788899999999999999999988643221111357888999999999999999999987543    2122 


Q ss_pred             ChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCC-CC----HHHHHHHHHHHHhcCc--------------------HhH
Q 044084           94 DPSVYASLICSFASIAEVKVAEELFKEAEEKGML-RD----LEVFLKLVLMYIEEGM--------------------VEK  148 (343)
Q Consensus        94 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~--------------------~~~  148 (343)
                      ...++..+...+...|++++|...+++..+.... ++    ..++..+...|...|+                    +++
T Consensus        86 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~  165 (406)
T 3sf4_A           86 EAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQA  165 (406)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHH
Confidence            2456777888999999999999999887763211 12    4578889999999999                    999


Q ss_pred             HHHHHHHHHhc----C-CCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCC-CCC----HhhHHHHHHHHHccCChhH
Q 044084          149 TLEVVESMKNA----E-LNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGC-IPG----QVTYASIINAYCRIGLYSK  218 (343)
Q Consensus       149 a~~~~~~~~~~----~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~p~----~~~~~~ll~~~~~~~~~~~  218 (343)
                      |...+++....    + .+....++..+...+...|++++|...+++..+... .++    ..++..+...|...|++++
T Consensus       166 A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~  245 (406)
T 3sf4_A          166 AVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFET  245 (406)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHH
Confidence            99999886542    1 111234677888899999999999999998875410 111    2367888889999999999


Q ss_pred             HHHHHHHHHHcC----CCc-ChhhHHHHHHHHHccCChHHHHHHHHHHhhCCC-CchHHHHHHHHHHHhcccChhHHHhH
Q 044084          219 AEKVFIEMQQKG----FDK-CVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGC-EPNVWIYNSLMDMHGRAKNLRQLEKY  292 (343)
Q Consensus       219 a~~~~~~~~~~~----~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~-~p~~~~~~~l~~~~~~~~~~~~a~~~  292 (343)
                      |...++...+..    ..+ ...++..+...|...|++++|...+++..+... .++.               ...+..+
T Consensus       246 A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~---------------~~~~~~~  310 (406)
T 3sf4_A          246 ASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDR---------------IGEGRAC  310 (406)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCH---------------HHHHHHH
T ss_pred             HHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCc---------------HHHHHHH
Confidence            999999877542    111 155788889999999999999999998765310 0010               0011113


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhC----CCCcc-HHHHHHHHHHHhccccc
Q 044084          293 TTVISAYNMAREFDMCVKFYNEFRMN----GGVID-RAMAGIMVGVFSKLSQI  340 (343)
Q Consensus       293 ~~l~~~~~~~g~~~~a~~~~~~m~~~----~~~p~-~~~~~~l~~~~~~~g~~  340 (343)
                      ..+...|...|++++|.+.+++..+.    +..+. ..++..+..++...|+.
T Consensus       311 ~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  363 (406)
T 3sf4_A          311 WSLGNAYTALGNHDQAMHFAEKHLEISREVGDKSGELTARLNLSDLQMVLGLS  363 (406)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHhhHh
Confidence            44555566666666676666665332    22222 23466666777766655

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.67  E-value=2.6e-15  Score=127.78  Aligned_cols=242  Identities=10%  Similarity=0.052  Sum_probs=183.3

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhc----CC-CCChHh
Q 044084           23 GCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEK----GI-LEDPSV   97 (343)
Q Consensus        23 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~----~~-~~~~~~   97 (343)
                      ..+..+...+...|++++|...|+++.+...........+|..+...+...|++++|++.+++..+.    +. .....+
T Consensus        49 ~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~  128 (411)
T 4a1s_A           49 LELALEGERLCNAGDCRAGVAFFQAAIQAGTEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKS  128 (411)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHH
Confidence            3455677788999999999999999988643211111257888999999999999999999988653    11 123456


Q ss_pred             HHHHHHHHhcccCHHHHHHHHHHHHHcC-----CCCCHHHHHHHHHHHHhcCc-----------------HhHHHHHHHH
Q 044084           98 YASLICSFASIAEVKVAEELFKEAEEKG-----MLRDLEVFLKLVLMYIEEGM-----------------VEKTLEVVES  155 (343)
Q Consensus        98 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~~~-----------------~~~a~~~~~~  155 (343)
                      +..+...+...|++++|...+++..+..     ......++..+...|...|+                 +++|++.+++
T Consensus       129 ~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~  208 (411)
T 4a1s_A          129 SGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQE  208 (411)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHHH
Confidence            7788889999999999999999877641     11235678889999999999                 9999999888


Q ss_pred             HHhc----CC-CCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCC-CCC----HhhHHHHHHHHHccCChhHHHHHHHH
Q 044084          156 MKNA----EL-NISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGC-IPG----QVTYASIINAYCRIGLYSKAEKVFIE  225 (343)
Q Consensus       156 ~~~~----~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~  225 (343)
                      ..+.    +. .....++..+...+...|++++|...+++..+... .++    ...+..+...|...|++++|...+++
T Consensus       209 al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~  288 (411)
T 4a1s_A          209 NLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHYKR  288 (411)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHHHH
Confidence            6542    11 11234677888999999999999999998876411 011    23678888999999999999999998


Q ss_pred             HHHcCCC-----cChhhHHHHHHHHHccCChHHHHHHHHHHhhC
Q 044084          226 MQQKGFD-----KCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       226 ~~~~~~~-----~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                      ..+....     ....++..+...|...|++++|...+++..+.
T Consensus       289 al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  332 (411)
T 4a1s_A          289 TLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAI  332 (411)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            7764211     12567888999999999999999999988753

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.65  E-value=2.5e-14  Score=121.38  Aligned_cols=269  Identities=13%  Similarity=0.103  Sum_probs=194.1

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCC----hHhHHHHHHHHhcccCHHHHHHHHHHHHHc----CCCC-CH
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEKGILED----PSVYASLICSFASIAEVKVAEELFKEAEEK----GMLR-DL  130 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~  130 (343)
                      ...+......+...|++++|+..|++..+.+.. +    ...+..+...+...|+++.|...+++..+.    +..| ..
T Consensus         9 ~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~   87 (406)
T 3sf4_A            9 CLELALEGERLCKSGDCRAGVSFFEAAVQVGTE-DLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEA   87 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhcCcc-cHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHHHH
Confidence            466777888999999999999999999887422 3    356778888999999999999999987653    2112 25


Q ss_pred             HHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCC-C----chhhHHHHHHHHhcCCc--------------------HHHHH
Q 044084          131 EVFLKLVLMYIEEGMVEKTLEVVESMKNAELN-I----SDCISCVIVNGFSKRRA--------------------YWAAV  185 (343)
Q Consensus       131 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~----~~~~~~~l~~~~~~~~~--------------------~~~a~  185 (343)
                      .++..+...|...|++++|...+++....... .    ...++..+...+...|+                    +++|.
T Consensus        88 ~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A~  167 (406)
T 3sf4_A           88 KASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAAV  167 (406)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHHHH
Confidence            67888999999999999999999987653210 1    13367888889999999                    99999


Q ss_pred             HHHHHHHHc----CCCC-CHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCC-c----ChhhHHHHHHHHHccCChHHHH
Q 044084          186 KVYEQLISQ----GCIP-GQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFD-K----CVVAYSSMVAMYGKTGRIRDAM  255 (343)
Q Consensus       186 ~~~~~~~~~----~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~----~~~~~~~l~~~~~~~~~~~~a~  255 (343)
                      ..+++....    +..| ...++..+...|...|++++|...+++..+.... +    ...++..+...|...|++++|.
T Consensus       168 ~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~  247 (406)
T 3sf4_A          168 DFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETAS  247 (406)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHH
Confidence            999887543    2111 2346778888999999999999999988764110 1    1347888999999999999999


Q ss_pred             HHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCcc-HHHHHHH
Q 044084          256 RLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMN----GGVID-RAMAGIM  330 (343)
Q Consensus       256 ~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~~~----~~~p~-~~~~~~l  330 (343)
                      ..+++..+..  |+..            .....+..+..+...|...|++++|...+++..+.    +-.+. ..++..+
T Consensus       248 ~~~~~al~~~--~~~~------------~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l  313 (406)
T 3sf4_A          248 EYYKKTLLLA--RQLK------------DRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSL  313 (406)
T ss_dssp             HHHHHHHHHH--HHTT------------CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHH--HhCc------------CchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHH
Confidence            9999887531  1100            00001111455666677778888888888776543    21122 3467888


Q ss_pred             HHHHhcccccccC
Q 044084          331 VGVFSKLSQIEEL  343 (343)
Q Consensus       331 ~~~~~~~g~~~~a  343 (343)
                      ..+|.+.|++++|
T Consensus       314 a~~~~~~g~~~~A  326 (406)
T 3sf4_A          314 GNAYTALGNHDQA  326 (406)
T ss_dssp             HHHHHHHTCHHHH
T ss_pred             HHHHHHcCCHHHH
Confidence            8899998888764

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.65  E-value=1.4e-14  Score=123.26  Aligned_cols=258  Identities=13%  Similarity=0.036  Sum_probs=198.6

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCCh----HhHHHHHHHHhcccCHHHHHHHHHHHHHc----CC-CCCH
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDP----SVYASLICSFASIAEVKVAEELFKEAEEK----GM-LRDL  130 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~-~~~~  130 (343)
                      ...+..+...+...|++++|+..|++..+.+.. +.    ..+..+...+...|++++|...+++..+.    +. ....
T Consensus        48 ~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  126 (411)
T 4a1s_A           48 CLELALEGERLCNAGDCRAGVAFFQAAIQAGTE-DLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEA  126 (411)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHHhccc-ChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHH
Confidence            455667788899999999999999999887432 33    46788888999999999999999988763    11 1246


Q ss_pred             HHHHHHHHHHHhcCcHhHHHHHHHHHHhcC-----CCCchhhHHHHHHHHhcCCc-----------------HHHHHHHH
Q 044084          131 EVFLKLVLMYIEEGMVEKTLEVVESMKNAE-----LNISDCISCVIVNGFSKRRA-----------------YWAAVKVY  188 (343)
Q Consensus       131 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~~~-----------------~~~a~~~~  188 (343)
                      .++..+...|...|++++|...+++.....     .+....++..+...|...|+                 +++|...+
T Consensus       127 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~  206 (411)
T 4a1s_A          127 KSSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFY  206 (411)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHH
Confidence            778889999999999999999999876531     11234467888889999999                 99999999


Q ss_pred             HHHHHc----CCCC-CHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCC-cC----hhhHHHHHHHHHccCChHHHHHHH
Q 044084          189 EQLISQ----GCIP-GQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFD-KC----VVAYSSMVAMYGKTGRIRDAMRLV  258 (343)
Q Consensus       189 ~~~~~~----~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~~~~a~~~~  258 (343)
                      ++..+.    +..+ ...++..+...|...|++++|...+++..+.... ++    ..++..+...|...|++++|...+
T Consensus       207 ~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~  286 (411)
T 4a1s_A          207 QENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHY  286 (411)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHH
Confidence            887543    2112 2346778888999999999999999988764211 11    237888999999999999999999


Q ss_pred             HHHhhCC----CC-chHHHHHHHHHHHhcccChhHHHh---------------------HHHHHHHHHhcCCHHHHHHHH
Q 044084          259 AKMKPKG----CE-PNVWIYNSLMDMHGRAKNLRQLEK---------------------YTTVISAYNMAREFDMCVKFY  312 (343)
Q Consensus       259 ~~m~~~~----~~-p~~~~~~~l~~~~~~~~~~~~a~~---------------------~~~l~~~~~~~g~~~~a~~~~  312 (343)
                      ++..+..    .. ....++..+...|...|++++|..                     +..+...|...|++++|.+.+
T Consensus       287 ~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~  366 (411)
T 4a1s_A          287 KRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAIGGHERALKYA  366 (411)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccHHHHHHHH
Confidence            9887531    11 124667788888888999888876                     566777888889999999888


Q ss_pred             HHHHhC
Q 044084          313 NEFRMN  318 (343)
Q Consensus       313 ~~m~~~  318 (343)
                      ++..+.
T Consensus       367 ~~al~~  372 (411)
T 4a1s_A          367 EQHLQL  372 (411)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            887654

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.64  E-value=1.9e-14  Score=118.63  Aligned_cols=282  Identities=13%  Similarity=0.049  Sum_probs=204.1

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhc----CCCC-ChHh
Q 044084           23 GCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEK----GILE-DPSV   97 (343)
Q Consensus        23 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~   97 (343)
                      ..+......+...|++++|...|+++.+............+..+...+...|++++|.+.+++....    +..| ...+
T Consensus         6 ~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~   85 (338)
T 3ro2_A            6 LELALEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKA   85 (338)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHHH
Confidence            3455667788999999999999999988643221111367888999999999999999999887543    2122 2456


Q ss_pred             HHHHHHHHhcccCHHHHHHHHHHHHHcCCC-CC----HHHHHHHHHHHHhcCc--------------------HhHHHHH
Q 044084           98 YASLICSFASIAEVKVAEELFKEAEEKGML-RD----LEVFLKLVLMYIEEGM--------------------VEKTLEV  152 (343)
Q Consensus        98 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~--------------------~~~a~~~  152 (343)
                      +..+...+...|++++|...+++..+.... ++    ..++..+...|...|+                    +++|.+.
T Consensus        86 ~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~  165 (338)
T 3ro2_A           86 SGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDL  165 (338)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHH
Confidence            778888999999999999999987753211 12    4478888999999999                    9999999


Q ss_pred             HHHHHhc----C-CCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHc----CCC-CCHhhHHHHHHHHHccCChhHHHHH
Q 044084          153 VESMKNA----E-LNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQ----GCI-PGQVTYASIINAYCRIGLYSKAEKV  222 (343)
Q Consensus       153 ~~~~~~~----~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~-p~~~~~~~ll~~~~~~~~~~~a~~~  222 (343)
                      +++....    + ......++..+...+...|++++|...+++..+.    +.. ....++..+...+...|++++|...
T Consensus       166 ~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  245 (338)
T 3ro2_A          166 YEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEY  245 (338)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            8876532    1 1112346778888899999999999999987654    111 1123677888889999999999999


Q ss_pred             HHHHHHcCC----Cc-ChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHhHHHHHH
Q 044084          223 FIEMQQKGF----DK-CVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVIS  297 (343)
Q Consensus       223 ~~~~~~~~~----~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~  297 (343)
                      ++...+...    ++ ...++..+...+...|++++|...+++..+.  .+....            ....+..+..+..
T Consensus       246 ~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~--~~~~~~------------~~~~~~~~~~la~  311 (338)
T 3ro2_A          246 YKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAI--AQELKD------------RIGEGRACWSLGN  311 (338)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--HHHHTC------------HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH--HHhcCC------------cHHHHHHHHHHHH
Confidence            998775421    11 1557788889999999999999999988753  111100            0111111555677


Q ss_pred             HHHhcCCHHHHHHHHHHHHhC
Q 044084          298 AYNMAREFDMCVKFYNEFRMN  318 (343)
Q Consensus       298 ~~~~~g~~~~a~~~~~~m~~~  318 (343)
                      .|...|++++|...+++..+.
T Consensus       312 ~~~~~g~~~~A~~~~~~a~~~  332 (338)
T 3ro2_A          312 AYTALGNHDQAMHFAEKHLEI  332 (338)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHC
T ss_pred             HHHHcCChHHHHHHHHHHHHH
Confidence            788888899999999888764

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.63  E-value=4.8e-13  Score=109.22  Aligned_cols=218  Identities=8%  Similarity=0.074  Sum_probs=154.9

Q ss_pred             HHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhc-------cCcH-------HHHHHHHHHHHhcCCCC-ChHhHHHHHH
Q 044084           39 EKVAALFLECESRKLDLTPSSTHMYKILCDSLGK-------SGRA-------FEILKFFRDMKEKGILE-DPSVYASLIC  103 (343)
Q Consensus        39 ~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~-------~~~~-------~~a~~~~~~~~~~~~~~-~~~~~~~l~~  103 (343)
                      ++|..+|+++....    |.+...|..++..+..       .|++       ++|..+|++..+. +.| +...|..++.
T Consensus        33 ~~a~~~~~~al~~~----p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~-~~p~~~~~~~~~~~  107 (308)
T 2ond_A           33 KRVMFAYEQCLLVL----GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAIST-LLKKNMLLYFAYAD  107 (308)
T ss_dssp             HHHHHHHHHHHHHH----TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTT-TTTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHc----CCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHH-hCcccHHHHHHHHH
Confidence            67778888876654    3335678777776653       4664       7888888888773 123 4557778888


Q ss_pred             HHhcccCHHHHHHHHHHHHHcCCCCCHH-HHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHH-hcCCcH
Q 044084          104 SFASIAEVKVAEELFKEAEEKGMLRDLE-VFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGF-SKRRAY  181 (343)
Q Consensus       104 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~  181 (343)
                      .+.+.|++++|..+|+++.+..+. +.. +|..++..+.+.|++++|..+|++..+..+ .+...|....... ...|++
T Consensus       108 ~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p-~~~~~~~~~a~~~~~~~~~~  185 (308)
T 2ond_A          108 YEESRMKYEKVHSIYNRLLAIEDI-DPTLVYIQYMKFARRAEGIKSGRMIFKKAREDAR-TRHHVYVTAALMEYYCSKDK  185 (308)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTSSSS-CTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTT-CCTHHHHHHHHHHHHTSCCH
T ss_pred             HHHhcCCHHHHHHHHHHHHhcccc-CccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHHHcCCH
Confidence            888888888888888888875432 343 788888888888888888888888877654 3344444333332 236888


Q ss_pred             HHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcC-CCc--ChhhHHHHHHHHHccCChHHHHHHH
Q 044084          182 WAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKG-FDK--CVVAYSSMVAMYGKTGRIRDAMRLV  258 (343)
Q Consensus       182 ~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~-~~~--~~~~~~~l~~~~~~~~~~~~a~~~~  258 (343)
                      ++|.++|++..+.. +-+...|..++..+.+.|++++|..+|+...+.. ++|  ....|..++..+.+.|+.+.|..++
T Consensus       186 ~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~  264 (308)
T 2ond_A          186 SVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVE  264 (308)
T ss_dssp             HHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            88888888877653 3356677777888888888888888888888752 344  3567777888888888888888888


Q ss_pred             HHHhhC
Q 044084          259 AKMKPK  264 (343)
Q Consensus       259 ~~m~~~  264 (343)
                      +++.+.
T Consensus       265 ~~a~~~  270 (308)
T 2ond_A          265 KRRFTA  270 (308)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            887764

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.63  E-value=2.5e-13  Score=102.07  Aligned_cols=166  Identities=16%  Similarity=0.155  Sum_probs=89.4

Q ss_pred             hHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHH
Q 044084           95 PSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNG  174 (343)
Q Consensus        95 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  174 (343)
                      +..|..+...+...|++++|...|++..+..+. +..++..+..+|.+.|++++|...+........ .+...+..+...
T Consensus         5 ~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~~~   82 (184)
T 3vtx_A            5 TTIYMDIGDKKRTKGDFDGAIRAYKKVLKADPN-NVETLLKLGKTYMDIGLPNDAIESLKKFVVLDT-TSAEAYYILGSA   82 (184)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCC-CCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCc-hhHHHHHHHHHH
Confidence            344555555555555555555555555554432 455555555555555555555555555544433 233344444555


Q ss_pred             HhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHH
Q 044084          175 FSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDA  254 (343)
Q Consensus       175 ~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  254 (343)
                      +...++++.+...+.+..... +.+...+..+..+|.+.|++++|...|++..+.. +.+..+|..+..+|.+.|++++|
T Consensus        83 ~~~~~~~~~a~~~~~~a~~~~-~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~lg~~~~~~g~~~~A  160 (184)
T 3vtx_A           83 NFMIDEKQAAIDALQRAIALN-TVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIK-PGFIRAYQSIGLAYEGKGLRDEA  160 (184)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhc-chhhhHHHHHHHHHHHCCCHHHH
Confidence            555555555555555555442 2234445555555666666666666666655543 33455566666666666666666


Q ss_pred             HHHHHHHhhC
Q 044084          255 MRLVAKMKPK  264 (343)
Q Consensus       255 ~~~~~~m~~~  264 (343)
                      ...|++..+.
T Consensus       161 ~~~~~~al~~  170 (184)
T 3vtx_A          161 VKYFKKALEK  170 (184)
T ss_dssp             HHHHHHHHHT
T ss_pred             HHHHHHHHhC
Confidence            6666666553

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.63  E-value=1.8e-13  Score=102.79  Aligned_cols=167  Identities=15%  Similarity=0.114  Sum_probs=110.3

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHH
Q 044084           21 DSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYAS  100 (343)
Q Consensus        21 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  100 (343)
                      ++..|..+...|.+.|++++|.+.|++..+.+    |.+..+|..+...+.+.|++++|+..+......... +...+..
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~----p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~   78 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKAD----PNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLDTT-SAEAYYI   78 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCC-CHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC----CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCch-hHHHHHH
Confidence            45566777777777777777777777766554    333566777777777777777777777776665322 4455555


Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCc
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRA  180 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  180 (343)
                      +...+...++++.+...+.+..+..+. +...+..+...|.+.|++++|++.|++..+..+ .+..+|..+..+|...|+
T Consensus        79 ~~~~~~~~~~~~~a~~~~~~a~~~~~~-~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p-~~~~~~~~lg~~~~~~g~  156 (184)
T 3vtx_A           79 LGSANFMIDEKQAAIDALQRAIALNTV-YADAYYKLGLVYDSMGEHDKAIEAYEKTISIKP-GFIRAYQSIGLAYEGKGL  156 (184)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCcc-chHHHHHHHHHHHHhCCchhHHHHHHHHHHhcc-hhhhHHHHHHHHHHHCCC
Confidence            666666677777777777776665433 566666777777777777777777777666554 345566666677777777


Q ss_pred             HHHHHHHHHHHHHc
Q 044084          181 YWAAVKVYEQLISQ  194 (343)
Q Consensus       181 ~~~a~~~~~~~~~~  194 (343)
                      +++|.+.|++..+.
T Consensus       157 ~~~A~~~~~~al~~  170 (184)
T 3vtx_A          157 RDEAVKYFKKALEK  170 (184)
T ss_dssp             HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhC
Confidence            77777777766654

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.62  E-value=3.1e-13  Score=113.95  Aligned_cols=286  Identities=13%  Similarity=0.029  Sum_probs=192.0

Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCC-CCchHHHHHHHHHH--hhccCcHHHHH-----------HHHHHHHhcCCCCCh--
Q 044084           32 FYKIGDSEKVAALFLECESRKLDL-TPSSTHMYKILCDS--LGKSGRAFEIL-----------KFFRDMKEKGILEDP--   95 (343)
Q Consensus        32 ~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~~~~li~~--~~~~~~~~~a~-----------~~~~~~~~~~~~~~~--   95 (343)
                      +.+.+++++|..+++++.+.-... ...+...|-.++..  ....++++.+.           +.++.+.......+.  
T Consensus        22 ~i~~~~~~~A~~l~~~i~~~~~~~~~~~~~~~y~~ll~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~i~~~~~~~~~~l  101 (383)
T 3ulq_A           22 YIRRFSIPDAEYLRREIKQELDQMEEDQDLHLYYSLMEFRHNLMLEYLEPLEKMRIEEQPRLSDLLLEIDKKQARLTGLL  101 (383)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHGGGGGSCGGGSCCHHHHHHHHHHHTHHHHHHH
T ss_pred             HHHHcCHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHhhcCcccccccccccchhhHHHHHHhcCCCchhHH
Confidence            467899999999999986643221 11223333333332  11223333343           566665442111010  


Q ss_pred             --HhHHHHHHHHhcccCHHHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCC------
Q 044084           96 --SVYASLICSFASIAEVKVAEELFKEAEEK----GMLR-DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELN------  162 (343)
Q Consensus        96 --~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~------  162 (343)
                        ..+......+...|++++|...+++..+.    +..+ ...++..+...|...|++++|...+++..+....      
T Consensus       102 ~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~  181 (383)
T 3ulq_A          102 EYYFNFFRGMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNI  181 (383)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHH
T ss_pred             HHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchH
Confidence              01122455677889999999999998764    1111 3567888999999999999999999887653211      


Q ss_pred             CchhhHHHHHHHHhcCCcHHHHHHHHHHHHHc----CCCC-CHhhHHHHHHHHHccCChhHHHHHHHHHHHc----CC-C
Q 044084          163 ISDCISCVIVNGFSKRRAYWAAVKVYEQLISQ----GCIP-GQVTYASIINAYCRIGLYSKAEKVFIEMQQK----GF-D  232 (343)
Q Consensus       163 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~----~~-~  232 (343)
                      ....+++.+...|...|++++|...+++..+.    +-.+ ...++..+...|...|++++|...+++..+.    +. +
T Consensus       182 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~  261 (383)
T 3ulq_A          182 RLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILP  261 (383)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGG
T ss_pred             HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccch
Confidence            11346778888999999999999999887754    1111 1246788888999999999999999988772    32 3


Q ss_pred             cChhhHHHHHHHHHccCChHHHHHHHHHHhhC----CCCchHHHHHHHHHHHhcccC---hhHHHh--------------
Q 044084          233 KCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK----GCEPNVWIYNSLMDMHGRAKN---LRQLEK--------------  291 (343)
Q Consensus       233 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~----~~~p~~~~~~~l~~~~~~~~~---~~~a~~--------------  291 (343)
                      ....++..+...|.+.|++++|...+++..+.    +-......+..+...+...|+   .++|..              
T Consensus       262 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~~~~~~~~~~  341 (383)
T 3ulq_A          262 SLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESKMLYADLEDF  341 (383)
T ss_dssp             GHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCcCHHHHHHH
Confidence            34667888999999999999999999887753    111122335566677777777   444443              


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHh
Q 044084          292 YTTVISAYNMAREFDMCVKFYNEFRM  317 (343)
Q Consensus       292 ~~~l~~~~~~~g~~~~a~~~~~~m~~  317 (343)
                      +..+...|...|++++|...+++..+
T Consensus       342 ~~~la~~y~~~g~~~~A~~~~~~al~  367 (383)
T 3ulq_A          342 AIDVAKYYHERKNFQKASAYFLKVEQ  367 (383)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            66778888888888888888887754

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.61  E-value=1e-12  Score=107.27  Aligned_cols=218  Identities=13%  Similarity=0.093  Sum_probs=178.5

Q ss_pred             hhHHHHHHHHHhCCCCCChhhHHHHHHHHH-------hcCCH-------HHHHHHHHHHHhC-CCCCCCchHHHHHHHHH
Q 044084            4 QSKLHYYEKMKSAGIVLDSGCYCQIMEAFY-------KIGDS-------EKVAALFLECESR-KLDLTPSSTHMYKILCD   68 (343)
Q Consensus         4 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~-------~~~~~-------~~a~~~~~~~~~~-~~~~~~~~~~~~~~li~   68 (343)
                      ++|+.+|++..+.. +.+...|..++..+.       +.|++       ++|..+|++..+. .    |.+...|..++.
T Consensus        33 ~~a~~~~~~al~~~-p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~----p~~~~~~~~~~~  107 (308)
T 2ond_A           33 KRVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLL----KKNMLLYFAYAD  107 (308)
T ss_dssp             HHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTT----TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhC----cccHHHHHHHHH
Confidence            67889999999864 357778888888776       35886       8999999998773 3    333678999999


Q ss_pred             HhhccCcHHHHHHHHHHHHhcCCCCC-hH-hHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH-hcCc
Q 044084           69 SLGKSGRAFEILKFFRDMKEKGILED-PS-VYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYI-EEGM  145 (343)
Q Consensus        69 ~~~~~~~~~~a~~~~~~~~~~~~~~~-~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~  145 (343)
                      .+...|++++|.++|++..+.  .|+ .. .|..+...+.+.|++++|..+|++..+... .+...|........ ..|+
T Consensus       108 ~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p-~~~~~~~~~a~~~~~~~~~  184 (308)
T 2ond_A          108 YEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDAR-TRHHVYVTAALMEYYCSKD  184 (308)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTS--SSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTT-CCTHHHHHHHHHHHHTSCC
T ss_pred             HHHhcCCHHHHHHHHHHHHhc--cccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHHHcCC
Confidence            999999999999999999985  444 33 799999999999999999999999998754 35556654444432 3699


Q ss_pred             HhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcC-CCCC--HhhHHHHHHHHHccCChhHHHHH
Q 044084          146 VEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQG-CIPG--QVTYASIINAYCRIGLYSKAEKV  222 (343)
Q Consensus       146 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~p~--~~~~~~ll~~~~~~~~~~~a~~~  222 (343)
                      +++|..+|++..+..+ .+...|..++..+...|++++|..+|++..... ++|+  ...|..++....+.|+.+.|..+
T Consensus       185 ~~~A~~~~~~al~~~p-~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~  263 (308)
T 2ond_A          185 KSVAFKIFELGLKKYG-DIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKV  263 (308)
T ss_dssp             HHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            9999999999987654 467789999999999999999999999999863 4553  56788888888999999999999


Q ss_pred             HHHHHHcC
Q 044084          223 FIEMQQKG  230 (343)
Q Consensus       223 ~~~~~~~~  230 (343)
                      ++.+.+..
T Consensus       264 ~~~a~~~~  271 (308)
T 2ond_A          264 EKRRFTAF  271 (308)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHHc
Confidence            99998864

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.60  E-value=1e-13  Score=119.93  Aligned_cols=217  Identities=11%  Similarity=0.013  Sum_probs=175.5

Q ss_pred             CCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcH-HHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHH
Q 044084           36 GDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRA-FEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVA  114 (343)
Q Consensus        36 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  114 (343)
                      +.++++...++......    +.....+..+...+...|++ ++|++.|++..+... -+...|..+...+...|++++|
T Consensus        82 ~~~~~al~~l~~~~~~~----~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~g~~~~A  156 (474)
T 4abn_A           82 EEMEKTLQQMEEVLGSA----QVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLEP-ELVEAWNQLGEVYWKKGDVTSA  156 (474)
T ss_dssp             HHHHHHHHHHHHHHTTC----CCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHHHhccC----chhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhCC-CCHHHHHHHHHHHHHcCCHHHH
Confidence            34677777777765543    22367888888999999999 999999999887642 2577888888999999999999


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHhc---------CcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcC-------
Q 044084          115 EELFKEAEEKGMLRDLEVFLKLVLMYIEE---------GMVEKTLEVVESMKNAELNISDCISCVIVNGFSKR-------  178 (343)
Q Consensus       115 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-------  178 (343)
                      ...|++..+..  |+...+..+...|...         |++++|++.|++..+..+ .+...|..+..+|...       
T Consensus       157 ~~~~~~al~~~--p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~~~~~~~~  233 (474)
T 4abn_A          157 HTCFSGALTHC--KNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMDV-LDGRSWYILGNAYLSLYFNTGQN  233 (474)
T ss_dssp             HHHHHHHHTTC--CCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHhhC--CCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHHHhhccc
Confidence            99999988765  5678888888889888         999999999999888765 4567788888888888       


Q ss_pred             -CcHHHHHHHHHHHHHcCCC---CCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHH
Q 044084          179 -RAYWAAVKVYEQLISQGCI---PGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDA  254 (343)
Q Consensus       179 -~~~~~a~~~~~~~~~~~~~---p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  254 (343)
                       |++++|...|++..+.. +   -+...+..+..+|...|++++|...|+...+.. +.+...+..+...+...|++++|
T Consensus       234 ~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~a~~~l~~~~~~lg~~~eA  311 (474)
T 4abn_A          234 PKISQQALSAYAQAEKVD-RKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALD-PAWPEPQQREQQLLEFLSRLTSL  311 (474)
T ss_dssp             HHHHHHHHHHHHHHHHHC-GGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHhC-CCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHH
Confidence             88999999999988863 2   367788888899999999999999999988875 44567788888888888999988


Q ss_pred             HHHHHHHh
Q 044084          255 MRLVAKMK  262 (343)
Q Consensus       255 ~~~~~~m~  262 (343)
                      .+.+.++.
T Consensus       312 i~~~~~~~  319 (474)
T 4abn_A          312 LESKGKTK  319 (474)
T ss_dssp             HHHTTTCC
T ss_pred             HHHhcccc
Confidence            87766654

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.60  E-value=4.4e-14  Score=116.44  Aligned_cols=263  Identities=15%  Similarity=0.083  Sum_probs=198.9

Q ss_pred             CchhhHHHHHHHHHhCCCCCC----hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCC--CCCCCchHHHHHHHHHHhhccC
Q 044084            1 TNSQSKLHYYEKMKSAGIVLD----SGCYCQIMEAFYKIGDSEKVAALFLECESRK--LDLTPSSTHMYKILCDSLGKSG   74 (343)
Q Consensus         1 ~~~~~A~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~~~~li~~~~~~~   74 (343)
                      .++++|+..|+++.+.+.. +    ...+..+...+...|++++|.+.+++.....  ....+....++..+...+...|
T Consensus        19 g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g   97 (338)
T 3ro2_A           19 GDCRAGVSFFEAAVQVGTE-DLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTLKVLG   97 (338)
T ss_dssp             TCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTT
T ss_pred             ccHHHHHHHHHHHHhhCcc-cHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHHHHcc
Confidence            3678999999999986432 3    3678889999999999999999998865431  1112233567888999999999


Q ss_pred             cHHHHHHHHHHHHhcCC-CCC----hHhHHHHHHHHhcccC--------------------HHHHHHHHHHHHHc----C
Q 044084           75 RAFEILKFFRDMKEKGI-LED----PSVYASLICSFASIAE--------------------VKVAEELFKEAEEK----G  125 (343)
Q Consensus        75 ~~~~a~~~~~~~~~~~~-~~~----~~~~~~l~~~~~~~~~--------------------~~~a~~~~~~~~~~----~  125 (343)
                      ++++|.+.+++..+... .++    ..++..+...+...|+                    ++.|...+++..+.    +
T Consensus        98 ~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a~~~~~~~~  177 (338)
T 3ro2_A           98 NFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDLYEENLSLVTALG  177 (338)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHhcC
Confidence            99999999998765311 112    3367788888999999                    99999998876542    2


Q ss_pred             CCC-CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCC-----CCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcC----
Q 044084          126 MLR-DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAEL-----NISDCISCVIVNGFSKRRAYWAAVKVYEQLISQG----  195 (343)
Q Consensus       126 ~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----  195 (343)
                      ..+ ...++..+...+...|++++|...+++..+...     .....++..+...+...|++++|...+++.....    
T Consensus       178 ~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~  257 (338)
T 3ro2_A          178 DRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLK  257 (338)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhc
Confidence            111 245788889999999999999999998764321     1112367788889999999999999999877541    


Q ss_pred             CCC-CHhhHHHHHHHHHccCChhHHHHHHHHHHHcC----C-CcChhhHHHHHHHHHccCChHHHHHHHHHHhhC
Q 044084          196 CIP-GQVTYASIINAYCRIGLYSKAEKVFIEMQQKG----F-DKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       196 ~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~----~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                      ..+ ...++..+...+...|++++|...++...+..    - .....++..+...|...|++++|...+++..+.
T Consensus       258 ~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~  332 (338)
T 3ro2_A          258 DRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEI  332 (338)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHC
T ss_pred             chhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHH
Confidence            111 14567778889999999999999999877641    1 112447788999999999999999999998864

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.60  E-value=1.5e-13  Score=118.99  Aligned_cols=211  Identities=9%  Similarity=-0.006  Sum_probs=181.6

Q ss_pred             CcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCH-HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHH
Q 044084           74 GRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEV-KVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEV  152 (343)
Q Consensus        74 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  152 (343)
                      +.+++++..+++..... +.+...+..+...+...|++ ++|...|++..+..+. +...|..+...|...|++++|.+.
T Consensus        82 ~~~~~al~~l~~~~~~~-~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~g~~~~A~~~  159 (474)
T 4abn_A           82 EEMEKTLQQMEEVLGSA-QVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLEPE-LVEAWNQLGEVYWKKGDVTSAHTC  159 (474)
T ss_dssp             HHHHHHHHHHHHHHTTC-CCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccC-chhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhCCC-CHHHHHHHHHHHHHcCCHHHHHHH
Confidence            44778888888776643 34677888899999999999 9999999999987643 689999999999999999999999


Q ss_pred             HHHHHhcCCCCchhhHHHHHHHHhcC---------CcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHcc--------CC
Q 044084          153 VESMKNAELNISDCISCVIVNGFSKR---------RAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRI--------GL  215 (343)
Q Consensus       153 ~~~~~~~~~~~~~~~~~~l~~~~~~~---------~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~--------~~  215 (343)
                      |++..+..  |+...+..+...+...         |++++|...+++..+.. +.+...|..+..+|...        |+
T Consensus       160 ~~~al~~~--p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~~~~g~  236 (474)
T 4abn_A          160 FSGALTHC--KNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD-VLDGRSWYILGNAYLSLYFNTGQNPKI  236 (474)
T ss_dssp             HHHHHTTC--CCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHhhC--CCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHhhccccch
Confidence            99998876  4567888999999999         99999999999999874 34577888899999888        99


Q ss_pred             hhHHHHHHHHHHHcCCC---cChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh
Q 044084          216 YSKAEKVFIEMQQKGFD---KCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK  291 (343)
Q Consensus       216 ~~~a~~~~~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~  291 (343)
                      +++|...|+...+.. +   .+...|..+..+|...|++++|...|++..+.. +.+...+..+..++...|++++|..
T Consensus       237 ~~~A~~~~~~al~~~-p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~a~~~l~~~~~~lg~~~eAi~  313 (474)
T 4abn_A          237 SQQALSAYAQAEKVD-RKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALD-PAWPEPQQREQQLLEFLSRLTSLLE  313 (474)
T ss_dssp             HHHHHHHHHHHHHHC-GGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC-CCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999875 3   478899999999999999999999999998763 2256678888899999999999887

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=99.59  E-value=6e-12  Score=117.07  Aligned_cols=249  Identities=12%  Similarity=0.170  Sum_probs=140.3

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHH
Q 044084           22 SGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASL  101 (343)
Q Consensus        22 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  101 (343)
                      ..+|..+..++.+.|++++|.+.|.+.      .+   ...|..++.++.+.|++++|++.|...++..  +++...+.+
T Consensus      1105 p~vWsqLAKAql~~G~~kEAIdsYiKA------dD---~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~L 1173 (1630)
T 1xi4_A         1105 PAVWSQLAKAQLQKGMVKEAIDSYIKA------DD---PSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETEL 1173 (1630)
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHhc------CC---hHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHH
Confidence            445555555555555555555555332      11   2345555555555555555555555544432  222222235


Q ss_pred             HHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcH
Q 044084          102 ICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAY  181 (343)
Q Consensus       102 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  181 (343)
                      +.+|++.++++......    +   .++...|..+...|...|++++|..+|...         ..|..+..++.+.|++
T Consensus      1174 afaYAKl~rleele~fI----~---~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~ 1237 (1630)
T 1xi4_A         1174 IFALAKTNRLAELEEFI----N---GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEY 1237 (1630)
T ss_pred             HHHHHhhcCHHHHHHHH----h---CCCHHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCH
Confidence            55555555554322221    1   134444555666666666666666666653         1456666666666666


Q ss_pred             HHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHH
Q 044084          182 WAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKM  261 (343)
Q Consensus       182 ~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m  261 (343)
                      ++|.+.+++.      .+..+|..+-.+|...|++..|......     +..++..+..++..|.+.|.+++|+.+++..
T Consensus      1238 q~AIEaarKA------~n~~aWkev~~acve~~Ef~LA~~cgl~-----Iiv~~deLeeli~yYe~~G~feEAI~LlE~a 1306 (1630)
T 1xi4_A         1238 QAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLH-----IVVHADELEELINYYQDRGYFEELITMLEAA 1306 (1630)
T ss_pred             HHHHHHHHHh------CCHHHHHHHHHHHhhhhHHHHHHHHHHh-----hhcCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            6666666654      2345566666666666666665554432     2334566778888999999999999999887


Q ss_pred             hhCCCCchHHHHHHHHHHHhc---------------ccChhHHHh-------HHHHHHHHHhcCCHHHHH
Q 044084          262 KPKGCEPNVWIYNSLMDMHGR---------------AKNLRQLEK-------YTTVISAYNMAREFDMCV  309 (343)
Q Consensus       262 ~~~~~~p~~~~~~~l~~~~~~---------------~~~~~~a~~-------~~~l~~~~~~~g~~~~a~  309 (343)
                      .... +-....|+-+...|.+               .++.....+       |..++..|.+.|+++.|.
T Consensus      1307 L~Le-raH~gmftELaiLyaKy~peklmEhlk~f~~rini~k~~r~~e~~~lW~elv~LY~~~~e~dnA~ 1375 (1630)
T 1xi4_A         1307 LGLE-RAHMGMFTELAILYSKFKPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAI 1375 (1630)
T ss_pred             hccC-hhHhHHHHHHHHHHHhCCHHHHHHHHHHHHHhcccchHhHHHHHHHHHHHHHHHHHhcccHHHHH
Confidence            7543 2233444444444333               223222111       888889999999999888

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.57  E-value=1.4e-13  Score=112.29  Aligned_cols=242  Identities=12%  Similarity=0.069  Sum_probs=149.2

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCC----CCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhc------C
Q 044084           21 DSGCYCQIMEAFYKIGDSEKVAALFLECESRKL----DLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEK------G   90 (343)
Q Consensus        21 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~------~   90 (343)
                      +..++..+...+...|++++|...|+++.+...    ...+....++..+...+...|++++|...+++....      +
T Consensus        26 ~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~  105 (311)
T 3nf1_A           26 RLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGK  105 (311)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCC
Confidence            345677788888888888888888888876310    012333567778888888888888888888887654      1


Q ss_pred             CCC-ChHhHHHHHHHHhcccCHHHHHHHHHHHHHc------CCCC-CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhc---
Q 044084           91 ILE-DPSVYASLICSFASIAEVKVAEELFKEAEEK------GMLR-DLEVFLKLVLMYIEEGMVEKTLEVVESMKNA---  159 (343)
Q Consensus        91 ~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---  159 (343)
                      -.| ...++..+...+...|++++|...+++..+.      +..| ...++..+...+...|++++|++.+++....   
T Consensus       106 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~  185 (311)
T 3nf1_A          106 DHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQT  185 (311)
T ss_dssp             TCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence            112 3456677777888888888888888877764      2112 3556777778888888888888888877653   


Q ss_pred             ---CCCC-chhhHHHHHHHHhcCCcHHHHHHHHHHHHHc-------CCCCCHhh-------HHHHHHHHHccCChhHHHH
Q 044084          160 ---ELNI-SDCISCVIVNGFSKRRAYWAAVKVYEQLISQ-------GCIPGQVT-------YASIINAYCRIGLYSKAEK  221 (343)
Q Consensus       160 ---~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-------~~~p~~~~-------~~~ll~~~~~~~~~~~a~~  221 (343)
                         +..| ...++..+...+...|++++|...++++.+.       ...+....       +..+...+...+.+.++..
T Consensus       186 ~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~  265 (311)
T 3nf1_A          186 KLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEEREECKGKQKDGTSFGEYGG  265 (311)
T ss_dssp             TSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHHHC-------CCSCCCC-
T ss_pred             HhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHhcCchhhHHHHHHHHH
Confidence               1112 2345677777888888888888888877653       11122111       1122222334445555556


Q ss_pred             HHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhh
Q 044084          222 VFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                      .+....... +.+..++..+...|.+.|++++|...|++..+
T Consensus       266 ~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  306 (311)
T 3nf1_A          266 WYKACKVDS-PTVTTTLKNLGALYRRQGKFEAAETLEEAAMR  306 (311)
T ss_dssp             --------C-HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHhhcCCCC-chHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            666555432 33456677777888888888888888777654

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.56  E-value=4.1e-12  Score=109.27  Aligned_cols=293  Identities=11%  Similarity=0.067  Sum_probs=160.7

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCH---HHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccC----
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDS---EKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSG----   74 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~---~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~----   74 (343)
                      ++++|+++|++..+.|   +...+..|...|...|+.   ++|...|++..+.  .     ...+..|...+...+    
T Consensus        18 ~~~~A~~~~~~aa~~g---~~~A~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~~--~-----~~A~~~Lg~~~~~~~~~~~   87 (452)
T 3e4b_A           18 DTVTAQQNYQQLAELG---YSEAQVGLADIQVGTRDPAQIKQAEATYRAAADT--S-----PRAQARLGRLLAAKPGATE   87 (452)
T ss_dssp             HHHHHHHHHHHHHHHT---CCTGGGTCC-----------------------------------CHHHHHHHHHTC--CCH
T ss_pred             CHHHHHHHHHHHHHCC---CHHHHHHHHHHHHccCCCCCHHHHHHHHHHHHhC--C-----HHHHHHHHHHHHhCCCCCC
Confidence            5678888888887765   334455566666667777   8888888877654  2     234555666444443    


Q ss_pred             -cHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHH---HHHHHHHHHHHcC-------------------------
Q 044084           75 -RAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVK---VAEELFKEAEEKG-------------------------  125 (343)
Q Consensus        75 -~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~---~a~~~~~~~~~~~-------------------------  125 (343)
                       ++++|+.+|++..+.|.. +  .+..|...|...+..+   .+.+.+......|                         
T Consensus        88 ~~~~~A~~~~~~Aa~~g~~-~--A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g~~~a~~~Lg~~y~~~~~~~~~~~~a  164 (452)
T 3e4b_A           88 AEHHEAESLLKKAFANGEG-N--TLIPLAMLYLQYPHSFPNVNAQQQISQWQAAGYPEAGLAQVLLYRTQGTYDQHLDDV  164 (452)
T ss_dssp             HHHHHHHHHHHHHHHTTCS-S--CHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHTCTTHHHHHHHHHHHHTCGGGGHHHH
T ss_pred             cCHHHHHHHHHHHHHCCCH-H--HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCcccCHHHH
Confidence             778888888887776532 2  3444444443332211   1111111111111                         


Q ss_pred             -------CCCCHHHHHHHHHHHHhcC---cHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcC----CcHHHHHHHHHHH
Q 044084          126 -------MLRDLEVFLKLVLMYIEEG---MVEKTLEVVESMKNAELNISDCISCVIVNGFSKR----RAYWAAVKVYEQL  191 (343)
Q Consensus       126 -------~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----~~~~~a~~~~~~~  191 (343)
                             ...++..+..|...|...|   +.++|++.|++..+.+. ++...+..+...|...    +++++|...|++.
T Consensus       165 ~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~-~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~a  243 (452)
T 3e4b_A          165 ERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRGT-VTAQRVDSVARVLGDATLGTPDEKTAQALLEKI  243 (452)
T ss_dssp             HHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTC-SCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCC-HHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHH
Confidence                   1123336677777777777   77888888888777775 4444445555555443    6778888888887


Q ss_pred             HHcCCCCCHhhHHHHHHH-H--HccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccC-----ChHHHHHHHHHHhh
Q 044084          192 ISQGCIPGQVTYASIINA-Y--CRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTG-----RIRDAMRLVAKMKP  263 (343)
Q Consensus       192 ~~~~~~p~~~~~~~ll~~-~--~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-----~~~~a~~~~~~m~~  263 (343)
                      . .|   +...+..+... +  ...+++++|...|+...+.|   +...+..|...|. .|     ++++|...|++.. 
T Consensus       244 a-~g---~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~-~G~g~~~d~~~A~~~~~~Aa-  314 (452)
T 3e4b_A          244 A-PG---YPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAAD---QPRAELLLGKLYY-EGKWVPADAKAAEAHFEKAV-  314 (452)
T ss_dssp             G-GG---STHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH-HCSSSCCCHHHHHHHHHTTT-
T ss_pred             c-CC---CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHH-cCCCCCCCHHHHHHHHHHHh-
Confidence            6 33   33445555554 3  45778888888888877766   5566666666666 44     7888888888777 


Q ss_pred             CCCCchHHHHHHHHHHHhc----ccChhHHHh-------------HHHHHHHHHh----cCCHHHHHHHHHHHHhCCC
Q 044084          264 KGCEPNVWIYNSLMDMHGR----AKNLRQLEK-------------YTTVISAYNM----AREFDMCVKFYNEFRMNGG  320 (343)
Q Consensus       264 ~~~~p~~~~~~~l~~~~~~----~~~~~~a~~-------------~~~l~~~~~~----~g~~~~a~~~~~~m~~~~~  320 (343)
                      .|   +......|...|..    ..+.++|..             ...+...|..    ..++++|..+|+...+.|.
T Consensus       315 ~g---~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~A~~~g~  389 (452)
T 3e4b_A          315 GR---EVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNGQNSADFAIAQLFSQGKGTKPDPLNAYVFSQLAKAQDT  389 (452)
T ss_dssp             TT---CHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTTCTTHHHHHHHHHHSCTTBCCCHHHHHHHHHHHHTTCC
T ss_pred             CC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhChHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHCCC
Confidence            32   44555555555554    235666655             4445555543    3577778887777777664

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.56  E-value=1.8e-12  Score=111.46  Aligned_cols=272  Identities=15%  Similarity=0.138  Sum_probs=168.6

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcH---HHHHHHHHHHHhcCCCCChHhHHHHHH
Q 044084           27 QIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRA---FEILKFFRDMKEKGILEDPSVYASLIC  103 (343)
Q Consensus        27 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~---~~a~~~~~~~~~~~~~~~~~~~~~l~~  103 (343)
                      .+...+.+.|++++|.++|++..+.+..      .++..|...+...|++   ++|+++|++..+.    ++..+..+..
T Consensus         8 ~la~~~~~~g~~~~A~~~~~~aa~~g~~------~A~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~~----~~~A~~~Lg~   77 (452)
T 3e4b_A            8 RLANEALKRGDTVTAQQNYQQLAELGYS------EAQVGLADIQVGTRDPAQIKQAEATYRAAADT----SPRAQARLGR   77 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTCC------TGGGTCC--------------------------------CHHHHHH
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHCCCH------HHHHHHHHHHHccCCCCCHHHHHHHHHHHHhC----CHHHHHHHHH
Confidence            3667788999999999999999877632      2456677777778888   9999999998754    5555666666


Q ss_pred             HHhccc-----CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCc---------------------------------
Q 044084          104 SFASIA-----EVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGM---------------------------------  145 (343)
Q Consensus       104 ~~~~~~-----~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---------------------------------  145 (343)
                      .+...+     +.++|...|++..+.|.. +  .+..|...|...+.                                 
T Consensus        78 ~~~~~~~~~~~~~~~A~~~~~~Aa~~g~~-~--A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g~~~a~~~Lg~~y~~~  154 (452)
T 3e4b_A           78 LLAAKPGATEAEHHEAESLLKKAFANGEG-N--TLIPLAMLYLQYPHSFPNVNAQQQISQWQAAGYPEAGLAQVLLYRTQ  154 (452)
T ss_dssp             HHHTC--CCHHHHHHHHHHHHHHHHTTCS-S--CHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHTCTTHHHHHHHHHHHH
T ss_pred             HHHhCCCCCCcCHHHHHHHHHHHHHCCCH-H--HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHcC
Confidence            444444     789999999999887643 2  44444444444333                                 


Q ss_pred             --HhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCC---cHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHcc----CCh
Q 044084          146 --VEKTLEVVESMKNAELNISDCISCVIVNGFSKRR---AYWAAVKVYEQLISQGCIPGQVTYASIINAYCRI----GLY  216 (343)
Q Consensus       146 --~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~----~~~  216 (343)
                        ++++......+.+.-...+...+..+...|...|   ++++|.+.|++..+.| .++...+..+...|...    +++
T Consensus       155 ~~~~~~~~~a~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g-~~~a~~~~~Lg~~y~~g~~~~~d~  233 (452)
T 3e4b_A          155 GTYDQHLDDVERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRG-TVTAQRVDSVARVLGDATLGTPDE  233 (452)
T ss_dssp             TCGGGGHHHHHHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT-CSCHHHHHHHHHHHTCGGGSSCCH
T ss_pred             CCcccCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCCCCCH
Confidence              2222222111111111123336777888888888   8999999999998887 45555556666777554    689


Q ss_pred             hHHHHHHHHHHHcCCCcChhhHHHHHHH-H--HccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhccc-----ChhH
Q 044084          217 SKAEKVFIEMQQKGFDKCVVAYSSMVAM-Y--GKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAK-----NLRQ  288 (343)
Q Consensus       217 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~--~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~-----~~~~  288 (343)
                      ++|...|+... .   -++..+..+... +  ...+++++|...|++..+.|   +...+..|...|. .|     +.++
T Consensus       234 ~~A~~~~~~aa-~---g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~-~G~g~~~d~~~  305 (452)
T 3e4b_A          234 KTAQALLEKIA-P---GYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAAD---QPRAELLLGKLYY-EGKWVPADAKA  305 (452)
T ss_dssp             HHHHHHHHHHG-G---GSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH-HCSSSCCCHHH
T ss_pred             HHHHHHHHHHc-C---CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHH-cCCCCCCCHHH
Confidence            99999999877 3   356677777776 4  56889999999999998876   5556666666666 44     7777


Q ss_pred             HHh------------HHHHHHHHHh----cCCHHHHHHHHHHHHhCCC
Q 044084          289 LEK------------YTTVISAYNM----AREFDMCVKFYNEFRMNGG  320 (343)
Q Consensus       289 a~~------------~~~l~~~~~~----~g~~~~a~~~~~~m~~~~~  320 (343)
                      |..            +..+...|..    ..++++|..+|++..+.|.
T Consensus       306 A~~~~~~Aa~g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  353 (452)
T 3e4b_A          306 AEAHFEKAVGREVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNGQ  353 (452)
T ss_dssp             HHHHHHTTTTTCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhCh
Confidence            766            4455566655    3489999999999888764

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.55  E-value=6.2e-13  Score=108.46  Aligned_cols=173  Identities=13%  Similarity=0.099  Sum_probs=120.1

Q ss_pred             CCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhc-------CCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHc----
Q 044084           56 TPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEK-------GILEDPSVYASLICSFASIAEVKVAEELFKEAEEK----  124 (343)
Q Consensus        56 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----  124 (343)
                      +|....++..+...+...|++++|+.+++++.+.       .......++..+...+...|++++|...+++..+.    
T Consensus        23 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~  102 (311)
T 3nf1_A           23 IPARLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKT  102 (311)
T ss_dssp             SCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            3555678888888888889999999888888763       12223456777778888888888888888877764    


Q ss_pred             --CC-CCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhc------CC-CCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHc
Q 044084          125 --GM-LRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNA------EL-NISDCISCVIVNGFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       125 --~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  194 (343)
                        +. .....++..+...|...|++++|...+++..+.      +. +.....+..+...+...|++++|...++++.+.
T Consensus       103 ~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~  182 (311)
T 3nf1_A          103 LGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEI  182 (311)
T ss_dssp             HCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH
T ss_pred             hCCCChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence              21 123566777888888888888888888877653      11 123345667777777788888888888777654


Q ss_pred             ------CCCC-CHhhHHHHHHHHHccCChhHHHHHHHHHHH
Q 044084          195 ------GCIP-GQVTYASIINAYCRIGLYSKAEKVFIEMQQ  228 (343)
Q Consensus       195 ------~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  228 (343)
                            +..| ...++..+...|...|++++|...++.+.+
T Consensus       183 ~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  223 (311)
T 3nf1_A          183 YQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILT  223 (311)
T ss_dssp             HHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                  1122 234566667777777777777777777665

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.51  E-value=3.4e-12  Score=107.53  Aligned_cols=233  Identities=9%  Similarity=-0.033  Sum_probs=159.8

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCC--CCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCC-CC-----ChHhHH
Q 044084           28 IMEAFYKIGDSEKVAALFLECESRKL--DLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGI-LE-----DPSVYA   99 (343)
Q Consensus        28 l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~-~~-----~~~~~~   99 (343)
                      ....+...|++++|...|++..+.-.  ..++....+|..+...+...|+++.|+..+++..+... .+     ...++.
T Consensus       109 ~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  188 (383)
T 3ulq_A          109 RGMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHS  188 (383)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHH
Confidence            55667788999999999988865411  11122356788888888899999999988888765311 11     134677


Q ss_pred             HHHHHHhcccCHHHHHHHHHHHHHcCCC-CC----HHHHHHHHHHHHhcCcHhHHHHHHHHHHh-----cCCCCchhhHH
Q 044084          100 SLICSFASIAEVKVAEELFKEAEEKGML-RD----LEVFLKLVLMYIEEGMVEKTLEVVESMKN-----AELNISDCISC  169 (343)
Q Consensus       100 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~~~  169 (343)
                      .+...+...|++++|...+++..+.... ++    ..++..+...|...|++++|++.+++..+     ...+....++.
T Consensus       189 ~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  268 (383)
T 3ulq_A          189 LFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYF  268 (383)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHH
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHH
Confidence            7778888888899888888877653211 11    34677888888888888888888888765     22123355677


Q ss_pred             HHHHHHhcCCcHHHHHHHHHHHHHc----CCCCCHhhHHHHHHHHHccCC---hhHHHHHHHHHHHcCCCc-ChhhHHHH
Q 044084          170 VIVNGFSKRRAYWAAVKVYEQLISQ----GCIPGQVTYASIINAYCRIGL---YSKAEKVFIEMQQKGFDK-CVVAYSSM  241 (343)
Q Consensus       170 ~l~~~~~~~~~~~~a~~~~~~~~~~----~~~p~~~~~~~ll~~~~~~~~---~~~a~~~~~~~~~~~~~~-~~~~~~~l  241 (343)
                      .+...+...|++++|...+++..+.    +-+.....+..+...+...|+   +++|..+++..   +..| ....+..+
T Consensus       269 ~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~---~~~~~~~~~~~~l  345 (383)
T 3ulq_A          269 LITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESK---MLYADLEDFAIDV  345 (383)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHT---TCHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHC---cCHHHHHHHHHHH
Confidence            8888888888888888888887653    111122335566677777787   55566555544   2222 23466678


Q ss_pred             HHHHHccCChHHHHHHHHHHhh
Q 044084          242 VAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       242 ~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                      ...|...|++++|...+++..+
T Consensus       346 a~~y~~~g~~~~A~~~~~~al~  367 (383)
T 3ulq_A          346 AKYYHERKNFQKASAYFLKVEQ  367 (383)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHH
Confidence            8888888888888888887754

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=99.51  E-value=2.5e-12  Score=115.92  Aligned_cols=168  Identities=10%  Similarity=0.037  Sum_probs=99.6

Q ss_pred             CchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHH
Q 044084           57 PSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKL  136 (343)
Q Consensus        57 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  136 (343)
                      |.+..+|+.|...+.+.|++++|++.|++..+.... +..+|..+..++.+.|++++|...|++..+.... +...|..+
T Consensus         6 P~~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~P~-~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~P~-~~~a~~nL   83 (723)
T 4gyw_A            6 PTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPE-FAAAHSNLASVLQQQGKLQEALMHYKEAIRISPT-FADAYSNM   83 (723)
T ss_dssp             CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHH
Confidence            444556666666666666666666666666554211 3455556666666666666666666666655432 45666666


Q ss_pred             HHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCCh
Q 044084          137 VLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLY  216 (343)
Q Consensus       137 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~  216 (343)
                      ..+|.+.|++++|++.|++..+.++ -+...|..+..+|...|++++|++.|++..+.. +-+...+..+..++...|++
T Consensus        84 g~~l~~~g~~~~A~~~~~kAl~l~P-~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~-P~~~~a~~~L~~~l~~~g~~  161 (723)
T 4gyw_A           84 GNTLKEMQDVQGALQCYTRAIQINP-AFADAHSNLASIHKDSGNIPEAIASYRTALKLK-PDFPDAYCNLAHCLQIVCDW  161 (723)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHhhhhhHHHhcccH
Confidence            6666666666666666666655543 344556666666666666666666666666552 22345566666666666666


Q ss_pred             hHHHHHHHHHHH
Q 044084          217 SKAEKVFIEMQQ  228 (343)
Q Consensus       217 ~~a~~~~~~~~~  228 (343)
                      ++|.+.++++.+
T Consensus       162 ~~A~~~~~kal~  173 (723)
T 4gyw_A          162 TDYDERMKKLVS  173 (723)
T ss_dssp             TTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            666666655543

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.50  E-value=1.1e-11  Score=104.32  Aligned_cols=298  Identities=13%  Similarity=0.047  Sum_probs=197.2

Q ss_pred             CCChhhHHHHHHHH--HhcCCHHHHHHHHHHHHhCC--CCCCCchHHHHHHHHHHh--hccCc---------HHHHHHHH
Q 044084           19 VLDSGCYCQIMEAF--YKIGDSEKVAALFLECESRK--LDLTPSSTHMYKILCDSL--GKSGR---------AFEILKFF   83 (343)
Q Consensus        19 ~~~~~~~~~l~~~~--~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~~~~li~~~--~~~~~---------~~~a~~~~   83 (343)
                      .|+..+-+.|-..|  .+.+++++|..+++++....  ...++. ...|-.++..-  ...+.         .....+.+
T Consensus         7 ~~~~~v~~~l~~wy~~i~~~~~~~A~~l~~~i~~~~~~~~~~~~-~~~yy~l~~~r~~~~~~~~~~~~~~~~~~~~~~~l   85 (378)
T 3q15_A            7 IPSSRVGVKINEWYKMIRQFSVPDAEILKAEVEQDIQQMEEDQD-LLIYYSLMCFRHQLMLDYLEPGKTYGNRPTVTELL   85 (378)
T ss_dssp             BCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHGGGBCCCHH-HHHHHHHHHHHHHHHHHTCCC--------CHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhcccHH-HHHHHHHHHHHHHHHHhhcCcccccccccchHHHH
Confidence            45566666666666  78899999999999876532  222221 33334333321  11111         12222555


Q ss_pred             HHHHhcCCCCCh--H--hHHHHHHHHhcccCHHHHHHHHHHHHHcCCC-C----CHHHHHHHHHHHHhcCcHhHHHHHHH
Q 044084           84 RDMKEKGILEDP--S--VYASLICSFASIAEVKVAEELFKEAEEKGML-R----DLEVFLKLVLMYIEEGMVEKTLEVVE  154 (343)
Q Consensus        84 ~~~~~~~~~~~~--~--~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~----~~~~~~~l~~~~~~~~~~~~a~~~~~  154 (343)
                      +.+.....+.+.  .  .+......+...|++++|...+++..+.... +    ...++..+...|...|+++.|...++
T Consensus        86 ~~i~~~~~~~~~~l~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~  165 (378)
T 3q15_A           86 ETIETPQKKLTGLLKYYSLFFRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHIL  165 (378)
T ss_dssp             HHHHGGGHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHhccCCCCccHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHH
Confidence            555432111111  1  1223345567889999999999998764211 2    25678888999999999999999998


Q ss_pred             HHHhcCC-----CC-chhhHHHHHHHHhcCCcHHHHHHHHHHHHHc----CCCC-CHhhHHHHHHHHHccCChhHHHHHH
Q 044084          155 SMKNAEL-----NI-SDCISCVIVNGFSKRRAYWAAVKVYEQLISQ----GCIP-GQVTYASIINAYCRIGLYSKAEKVF  223 (343)
Q Consensus       155 ~~~~~~~-----~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~  223 (343)
                      +..+...     .+ ...+++.+...|...|++++|.+.+++..+.    +..+ ...++..+..+|...|++++|...+
T Consensus       166 ~al~~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~  245 (378)
T 3q15_A          166 QALDIYQNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHF  245 (378)
T ss_dssp             HHHHHHHTSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHhCCCchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            8764311     11 2346778888999999999999999887653    1111 2346777888899999999999999


Q ss_pred             HHHHHc----CCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhC----CCCchHHHHHHHHHHHhcccC---hhHHHh-
Q 044084          224 IEMQQK----GFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK----GCEPNVWIYNSLMDMHGRAKN---LRQLEK-  291 (343)
Q Consensus       224 ~~~~~~----~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~----~~~p~~~~~~~l~~~~~~~~~---~~~a~~-  291 (343)
                      ++..+.    +.+....++..+...|.+.|++++|...+++..+.    +.......+..+...+...++   ..+|.. 
T Consensus       246 ~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~  325 (378)
T 3q15_A          246 QKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSY  325 (378)
T ss_dssp             HHHHHHHHHHCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHH
T ss_pred             HHHHHHHHhhCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHH
Confidence            988762    22334677888999999999999999999988753    122233445555556666666   444443 


Q ss_pred             -------------HHHHHHHHHhcCCHHHHHHHHHHHHh
Q 044084          292 -------------YTTVISAYNMAREFDMCVKFYNEFRM  317 (343)
Q Consensus       292 -------------~~~l~~~~~~~g~~~~a~~~~~~m~~  317 (343)
                                   +..+...|...|++++|...|++..+
T Consensus       326 ~~~~~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          326 FEKKNLHAYIEACARSAAAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHhCCChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                         66788888899999999999888754

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.49  E-value=2.3e-11  Score=102.00  Aligned_cols=296  Identities=7%  Similarity=-0.084  Sum_probs=185.2

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCc-hHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCC-CCCh----Hh
Q 044084           24 CYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPS-STHMYKILCDSLGKSGRAFEILKFFRDMKEKGI-LEDP----SV   97 (343)
Q Consensus        24 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~-~~~~----~~   97 (343)
                      ........+...|++++|...+++........++. ...+++.+...+...|++++|.+.+++...... .++.    .+
T Consensus        16 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~   95 (373)
T 1hz4_A           16 FNALRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWS   95 (373)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHH
Confidence            45555667778888888888888876654222211 123577777888888888888888887765311 1121    23


Q ss_pred             HHHHHHHHhcccCHHHHHHHHHHHHHc----CCC--C-CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCC----chh
Q 044084           98 YASLICSFASIAEVKVAEELFKEAEEK----GML--R-DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNI----SDC  166 (343)
Q Consensus        98 ~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~----~~~  166 (343)
                      +..+...+...|++++|...+++..+.    +..  | ....+..+...+...|++++|...+++........    ...
T Consensus        96 ~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  175 (373)
T 1hz4_A           96 LIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQ  175 (373)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHH
Confidence            455667778888888888888877653    211  2 23456667778888888888888888876543211    123


Q ss_pred             hHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCH-hhHH-----HHHHHHHccCChhHHHHHHHHHHHcCCCc---Chhh
Q 044084          167 ISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQ-VTYA-----SIINAYCRIGLYSKAEKVFIEMQQKGFDK---CVVA  237 (343)
Q Consensus       167 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~-~~~~-----~ll~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~  237 (343)
                      ++..+...+...|++++|...+++.......++. ..+.     ..+..+...|++++|...++........+   ....
T Consensus       176 ~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~  255 (373)
T 1hz4_A          176 CLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQ  255 (373)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHH
Confidence            5667777788888888888888887654211111 1111     22334667888888888887766543211   1224


Q ss_pred             HHHHHHHHHccCChHHHHHHHHHHhhC----CCCchH-HHHHHHHHHHhcccChhHHHh-HHHHHHHHHhcC-------C
Q 044084          238 YSSMVAMYGKTGRIRDAMRLVAKMKPK----GCEPNV-WIYNSLMDMHGRAKNLRQLEK-YTTVISAYNMAR-------E  304 (343)
Q Consensus       238 ~~~l~~~~~~~~~~~~a~~~~~~m~~~----~~~p~~-~~~~~l~~~~~~~~~~~~a~~-~~~l~~~~~~~g-------~  304 (343)
                      +..+...+...|++++|...+++....    |..++. ..+..+..++...|+.++|.. +...+......|       .
T Consensus       256 ~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~~~~~~g~~~~~~~~  335 (373)
T 1hz4_A          256 WRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALKLANRTGFISHFVIE  335 (373)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCCCHHHHTT
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhccccHHHHHHHc
Confidence            566777888888888888888776542    222233 256666777888888888877 333333322221       1


Q ss_pred             HHHHHHHHHHHHhCC
Q 044084          305 FDMCVKFYNEFRMNG  319 (343)
Q Consensus       305 ~~~a~~~~~~m~~~~  319 (343)
                      .+....+++.+....
T Consensus       336 g~~~~~ll~~~~~~~  350 (373)
T 1hz4_A          336 GEAMAQQLRQLIQLN  350 (373)
T ss_dssp             HHHHHHHHHHHHHTT
T ss_pred             cHHHHHHHHHHHhCC
Confidence            145666777776654

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=99.48  E-value=8.8e-12  Score=93.30  Aligned_cols=160  Identities=11%  Similarity=0.071  Sum_probs=64.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHH
Q 044084           25 YCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICS  104 (343)
Q Consensus        25 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  104 (343)
                      +..+...+...|++++|...++++.+..    |.+..++..+...+...|++++|.+.++++.+.. +.+...+..+...
T Consensus        11 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~   85 (186)
T 3as5_A           11 YRDKGISHAKAGRYSQAVMLLEQVYDAD----AFDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLT   85 (186)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHTTTCCTT----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHhC----ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHH
Confidence            3344444444444444444444433221    1123344444444444444444444444444331 1123333334444


Q ss_pred             HhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHH
Q 044084          105 FASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAA  184 (343)
Q Consensus       105 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  184 (343)
                      +...|++++|...++++.+... .+...+..+...+...|++++|...+++..+... .+...+..+...+...|++++|
T Consensus        86 ~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~la~~~~~~~~~~~A  163 (186)
T 3as5_A           86 YVQVQKYDLAVPLLIKVAEANP-INFNVRFRLGVALDNLGRFDEAIDSFKIALGLRP-NEGKVHRAIAFSYEQMGRHEEA  163 (186)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHhcCc-HhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcCc-cchHHHHHHHHHHHHcCCHHHH
Confidence            4444444444444444443322 1333444444444444444444444444333322 2223333333344444444444


Q ss_pred             HHHHHHH
Q 044084          185 VKVYEQL  191 (343)
Q Consensus       185 ~~~~~~~  191 (343)
                      ...+++.
T Consensus       164 ~~~~~~~  170 (186)
T 3as5_A          164 LPHFKKA  170 (186)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            4444333

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=99.48  E-value=5.4e-12  Score=94.48  Aligned_cols=166  Identities=14%  Similarity=0.128  Sum_probs=110.5

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLM  139 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  139 (343)
                      ...|..+...+...|++++|.+.++++.... +.+...+..+...+...|++++|...++++.+... .+..++..+...
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~   85 (186)
T 3as5_A            8 QVYYRDKGISHAKAGRYSQAVMLLEQVYDAD-AFDVDVALHLGIAYVKTGAVDRGTELLERSLADAP-DNVKVATVLGLT   85 (186)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHTTTCCTT-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC-CCHHHHHHHHHH
Confidence            3556667777777778888877777766543 22456666677777777777777777777776543 256677777777


Q ss_pred             HHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHH
Q 044084          140 YIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKA  219 (343)
Q Consensus       140 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a  219 (343)
                      +...|++++|.+.++++..... .+...+..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|
T Consensus        86 ~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A  163 (186)
T 3as5_A           86 YVQVQKYDLAVPLLIKVAEANP-INFNVRFRLGVALDNLGRFDEAIDSFKIALGLR-PNEGKVHRAIAFSYEQMGRHEEA  163 (186)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHhcCc-HhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCHHHH
Confidence            7777777777777777766543 345556666666667777777777777666553 23445566666666666666666


Q ss_pred             HHHHHHHHHc
Q 044084          220 EKVFIEMQQK  229 (343)
Q Consensus       220 ~~~~~~~~~~  229 (343)
                      ...++...+.
T Consensus       164 ~~~~~~~~~~  173 (186)
T 3as5_A          164 LPHFKKANEL  173 (186)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHc
Confidence            6666666554

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.48  E-value=1.4e-10  Score=97.18  Aligned_cols=256  Identities=10%  Similarity=-0.035  Sum_probs=182.7

Q ss_pred             HHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChH----hHHHHHHHHhcccCHHHHHHHHHHHHHcCCC-CC----HHH
Q 044084           62 MYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPS----VYASLICSFASIAEVKVAEELFKEAEEKGML-RD----LEV  132 (343)
Q Consensus        62 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~  132 (343)
                      ........+...|++++|...+++........+..    ++..+...+...|+++.|...+++....... .+    ..+
T Consensus        16 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~   95 (373)
T 1hz4_A           16 FNALRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWS   95 (373)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHH
Confidence            34445566778999999999999988764222222    4556667788899999999999987763211 12    234


Q ss_pred             HHHHHHHHHhcCcHhHHHHHHHHHHhc----CCC--C-chhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCC--C--CHh
Q 044084          133 FLKLVLMYIEEGMVEKTLEVVESMKNA----ELN--I-SDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCI--P--GQV  201 (343)
Q Consensus       133 ~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--p--~~~  201 (343)
                      +..+...+...|++++|...+++....    +..  | ....+..+...+...|++++|...+++.......  +  ...
T Consensus        96 ~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  175 (373)
T 1hz4_A           96 LIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQ  175 (373)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHH
Confidence            677888899999999999999987643    221  2 2345667788899999999999999998765321  1  234


Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHHHHcCCCcC-hhhHH-----HHHHHHHccCChHHHHHHHHHHhhCCCCc---hHHH
Q 044084          202 TYASIINAYCRIGLYSKAEKVFIEMQQKGFDKC-VVAYS-----SMVAMYGKTGRIRDAMRLVAKMKPKGCEP---NVWI  272 (343)
Q Consensus       202 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~-----~l~~~~~~~~~~~~a~~~~~~m~~~~~~p---~~~~  272 (343)
                      ++..+...+...|++++|...++........++ ...+.     ..+..+...|++++|...+++.......+   ....
T Consensus       176 ~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~  255 (373)
T 1hz4_A          176 CLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQ  255 (373)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHH
Confidence            577788889999999999999999876421211 11222     23345779999999999999988653221   1335


Q ss_pred             HHHHHHHHhcccChhHHHh---------------------HHHHHHHHHhcCCHHHHHHHHHHHHh
Q 044084          273 YNSLMDMHGRAKNLRQLEK---------------------YTTVISAYNMAREFDMCVKFYNEFRM  317 (343)
Q Consensus       273 ~~~l~~~~~~~~~~~~a~~---------------------~~~l~~~~~~~g~~~~a~~~~~~m~~  317 (343)
                      +..+...+...|++++|..                     +..+..++...|+.++|...+++...
T Consensus       256 ~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~  321 (373)
T 1hz4_A          256 WRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  321 (373)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            6677788888899888866                     33446667788999999998888754

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=99.47  E-value=3.4e-12  Score=115.05  Aligned_cols=166  Identities=11%  Similarity=0.103  Sum_probs=148.1

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHH
Q 044084           21 DSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYAS  100 (343)
Q Consensus        21 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  100 (343)
                      +..+|+.|...+.+.|++++|++.|++..+..    |....+|+.+..++.+.|++++|++.|++..+.... +...|..
T Consensus         8 ~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~----P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~P~-~~~a~~n   82 (723)
T 4gyw_A            8 HADSLNNLANIKREQGNIEEAVRLYRKALEVF----PEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPT-FADAYSN   82 (723)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC----CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHH
Confidence            46789999999999999999999999998765    344689999999999999999999999999887432 5778999


Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCc
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRA  180 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  180 (343)
                      +..++...|++++|.+.|++..+.... +...|+.+...|.+.|++++|++.|++..+..+ -+...+..+..++...|+
T Consensus        83 Lg~~l~~~g~~~~A~~~~~kAl~l~P~-~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P-~~~~a~~~L~~~l~~~g~  160 (723)
T 4gyw_A           83 MGNTLKEMQDVQGALQCYTRAIQINPA-FADAHSNLASIHKDSGNIPEAIASYRTALKLKP-DFPDAYCNLAHCLQIVCD  160 (723)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCS-CCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CChHHHhhhhhHHHhccc
Confidence            999999999999999999999997654 789999999999999999999999999998775 456789999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 044084          181 YWAAVKVYEQLIS  193 (343)
Q Consensus       181 ~~~a~~~~~~~~~  193 (343)
                      +++|.+.++++.+
T Consensus       161 ~~~A~~~~~kal~  173 (723)
T 4gyw_A          161 WTDYDERMKKLVS  173 (723)
T ss_dssp             CTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999998888764

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=99.47  E-value=7.7e-11  Score=91.63  Aligned_cols=196  Identities=12%  Similarity=0.033  Sum_probs=98.9

Q ss_pred             ChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHH
Q 044084           94 DPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVN  173 (343)
Q Consensus        94 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  173 (343)
                      |+..+......+...|++++|...|++..+....++...+..+..++...|++++|+..|++..+..+ .+...|..+..
T Consensus         6 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~l~~   84 (228)
T 4i17_A            6 DPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKNY-NLANAYIGKSA   84 (228)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTC-SHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCc-chHHHHHHHHH
Confidence            34455555555666666666666666666554434555555556666666666666666666555443 23445555555


Q ss_pred             HHhcCCcHHHHHHHHHHHHHcCCCCCH-------hhHHHHHHHHHccCChhHHHHHHHHHHHcCCCc--ChhhHHHHHHH
Q 044084          174 GFSKRRAYWAAVKVYEQLISQGCIPGQ-------VTYASIINAYCRIGLYSKAEKVFIEMQQKGFDK--CVVAYSSMVAM  244 (343)
Q Consensus       174 ~~~~~~~~~~a~~~~~~~~~~~~~p~~-------~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~  244 (343)
                      ++...|++++|...+++..+.. +.+.       ..|..+...+...|++++|...|+...+.. +.  +...+..+..+
T Consensus        85 ~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~~l~~~  162 (228)
T 4i17_A           85 AYRDMKNNQEYIATLTEGIKAV-PGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDVT-SKKWKTDALYSLGVL  162 (228)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSS-CHHHHHHHHHHHHHH
T ss_pred             HHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhcC-CCcccHHHHHHHHHH
Confidence            5666666666666666555542 1122       224444444455555555555555554432 11  23344444444


Q ss_pred             HHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 044084          245 YGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNG  319 (343)
Q Consensus       245 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~  319 (343)
                      |...|     ...++++...+. .+...+.                   ..  .....+.+++|+..+++..+..
T Consensus       163 ~~~~~-----~~~~~~a~~~~~-~~~~~~~-------------------~~--~~~~~~~~~~A~~~~~~a~~l~  210 (228)
T 4i17_A          163 FYNNG-----ADVLRKATPLAS-SNKEKYA-------------------SE--KAKADAAFKKAVDYLGEAVTLS  210 (228)
T ss_dssp             HHHHH-----HHHHHHHGGGTT-TCHHHHH-------------------HH--HHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHH-----HHHHHHHHhccc-CCHHHHH-------------------HH--HHHHHHHHHHHHHHHHHHhhcC
Confidence            43222     222233332211 1111111                   11  1223466789999999998864

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.46  E-value=1.2e-11  Score=104.05  Aligned_cols=233  Identities=8%  Similarity=-0.057  Sum_probs=165.0

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCC--CCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCC-----CC-ChHhH
Q 044084           27 QIMEAFYKIGDSEKVAALFLECESRKL--DLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGI-----LE-DPSVY   98 (343)
Q Consensus        27 ~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~-----~~-~~~~~   98 (343)
                      .....+...|++++|...|++..+...  ...+....++..+...+...|+++.|+..+++..+...     .+ ...++
T Consensus       106 ~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  185 (378)
T 3q15_A          106 FRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSL  185 (378)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHH
T ss_pred             HHHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHH
Confidence            345567788999999999998865422  21223356788888999999999999999988765311     11 23467


Q ss_pred             HHHHHHHhcccCHHHHHHHHHHHHHc----CCC-CCHHHHHHHHHHHHhcCcHhHHHHHHHHHHh-----cCCCCchhhH
Q 044084           99 ASLICSFASIAEVKVAEELFKEAEEK----GML-RDLEVFLKLVLMYIEEGMVEKTLEVVESMKN-----AELNISDCIS  168 (343)
Q Consensus        99 ~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~~  168 (343)
                      +.+...+...|++++|...+++..+.    +.. ....++..+...|...|++++|++.|++...     ..+ ....++
T Consensus       186 ~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~-~~~~~~  264 (378)
T 3q15_A          186 FVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPD-LLPKVL  264 (378)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGG-GHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCh-hHHHHH
Confidence            77888889999999999998887763    111 1245678888899999999999999988766     333 335667


Q ss_pred             HHHHHHHhcCCcHHHHHHHHHHHHHcCC----CCCHhhHHHHHHHHHccCC---hhHHHHHHHHHHHcCCCc-ChhhHHH
Q 044084          169 CVIVNGFSKRRAYWAAVKVYEQLISQGC----IPGQVTYASIINAYCRIGL---YSKAEKVFIEMQQKGFDK-CVVAYSS  240 (343)
Q Consensus       169 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~----~p~~~~~~~ll~~~~~~~~---~~~a~~~~~~~~~~~~~~-~~~~~~~  240 (343)
                      ..+...+...|++++|...+++..+...    +.....+..+...+...++   +.+|...++.   .+..| ....+..
T Consensus       265 ~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~---~~~~~~~~~~~~~  341 (378)
T 3q15_A          265 FGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEK---KNLHAYIEACARS  341 (378)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHH---TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHh---CCChhHHHHHHHH
Confidence            7888889999999999999998876521    1122345555556667777   6666666554   22222 2345667


Q ss_pred             HHHHHHccCChHHHHHHHHHHhh
Q 044084          241 MVAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       241 l~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                      +...|...|++++|...|++..+
T Consensus       342 la~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          342 AAAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHH
Confidence            88888899999999988888764

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=99.45  E-value=3.1e-11  Score=93.85  Aligned_cols=150  Identities=9%  Similarity=-0.052  Sum_probs=86.6

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHH
Q 044084           21 DSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYAS  100 (343)
Q Consensus        21 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  100 (343)
                      |+..+......+.+.|++++|...|++..+....++   ...+..+..++...|++++|++.|++..+.... +...+..
T Consensus         6 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~---~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~   81 (228)
T 4i17_A            6 DPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQD---SVTAYNCGVCADNIKKYKEAADYFDIAIKKNYN-LANAYIG   81 (228)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCC---HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCS-HHHHHHH
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCC---cHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCcc-hHHHHHH
Confidence            455666666666666777777777766665543222   344555666666666666666666666654321 3445666


Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCCCCH-------HHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCC--chhhHHHH
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGMLRDL-------EVFLKLVLMYIEEGMVEKTLEVVESMKNAELNI--SDCISCVI  171 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l  171 (343)
                      +...+...|++++|...+++..+..+. +.       .+|..+...+...|++++|++.|++..+.++ .  +...+..+
T Consensus        82 l~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~~~l  159 (228)
T 4i17_A           82 KSAAYRDMKNNQEYIATLTEGIKAVPG-NATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDVTS-KKWKTDALYSL  159 (228)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSSC-HHHHHHHHHHH
T ss_pred             HHHHHHHcccHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhcCC-CcccHHHHHHH
Confidence            666666666666666666666665432 33       3455555666666666666666666655432 1  23344444


Q ss_pred             HHHHh
Q 044084          172 VNGFS  176 (343)
Q Consensus       172 ~~~~~  176 (343)
                      ..++.
T Consensus       160 ~~~~~  164 (228)
T 4i17_A          160 GVLFY  164 (228)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            44443

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=99.44  E-value=1.4e-12  Score=104.71  Aligned_cols=227  Identities=12%  Similarity=0.019  Sum_probs=155.4

Q ss_pred             chhhHHHHHHHHHh-------CCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCC----CCCCCchHHHHHHHHHHh
Q 044084            2 NSQSKLHYYEKMKS-------AGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRK----LDLTPSSTHMYKILCDSL   70 (343)
Q Consensus         2 ~~~~A~~~~~~~~~-------~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~~~~~~~~~~~li~~~   70 (343)
                      ++++|+..|++..+       .+.+....++..+...+...|++++|...++++.+..    ...++....++..+...+
T Consensus        16 ~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~   95 (283)
T 3edt_B           16 PRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLY   95 (283)
T ss_dssp             CSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHH
Confidence            44555555555544       2333356788999999999999999999999886541    012244467899999999


Q ss_pred             hccCcHHHHHHHHHHHHhc------CC-CCChHhHHHHHHHHhcccCHHHHHHHHHHHHHc------CCCC-CHHHHHHH
Q 044084           71 GKSGRAFEILKFFRDMKEK------GI-LEDPSVYASLICSFASIAEVKVAEELFKEAEEK------GMLR-DLEVFLKL  136 (343)
Q Consensus        71 ~~~~~~~~a~~~~~~~~~~------~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~~~~-~~~~~~~l  136 (343)
                      ...|++++|++.+++....      .. +....++..+...+...|++++|...+++..+.      +..| ...++..+
T Consensus        96 ~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l  175 (283)
T 3edt_B           96 GKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKTKNNL  175 (283)
T ss_dssp             HTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence            9999999999999998764      11 223567888889999999999999999998875      1122 46778899


Q ss_pred             HHHHHhcCcHhHHHHHHHHHHhc-------CCCCc-hhhHHHHHHHHhcCCc------HHHHHHHHHHHHHcCCCCCHhh
Q 044084          137 VLMYIEEGMVEKTLEVVESMKNA-------ELNIS-DCISCVIVNGFSKRRA------YWAAVKVYEQLISQGCIPGQVT  202 (343)
Q Consensus       137 ~~~~~~~~~~~~a~~~~~~~~~~-------~~~~~-~~~~~~l~~~~~~~~~------~~~a~~~~~~~~~~~~~p~~~~  202 (343)
                      ...|...|++++|...+++..+.       ...+. ...|..+...+...+.      +..+...++..... .+....+
T Consensus       176 a~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~  254 (283)
T 3edt_B          176 ASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKVD-SPTVNTT  254 (283)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC------------CCCCC-CHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCCC-CHHHHHH
Confidence            99999999999999999988653       11122 2234333333333222      22222222222111 1223457


Q ss_pred             HHHHHHHHHccCChhHHHHHHHHHHHc
Q 044084          203 YASIINAYCRIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       203 ~~~ll~~~~~~~~~~~a~~~~~~~~~~  229 (343)
                      +..+...|...|++++|..+++...+.
T Consensus       255 ~~~la~~~~~~g~~~~A~~~~~~al~~  281 (283)
T 3edt_B          255 LRSLGALYRRQGKLEAAHTLEDCASRN  281 (283)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            788899999999999999999987753

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=99.41  E-value=5.5e-12  Score=101.22  Aligned_cols=230  Identities=13%  Similarity=0.062  Sum_probs=148.4

Q ss_pred             HhcCCHHHHHHHHHHHHhCC----CCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhc------CCCC-ChHhHHHH
Q 044084           33 YKIGDSEKVAALFLECESRK----LDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEK------GILE-DPSVYASL  101 (343)
Q Consensus        33 ~~~~~~~~a~~~~~~~~~~~----~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~------~~~~-~~~~~~~l  101 (343)
                      ...|++++|...|++..+.-    ....|....++..+...+...|++++|+..+++..+.      +-.| ...++..+
T Consensus        12 ~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l   91 (283)
T 3edt_B           12 SGLVPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNL   91 (283)
T ss_dssp             -CCSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHH
Confidence            35567777777776654421    1112344678888889999999999999999888754      2122 34567788


Q ss_pred             HHHHhcccCHHHHHHHHHHHHHcC-----C--CCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhc------C-CCCchhh
Q 044084          102 ICSFASIAEVKVAEELFKEAEEKG-----M--LRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNA------E-LNISDCI  167 (343)
Q Consensus       102 ~~~~~~~~~~~~a~~~~~~~~~~~-----~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~-~~~~~~~  167 (343)
                      ...+...|++++|...+.+..+..     .  +....++..+...|...|++++|...+++..+.      + .+....+
T Consensus        92 ~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  171 (283)
T 3edt_B           92 AVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKT  171 (283)
T ss_dssp             HHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHH
T ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence            888889999999999988887641     1  124667888888889999999999999887654      1 1123456


Q ss_pred             HHHHHHHHhcCCcHHHHHHHHHHHHHc-------CCCCCHh-hHHHHHHHHHccCChhHHHHHHHHHHH----c--CCCc
Q 044084          168 SCVIVNGFSKRRAYWAAVKVYEQLISQ-------GCIPGQV-TYASIINAYCRIGLYSKAEKVFIEMQQ----K--GFDK  233 (343)
Q Consensus       168 ~~~l~~~~~~~~~~~~a~~~~~~~~~~-------~~~p~~~-~~~~ll~~~~~~~~~~~a~~~~~~~~~----~--~~~~  233 (343)
                      +..+...+...|++++|...+++..+.       ...+... .+..+...+...+....+.. +.....    .  ..+.
T Consensus       172 ~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~  250 (283)
T 3edt_B          172 KNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAP-YGEYGSWYKACKVDSPT  250 (283)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC-------------CCCCCCHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHH-HHHHHHHHHhcCCCCHH
Confidence            778888888889999999998887753       1223322 23333333333333222222 111111    1  1122


Q ss_pred             ChhhHHHHHHHHHccCChHHHHHHHHHHhh
Q 044084          234 CVVAYSSMVAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       234 ~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                      ...++..+...|...|++++|..++++..+
T Consensus       251 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~  280 (283)
T 3edt_B          251 VNTTLRSLGALYRRQGKLEAAHTLEDCASR  280 (283)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            345677888888888999999888888765

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=99.31  E-value=1.4e-10  Score=93.84  Aligned_cols=239  Identities=12%  Similarity=0.021  Sum_probs=163.8

Q ss_pred             hhHHHHHHHHHhCCCCCChhhHHHHHHHHHhc--C-CHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHH
Q 044084            4 QSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKI--G-DSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEIL   80 (343)
Q Consensus         4 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~-~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~   80 (343)
                      .+|.+++.+..+. .+++...| .+   + +.  + ++++|...|++.                  ...+...|++++|.
T Consensus         2 ~~a~~~~~~a~k~-~~~~~~~~-~~---~-~~~~~~~~~~A~~~~~~a------------------~~~~~~~g~~~~A~   57 (292)
T 1qqe_A            2 SDPVELLKRAEKK-GVPSSGFM-KL---F-SGSDSYKFEEAADLCVQA------------------ATIYRLRKELNLAG   57 (292)
T ss_dssp             CCHHHHHHHHHHH-SSCCCTHH-HH---H-SCCSHHHHHHHHHHHHHH------------------HHHHHHTTCTHHHH
T ss_pred             CcHHHHHHHHHHH-hCcCCCcc-hh---c-CCCCCccHHHHHHHHHHH------------------HHHHHHcCCHHHHH
Confidence            4577777777765 22222223 22   2 32  2 478888777665                  33456788899999


Q ss_pred             HHHHHHHhc----CCCCC-hHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCC-C----HHHHHHHHHHHHhc-CcHhHH
Q 044084           81 KFFRDMKEK----GILED-PSVYASLICSFASIAEVKVAEELFKEAEEKGMLR-D----LEVFLKLVLMYIEE-GMVEKT  149 (343)
Q Consensus        81 ~~~~~~~~~----~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~----~~~~~~l~~~~~~~-~~~~~a  149 (343)
                      +.|++....    |-.++ ..+|+.+..+|.+.|++++|...+++..+..... +    ..+++.+...|... |++++|
T Consensus        58 ~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A  137 (292)
T 1qqe_A           58 DSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKA  137 (292)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHH
Confidence            888877653    22222 4578888889999999999999888877632111 1    45788899999996 999999


Q ss_pred             HHHHHHHHhcCCCC-c----hhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCH------hhHHHHHHHHHccCChhH
Q 044084          150 LEVVESMKNAELNI-S----DCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQ------VTYASIINAYCRIGLYSK  218 (343)
Q Consensus       150 ~~~~~~~~~~~~~~-~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~------~~~~~ll~~~~~~~~~~~  218 (343)
                      +..|++..+..... +    ..++..+...+...|++++|...|++..+.......      ..+..+..++...|++++
T Consensus       138 ~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~  217 (292)
T 1qqe_A          138 IDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVA  217 (292)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHH
Confidence            99999876543211 1    346788889999999999999999999886422221      146677788889999999


Q ss_pred             HHHHHHHHHHcCCCcC------hhhHHHHHHHHH--ccCChHHHHHHHHHHhhCCCCchH
Q 044084          219 AEKVFIEMQQKGFDKC------VVAYSSMVAMYG--KTGRIRDAMRLVAKMKPKGCEPNV  270 (343)
Q Consensus       219 a~~~~~~~~~~~~~~~------~~~~~~l~~~~~--~~~~~~~a~~~~~~m~~~~~~p~~  270 (343)
                      |...|+...+..  |+      ...+..++..+.  ..+++++|+..|+++...  .|+.
T Consensus       218 A~~~~~~al~l~--p~~~~~~~~~~l~~l~~~~~~~~~~~~~~A~~~~~~~~~l--~~~~  273 (292)
T 1qqe_A          218 AARTLQEGQSED--PNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFMRL--DKWK  273 (292)
T ss_dssp             HHHHHHGGGCC-----------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSSCC--CHHH
T ss_pred             HHHHHHHHHhhC--CCCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCcc--HHHH
Confidence            999999877642  32      123445566664  456788899988887653  4444

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=99.29  E-value=4.2e-10  Score=89.40  Aligned_cols=105  Identities=9%  Similarity=0.011  Sum_probs=70.0

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCC-CC-hHhH
Q 044084           21 DSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGIL-ED-PSVY   98 (343)
Q Consensus        21 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~-~~-~~~~   98 (343)
                      +...+-.+...+.+.|++++|...|+.+.+..... +....++..+..++.+.|++++|+..|++..+.... |. ...+
T Consensus        14 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~-~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~   92 (261)
T 3qky_A           14 SPQEAFERAMEFYNQGKYDRAIEYFKAVFTYGRTH-EWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAE   92 (261)
T ss_dssp             SHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGCSCS-TTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCC-cchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHH
Confidence            45566667777778888888888888877654322 111456777777788888888888888887775321 11 3345


Q ss_pred             HHHHHHHhc--------ccCHHHHHHHHHHHHHcCC
Q 044084           99 ASLICSFAS--------IAEVKVAEELFKEAEEKGM  126 (343)
Q Consensus        99 ~~l~~~~~~--------~~~~~~a~~~~~~~~~~~~  126 (343)
                      ..+..++..        .|++++|...|+++.+..+
T Consensus        93 ~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~p  128 (261)
T 3qky_A           93 YERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRYP  128 (261)
T ss_dssp             HHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHhcccccccchhHHHHHHHHHHHHHHCc
Confidence            556666666        7778888888877777543

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=99.29  E-value=4.5e-10  Score=90.77  Aligned_cols=200  Identities=12%  Similarity=0.101  Sum_probs=139.6

Q ss_pred             cHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHhcCcHhHH
Q 044084           75 RAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEK----GMLR-DLEVFLKLVLMYIEEGMVEKT  149 (343)
Q Consensus        75 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a  149 (343)
                      ++++|.+.|++.               ...+...|++++|...|.+..+.    |..+ ...+|+.+..+|.+.|++++|
T Consensus        32 ~~~~A~~~~~~a---------------~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A   96 (292)
T 1qqe_A           32 KFEEAADLCVQA---------------ATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNA   96 (292)
T ss_dssp             HHHHHHHHHHHH---------------HHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             cHHHHHHHHHHH---------------HHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHH
Confidence            588888888776               33566788899998888877653    2211 256788889999999999999


Q ss_pred             HHHHHHHHhcCCC---C--chhhHHHHHHHHhcC-CcHHHHHHHHHHHHHcCC---CC-C-HhhHHHHHHHHHccCChhH
Q 044084          150 LEVVESMKNAELN---I--SDCISCVIVNGFSKR-RAYWAAVKVYEQLISQGC---IP-G-QVTYASIINAYCRIGLYSK  218 (343)
Q Consensus       150 ~~~~~~~~~~~~~---~--~~~~~~~l~~~~~~~-~~~~~a~~~~~~~~~~~~---~p-~-~~~~~~ll~~~~~~~~~~~  218 (343)
                      +..|++..+....   +  -..+++.+...|... |++++|...|++..+...   .+ . ..++..+...+.+.|++++
T Consensus        97 ~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~  176 (292)
T 1qqe_A           97 VDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIE  176 (292)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHH
Confidence            9988887643211   1  134677888888886 999999999988776411   01 1 3467788888999999999


Q ss_pred             HHHHHHHHHHcCCCcCh------hhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchH------HHHHHHHHHHh--ccc
Q 044084          219 AEKVFIEMQQKGFDKCV------VAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNV------WIYNSLMDMHG--RAK  284 (343)
Q Consensus       219 a~~~~~~~~~~~~~~~~------~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~------~~~~~l~~~~~--~~~  284 (343)
                      |...|+...+.......      ..|..+..++...|++++|...|++..+.  .|+.      ..+..++.++.  ..+
T Consensus       177 A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~~~~~~~~~l~~l~~~~~~~~~~  254 (292)
T 1qqe_A          177 ASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSE--DPNFADSRESNFLKSLIDAVNEGDSE  254 (292)
T ss_dssp             HHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC-----------HHHHHHHHHHHHTTCTT
T ss_pred             HHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCCCCcHHHHHHHHHHHHHHcCCHH
Confidence            99999988876432221      14677778888899999999999988764  3332      23445566664  445


Q ss_pred             ChhHHHh
Q 044084          285 NLRQLEK  291 (343)
Q Consensus       285 ~~~~a~~  291 (343)
                      ++++|..
T Consensus       255 ~~~~A~~  261 (292)
T 1qqe_A          255 QLSEHCK  261 (292)
T ss_dssp             THHHHHH
T ss_pred             HHHHHHH
Confidence            6766665

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=99.28  E-value=6.9e-10  Score=88.12  Aligned_cols=188  Identities=13%  Similarity=0.073  Sum_probs=117.0

Q ss_pred             CchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCC---hHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCC-C-CHH
Q 044084           57 PSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILED---PSVYASLICSFASIAEVKVAEELFKEAEEKGML-R-DLE  131 (343)
Q Consensus        57 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~-~~~  131 (343)
                      +.+...+..+...+.+.|++++|+..|+++.+.... +   ...+..+..++.+.|++++|...|++..+..+. | ...
T Consensus        12 ~~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~-~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~   90 (261)
T 3qky_A           12 HSSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYGRT-HEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQ   90 (261)
T ss_dssp             CSSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGCSC-STTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHH
T ss_pred             CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCC-CcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHH
Confidence            344567777888889999999999999999886422 2   556777888899999999999999999886532 2 256


Q ss_pred             HHHHHHHHHHh--------cCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhH
Q 044084          132 VFLKLVLMYIE--------EGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTY  203 (343)
Q Consensus       132 ~~~~l~~~~~~--------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~  203 (343)
                      .+..+..++..        .|++++|+..|+++....+. +......+..              +..+...    -...+
T Consensus        91 a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~p~-~~~~~~a~~~--------------~~~~~~~----~~~~~  151 (261)
T 3qky_A           91 AEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRYPN-HELVDDATQK--------------IRELRAK----LARKQ  151 (261)
T ss_dssp             HHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHCTT-CTTHHHHHHH--------------HHHHHHH----HHHHH
T ss_pred             HHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHCcC-chhHHHHHHH--------------HHHHHHH----HHHHH
Confidence            67778888888        89999999999988876542 2222221100              0000000    00113


Q ss_pred             HHHHHHHHccCChhHHHHHHHHHHHcCCCc--ChhhHHHHHHHHHcc----------CChHHHHHHHHHHhhC
Q 044084          204 ASIINAYCRIGLYSKAEKVFIEMQQKGFDK--CVVAYSSMVAMYGKT----------GRIRDAMRLVAKMKPK  264 (343)
Q Consensus       204 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~----------~~~~~a~~~~~~m~~~  264 (343)
                      ..+...|.+.|++++|...|+.+.+.....  ....+..+..+|...          |++++|...|+++.+.
T Consensus       152 ~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~  224 (261)
T 3qky_A          152 YEAARLYERRELYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQI  224 (261)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHH
Confidence            344455555666666666666655543111  123444555555544          5556666666666553

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=99.28  E-value=9.1e-10  Score=87.81  Aligned_cols=144  Identities=12%  Similarity=0.109  Sum_probs=66.5

Q ss_pred             HHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHhcCcHhHHHHHHHHHH
Q 044084           79 ILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGM-LRDLEVFLKLVLMYIEEGMVEKTLEVVESMK  157 (343)
Q Consensus        79 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  157 (343)
                      ++..|++....+ .++..++..+..++...|++++|++++.+.+..+. .-+...+..++..+.+.|+.+.|.+.+++|.
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            444444444332 23333334445555555555555555555544332 1134445555555555555555555555554


Q ss_pred             hcCCCC-----chhhHHHHHHHHh----cCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHH
Q 044084          158 NAELNI-----SDCISCVIVNGFS----KRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQ  227 (343)
Q Consensus       158 ~~~~~~-----~~~~~~~l~~~~~----~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  227 (343)
                      +..  |     +..+...++.+++    ..+++.+|..+|+++.+.  .|+..+-..++.++.+.|++++|+..++.+.
T Consensus       164 ~~~--~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~--~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~  238 (310)
T 3mv2_B          164 NAI--EDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT--FPTWKTQLGLLNLHLQQRNIAEAQGIVELLL  238 (310)
T ss_dssp             HHS--CHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             hcC--ccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            432  2     1223333333311    122555555555555443  2332222333335555555555555555443

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=99.28  E-value=6.8e-10  Score=78.10  Aligned_cols=124  Identities=18%  Similarity=0.214  Sum_probs=46.2

Q ss_pred             HHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC
Q 044084           65 ILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEG  144 (343)
Q Consensus        65 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  144 (343)
                      .+...+...|++++|..+++++.+.+. .+...+..+...+...|++++|...++++.+.+. .+...+..+...+...|
T Consensus         6 ~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~   83 (136)
T 2fo7_A            6 NLGNAYYKQGDYDEAIEYYQKALELDP-RSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDP-RSAEAWYNLGNAYYKQG   83 (136)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHcCcHHHHHHHHHHHHHcCC-cchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHCC-CchHHHHHHHHHHHHhc
Confidence            333333344444444444444333211 1223333333333334444444444444333321 12333333444444444


Q ss_pred             cHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHH
Q 044084          145 MVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQL  191 (343)
Q Consensus       145 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  191 (343)
                      ++++|.+.++++....+ .+...+..+...+...|++++|...++++
T Consensus        84 ~~~~A~~~~~~~~~~~~-~~~~~~~~la~~~~~~~~~~~A~~~~~~~  129 (136)
T 2fo7_A           84 DYDEAIEYYQKALELDP-RSAEAWYNLGNAYYKQGDYDEAIEYYQKA  129 (136)
T ss_dssp             CHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCC-CChHHHHHHHHHHHHHccHHHHHHHHHHH
Confidence            44444444444333322 12223333333344444444444444433

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=99.28  E-value=8.6e-10  Score=77.56  Aligned_cols=128  Identities=17%  Similarity=0.215  Sum_probs=70.0

Q ss_pred             HHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhc
Q 044084           98 YASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSK  177 (343)
Q Consensus        98 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  177 (343)
                      |..+...+...|++++|..+++++.+.... +...+..+...+...|++++|...++++...+. .+...+..+...+..
T Consensus         4 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~   81 (136)
T 2fo7_A            4 WYNLGNAYYKQGDYDEAIEYYQKALELDPR-SAEAWYNLGNAYYKQGDYDEAIEYYQKALELDP-RSAEAWYNLGNAYYK   81 (136)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCcHHHHHHHHHHHHHcCCc-chhHHHHHHHHHHHhcCHHHHHHHHHHHHHHCC-CchHHHHHHHHHHHH
Confidence            444555555666666666666666554432 455555566666666666666666666555443 233445555555555


Q ss_pred             CCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHH
Q 044084          178 RRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQ  228 (343)
Q Consensus       178 ~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  228 (343)
                      .|++++|.+.++++.+.. +.+...+..+...+...|++++|...++.+.+
T Consensus        82 ~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  131 (136)
T 2fo7_A           82 QGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALE  131 (136)
T ss_dssp             TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHHccHHHHHHHHHHHHc
Confidence            566666665555555442 22344444555555555555555555555544

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=99.25  E-value=2.8e-08  Score=80.01  Aligned_cols=223  Identities=8%  Similarity=0.025  Sum_probs=177.1

Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccC--cHHHHHHHHHHHHhcCCCCChHhHHHHHHHH----hc
Q 044084           34 KIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSG--RAFEILKFFRDMKEKGILEDPSVYASLICSF----AS  107 (343)
Q Consensus        34 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~----~~  107 (343)
                      +....++|+++++.+...+    |....+|+.--..+...+  ++++++++++.+.....+ +..+|+.--..+    ..
T Consensus        45 ~~e~s~~aL~~t~~~L~~n----P~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nPk-~y~aW~~R~~iL~~~~~~  119 (306)
T 3dra_A           45 AEEYSERALHITELGINEL----ASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDNEK-NYQIWNYRQLIIGQIMEL  119 (306)
T ss_dssp             TTCCSHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCTT-CCHHHHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHHHC----cHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHCcc-cHHHHHHHHHHHHHHHHh
Confidence            3344579999999998876    334688998888888888  999999999999987544 555666544444    44


Q ss_pred             c---cCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHh--HHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCc--
Q 044084          108 I---AEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVE--KTLEVVESMKNAELNISDCISCVIVNGFSKRRA--  180 (343)
Q Consensus       108 ~---~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~--  180 (343)
                      .   +++++++.+++.+.+..++ +..+|+.-...+.+.|+++  ++++.++++.+.++ -|...|+.-...+...+.  
T Consensus       120 l~~~~~~~~EL~~~~~~l~~~pk-ny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~-~N~sAW~~R~~ll~~l~~~~  197 (306)
T 3dra_A          120 NNNDFDPYREFDILEAMLSSDPK-NHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDL-KNNSAWSHRFFLLFSKKHLA  197 (306)
T ss_dssp             TTTCCCTHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHSSGGGC
T ss_pred             ccccCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhccccc
Confidence            4   7899999999999998765 8999999988899999988  99999999999887 577788877777777776  


Q ss_pred             ----HHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhH-HHHHHHHHHHcC--CCcChhhHHHHHHHHHccCChHH
Q 044084          181 ----YWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSK-AEKVFIEMQQKG--FDKCVVAYSSMVAMYGKTGRIRD  253 (343)
Q Consensus       181 ----~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~-a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~  253 (343)
                          ++++++.++++.... +-|...|+-.-..+.+.|+... +..+...+.+.+  -+.+...+..+...|.+.|+.++
T Consensus       198 ~~~~~~eEl~~~~~aI~~~-p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~  276 (306)
T 3dra_A          198 TDNTIDEELNYVKDKIVKC-PQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNE  276 (306)
T ss_dssp             CHHHHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHH
T ss_pred             hhhhHHHHHHHHHHHHHhC-CCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHH
Confidence                899999999998875 4577888888888888777444 555666555432  13467888999999999999999


Q ss_pred             HHHHHHHHhhC
Q 044084          254 AMRLVAKMKPK  264 (343)
Q Consensus       254 a~~~~~~m~~~  264 (343)
                      |.++++.+.+.
T Consensus       277 A~~~~~~l~~~  287 (306)
T 3dra_A          277 SRTVYDLLKSK  287 (306)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHHHhc
Confidence            99999999864

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=99.25  E-value=9.7e-10  Score=84.07  Aligned_cols=178  Identities=15%  Similarity=0.066  Sum_probs=80.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHH
Q 044084           25 YCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICS  104 (343)
Q Consensus        25 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  104 (343)
                      +......+.+.|++++|...|++..+..    |.+...|...  .....                 ..........+..+
T Consensus         7 ~~~~g~~~~~~g~~~~A~~~~~~al~~~----p~~~~~~~~~--~~~~~-----------------~~~~~~~~~~lg~~   63 (208)
T 3urz_A            7 MLQKVSAAIEAGQNGQAVSYFRQTIALN----IDRTEMYYWT--NVDKN-----------------SEISSKLATELALA   63 (208)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC----HHHHHHHHHH--HSCTT-----------------SHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC----CCChHHHHHh--hhcch-----------------hhhhHHHHHHHHHH
Confidence            3344556667788888888887776644    3333444440  00000                 00001111224445


Q ss_pred             HhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCc--HH
Q 044084          105 FASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRA--YW  182 (343)
Q Consensus       105 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~--~~  182 (343)
                      +.+.|++++|...+++..+..+. +...+..+...+...|++++|+..|++..+.++ .+..++..+...|...|+  ..
T Consensus        64 ~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~P-~~~~a~~~lg~~~~~~~~~~~~  141 (208)
T 3urz_A           64 YKKNRNYDKAYLFYKELLQKAPN-NVDCLEACAEMQVCRGQEKDALRMYEKILQLEA-DNLAANIFLGNYYYLTAEQEKK  141 (208)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHHhHHHHH
Confidence            55555555555555555554432 455555555555555555555555555555443 233444444444433332  22


Q ss_pred             HHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHc
Q 044084          183 AAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       183 ~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  229 (343)
                      .+...++....  ..|....+.....++...|++++|...|++..+.
T Consensus       142 ~~~~~~~~~~~--~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~l  186 (208)
T 3urz_A          142 KLETDYKKLSS--PTKMQYARYRDGLSKLFTTRYEKARNSLQKVILR  186 (208)
T ss_dssp             HHHHHHC---C--CCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHhC--CCchhHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            33333333321  1122222222333344455555555555555543

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=99.25  E-value=7.3e-10  Score=84.76  Aligned_cols=139  Identities=14%  Similarity=0.000  Sum_probs=103.7

Q ss_pred             HHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHc
Q 044084          133 FLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCR  212 (343)
Q Consensus       133 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~  212 (343)
                      ...+...|.+.|++++|+..|++..+..+ -+...+..+..++...|++++|...|++..+.. +.+...+..+..+|..
T Consensus        57 ~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~  134 (208)
T 3urz_A           57 ATELALAYKKNRNYDKAYLFYKELLQKAP-NNVDCLEACAEMQVCRGQEKDALRMYEKILQLE-ADNLAANIFLGNYYYL  134 (208)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHH
Confidence            34588999999999999999999998875 467789999999999999999999999999874 3456778888877766


Q ss_pred             cCC--hhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHH
Q 044084          213 IGL--YSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLM  277 (343)
Q Consensus       213 ~~~--~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~  277 (343)
                      .|+  .+.+...+.....  ..|....+.....++...|++++|...|++.++.  .|+......+.
T Consensus       135 ~~~~~~~~~~~~~~~~~~--~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~l--~P~~~~~~~l~  197 (208)
T 3urz_A          135 TAEQEKKKLETDYKKLSS--PTKMQYARYRDGLSKLFTTRYEKARNSLQKVILR--FPSTEAQKTLD  197 (208)
T ss_dssp             HHHHHHHHHHHHHC---C--CCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTTT--SCCHHHHHHHH
T ss_pred             HhHHHHHHHHHHHHHHhC--CCchhHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCHHHHHHHH
Confidence            554  3445555555432  2333334555566777789999999999999975  67765544443

>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=99.24  E-value=5.6e-09  Score=80.02  Aligned_cols=177  Identities=14%  Similarity=0.079  Sum_probs=129.5

Q ss_pred             hhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccC----cHHHH
Q 044084            4 QSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSG----RAFEI   79 (343)
Q Consensus         4 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~----~~~~a   79 (343)
                      .+|++.|++..+.|   +...+..+...|...+++++|.+.|++..+.+.      ..++..|...|.. +    ++++|
T Consensus         3 ~eA~~~~~~aa~~g---~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g~------~~a~~~lg~~y~~-~g~~~~~~~A   72 (212)
T 3rjv_A            3 TEPGSQYQQQAEAG---DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQGD------GDALALLAQLKIR-NPQQADYPQA   72 (212)
T ss_dssp             -CTTHHHHHHHHTT---CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTC------HHHHHHHHHHTTS-STTSCCHHHH
T ss_pred             chHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCC------HHHHHHHHHHHHc-CCCCCCHHHH
Confidence            46888888888864   567788888888888999999999988877652      4567778888877 6    78888


Q ss_pred             HHHHHHHHhcCCCCChHhHHHHHHHHhc----ccCHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHh----cCcHhHHH
Q 044084           80 LKFFRDMKEKGILEDPSVYASLICSFAS----IAEVKVAEELFKEAEEKGML-RDLEVFLKLVLMYIE----EGMVEKTL  150 (343)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~----~~~~~~a~  150 (343)
                      +++|++..+.|   +...+..|...|..    .+++++|...|++..+.|.. .++..+..|...|..    .+++++|+
T Consensus        73 ~~~~~~A~~~g---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~  149 (212)
T 3rjv_A           73 RQLAEKAVEAG---SKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKAS  149 (212)
T ss_dssp             HHHHHHHHHTT---CHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHH
T ss_pred             HHHHHHHHHCC---CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHH
Confidence            88888887754   56667777777776    77888888888888876631 026777788888877    77788888


Q ss_pred             HHHHHHHhcCCCCchhhHHHHHHHHhcC------CcHHHHHHHHHHHHHcC
Q 044084          151 EVVESMKNAELNISDCISCVIVNGFSKR------RAYWAAVKVYEQLISQG  195 (343)
Q Consensus       151 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~------~~~~~a~~~~~~~~~~~  195 (343)
                      ..|++..+.+  .+...+..+...|...      .++++|...|++..+.|
T Consensus       150 ~~~~~A~~~~--~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g  198 (212)
T 3rjv_A          150 EYFKGSSSLS--RTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEG  198 (212)
T ss_dssp             HHHHHHHHTS--CTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHcC--CCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcC
Confidence            8888877652  2233455566665432      27788888888777766

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=99.24  E-value=3.6e-09  Score=84.37  Aligned_cols=210  Identities=10%  Similarity=0.024  Sum_probs=144.8

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcc
Q 044084           29 MEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASI  108 (343)
Q Consensus        29 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  108 (343)
                      ++...-.|++..++.-   ..+.  .+..+ ...-.-+.+++...|++...         ....|....+..+.. |...
T Consensus        20 ikn~fy~G~yq~~i~e---~~~~--~~~~~-~~~~~~~~Rs~iAlg~~~~~---------~~~~~~~~a~~~la~-~~~~   83 (310)
T 3mv2_B           20 IKQNYYTGNFVQCLQE---IEKF--SKVTD-NTLLFYKAKTLLALGQYQSQ---------DPTSKLGKVLDLYVQ-FLDT   83 (310)
T ss_dssp             HHHHHTTTCHHHHTHH---HHTS--SCCCC-HHHHHHHHHHHHHTTCCCCC---------CSSSTTHHHHHHHHH-HHTT
T ss_pred             HHHHHHhhHHHHHHHH---HHhc--Cccch-HHHHHHHHHHHHHcCCCccC---------CCCCHHHHHHHHHHH-Hhcc
Confidence            4455567888888873   3322  22222 23333456778777776632         122344334443333 3332


Q ss_pred             cCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCC-CCchhhHHHHHHHHhcCCcHHHHHHH
Q 044084          109 AEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAEL-NISDCISCVIVNGFSKRRAYWAAVKV  187 (343)
Q Consensus       109 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~  187 (343)
                      +    +...+++..+.+ .++..++..+..++...|++++|++++.+....+. .-+...+...+..+.+.|+++.|.+.
T Consensus        84 ~----a~~~l~~l~~~~-~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~  158 (310)
T 3mv2_B           84 K----NIEELENLLKDK-QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTI  158 (310)
T ss_dssp             T----CCHHHHHTTTTS-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             c----HHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHH
Confidence            2    677777777655 35666677889999999999999999999876664 23556788889999999999999999


Q ss_pred             HHHHHHcCCCC-----CHhhHHHHHHHHH--ccC--ChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHH
Q 044084          188 YEQLISQGCIP-----GQVTYASIINAYC--RIG--LYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLV  258 (343)
Q Consensus       188 ~~~~~~~~~~p-----~~~~~~~ll~~~~--~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  258 (343)
                      +++|.+.  .|     +..+...+..++.  ..|  +..+|..+|+++.+..  |+..+-..++.++.+.|++++|.+.+
T Consensus       159 l~~~~~~--~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~~--p~~~~~~lLln~~~~~g~~~eAe~~L  234 (310)
T 3mv2_B          159 FDNYTNA--IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQTF--PTWKTQLGLLNLHLQQRNIAEAQGIV  234 (310)
T ss_dssp             HHHHHHH--SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTTS--CSHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHhc--CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhC--CCcccHHHHHHHHHHcCCHHHHHHHH
Confidence            9999886  56     3566666776633  334  8999999999987653  54333344455899999999999999


Q ss_pred             HHHhh
Q 044084          259 AKMKP  263 (343)
Q Consensus       259 ~~m~~  263 (343)
                      +.+.+
T Consensus       235 ~~l~~  239 (310)
T 3mv2_B          235 ELLLS  239 (310)
T ss_dssp             HHHHS
T ss_pred             HHHHH
Confidence            97665

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=99.23  E-value=4.4e-10  Score=101.61  Aligned_cols=186  Identities=11%  Similarity=-0.000  Sum_probs=142.7

Q ss_pred             hccCcHHHHHHHHHHHH--------hcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 044084           71 GKSGRAFEILKFFRDMK--------EKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIE  142 (343)
Q Consensus        71 ~~~~~~~~a~~~~~~~~--------~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  142 (343)
                      ...|++++|++.+++..        +.. +.+...+..+..++...|++++|...++++.+.... +...|..+...|..
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~  479 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDF-SESVELPLMEVRALLDLGDVAKATRKLDDLAERVGW-RWRLVWYRAVAELL  479 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CC-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhccccccccc-ccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccCcc-hHHHHHHHHHHHHH
Confidence            67888999999999887        332 335667888888889999999999999998887643 78888899999999


Q ss_pred             cCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHH
Q 044084          143 EGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKV  222 (343)
Q Consensus       143 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~  222 (343)
                      .|++++|++.|++..+..+ .+...|..+..++...|++++ .+.|++..+.. +.+...+..+..++.+.|++++|...
T Consensus       480 ~g~~~~A~~~~~~al~l~P-~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~  556 (681)
T 2pzi_A          480 TGDYDSATKHFTEVLDTFP-GELAPKLALAATAELAGNTDE-HKFYQTVWSTN-DGVISAAFGLARARSAEGDRVGAVRT  556 (681)
T ss_dssp             HTCHHHHHHHHHHHHHHST-TCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhCC-CChHHHHHHHHHHHHcCChHH-HHHHHHHHHhC-CchHHHHHHHHHHHHHcCCHHHHHHH
Confidence            9999999999999888765 456678888888999999999 99999988764 34567788888899999999999999


Q ss_pred             HHHHHHcCCCcChhhHHHHHHHHHccCC--------hHHHHHHHHHHh
Q 044084          223 FIEMQQKGFDKCVVAYSSMVAMYGKTGR--------IRDAMRLVAKMK  262 (343)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~--------~~~a~~~~~~m~  262 (343)
                      |++..+.+ +-+...+..+..++...++        +++|.+.+..+.
T Consensus       557 ~~~al~l~-P~~~~a~~~~~~~~~~~~~~~~~~~~~~~~A~~~l~~~~  603 (681)
T 2pzi_A          557 LDEVPPTS-RHFTTARLTSAVTLLSGRSTSEVTEEQIRDAARRVEALP  603 (681)
T ss_dssp             HHTSCTTS-TTHHHHHHHHHHHTC-------CCHHHHHHHHHHHHTSC
T ss_pred             HHhhcccC-cccHHHHHHHHHHHHccCCCCCCCHHHHHHHHHHHhhCC
Confidence            98887764 2345677777777766444        445555554443

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=99.19  E-value=3.1e-10  Score=81.91  Aligned_cols=141  Identities=11%  Similarity=-0.022  Sum_probs=68.7

Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccC
Q 044084           31 AFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAE  110 (343)
Q Consensus        31 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  110 (343)
                      .+...|++++|+..+......    +|.....+..+...|.+.|++++|++.|++..+.... +..+|..+..++...|+
T Consensus         6 ~~~~~~~~e~ai~~~~~a~~~----~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~~~   80 (150)
T 4ga2_A            6 MRRSKADVERYIASVQGSTPS----PRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQER-DPKAHRFLGLLYELEEN   80 (150)
T ss_dssp             -CCCHHHHHHHHHHHHHHSCS----HHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTC
T ss_pred             HHHHcChHHHHHHHHHHhccc----CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCc
Confidence            334445555555555544222    1222333444555555555555555555555554321 34455555555555555


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHH-HHHHHhcCCCCchhhHHHHHHHHhcC
Q 044084          111 VKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEV-VESMKNAELNISDCISCVIVNGFSKR  178 (343)
Q Consensus       111 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~  178 (343)
                      +++|...|++..+..+. +..++..+...|.+.|++++|.+. +++..+..+ -+..+|......+...
T Consensus        81 ~~~A~~~~~~al~~~p~-~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~P-~~~~~~~l~~~ll~~~  147 (150)
T 4ga2_A           81 TDKAVECYRRSVELNPT-QKDLVLKIAELLCKNDVTDGRAKYWVERAAKLFP-GSPAVYKLKEQLLDCE  147 (150)
T ss_dssp             HHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHST-TCHHHHHHHHHHHHTC
T ss_pred             hHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhCc-CCHHHHHHHHHHHHHh
Confidence            55555555555554432 455555555555555555544433 344444433 2333444444443333

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=99.19  E-value=1.7e-07  Score=83.80  Aligned_cols=150  Identities=11%  Similarity=0.079  Sum_probs=94.1

Q ss_pred             hhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCc---HHHHH
Q 044084            4 QSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGR---AFEIL   80 (343)
Q Consensus         4 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~---~~~a~   80 (343)
                      .+.+..|++.+..++ -|...|..++..+.+.+.++.+..+|+.+...-    |.....|...+..-.+.+.   ++.+.
T Consensus        49 ~d~i~~lE~~l~~np-~d~~~W~~yi~~~~~~~~~~~aR~vyEraL~~f----P~~~~lW~~Yi~~E~~~~~~~~~~~v~  123 (679)
T 4e6h_A           49 SDVIGKLNDMIEEQP-TDIFLYVKLLKHHVSLKQWKQVYETFDKLHDRF----PLMANIWCMRLSLEFDKMEELDAAVIE  123 (679)
T ss_dssp             SCHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHTC--CCCHHHHH
T ss_pred             HHHHHHHHHHHHHCc-CCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHC----CCCHHHHHHHHHHHHhhCCcchHHHHH
Confidence            344555666666554 577888888888888888888888888887764    2225678777777777777   88888


Q ss_pred             HHHHHHHhcC-CCCChHhHHHHHHHHhcccCH--------HHHHHHHHHHHH-cCC-CC-CHHHHHHHHHHHHh------
Q 044084           81 KFFRDMKEKG-ILEDPSVYASLICSFASIAEV--------KVAEELFKEAEE-KGM-LR-DLEVFLKLVLMYIE------  142 (343)
Q Consensus        81 ~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~--------~~a~~~~~~~~~-~~~-~~-~~~~~~~l~~~~~~------  142 (343)
                      .+|++..... ..|+...|...+....+.++.        +.+.++|+.... .|. .+ +...|...+.....      
T Consensus       124 ~lfeRal~~~~~~~sv~LW~~Yl~f~~~~~~~~~~~~~~r~~vr~~FErAl~~vG~~d~~s~~iW~~Yi~f~~~~~~~~~  203 (679)
T 4e6h_A          124 PVLARCLSKELGNNDLSLWLSYITYVRKKNDIITGGEEARNIVIQAFQVVVDKCAIFEPKSIQFWNEYLHFLEHWKPVNK  203 (679)
T ss_dssp             HHHHHHTCSSSCCCCHHHHHHHHHHHHHHSCSTTTHHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHTCCCCSH
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHhccccCc
Confidence            8888877753 136777777666554444332        334466666554 344 33 35667666654432      


Q ss_pred             ---cCcHhHHHHHHHHHHh
Q 044084          143 ---EGMVEKTLEVVESMKN  158 (343)
Q Consensus       143 ---~~~~~~a~~~~~~~~~  158 (343)
                         .++++.+..+|++...
T Consensus       204 ~eeq~~~~~~R~iy~raL~  222 (679)
T 4e6h_A          204 FEEQQRVQYIRKLYKTLLC  222 (679)
T ss_dssp             HHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHhHHHHHHHHHHHHHh
Confidence               2345566666666553

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=99.19  E-value=1.6e-07  Score=84.09  Aligned_cols=84  Identities=13%  Similarity=0.045  Sum_probs=50.4

Q ss_pred             hhhHHHHHHHHHhCC-CCCChhhHHHHHHHHHhcCCH--------HHHHHHHHHHHh-CCC-CCCCchHHHHHHHHHHhh
Q 044084            3 SQSKLHYYEKMKSAG-IVLDSGCYCQIMEAFYKIGDS--------EKVAALFLECES-RKL-DLTPSSTHMYKILCDSLG   71 (343)
Q Consensus         3 ~~~A~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~--------~~a~~~~~~~~~-~~~-~~~~~~~~~~~~li~~~~   71 (343)
                      .+.+..+|++..... .+|++..|...+....+.++.        +.+.++|+.... .|. .+  .+...|...+....
T Consensus       119 ~~~v~~lfeRal~~~~~~~sv~LW~~Yl~f~~~~~~~~~~~~~~r~~vr~~FErAl~~vG~~d~--~s~~iW~~Yi~f~~  196 (679)
T 4e6h_A          119 AAVIEPVLARCLSKELGNNDLSLWLSYITYVRKKNDIITGGEEARNIVIQAFQVVVDKCAIFEP--KSIQFWNEYLHFLE  196 (679)
T ss_dssp             HHHHHHHHHHHTCSSSCCCCHHHHHHHHHHHHHHSCSTTTHHHHHHHHHHHHHHHHHHTTTTCS--SCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHhCcccc--cchHHHHHHHHHHH
Confidence            677788888887754 136777777777766555543        334466666543 233 22  22457777665543


Q ss_pred             c---------cCcHHHHHHHHHHHHh
Q 044084           72 K---------SGRAFEILKFFRDMKE   88 (343)
Q Consensus        72 ~---------~~~~~~a~~~~~~~~~   88 (343)
                      .         .++.+.+..+|++.+.
T Consensus       197 ~~~~~~~~eeq~~~~~~R~iy~raL~  222 (679)
T 4e6h_A          197 HWKPVNKFEEQQRVQYIRKLYKTLLC  222 (679)
T ss_dssp             TCCCCSHHHHHHHHHHHHHHHHHHTT
T ss_pred             hccccCcHHHHhHHHHHHHHHHHHHh
Confidence            2         3346667777777764

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=99.19  E-value=8.4e-10  Score=99.80  Aligned_cols=177  Identities=8%  Similarity=-0.082  Sum_probs=144.6

Q ss_pred             HhcCCHHHHHHHHHHHHhC----CCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcc
Q 044084           33 YKIGDSEKVAALFLECESR----KLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASI  108 (343)
Q Consensus        33 ~~~~~~~~a~~~~~~~~~~----~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  108 (343)
                      ...|++++|.+.+++....    ....+|.+...+..+...+...|++++|++.|++..+.+. -+...|..+..++...
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~  480 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAERVG-WRWRLVWYRAVAELLT  480 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccCc-chHHHHHHHHHHHHHc
Confidence            7889999999999998711    1112233457899999999999999999999999988643 2677888899999999


Q ss_pred             cCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHH
Q 044084          109 AEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVY  188 (343)
Q Consensus       109 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  188 (343)
                      |++++|...|++..+..+. +...+..+..+|.+.|++++ ++.|++..+.++ .+...|..+..++...|++++|.+.|
T Consensus       481 g~~~~A~~~~~~al~l~P~-~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~P-~~~~a~~~lg~~~~~~g~~~~A~~~~  557 (681)
T 2pzi_A          481 GDYDSATKHFTEVLDTFPG-ELAPKLALAATAELAGNTDE-HKFYQTVWSTND-GVISAAFGLARARSAEGDRVGAVRTL  557 (681)
T ss_dssp             TCHHHHHHHHHHHHHHSTT-CSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHcCChHH-HHHHHHHHHhCC-chHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            9999999999999997654 68889999999999999999 999999988776 46678999999999999999999999


Q ss_pred             HHHHHcCCCCC-HhhHHHHHHHHHccCC
Q 044084          189 EQLISQGCIPG-QVTYASIINAYCRIGL  215 (343)
Q Consensus       189 ~~~~~~~~~p~-~~~~~~ll~~~~~~~~  215 (343)
                      ++..+.  .|+ ...+..+..++...++
T Consensus       558 ~~al~l--~P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          558 DEVPPT--SRHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             HTSCTT--STTHHHHHHHHHHHTC----
T ss_pred             Hhhccc--CcccHHHHHHHHHHHHccCC
Confidence            998876  354 4566677777766555

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=99.17  E-value=7.8e-09  Score=80.05  Aligned_cols=188  Identities=12%  Similarity=-0.013  Sum_probs=114.9

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCCh--HhH
Q 044084           21 DSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDP--SVY   98 (343)
Q Consensus        21 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~   98 (343)
                      +...+..+...+.+.|++++|...|+++.+..... +....++..+..++.+.|++++|+..|+++.+.......  ..+
T Consensus         3 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~-~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~   81 (225)
T 2yhc_A            3 PPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFG-PYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVM   81 (225)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTS-TTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC-hHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHH
Confidence            34456666778888999999999999988754322 222357788888999999999999999998876422111  133


Q ss_pred             HHHHHHHhc------------------ccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcC
Q 044084           99 ASLICSFAS------------------IAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus        99 ~~l~~~~~~------------------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  160 (343)
                      ..+..++..                  .|+.++|...|+++.+..+. +...+.......          .+...+.   
T Consensus        82 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~P~-~~~a~~a~~~l~----------~~~~~~~---  147 (225)
T 2yhc_A           82 YMRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGYPN-SQYTTDATKRLV----------FLKDRLA---  147 (225)
T ss_dssp             HHHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTTCTT-CTTHHHHHHHHH----------HHHHHHH---
T ss_pred             HHHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHCcC-ChhHHHHHHHHH----------HHHHHHH---
Confidence            333444433                  34555666666555554322 111111110000          0000000   


Q ss_pred             CCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCH----hhHHHHHHHHHccCChhHHHHHHHHHHHcC
Q 044084          161 LNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQ----VTYASIINAYCRIGLYSKAEKVFIEMQQKG  230 (343)
Q Consensus       161 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~----~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  230 (343)
                           .....+...+...|++++|...|+++.+..  |+.    ..+..+..+|.+.|+.++|.+.++.+...+
T Consensus       148 -----~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~  214 (225)
T 2yhc_A          148 -----KYEYSVAEYYTERGAWVAVVNRVEGMLRDY--PDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANS  214 (225)
T ss_dssp             -----HHHHHHHHHHHHHTCHHHHHHHHHHHHHHS--TTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCC
T ss_pred             -----HHHHHHHHHHHHcCcHHHHHHHHHHHHHHC--cCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC
Confidence                 011245567777888888888888887762  332    456777788888888888888888877764

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=99.16  E-value=1.1e-09  Score=88.23  Aligned_cols=165  Identities=6%  Similarity=0.001  Sum_probs=113.8

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHH-HHHH
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFL-KLVL  138 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~l~~  138 (343)
                      ...+..+...+...|++++|...|++..+.... +...+..+...+.+.|++++|...++++....  |+..... ....
T Consensus       117 ~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~P~-~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~--p~~~~~~~~~~~  193 (287)
T 3qou_A          117 EELXAQQAMQLMQESNYTDALPLLXDAWQLSNQ-NGEIGLLLAETLIALNRSEDAEAVLXTIPLQD--QDTRYQGLVAQI  193 (287)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTS-CHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGG--CSHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHhCCCHHHHHHHHHHHHHhCCc-chhHHHHHHHHHHHCCCHHHHHHHHHhCchhh--cchHHHHHHHHH
Confidence            456667777777888888888888887776322 45667777777888888888888887776653  3433322 2233


Q ss_pred             HHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCC-CCHhhHHHHHHHHHccCChh
Q 044084          139 MYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCI-PGQVTYASIINAYCRIGLYS  217 (343)
Q Consensus       139 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-p~~~~~~~ll~~~~~~~~~~  217 (343)
                      .+...++.++|...+++.....+ .+...+..+...+...|++++|...|.++.+.... .+...+..+...+...|+.+
T Consensus       194 ~l~~~~~~~~a~~~l~~al~~~P-~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~  272 (287)
T 3qou_A          194 ELLXQAADTPEIQQLQQQVAENP-EDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTGD  272 (287)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTTC
T ss_pred             HHHhhcccCccHHHHHHHHhcCC-ccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCCC
Confidence            35566777777888877777665 45667777778888888888888888887776321 12456777788888888888


Q ss_pred             HHHHHHHHHHH
Q 044084          218 KAEKVFIEMQQ  228 (343)
Q Consensus       218 ~a~~~~~~~~~  228 (343)
                      +|...+++...
T Consensus       273 ~a~~~~r~al~  283 (287)
T 3qou_A          273 ALASXYRRQLY  283 (287)
T ss_dssp             HHHHHHHHHHH
T ss_pred             cHHHHHHHHHH
Confidence            88777776543

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=99.16  E-value=4.9e-10  Score=83.30  Aligned_cols=162  Identities=11%  Similarity=0.065  Sum_probs=100.1

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHH
Q 044084           24 CYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLIC  103 (343)
Q Consensus        24 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  103 (343)
                      .+..+...+.+.|++++|...|++..+..    |.+...+..+...+...|++++|+..+++.....  |+...+..+..
T Consensus         8 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~----P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~--p~~~~~~~~~~   81 (176)
T 2r5s_A            8 QLLKQVSELLQQGEHAQALNVIQTLSDEL----QSRGDVKLAKADCLLETKQFELAQELLATIPLEY--QDNSYKSLIAK   81 (176)
T ss_dssp             THHHHHHHHHHTTCHHHHHHHHHTSCHHH----HTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGG--CCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHC----CCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhcc--CChHHHHHHHH
Confidence            45566677778888888888887765433    3345677788888888888888888887776543  23333222211


Q ss_pred             H-HhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCC-chhhHHHHHHHHhcCCcH
Q 044084          104 S-FASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNI-SDCISCVIVNGFSKRRAY  181 (343)
Q Consensus       104 ~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~  181 (343)
                      . +...+....+...+++..+..+. +...+..+...+...|++++|...|+++.+..+.+ +...+..+...+...|+.
T Consensus        82 ~~~~~~~~~~~a~~~~~~al~~~P~-~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~  160 (176)
T 2r5s_A           82 LELHQQAAESPELKRLEQELAANPD-NFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQG  160 (176)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSS
T ss_pred             HHHHhhcccchHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCC
Confidence            1 11212223356666666665432 56667777777777777777777777776655432 234566666666666777


Q ss_pred             HHHHHHHHHHH
Q 044084          182 WAAVKVYEQLI  192 (343)
Q Consensus       182 ~~a~~~~~~~~  192 (343)
                      ++|...|++..
T Consensus       161 ~~A~~~y~~al  171 (176)
T 2r5s_A          161 NAIASKYRRQL  171 (176)
T ss_dssp             CHHHHHHHHHH
T ss_pred             CcHHHHHHHHH
Confidence            66666666544

>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=99.16  E-value=9.1e-09  Score=78.85  Aligned_cols=175  Identities=14%  Similarity=0.061  Sum_probs=89.4

Q ss_pred             HHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC----cHhHHHHHHH
Q 044084           79 ILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEG----MVEKTLEVVE  154 (343)
Q Consensus        79 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~----~~~~a~~~~~  154 (343)
                      |++.|++..+.|   ++..+..+...+...+++++|...|++..+.|   ++..+..|...|.. +    ++++|.+.|+
T Consensus         5 A~~~~~~aa~~g---~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~   77 (212)
T 3rjv_A            5 PGSQYQQQAEAG---DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQLAE   77 (212)
T ss_dssp             TTHHHHHHHHTT---CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHHHH
T ss_pred             HHHHHHHHHHCC---CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHHHH
Confidence            444455444432   44445555555555555555555555555543   34455555555554 4    5555666555


Q ss_pred             HHHhcCCCCchhhHHHHHHHHhc----CCcHHHHHHHHHHHHHcCCC-CCHhhHHHHHHHHHc----cCChhHHHHHHHH
Q 044084          155 SMKNAELNISDCISCVIVNGFSK----RRAYWAAVKVYEQLISQGCI-PGQVTYASIINAYCR----IGLYSKAEKVFIE  225 (343)
Q Consensus       155 ~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~-p~~~~~~~ll~~~~~----~~~~~~a~~~~~~  225 (343)
                      +..+.+   +...+..+...|..    .+++++|.++|++..+.|.. .+...+..|...|..    .+++++|...|+.
T Consensus        78 ~A~~~g---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~  154 (212)
T 3rjv_A           78 KAVEAG---SKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKG  154 (212)
T ss_dssp             HHHHTT---CHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHH
T ss_pred             HHHHCC---CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence            554443   22244444444544    55566666666665554311 013445555555554    4556666666666


Q ss_pred             HHHcCCCcChhhHHHHHHHHHcc-C-----ChHHHHHHHHHHhhCC
Q 044084          226 MQQKGFDKCVVAYSSMVAMYGKT-G-----RIRDAMRLVAKMKPKG  265 (343)
Q Consensus       226 ~~~~~~~~~~~~~~~l~~~~~~~-~-----~~~~a~~~~~~m~~~~  265 (343)
                      ..+.  +.+...+..|...|..- |     +.++|...|++..+.|
T Consensus       155 A~~~--~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g  198 (212)
T 3rjv_A          155 SSSL--SRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEG  198 (212)
T ss_dssp             HHHT--SCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHT
T ss_pred             HHHc--CCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcC
Confidence            5554  12334455555555432 2     5666666666665554

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=99.16  E-value=1.9e-09  Score=86.85  Aligned_cols=162  Identities=10%  Similarity=0.022  Sum_probs=78.6

Q ss_pred             HhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchh-hHHHHHHH
Q 044084           96 SVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDC-ISCVIVNG  174 (343)
Q Consensus        96 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~  174 (343)
                      ..+..+...+...|++++|...+++..+..+. +...+..+...+.+.|++++|...++++....+  +.. ........
T Consensus       118 ~~~~~~a~~~~~~g~~~~A~~~~~~al~~~P~-~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~p--~~~~~~~~~~~~  194 (287)
T 3qou_A          118 ELXAQQAMQLMQESNYTDALPLLXDAWQLSNQ-NGEIGLLLAETLIALNRSEDAEAVLXTIPLQDQ--DTRYQGLVAQIE  194 (287)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTS-CHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGGC--SHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHhCCCHHHHHHHHHHHHHhCCc-chhHHHHHHHHHHHCCCHHHHHHHHHhCchhhc--chHHHHHHHHHH
Confidence            33444445555555555555555555554432 455555555555555555555555555544332  211 11111222


Q ss_pred             HhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCc-ChhhHHHHHHHHHccCChHH
Q 044084          175 FSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDK-CVVAYSSMVAMYGKTGRIRD  253 (343)
Q Consensus       175 ~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~  253 (343)
                      +...++.+.|...+++..... +.+...+..+...+...|++++|...|..+.+..... +...+..++..+...|+.++
T Consensus       195 l~~~~~~~~a~~~l~~al~~~-P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~  273 (287)
T 3qou_A          195 LLXQAADTPEIQQLQQQVAEN-PEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTGDA  273 (287)
T ss_dssp             HHHHHTSCHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTTCH
T ss_pred             HHhhcccCccHHHHHHHHhcC-CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCCCc
Confidence            334444444555555555442 2334445555555555555555555555555543111 13445555555555555555


Q ss_pred             HHHHHHHH
Q 044084          254 AMRLVAKM  261 (343)
Q Consensus       254 a~~~~~~m  261 (343)
                      |...+++.
T Consensus       274 a~~~~r~a  281 (287)
T 3qou_A          274 LASXYRRQ  281 (287)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            55555443

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=99.15  E-value=4.7e-10  Score=80.93  Aligned_cols=57  Identities=11%  Similarity=0.051  Sum_probs=22.1

Q ss_pred             HHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHH
Q 044084          136 LVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLIS  193 (343)
Q Consensus       136 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  193 (343)
                      +...|.+.|++++|++.|++..+..+ -+..+|..+..++...|++++|...|++..+
T Consensus        37 la~~y~~~~~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~   93 (150)
T 4ga2_A           37 FAKLYYEAKEYDLAKKYICTYINVQE-RDPKAHRFLGLLYELEENTDKAVECYRRSVE   93 (150)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCchHHHHHHHHHHHH
Confidence            33334444444444444444333332 2233333334444444444444444444333

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=99.14  E-value=4e-08  Score=79.04  Aligned_cols=231  Identities=6%  Similarity=0.005  Sum_probs=179.5

Q ss_pred             hhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcC--CHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHh----hcc---
Q 044084            3 SQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIG--DSEKVAALFLECESRKLDLTPSSTHMYKILCDSL----GKS---   73 (343)
Q Consensus         3 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~----~~~---   73 (343)
                      .++|+.+++.++..++ -+...|+.-..++...+  ++++++++++.+...++..    ..+|+.-...+    ...   
T Consensus        49 s~~aL~~t~~~L~~nP-~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nPk~----y~aW~~R~~iL~~~~~~l~~~  123 (306)
T 3dra_A           49 SERALHITELGINELA-SHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDNEKN----YQIWNYRQLIIGQIMELNNND  123 (306)
T ss_dssp             SHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCTTC----CHHHHHHHHHHHHHHHHTTTC
T ss_pred             CHHHHHHHHHHHHHCc-HHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHCccc----HHHHHHHHHHHHHHHHhcccc
Confidence            3679999999998653 24556888888888888  9999999999998876443    46777655555    444   


Q ss_pred             CcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHH--HHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCc------
Q 044084           74 GRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVK--VAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGM------  145 (343)
Q Consensus        74 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~------  145 (343)
                      +++++++++++++.+...+ +..+|+.-.-.+.+.|.++  ++++.++++.+..+. |...|+.........++      
T Consensus       124 ~~~~~EL~~~~~~l~~~pk-ny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~~-N~sAW~~R~~ll~~l~~~~~~~~  201 (306)
T 3dra_A          124 FDPYREFDILEAMLSSDPK-NHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDLK-NNSAWSHRFFLLFSKKHLATDNT  201 (306)
T ss_dssp             CCTHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHSSGGGCCHHH
T ss_pred             CCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhccccchhhh
Confidence            7899999999999987544 7778888777777888888  999999999998765 88999988888877777      


Q ss_pred             HhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHH-HHHHHHHHHHcC--CCCCHhhHHHHHHHHHccCChhHHHHH
Q 044084          146 VEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWA-AVKVYEQLISQG--CIPGQVTYASIINAYCRIGLYSKAEKV  222 (343)
Q Consensus       146 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~~~--~~p~~~~~~~ll~~~~~~~~~~~a~~~  222 (343)
                      ++++++.++++...++ -|...|+-+-..+.+.|.... +..+..++.+.+  -+.+...+..+...|.+.|+.++|.++
T Consensus       202 ~~eEl~~~~~aI~~~p-~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A~~~  280 (306)
T 3dra_A          202 IDEELNYVKDKIVKCP-QNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNESRTV  280 (306)
T ss_dssp             HHHHHHHHHHHHHHCS-SCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCC-CCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHHHHH
Confidence            8999999999998877 677888888878877776443 555666655432  134667888899999999999999999


Q ss_pred             HHHHHHc-CCCcChhhHHHHH
Q 044084          223 FIEMQQK-GFDKCVVAYSSMV  242 (343)
Q Consensus       223 ~~~~~~~-~~~~~~~~~~~l~  242 (343)
                      ++.+.+. + +.....|+..+
T Consensus       281 ~~~l~~~~D-pir~~yW~~~~  300 (306)
T 3dra_A          281 YDLLKSKYN-PIRSNFWDYQI  300 (306)
T ss_dssp             HHHHHHTTC-GGGHHHHHHHH
T ss_pred             HHHHHhccC-hHHHHHHHHHH
Confidence            9999873 3 33445555443

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=99.13  E-value=2.1e-08  Score=77.57  Aligned_cols=186  Identities=11%  Similarity=0.015  Sum_probs=117.5

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCC-C-ChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCC--HHHHHH
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEKGIL-E-DPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRD--LEVFLK  135 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~-~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~  135 (343)
                      ...+..+...+...|++++|+..|+++...... | ....+..+..++.+.|++++|...|+++.+..+...  ...+..
T Consensus         4 ~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~~   83 (225)
T 2yhc_A            4 PNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYM   83 (225)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHHH
Confidence            345666778888889999999999998875322 1 134677778888889999999999999888654321  124555


Q ss_pred             HHHHHHh------------------cCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCC
Q 044084          136 LVLMYIE------------------EGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCI  197 (343)
Q Consensus       136 l~~~~~~------------------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  197 (343)
                      +..++..                  .|++++|+..|+++.+..+ -+...+.+....          ..+...+.     
T Consensus        84 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~P-~~~~a~~a~~~l----------~~~~~~~~-----  147 (225)
T 2yhc_A           84 RGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGYP-NSQYTTDATKRL----------VFLKDRLA-----  147 (225)
T ss_dssp             HHHHHHHHHC--------------CCHHHHHHHHHHHHHHTTCT-TCTTHHHHHHHH----------HHHHHHHH-----
T ss_pred             HHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHCc-CChhHHHHHHHH----------HHHHHHHH-----
Confidence            5555554                  3445555555555554432 111111111000          00000000     


Q ss_pred             CCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCc--ChhhHHHHHHHHHccCChHHHHHHHHHHhhC
Q 044084          198 PGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDK--CVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       198 p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                         .....+...|.+.|++++|...|+.+.+.....  ....+..+..+|.+.|+.++|.+.++.+...
T Consensus       148 ---~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~  213 (225)
T 2yhc_A          148 ---KYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAAN  213 (225)
T ss_dssp             ---HHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHC
T ss_pred             ---HHHHHHHHHHHHcCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhh
Confidence               011235567788899999999999988864111  1256788889999999999999999988776

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=99.12  E-value=3.3e-09  Score=94.11  Aligned_cols=153  Identities=10%  Similarity=0.029  Sum_probs=95.7

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      ++++|+..|++..+... .+...+..+...+.+.|++++|.+.|++..+..    |.+..+|..+...+...|++++|.+
T Consensus         4 ~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~----p~~~~~~~~lg~~~~~~g~~~~A~~   78 (568)
T 2vsy_A            4 DGPRELLQLRAAVRHRP-QDFVAWLMLADAELGMGDTTAGEMAVQRGLALH----PGHPEAVARLGRVRWTQQRHAEAAV   78 (568)
T ss_dssp             ------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTS----TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC----CCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            45677777777766542 346677777777777777777777777776654    2235677777777777777777777


Q ss_pred             HHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc---CcHhHHHHHHHHHHh
Q 044084           82 FFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEE---GMVEKTLEVVESMKN  158 (343)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~a~~~~~~~~~  158 (343)
                      .+++..+... .+...+..+..++.+.|++++|.+.+++..+.... +...+..+...+...   |+.++|.+.+++..+
T Consensus        79 ~~~~al~~~p-~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~  156 (568)
T 2vsy_A           79 LLQQASDAAP-EHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPE-EPYITAQLLNWRRRLCDWRALDVLSAQVRAAVA  156 (568)
T ss_dssp             HHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhhccccHHHHHHHHHHHHh
Confidence            7777776532 24566777777777777777777777777776543 566777777777777   777777777777766


Q ss_pred             cCC
Q 044084          159 AEL  161 (343)
Q Consensus       159 ~~~  161 (343)
                      .+.
T Consensus       157 ~~p  159 (568)
T 2vsy_A          157 QGV  159 (568)
T ss_dssp             HTC
T ss_pred             cCC
Confidence            654

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=99.12  E-value=3.5e-09  Score=93.93  Aligned_cols=154  Identities=14%  Similarity=0.019  Sum_probs=111.4

Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHH
Q 044084           35 IGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVA  114 (343)
Q Consensus        35 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  114 (343)
                      .|++++|.+.|++..+..    |.+...|..+...+...|++++|.+.+++..+... .+...+..+...+...|++++|
T Consensus         2 ~g~~~~A~~~~~~al~~~----p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A   76 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHR----PQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHP-GHPEAVARLGRVRWTQQRHAEA   76 (568)
T ss_dssp             -----------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTST-TCHHHHHHHHHHHHHTTCHHHH
T ss_pred             CccHHHHHHHHHHHHHhC----CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHCCCHHHH
Confidence            478888999888876654    33467888888999999999999999998887642 2567788888888899999999


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcC---CcHHHHHHHHHHH
Q 044084          115 EELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKR---RAYWAAVKVYEQL  191 (343)
Q Consensus       115 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~a~~~~~~~  191 (343)
                      ...+++..+.... +...+..+...|.+.|++++|.+.|++..+... .+...+..+..++...   |++++|.+.+++.
T Consensus        77 ~~~~~~al~~~p~-~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~a  154 (568)
T 2vsy_A           77 AVLLQQASDAAPE-HPGIALWLGHALEDAGQAEAAAAAYTRAHQLLP-EEPYITAQLLNWRRRLCDWRALDVLSAQVRAA  154 (568)
T ss_dssp             HHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhhccccHHHHHHHHHHH
Confidence            9999988887643 678888889999999999999999998887765 4566778888888888   8999999999988


Q ss_pred             HHcC
Q 044084          192 ISQG  195 (343)
Q Consensus       192 ~~~~  195 (343)
                      .+.+
T Consensus       155 l~~~  158 (568)
T 2vsy_A          155 VAQG  158 (568)
T ss_dssp             HHHT
T ss_pred             HhcC
Confidence            8774

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=99.10  E-value=1.1e-09  Score=81.40  Aligned_cols=156  Identities=10%  Similarity=0.059  Sum_probs=67.7

Q ss_pred             HHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHH-HhcCCc
Q 044084          102 ICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNG-FSKRRA  180 (343)
Q Consensus       102 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~  180 (343)
                      ...+...|++++|...+++..+..+. +...+..+...+...|++++|+..|++.....+  +...+...... +...+.
T Consensus        13 a~~~~~~g~~~~A~~~~~~al~~~P~-~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~p--~~~~~~~~~~~~~~~~~~   89 (176)
T 2r5s_A           13 VSELLQQGEHAQALNVIQTLSDELQS-RGDVKLAKADCLLETKQFELAQELLATIPLEYQ--DNSYKSLIAKLELHQQAA   89 (176)
T ss_dssp             HHHHHHTTCHHHHHHHHHTSCHHHHT-SHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGGC--CHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHHCCCHHHHHHHHHHhhhccC--ChHHHHHHHHHHHHhhcc
Confidence            33444445555555555444433221 344444455555555555555555544433322  11111111101 011111


Q ss_pred             HHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCc-ChhhHHHHHHHHHccCChHHHHHHHH
Q 044084          181 YWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDK-CVVAYSSMVAMYGKTGRIRDAMRLVA  259 (343)
Q Consensus       181 ~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~  259 (343)
                      ...+...+++..+.. +-+...+..+..++...|++++|...|+.+.+....+ +...+..+...+...|+.++|...|+
T Consensus        90 ~~~a~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y~  168 (176)
T 2r5s_A           90 ESPELKRLEQELAAN-PDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYR  168 (176)
T ss_dssp             SCHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHHH
T ss_pred             cchHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHHH
Confidence            122444455544432 1234444555555555555555555555555543211 23345555555555555555555555


Q ss_pred             HH
Q 044084          260 KM  261 (343)
Q Consensus       260 ~m  261 (343)
                      +.
T Consensus       169 ~a  170 (176)
T 2r5s_A          169 RQ  170 (176)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=99.08  E-value=1.8e-08  Score=82.05  Aligned_cols=200  Identities=8%  Similarity=-0.033  Sum_probs=141.2

Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHH
Q 044084           34 KIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKV  113 (343)
Q Consensus        34 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  113 (343)
                      ..|++++|.+++++..+.... .            .+...++++.|...|.+.               ...|...|++++
T Consensus         3 ~~~~~~eA~~~~~~a~k~~~~-~------------~~~~~~~~~~A~~~~~~a---------------~~~~~~~g~~~~   54 (307)
T 2ifu_A            3 AAQKISEAHEHIAKAEKYLKT-S------------FMKWKPDYDSAASEYAKA---------------AVAFKNAKQLEQ   54 (307)
T ss_dssp             CHHHHHHHHHHHHHHHHHHCC-C------------SSSCSCCHHHHHHHHHHH---------------HHHHHHTTCHHH
T ss_pred             ccchHHHHHHHHHHHHHHccc-c------------ccCCCCCHHHHHHHHHHH---------------HHHHHHcCCHHH
Confidence            356788888888887654321 0            011146777777777654               345667888999


Q ss_pred             HHHHHHHHHHcCCCC-----CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCC---CC--chhhHHHHHHHHhcCCcHHH
Q 044084          114 AEELFKEAEEKGMLR-----DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAEL---NI--SDCISCVIVNGFSKRRAYWA  183 (343)
Q Consensus       114 a~~~~~~~~~~~~~~-----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---~~--~~~~~~~l~~~~~~~~~~~~  183 (343)
                      |...+.+..+.....     -..+|+.+...|...|++++|+..|++..+...   .+  ...++..+...|.. |++++
T Consensus        55 A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~  133 (307)
T 2ifu_A           55 AKDAYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSK  133 (307)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHH
Confidence            988888776532111     145788888999999999999999988654311   11  13467778888888 99999


Q ss_pred             HHHHHHHHHHcCC---CC--CHhhHHHHHHHHHccCChhHHHHHHHHHHHc----CCCcC-hhhHHHHHHHHHccCChHH
Q 044084          184 AVKVYEQLISQGC---IP--GQVTYASIINAYCRIGLYSKAEKVFIEMQQK----GFDKC-VVAYSSMVAMYGKTGRIRD  253 (343)
Q Consensus       184 a~~~~~~~~~~~~---~p--~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~----~~~~~-~~~~~~l~~~~~~~~~~~~  253 (343)
                      |+..|++......   .+  ...++..+...|.+.|++++|...|++..+.    +..+. ...+..+..++...|++++
T Consensus       134 A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~  213 (307)
T 2ifu_A          134 AVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVA  213 (307)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHH
Confidence            9999998775410   11  1356778888999999999999999988764    11111 2356677778888899999


Q ss_pred             HHHHHHHHh
Q 044084          254 AMRLVAKMK  262 (343)
Q Consensus       254 a~~~~~~m~  262 (343)
                      |...|++..
T Consensus       214 A~~~~~~al  222 (307)
T 2ifu_A          214 AQKCVRESY  222 (307)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHHh
Confidence            999999988

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=99.05  E-value=2e-08  Score=81.73  Aligned_cols=190  Identities=12%  Similarity=0.011  Sum_probs=89.0

Q ss_pred             chhhHHHHHHHHHhCCC------CCC----hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC--CchHHHHHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGI------VLD----SGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLT--PSSTHMYKILCDS   69 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~------~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~~~~li~~   69 (343)
                      ++++|.+++++..+...      .++    ...|......|...|++++|...|.+..+......  .....+|+.+...
T Consensus         6 ~~~eA~~~~~~a~k~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~   85 (307)
T 2ifu_A            6 KISEAHEHIAKAEKYLKTSFMKWKPDYDSAASEYAKAAVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGMM   85 (307)
T ss_dssp             HHHHHHHHHHHHHHHHCCCSSSCSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHccccccCCCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            46788888887765311      122    11344555555556666666666555433211100  1112355555555


Q ss_pred             hhccCcHHHHHHHHHHHHhcC---CCCC--hHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCC-----CHHHHHHHHHH
Q 044084           70 LGKSGRAFEILKFFRDMKEKG---ILED--PSVYASLICSFASIAEVKVAEELFKEAEEKGMLR-----DLEVFLKLVLM  139 (343)
Q Consensus        70 ~~~~~~~~~a~~~~~~~~~~~---~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-----~~~~~~~l~~~  139 (343)
                      |...|++++|+..|++..+..   -.+.  ..++..+...|.. |++++|...+++..+.....     ...++..+...
T Consensus        86 ~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~  164 (307)
T 2ifu_A           86 LKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKASRL  164 (307)
T ss_dssp             HHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHH
Confidence            666666666666655544320   0111  2334444455555 55555555555544321110     12345555555


Q ss_pred             HHhcCcHhHHHHHHHHHHhcCC----CCc-hhhHHHHHHHHhcCCcHHHHHHHHHHHH
Q 044084          140 YIEEGMVEKTLEVVESMKNAEL----NIS-DCISCVIVNGFSKRRAYWAAVKVYEQLI  192 (343)
Q Consensus       140 ~~~~~~~~~a~~~~~~~~~~~~----~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~  192 (343)
                      |.+.|++++|+..|++......    .+. ...+..+..++...|++++|...|++..
T Consensus       165 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~al  222 (307)
T 2ifu_A          165 LVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRESY  222 (307)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            5555555555555555443211    000 1133334444444555555555555554

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=99.02  E-value=1.9e-06  Score=74.64  Aligned_cols=299  Identities=11%  Similarity=0.018  Sum_probs=175.8

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCC-HHHHHHHHHHHHhC-CCCCCCchHHHHHHHHHHhhc----cCc
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGD-SEKVAALFLECESR-KLDLTPSSTHMYKILCDSLGK----SGR   75 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~-~~~~~~~~~~~~~~li~~~~~----~~~   75 (343)
                      +.+.+..+|++....  .|+...|...+....+.++ .+....+|+..... |.  ++.+...|...+..+..    .++
T Consensus        29 ~~e~~~~iferal~~--~ps~~LW~~Y~~f~~~~~~~~~~i~~~fe~al~~vg~--d~~s~~iW~~Yi~f~~~~~~~~~~  104 (493)
T 2uy1_A           29 DYRSLESLFGRCLKK--SYNLDLWMLYIEYVRKVSQKKFKLYEVYEFTLGQFEN--YWDSYGLYKEYIEEEGKIEDEQTR  104 (493)
T ss_dssp             CHHHHHHHHHHHSTT--CCCHHHHHHHHHHHHHHC----CTHHHHHHHHHHSTT--CTTCHHHHHHHHHHTSSCSSHHHH
T ss_pred             CHHHHHHHHHHHhcc--CCCHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHcCC--CcccHHHHHHHHHHHHhchhhhHH
Confidence            578889999998884  4799999999988888774 45677788776653 32  23335789888887653    467


Q ss_pred             HHHHHHHHHHHHhcCCCCChHhHHHHHH--------------------------------------------HHhc--cc
Q 044084           76 AFEILKFFRDMKEKGILEDPSVYASLIC--------------------------------------------SFAS--IA  109 (343)
Q Consensus        76 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~--------------------------------------------~~~~--~~  109 (343)
                      .+.+.++|++.+......-...|.....                                            .|+.  .+
T Consensus       105 ~~~vR~iy~rAL~~P~~~~~~lw~~Y~~fE~~~~~~~~~~~~~~~~~~y~~ar~~y~~~~~~~~~~s~~~W~~y~~~E~~  184 (493)
T 2uy1_A          105 IEKIRNGYMRALQTPMGSLSELWKDFENFELELNKITGKKIVGDTLPIFQSSFQRYQQIQPLIRGWSVKNAARLIDLEME  184 (493)
T ss_dssp             HHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhChhhhHHHHHHHHHHHHHHhccccHHHHHHHHhHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHhc
Confidence            8889999999887321100111111110                                            0000  01


Q ss_pred             C---------HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCc
Q 044084          110 E---------VKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRA  180 (343)
Q Consensus       110 ~---------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  180 (343)
                      +         .+.+..+|+++....+ .+...|...+..+.+.|+.+.|..+|++....  +.+...|...... ...++
T Consensus       185 ~~~~~~~~~~~~Rv~~~ye~al~~~p-~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~--P~~~~l~~~y~~~-~e~~~  260 (493)
T 2uy1_A          185 NGMKLGGRPHESRMHFIHNYILDSFY-YAEEVYFFYSEYLIGIGQKEKAKKVVERGIEM--SDGMFLSLYYGLV-MDEEA  260 (493)
T ss_dssp             CTTCCCHHHHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCSSHHHHHHHHH-TTCTH
T ss_pred             CCccCcchhhHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC--CCcHHHHHHHHhh-cchhH
Confidence            0         2234456666665433 35667777777777778888888888877766  2333222221111 11111


Q ss_pred             HHHHHHHHHHHHHcC---------CCC---CHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHcc
Q 044084          181 YWAAVKVYEQLISQG---------CIP---GQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKT  248 (343)
Q Consensus       181 ~~~a~~~~~~~~~~~---------~~p---~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  248 (343)
                            +++.+.+.-         ..+   ....|...+....+.++.+.|..+|+.. +.. +.+...|...+..-...
T Consensus       261 ------~~~~l~~~~~~~~~~~~~~~~~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A-~~~-~~~~~v~i~~A~lE~~~  332 (493)
T 2uy1_A          261 ------VYGDLKRKYSMGEAESAEKVFSKELDLLRINHLNYVLKKRGLELFRKLFIEL-GNE-GVGPHVFIYCAFIEYYA  332 (493)
T ss_dssp             ------HHHHHHHHTC----------CHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH-TTS-CCCHHHHHHHHHHHHHH
T ss_pred             ------HHHHHHHHHHhhccchhhhhcccccHHHHHHHHHHHHHcCCHHHHHHHHHHh-hCC-CCChHHHHHHHHHHHHH
Confidence                  122222110         001   1234555556555677899999999988 321 22334444333222223


Q ss_pred             C-ChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh-----------HHHHHHHHHhcCCHHHHHHHHHHHH
Q 044084          249 G-RIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK-----------YTTVISAYNMAREFDMCVKFYNEFR  316 (343)
Q Consensus       249 ~-~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~-----------~~~l~~~~~~~g~~~~a~~~~~~m~  316 (343)
                      + +.+.|..+|+...+.- .-++..+...++...+.|+.+.|..           |...+.--...|+.+.+.++++++.
T Consensus       333 ~~d~~~ar~ife~al~~~-~~~~~~~~~yid~e~~~~~~~~aR~l~er~~k~~~lw~~~~~fE~~~G~~~~~r~v~~~~~  411 (493)
T 2uy1_A          333 TGSRATPYNIFSSGLLKH-PDSTLLKEEFFLFLLRIGDEENARALFKRLEKTSRMWDSMIEYEFMVGSMELFRELVDQKM  411 (493)
T ss_dssp             HCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHSCCBHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             CCChHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3 6899999999988752 2134455666777777888887764           6666666667799999988888875


Q ss_pred             h
Q 044084          317 M  317 (343)
Q Consensus       317 ~  317 (343)
                      +
T Consensus       412 ~  412 (493)
T 2uy1_A          412 D  412 (493)
T ss_dssp             H
T ss_pred             H
Confidence            3

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=99.01  E-value=1.9e-08  Score=70.02  Aligned_cols=103  Identities=10%  Similarity=0.087  Sum_probs=67.6

Q ss_pred             CchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHH
Q 044084           57 PSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKL  136 (343)
Q Consensus        57 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  136 (343)
                      |.....+......+.+.|++++|++.|++..+... .+...|..+..++.+.|++++|...+++.++..+. +...|..+
T Consensus        10 P~~a~~~~~~G~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~-~~~a~~~l   87 (126)
T 4gco_A           10 PELAQEEKNKGNEYFKKGDYPTAMRHYNEAVKRDP-ENAILYSNRAACLTKLMEFQRALDDCDTCIRLDSK-FIKGYIRK   87 (126)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhh-hhHHHHHH
Confidence            44455666666777777777777777777666532 24556666666777777777777777776665533 56667777


Q ss_pred             HHHHHhcCcHhHHHHHHHHHHhcCC
Q 044084          137 VLMYIEEGMVEKTLEVVESMKNAEL  161 (343)
Q Consensus       137 ~~~~~~~~~~~~a~~~~~~~~~~~~  161 (343)
                      ..+|...|++++|++.|++..+..+
T Consensus        88 g~~~~~~~~~~~A~~~~~~al~l~P  112 (126)
T 4gco_A           88 AACLVAMREWSKAQRAYEDALQVDP  112 (126)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHCc
Confidence            7777777777777777777666543

>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=98.99  E-value=8.6e-08  Score=73.28  Aligned_cols=127  Identities=9%  Similarity=0.039  Sum_probs=75.7

Q ss_pred             HHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 044084           63 YKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIE  142 (343)
Q Consensus        63 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  142 (343)
                      +..+...+...|++++|++.|++..    .|+...+..+...+...|++++|...+++..+... .+...+..+..+|..
T Consensus         9 ~~~~g~~~~~~~~~~~A~~~~~~a~----~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~-~~~~~~~~lg~~~~~   83 (213)
T 1hh8_A            9 LWNEGVLAADKKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDK-HLAVAYFQRGMLYYQ   83 (213)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHc----CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-cchHHHHHHHHHHHH
Confidence            3444555566666666666665542    34555666666666666666666666666666543 255666666666666


Q ss_pred             cCcHhHHHHHHHHHHhcCCCC---------------chhhHHHHHHHHhcCCcHHHHHHHHHHHHHc
Q 044084          143 EGMVEKTLEVVESMKNAELNI---------------SDCISCVIVNGFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       143 ~~~~~~a~~~~~~~~~~~~~~---------------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  194 (343)
                      .|++++|++.|++..+.....               ....+..+..++...|++++|...|++..+.
T Consensus        84 ~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  150 (213)
T 1hh8_A           84 TEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSM  150 (213)
T ss_dssp             TTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             cccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHc
Confidence            666666666666665543211               1134555666666666666666666666654

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=98.98  E-value=2.2e-07  Score=75.02  Aligned_cols=91  Identities=15%  Similarity=0.081  Sum_probs=39.9

Q ss_pred             HHHhhccCcHHHHHHHHHHHHhcCC-CCChH----hHHHHHHHHhcccCHHHHHHHHHHHHHcCCC-CC----HHHHHHH
Q 044084           67 CDSLGKSGRAFEILKFFRDMKEKGI-LEDPS----VYASLICSFASIAEVKVAEELFKEAEEKGML-RD----LEVFLKL  136 (343)
Q Consensus        67 i~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l  136 (343)
                      +..+...|++++|.+.+++...... .|+..    .+..+...+...+++++|...+++..+.... ++    ..+++.+
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            4445555555555555555544211 11110    1122333344444555555555555542111 11    2234555


Q ss_pred             HHHHHhcCcHhHHHHHHHHHH
Q 044084          137 VLMYIEEGMVEKTLEVVESMK  157 (343)
Q Consensus       137 ~~~~~~~~~~~~a~~~~~~~~  157 (343)
                      ...|...|++++|+..|+++.
T Consensus       162 g~~y~~~g~~~~A~~~~~~al  182 (293)
T 3u3w_A          162 ANIYAENGYLKKGIDLFEQIL  182 (293)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHH
Confidence            555555555555555555543

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=98.98  E-value=9.1e-08  Score=77.23  Aligned_cols=165  Identities=9%  Similarity=-0.029  Sum_probs=120.4

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCCCch---HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCC-CC----hHhHH
Q 044084           28 IMEAFYKIGDSEKVAALFLECESRKLDLTPSS---THMYKILCDSLGKSGRAFEILKFFRDMKEKGIL-ED----PSVYA   99 (343)
Q Consensus        28 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~   99 (343)
                      .+..+...|++++|..++++..+..... +..   ...+..+...+...+++++|+..|++....... ++    ..+++
T Consensus        81 ~i~~~~~~~~y~~a~~~~~~~l~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~  159 (293)
T 3u3w_A           81 QVIMLCKQKRYKEIYNKVWNELKKEEYH-PEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIEN  159 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTCCCC-HHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHH
T ss_pred             HHHHHHHHhhHHHHHHHHHHHhccccCC-hHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHH
Confidence            4677889999999999999987743221 111   123445777888889999999999999884322 22    23688


Q ss_pred             HHHHHHhcccCHHHHHHHHHHHHHc-----CCCC-CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhc----CCCC-chhhH
Q 044084          100 SLICSFASIAEVKVAEELFKEAEEK-----GMLR-DLEVFLKLVLMYIEEGMVEKTLEVVESMKNA----ELNI-SDCIS  168 (343)
Q Consensus       100 ~l~~~~~~~~~~~~a~~~~~~~~~~-----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~  168 (343)
                      .+...|...|+++.|...++++.+.     +..+ ...++..+...|.+.|++++|+..+++..+.    +..+ -..+|
T Consensus       160 ~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~  239 (293)
T 3u3w_A          160 AIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLY  239 (293)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHH
Confidence            8999999999999999999998841     1111 2447888899999999999999999887542    2111 14567


Q ss_pred             HHHHHHHhcCC-cHHHHHHHHHHHHH
Q 044084          169 CVIVNGFSKRR-AYWAAVKVYEQLIS  193 (343)
Q Consensus       169 ~~l~~~~~~~~-~~~~a~~~~~~~~~  193 (343)
                      ..+..++...| ++++|.+.+++...
T Consensus       240 ~~lg~~~~~~g~~~~~A~~~~~~Al~  265 (293)
T 3u3w_A          240 YQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCcHHHHHHHHHHHHH
Confidence            77888888888 46888888877654

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=98.98  E-value=7.6e-07  Score=72.51  Aligned_cols=226  Identities=11%  Similarity=0.029  Sum_probs=164.1

Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccC-cHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcc-
Q 044084           31 AFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSG-RAFEILKFFRDMKEKGILEDPSVYASLICSFASI-  108 (343)
Q Consensus        31 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-  108 (343)
                      ...+.+..++|+++++.+...+    |.+..+|+.--..+...+ .+++++++++.+.....+ +..+|+.-...+.+. 
T Consensus        63 ~~~~~e~se~AL~lt~~~L~~n----P~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~nPK-ny~aW~hR~wlL~~l~  137 (349)
T 3q7a_A           63 IAAKEEKSERALELTEIIVRMN----PAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQNLK-SYQVWHHRLLLLDRIS  137 (349)
T ss_dssp             HHHTTCCSHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTCC-CHHHHHHHHHHHHHHC
T ss_pred             HHHhCCCCHHHHHHHHHHHHhC----chhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHhc
Confidence            3444556678999999998876    334578888777777777 599999999999987544 667777766666665 


Q ss_pred             c-CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHh--------HHHHHHHHHHhcCCCCchhhHHHHHHHHhcCC
Q 044084          109 A-EVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVE--------KTLEVVESMKNAELNISDCISCVIVNGFSKRR  179 (343)
Q Consensus       109 ~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--------~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  179 (343)
                      + ++++++.+++.+.+...+ +..+|+.-...+.+.|.++        ++++.++++.+.++ -|...|+.....+.+.+
T Consensus       138 ~~~~~~EL~~~~k~L~~dpk-Ny~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp-~N~SAW~~R~~lL~~l~  215 (349)
T 3q7a_A          138 PQDPVSEIEYIHGSLLPDPK-NYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDG-RNNSAWGWRWYLRVSRP  215 (349)
T ss_dssp             CSCCHHHHHHHHHHTSSCTT-CHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHTTST
T ss_pred             CCChHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhcc
Confidence            6 788999999999887654 8888888777777777776        89999999998877 57778888777777776


Q ss_pred             c-------HHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCCh--------------------hHHHHHHHHHHHcC--
Q 044084          180 A-------YWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLY--------------------SKAEKVFIEMQQKG--  230 (343)
Q Consensus       180 ~-------~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~--------------------~~a~~~~~~~~~~~--  230 (343)
                      .       ++++++.+++..... +-|...|+-+-..+.+.|+.                    .........+...+  
T Consensus       216 ~~~~~~~~~~eELe~~~~aI~~~-P~n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  294 (349)
T 3q7a_A          216 GAETSSRSLQDELIYILKSIHLI-PHNVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDIETVEAFGFPMPSDPLP  294 (349)
T ss_dssp             TCCCCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC--------------CCCCC-CCC
T ss_pred             ccccchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCCcccccccccccccccccccchhHHHHHHHHHhcccc
Confidence            5       688888888888764 44666777666666655543                    12222222222211  


Q ss_pred             ---CCcChhhHHHHHHHHHccCChHHHHHHHHHHhhC
Q 044084          231 ---FDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       231 ---~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                         -.+.......+++.|...|+.++|.++++.+.+.
T Consensus       295 ~~~~~~s~~al~~l~d~~~~~~~~~~a~~~~~~l~~~  331 (349)
T 3q7a_A          295 EDTPLPVPLALEYLADSFIEQNRVDDAAKVFEKLSSE  331 (349)
T ss_dssp             SSCCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             cccCCCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhh
Confidence               1356778888999999999999999999998754

>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=98.96  E-value=1e-07  Score=72.87  Aligned_cols=126  Identities=13%  Similarity=-0.001  Sum_probs=78.0

Q ss_pred             HHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhc
Q 044084           98 YASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSK  177 (343)
Q Consensus        98 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  177 (343)
                      +..+...+...|++++|...+++..    .|+..++..+...|...|++++|+..|++...... .+...+..+..++..
T Consensus         9 ~~~~g~~~~~~~~~~~A~~~~~~a~----~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~-~~~~~~~~lg~~~~~   83 (213)
T 1hh8_A            9 LWNEGVLAADKKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDK-HLAVAYFQRGMLYYQ   83 (213)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHc----CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-cchHHHHHHHHHHHH
Confidence            3445556666677777777766552    45666777777777777777777777777666543 345566666667777


Q ss_pred             CCcHHHHHHHHHHHHHcCCCCCH----------------hhHHHHHHHHHccCChhHHHHHHHHHHHc
Q 044084          178 RRAYWAAVKVYEQLISQGCIPGQ----------------VTYASIINAYCRIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       178 ~~~~~~a~~~~~~~~~~~~~p~~----------------~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  229 (343)
                      .|++++|...|++..+... .+.                ..+..+..+|...|++++|...|+...+.
T Consensus        84 ~~~~~~A~~~~~~al~~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  150 (213)
T 1hh8_A           84 TEKYDLAIKDLKEALIQLR-GNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSM  150 (213)
T ss_dssp             TTCHHHHHHHHHHHHHTTT-TCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             cccHHHHHHHHHHHHHhCC-CccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHc
Confidence            7777777777777666421 111                34455555566666666666666665554

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.95  E-value=2.7e-08  Score=71.42  Aligned_cols=102  Identities=15%  Similarity=0.040  Sum_probs=67.4

Q ss_pred             CchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHH
Q 044084           57 PSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKL  136 (343)
Q Consensus        57 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  136 (343)
                      |.+...+..+...+.+.|++++|+..|++...... .+...|..+..++...|++++|...|++..+..+. ++..|..+
T Consensus        33 p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~P-~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P~-~~~~~~~l  110 (151)
T 3gyz_A           33 DDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDF-YNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKN-DYTPVFHT  110 (151)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSS-CCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCCC-CcHHHHHH
Confidence            44456666666777777777777777777766532 24556666666777777777777777777665543 56666667


Q ss_pred             HHHHHhcCcHhHHHHHHHHHHhcC
Q 044084          137 VLMYIEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus       137 ~~~~~~~~~~~~a~~~~~~~~~~~  160 (343)
                      ..+|...|++++|+..|++..+..
T Consensus       111 g~~~~~lg~~~eA~~~~~~al~l~  134 (151)
T 3gyz_A          111 GQCQLRLKAPLKAKECFELVIQHS  134 (151)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC
Confidence            777777777777777777766554

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=98.91  E-value=2.4e-08  Score=80.08  Aligned_cols=195  Identities=7%  Similarity=-0.052  Sum_probs=108.9

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLM  139 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  139 (343)
                      ...+..+...+...|++++|+..|++...... .+...|..+..++.+.|++++|...+++..+.... +...+..+..+
T Consensus         4 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~lg~~   81 (281)
T 2c2l_A            4 AQELKEQGNRLFVGRKYPEAAACYGRAITRNP-LVAVYYTNRALCYLKMQQPEQALADCRRALELDGQ-SVKAHFFLGQC   81 (281)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCS-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTT-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-CHHHHHHHHHH
Confidence            45666667777777777777777777766532 25566667777777777777777777777765432 56777777777


Q ss_pred             HHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHH
Q 044084          140 YIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKA  219 (343)
Q Consensus       140 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a  219 (343)
                      |...|++++|...|++..+.++. +...+...+....+   ..... -+........+.+..... .+..+. .|+.++|
T Consensus        82 ~~~~g~~~~A~~~~~~al~l~p~-~~~~~~~~~~~~~~---~~~~~-~~~~~~~~~~~~~~~i~~-~l~~l~-~~~~~~A  154 (281)
T 2c2l_A           82 QLEMESYDEAIANLQRAYSLAKE-QRLNFGDDIPSALR---IAKKK-RWNSIEERRIHQESELHS-YLTRLI-AAERERE  154 (281)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHH-TTCCCCSHHHHHHH---HHHHH-HHHHHHHTCCCCCCHHHH-HHHHHH-HHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhCcc-chhhHHHHHHHHHH---HHHHH-HHHHHHHHHHhhhHHHHH-HHHHHH-HHHHHHH
Confidence            88888888888877776554321 11111111111111   11111 112222222233333322 233222 5777777


Q ss_pred             HHHHHHHHHcCCCcChhhHHHHHHHHHcc-CChHHHHHHHHHHhhC
Q 044084          220 EKVFIEMQQKGFDKCVVAYSSMVAMYGKT-GRIRDAMRLVAKMKPK  264 (343)
Q Consensus       220 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~a~~~~~~m~~~  264 (343)
                      .+.++...+.. +.+......+...+.+. +.+++|.++|.++.+.
T Consensus       155 ~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~~~  199 (281)
T 2c2l_A          155 LEECQRNHEGH-EDDGHIRAQQACIEAKHDKYMADMDELFSQVDEK  199 (281)
T ss_dssp             HTTTSGGGTTT-SCHHHHTHHHHHHHHHHHHHHHHHHHHHHHSSCT
T ss_pred             HHHHHhhhccc-cchhhhhhHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence            77777666543 22333333444444444 5577788888777653

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=98.91  E-value=1.3e-07  Score=69.05  Aligned_cols=127  Identities=13%  Similarity=0.058  Sum_probs=61.9

Q ss_pred             HHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 044084           62 MYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYI  141 (343)
Q Consensus        62 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  141 (343)
                      .|..+...+...|++++|...|++..+.. +.+..++..+...+...|++++|...+++..+... .+...+..+...+.
T Consensus        15 ~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~~a~~~~   92 (166)
T 1a17_A           15 ELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDK-KYIKGYYRRAASNM   92 (166)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-ccHHHHHHHHHHHH
Confidence            34445555555555555555555555432 11344455555555555555555555555555432 24455555555555


Q ss_pred             hcCcHhHHHHHHHHHHhcCCCCchhhHH--HHHHHHhcCCcHHHHHHHHHHH
Q 044084          142 EEGMVEKTLEVVESMKNAELNISDCISC--VIVNGFSKRRAYWAAVKVYEQL  191 (343)
Q Consensus       142 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~--~l~~~~~~~~~~~~a~~~~~~~  191 (343)
                      ..|++++|...|++.....+ .+...+.  .....+...|++++|...+...
T Consensus        93 ~~~~~~~A~~~~~~a~~~~p-~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~  143 (166)
T 1a17_A           93 ALGKFRAALRDYETVVKVKP-HDKDAKMKYQECNKIVKQKAFERAIAGDEHK  143 (166)
T ss_dssp             HTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhccHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHHHHHHHHHHHcccch
Confidence            55555555555555554432 1222221  1222244445555555555443

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=98.90  E-value=1.1e-07  Score=69.48  Aligned_cols=126  Identities=9%  Similarity=-0.054  Sum_probs=56.5

Q ss_pred             HHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHc
Q 044084          133 FLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCR  212 (343)
Q Consensus       133 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~  212 (343)
                      +..+...+...|++++|...|++..+... .+..++..+..++...|++++|...+++..+.. +.+...+..+..++..
T Consensus        16 ~~~~a~~~~~~~~~~~A~~~~~~al~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~   93 (166)
T 1a17_A           16 LKTQANDYFKAKDYENAIKFYSQAIELNP-SNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMA   93 (166)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHhCC-CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHH
Confidence            34444444445555555555554444332 233344444444455555555555555544432 2233444444455555


Q ss_pred             cCChhHHHHHHHHHHHcCCCcChhhHH--HHHHHHHccCChHHHHHHHHHH
Q 044084          213 IGLYSKAEKVFIEMQQKGFDKCVVAYS--SMVAMYGKTGRIRDAMRLVAKM  261 (343)
Q Consensus       213 ~~~~~~a~~~~~~~~~~~~~~~~~~~~--~l~~~~~~~~~~~~a~~~~~~m  261 (343)
                      .|++++|...++...+.. +.+...+.  ..+..+...|++++|...+...
T Consensus        94 ~~~~~~A~~~~~~a~~~~-p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~  143 (166)
T 1a17_A           94 LGKFRAALRDYETVVKVK-PHDKDAKMKYQECNKIVKQKAFERAIAGDEHK  143 (166)
T ss_dssp             TTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHHHHcccch
Confidence            555555555555554432 12222222  2222244445555555554443

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=98.89  E-value=9.2e-07  Score=72.01  Aligned_cols=219  Identities=9%  Similarity=-0.007  Sum_probs=162.2

Q ss_pred             hhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcC-CHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhcc-C-cHHHH
Q 044084            3 SQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIG-DSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKS-G-RAFEI   79 (343)
Q Consensus         3 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~-~-~~~~a   79 (343)
                      .++|+++++.++..++ -+..+|+.--.++...| .+++++++++.+...+.    .+..+|+.-...+... + +++++
T Consensus        70 se~AL~lt~~~L~~nP-~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~nP----Kny~aW~hR~wlL~~l~~~~~~~E  144 (349)
T 3q7a_A           70 SERALELTEIIVRMNP-AHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQNL----KSYQVWHHRLLLLDRISPQDPVSE  144 (349)
T ss_dssp             SHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTC----CCHHHHHHHHHHHHHHCCSCCHHH
T ss_pred             CHHHHHHHHHHHHhCc-hhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCC----CcHHHHHHHHHHHHHhcCCChHHH
Confidence            3679999999998654 35556888888888888 59999999999988763    3468888877777666 6 88999


Q ss_pred             HHHHHHHHhcCCCCChHhHHHHHHHHhcccCHH--------HHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCc------
Q 044084           80 LKFFRDMKEKGILEDPSVYASLICSFASIAEVK--------VAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGM------  145 (343)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--------~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~------  145 (343)
                      +++++++.+...+ |..+|+.-.-.+.+.+.++        ++++.++++.+..+. |...|+.....+.+.++      
T Consensus       145 L~~~~k~L~~dpk-Ny~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp~-N~SAW~~R~~lL~~l~~~~~~~~  222 (349)
T 3q7a_A          145 IEYIHGSLLPDPK-NYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDGR-NNSAWGWRWYLRVSRPGAETSSR  222 (349)
T ss_dssp             HHHHHHHTSSCTT-CHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHTTSTTCCCCHH
T ss_pred             HHHHHHHHHhCCC-CHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhccccccchH
Confidence            9999999987543 6777776665665555555        889999999998765 89999998888888776      


Q ss_pred             -HhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcH--------------------HHHHHHHHHHHHcC-----CCCC
Q 044084          146 -VEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAY--------------------WAAVKVYEQLISQG-----CIPG  199 (343)
Q Consensus       146 -~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--------------------~~a~~~~~~~~~~~-----~~p~  199 (343)
                       ++++++.+++.....+ -|...|+-+-..+.+.|..                    ........++...+     -.++
T Consensus       223 ~~~eELe~~~~aI~~~P-~n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s  301 (349)
T 3q7a_A          223 SLQDELIYILKSIHLIP-HNVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDIETVEAFGFPMPSDPLPEDTPLPV  301 (349)
T ss_dssp             HHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC--------------CCCCC-CCCSSCCSCC
T ss_pred             HHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhcCCCcccccccccccccccccccchhHHHHHHHHHhcccccccCCCc
Confidence             6889999999888776 5777787665555554443                    22333333332221     1356


Q ss_pred             HhhHHHHHHHHHccCChhHHHHHHHHHHHc
Q 044084          200 QVTYASIINAYCRIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       200 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  229 (343)
                      ...+..++..|...|+.++|.++++.+.+.
T Consensus       302 ~~al~~l~d~~~~~~~~~~a~~~~~~l~~~  331 (349)
T 3q7a_A          302 PLALEYLADSFIEQNRVDDAAKVFEKLSSE  331 (349)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhh
Confidence            777888999999999999999999998754

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.88  E-value=1.4e-07  Score=65.99  Aligned_cols=100  Identities=11%  Similarity=0.115  Sum_probs=55.9

Q ss_pred             hHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 044084           59 STHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVL  138 (343)
Q Consensus        59 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  138 (343)
                      +...|..+...+...|++++|++.|++..+.. +.+...+..+...+...|++++|...+++..+.... +...+..+..
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~la~   92 (133)
T 2lni_A           15 LALMVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQLEPT-FIKGYTRKAA   92 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCC-chHHHHHHHH
Confidence            34555555556666666666666666555442 113445555555555666666666666655554322 4555555666


Q ss_pred             HHHhcCcHhHHHHHHHHHHhcC
Q 044084          139 MYIEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus       139 ~~~~~~~~~~a~~~~~~~~~~~  160 (343)
                      .+...|++++|.+.|++..+..
T Consensus        93 ~~~~~~~~~~A~~~~~~~~~~~  114 (133)
T 2lni_A           93 ALEAMKDYTKAMDVYQKALDLD  114 (133)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHhhHHHHHHHHHHHHHhC
Confidence            6666666666666666555443

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.88  E-value=1.2e-07  Score=65.83  Aligned_cols=94  Identities=11%  Similarity=0.038  Sum_probs=38.7

Q ss_pred             HHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHc
Q 044084          133 FLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCR  212 (343)
Q Consensus       133 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~  212 (343)
                      +......|.+.|++++|++.|++..+.++ .+...|..+..++...|++++|+..+++..+.. +.+...|..+..++..
T Consensus        16 ~~~~G~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~   93 (126)
T 4gco_A           16 EKNKGNEYFKKGDYPTAMRHYNEAVKRDP-ENAILYSNRAACLTKLMEFQRALDDCDTCIRLD-SKFIKGYIRKAACLVA   93 (126)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhh-hhhhHHHHHHHHHHHH
Confidence            33334444444444444444444443332 233334444444444444444444444444332 1223334444444444


Q ss_pred             cCChhHHHHHHHHHHH
Q 044084          213 IGLYSKAEKVFIEMQQ  228 (343)
Q Consensus       213 ~~~~~~a~~~~~~~~~  228 (343)
                      .|++++|...|+...+
T Consensus        94 ~~~~~~A~~~~~~al~  109 (126)
T 4gco_A           94 MREWSKAQRAYEDALQ  109 (126)
T ss_dssp             TTCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            4444444444444444

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.88  E-value=2.3e-06  Score=68.92  Aligned_cols=159  Identities=13%  Similarity=0.019  Sum_probs=101.9

Q ss_pred             HHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCch-----hhHHHHHHHHhcCCcHHHHHHHHHHHHHcCC---CCC--H
Q 044084          131 EVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISD-----CISCVIVNGFSKRRAYWAAVKVYEQLISQGC---IPG--Q  200 (343)
Q Consensus       131 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---~p~--~  200 (343)
                      ..+...+..+...|++++|.+.+++..+.....+.     ..+..+...+...|++++|...+++......   .+.  .
T Consensus        76 ~~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~  155 (293)
T 2qfc_A           76 KQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNL  155 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHH
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHH
Confidence            34555667777888888888888776654332111     1233455566777888888888888765321   111  3


Q ss_pred             hhHHHHHHHHHccCChhHHHHHHHHHHH---cC-CCc--ChhhHHHHHHHHHccCChHHHHHHHHHHhhCC----CC-ch
Q 044084          201 VTYASIINAYCRIGLYSKAEKVFIEMQQ---KG-FDK--CVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKG----CE-PN  269 (343)
Q Consensus       201 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~---~~-~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~----~~-p~  269 (343)
                      .+++.+...|...|++++|...+++..+   .. -.+  ...++..+...|...|++++|...+++..+..    .. .-
T Consensus       156 ~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~  235 (293)
T 2qfc_A          156 YIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALI  235 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHH
Confidence            4677778888888888888888888763   21 111  12577788888888888888888888876431    00 01


Q ss_pred             HHHHHHHHHHHhcccChhHH
Q 044084          270 VWIYNSLMDMHGRAKNLRQL  289 (343)
Q Consensus       270 ~~~~~~l~~~~~~~~~~~~a  289 (343)
                      ..+|..+..+|.+.|+.++|
T Consensus       236 ~~~~~~lg~~y~~~g~~~~A  255 (293)
T 2qfc_A          236 GQLYYQRGECLRKLEYEEAE  255 (293)
T ss_dssp             HHHHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHHHHcCCcHHH
Confidence            45556666666666666665

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.88  E-value=1.6e-07  Score=64.63  Aligned_cols=95  Identities=16%  Similarity=0.234  Sum_probs=38.3

Q ss_pred             HHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHH
Q 044084          132 VFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYC  211 (343)
Q Consensus       132 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~  211 (343)
                      .+..+...+...|++++|.+.++++..... .+..++..+...+...|++++|...++++.+.. +.+..++..+...+.
T Consensus        11 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~   88 (125)
T 1na0_A           11 AWYNLGNAYYKQGDYDEAIEYYQKALELDP-NNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYY   88 (125)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCc-CcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHH
Confidence            333444444444444444444444433322 222333344444444444444444444443331 122333334444444


Q ss_pred             ccCChhHHHHHHHHHHH
Q 044084          212 RIGLYSKAEKVFIEMQQ  228 (343)
Q Consensus       212 ~~~~~~~a~~~~~~~~~  228 (343)
                      ..|++++|...++.+.+
T Consensus        89 ~~~~~~~A~~~~~~~~~  105 (125)
T 1na0_A           89 KQGDYDEAIEYYQKALE  105 (125)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHH
Confidence            44444444444444443

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.86  E-value=2.2e-07  Score=75.02  Aligned_cols=166  Identities=10%  Similarity=-0.029  Sum_probs=94.9

Q ss_pred             hHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCC-----HHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCC---Cc--hh
Q 044084           97 VYASLICSFASIAEVKVAEELFKEAEEKGMLRD-----LEVFLKLVLMYIEEGMVEKTLEVVESMKNAELN---IS--DC  166 (343)
Q Consensus        97 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~--~~  166 (343)
                      .+...+..+...|++++|...+.+..+......     ...+..+...+...|++++|+..+++.......   +.  ..
T Consensus        77 ~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~  156 (293)
T 2qfc_A           77 QFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLY  156 (293)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHH
Confidence            344455556666667777666666655432211     122334555566666777777777766542211   11  23


Q ss_pred             hHHHHHHHHhcCCcHHHHHHHHHHHHH---cC-CCC--CHhhHHHHHHHHHccCChhHHHHHHHHHHHcC----CCc-Ch
Q 044084          167 ISCVIVNGFSKRRAYWAAVKVYEQLIS---QG-CIP--GQVTYASIINAYCRIGLYSKAEKVFIEMQQKG----FDK-CV  235 (343)
Q Consensus       167 ~~~~l~~~~~~~~~~~~a~~~~~~~~~---~~-~~p--~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~----~~~-~~  235 (343)
                      +++.+...|...|++++|...+++..+   .. ..+  ...++..+...|...|++++|...+++..+..    ... -.
T Consensus       157 ~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~  236 (293)
T 2qfc_A          157 IENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIG  236 (293)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHH
Confidence            566667777777777777777776652   11 111  11466666777777777777777777665431    001 14


Q ss_pred             hhHHHHHHHHHccCChHHH-HHHHHHHh
Q 044084          236 VAYSSMVAMYGKTGRIRDA-MRLVAKMK  262 (343)
Q Consensus       236 ~~~~~l~~~~~~~~~~~~a-~~~~~~m~  262 (343)
                      .+|..+..+|.+.|++++| ...+++..
T Consensus       237 ~~~~~lg~~y~~~g~~~~Ai~~~~~~Al  264 (293)
T 2qfc_A          237 QLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence            5666777777777777777 55565544

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.86  E-value=1.6e-07  Score=65.60  Aligned_cols=116  Identities=12%  Similarity=0.006  Sum_probs=63.2

Q ss_pred             CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHH
Q 044084          129 DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIIN  208 (343)
Q Consensus       129 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~  208 (343)
                      +...+..+...+...|++++|...|++..+... .+...+..+..++...|++++|...+++..+.. +.+...+..+..
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~-~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~   92 (133)
T 2lni_A           15 LALMVKNKGNECFQKGDYPQAMKHYTEAIKRNP-KDAKLYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTRKAA   92 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTCT-TCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC-CcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHHHHH
Confidence            345555566666666666666666666555433 234455555566666666666666666655542 223445555555


Q ss_pred             HHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHc
Q 044084          209 AYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGK  247 (343)
Q Consensus       209 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  247 (343)
                      ++...|++++|...|+...+.. +.+...+..+..++..
T Consensus        93 ~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~  130 (133)
T 2lni_A           93 ALEAMKDYTKAMDVYQKALDLD-SSCKEAADGYQRCMMA  130 (133)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-GGGTHHHHHHHHHHHH
T ss_pred             HHHHHhhHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHH
Confidence            5666666666666666655543 2233444444444443

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.84  E-value=6.2e-08  Score=73.41  Aligned_cols=133  Identities=7%  Similarity=-0.027  Sum_probs=56.3

Q ss_pred             HHHHHHHHHHHHhcCcHhHHHHHHHHHHhc----CC-CCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHc----CCCC--
Q 044084          130 LEVFLKLVLMYIEEGMVEKTLEVVESMKNA----EL-NISDCISCVIVNGFSKRRAYWAAVKVYEQLISQ----GCIP--  198 (343)
Q Consensus       130 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~p--  198 (343)
                      ..++..+...+...|++++|...+++....    +. +....++..+...+...|++++|...+++..+.    +-.|  
T Consensus        26 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  105 (203)
T 3gw4_A           26 SGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNWDAARRCFLEERELLASLPEDPLA  105 (203)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHH
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCccHHH
Confidence            344444444444555555555544443321    00 011223444444444555555555554443332    1011  


Q ss_pred             CHhhHHHHHHHHHccCChhHHHHHHHHHHHc----CCC-cChhhHHHHHHHHHccCChHHHHHHHHHHh
Q 044084          199 GQVTYASIINAYCRIGLYSKAEKVFIEMQQK----GFD-KCVVAYSSMVAMYGKTGRIRDAMRLVAKMK  262 (343)
Q Consensus       199 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~  262 (343)
                      ....+..+...+...|++++|...+++..+.    +.+ .-..++..+...+...|++++|.+.+++..
T Consensus       106 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  174 (203)
T 3gw4_A          106 ASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEKNLLEAQQHWLRAR  174 (203)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence            1123344444455555555555555544321    100 001223445555555555555555555444

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=98.84  E-value=5.8e-08  Score=71.95  Aligned_cols=120  Identities=9%  Similarity=0.096  Sum_probs=60.6

Q ss_pred             ccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH-HHhcCcH--hH
Q 044084           72 KSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLM-YIEEGMV--EK  148 (343)
Q Consensus        72 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~--~~  148 (343)
                      ..|++++|+..+++..... +.+...+..+...+...|++++|...+++..+..+. +...+..+... +...|++  ++
T Consensus        22 ~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~la~~l~~~~~~~~~~~   99 (177)
T 2e2e_A           22 SQQNPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLRGE-NAELYAALATVLYYQASQHMTAQ   99 (177)
T ss_dssp             -----CCCCHHHHHHHHHC-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHCS-CHHHHHHHHHHHHHHTTTCCCHH
T ss_pred             hccCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHhcCCcchHH
Confidence            3455555555555554432 123445555555555555555555555555554322 44555555555 4555555  55


Q ss_pred             HHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHc
Q 044084          149 TLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       149 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  194 (343)
                      |...|++.....+ .+...+..+...+...|++++|...|+++.+.
T Consensus       100 A~~~~~~al~~~p-~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  144 (177)
T 2e2e_A          100 TRAMIDKALALDS-NEITALMLLASDAFMQANYAQAIELWQKVMDL  144 (177)
T ss_dssp             HHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhCC-CcHHHHHHHHHHHHHcccHHHHHHHHHHHHhh
Confidence            6666555555443 23344555555555556666666665555554

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.84  E-value=1.7e-07  Score=65.19  Aligned_cols=96  Identities=13%  Similarity=0.027  Sum_probs=40.4

Q ss_pred             HHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHH
Q 044084          132 VFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYC  211 (343)
Q Consensus       132 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~  211 (343)
                      .+..+...+...|++++|...|++...... .+...+..+...+...|++++|...+++..+.. +.+...+..+...+.
T Consensus        14 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~   91 (131)
T 2vyi_A           14 RLKTEGNEQMKVENFEAAVHFYGKAIELNP-ANAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGRMGLALS   91 (131)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHHHHHHHH
Confidence            334444444444444444444444443322 223334444444444444444444444444331 122333444444444


Q ss_pred             ccCChhHHHHHHHHHHHc
Q 044084          212 RIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       212 ~~~~~~~a~~~~~~~~~~  229 (343)
                      ..|++++|...++...+.
T Consensus        92 ~~~~~~~A~~~~~~~~~~  109 (131)
T 2vyi_A           92 SLNKHVEAVAYYKKALEL  109 (131)
T ss_dssp             HTTCHHHHHHHHHHHHHH
T ss_pred             HhCCHHHHHHHHHHHHhc
Confidence            444444444444444443

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.84  E-value=2.3e-07  Score=70.19  Aligned_cols=164  Identities=11%  Similarity=0.064  Sum_probs=106.6

Q ss_pred             HhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHc----CCCC-CHhhHHHHHHHHHccCC
Q 044084          141 IEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQ----GCIP-GQVTYASIINAYCRIGL  215 (343)
Q Consensus       141 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~p-~~~~~~~ll~~~~~~~~  215 (343)
                      ...|++++|.++++.+.. .......++..+...+...|++++|...+++....    +..| ...++..+...+...|+
T Consensus         3 ~~~g~~~~A~~~~~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~   81 (203)
T 3gw4_A            3 FEAHDYALAERQAQALLA-HPATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGN   81 (203)
T ss_dssp             ----CHHHHHHHHHHHHT-STTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             cccccHHHHHHHHHHhcC-ChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCC
Confidence            467889999996655543 22245667888999999999999999999998762    2222 34567778888999999


Q ss_pred             hhHHHHHHHHHHHc----CCC--cChhhHHHHHHHHHccCChHHHHHHHHHHhhCC---CCch--HHHHHHHHHHHhccc
Q 044084          216 YSKAEKVFIEMQQK----GFD--KCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKG---CEPN--VWIYNSLMDMHGRAK  284 (343)
Q Consensus       216 ~~~a~~~~~~~~~~----~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~---~~p~--~~~~~~l~~~~~~~~  284 (343)
                      +++|...+++..+.    +-.  .....+..+...+...|++++|...+++..+..   -.+.  ..++..+...+...|
T Consensus        82 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g  161 (203)
T 3gw4_A           82 WDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEK  161 (203)
T ss_dssp             HHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCc
Confidence            99999999987764    211  124567888899999999999999998876421   0111  122344444455555


Q ss_pred             ChhHHHh-HHHHHHHHHhcCCH
Q 044084          285 NLRQLEK-YTTVISAYNMAREF  305 (343)
Q Consensus       285 ~~~~a~~-~~~l~~~~~~~g~~  305 (343)
                      ++++|.. +...+..+.+.|+.
T Consensus       162 ~~~~A~~~~~~al~~~~~~~~~  183 (203)
T 3gw4_A          162 NLLEAQQHWLRARDIFAELEDS  183 (203)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCH
T ss_pred             CHHHHHHHHHHHHHHHHHcCCH
Confidence            5554444 33333333333333

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.83  E-value=2.6e-07  Score=63.58  Aligned_cols=98  Identities=15%  Similarity=0.222  Sum_probs=52.5

Q ss_pred             HHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 044084           61 HMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMY  140 (343)
Q Consensus        61 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  140 (343)
                      ..|..+...+...|++++|.+.++++.... +.+..++..+...+...|++++|...++++.+... .+..++..+...+
T Consensus        10 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~la~~~   87 (125)
T 1na0_A           10 EAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDP-NNAEAWYNLGNAY   87 (125)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCC-ccHHHHHHHHHHH
Confidence            455555555566666666666666555442 12344455555555555555555555555555432 2445555555555


Q ss_pred             HhcCcHhHHHHHHHHHHhcC
Q 044084          141 IEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus       141 ~~~~~~~~a~~~~~~~~~~~  160 (343)
                      ...|++++|...|+++.+..
T Consensus        88 ~~~~~~~~A~~~~~~~~~~~  107 (125)
T 1na0_A           88 YKQGDYDEAIEYYQKALELD  107 (125)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC
T ss_pred             HHhcCHHHHHHHHHHHHHhC
Confidence            55555555555555554443

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=98.83  E-value=5.2e-08  Score=72.20  Aligned_cols=121  Identities=7%  Similarity=0.004  Sum_probs=61.6

Q ss_pred             hcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHH-HhcCCcH--H
Q 044084          106 ASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNG-FSKRRAY--W  182 (343)
Q Consensus       106 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~--~  182 (343)
                      ...|++++|...++...+..+. +...+..+...|...|++++|...|++..+..+ .+...+..+..+ +...|++  +
T Consensus        21 ~~~~~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~la~~l~~~~~~~~~~   98 (177)
T 2e2e_A           21 ASQQNPEAQLQALQDKIRANPQ-NSEQWALLGEYYLWQNDYSNSLLAYRQALQLRG-ENAELYAALATVLYYQASQHMTA   98 (177)
T ss_dssp             C-----CCCCHHHHHHHHHCCS-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHC-SCHHHHHHHHHHHHHHTTTCCCH
T ss_pred             hhccCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHhcCCcchH
Confidence            3445566666666665554432 455666666666666666666666666555443 233344444444 4455555  5


Q ss_pred             HHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHc
Q 044084          183 AAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       183 ~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  229 (343)
                      +|...+++..+.. +.+...+..+...|...|++++|...|+...+.
T Consensus        99 ~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  144 (177)
T 2e2e_A           99 QTRAMIDKALALD-SNEITALMLLASDAFMQANYAQAIELWQKVMDL  144 (177)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhh
Confidence            5555555555442 223344444555555555555555555555554

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.82  E-value=2.7e-07  Score=66.21  Aligned_cols=97  Identities=11%  Similarity=0.058  Sum_probs=69.8

Q ss_pred             HhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHH
Q 044084           96 SVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGF  175 (343)
Q Consensus        96 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  175 (343)
                      ..+..+...+.+.|++++|...|+++.+..+. +...|..+..+|...|++++|+..|++.....+ .+...|..+..+|
T Consensus        37 ~~~~~lg~~~~~~g~~~eA~~~~~~al~~~P~-~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P-~~~~~~~~lg~~~  114 (151)
T 3gyz_A           37 DDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFY-NVDYIMGLAAIYQIKEQFQQAADLYAVAFALGK-NDYTPVFHTGQCQ  114 (151)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSS-SCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCC-CCcHHHHHHHHHH
Confidence            35556666777777777777777777776543 677777777777777777777777777776665 3455677777777


Q ss_pred             hcCCcHHHHHHHHHHHHHc
Q 044084          176 SKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       176 ~~~~~~~~a~~~~~~~~~~  194 (343)
                      ...|++++|...|++..+.
T Consensus       115 ~~lg~~~eA~~~~~~al~l  133 (151)
T 3gyz_A          115 LRLKAPLKAKECFELVIQH  133 (151)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHh
Confidence            7777777777777777765

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=98.82  E-value=1.6e-07  Score=77.41  Aligned_cols=123  Identities=11%  Similarity=-0.057  Sum_probs=67.5

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCC--------------hHhHHHHHHHHhcccCHHHHHHHHHHHHHcC
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEKGILED--------------PSVYASLICSFASIAEVKVAEELFKEAEEKG  125 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~--------------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  125 (343)
                      ...|..+...+.+.|++++|+..|++..+......              ...|..+..++.+.|++++|...+++..+..
T Consensus       147 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~  226 (336)
T 1p5q_A          147 STIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD  226 (336)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            45666667777777777777777777666532211              2445555555555555555555555555544


Q ss_pred             CCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHH
Q 044084          126 MLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAA  184 (343)
Q Consensus       126 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  184 (343)
                      +. +...+..+..+|...|++++|+..|++..+..+ .+...+..+..++...|+.+++
T Consensus       227 p~-~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P-~~~~a~~~l~~~~~~~~~~~~a  283 (336)
T 1p5q_A          227 SN-NEKGLSRRGEAHLAVNDFELARADFQKVLQLYP-NNKAAKTQLAVCQQRIRRQLAR  283 (336)
T ss_dssp             TT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCS-SCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CC-cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHH
Confidence            32 455555555555555555555555555554443 2334444555555555555544

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=98.81  E-value=1.4e-05  Score=64.73  Aligned_cols=132  Identities=10%  Similarity=0.001  Sum_probs=64.2

Q ss_pred             hhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCC----------HHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhcc
Q 044084            4 QSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGD----------SEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKS   73 (343)
Q Consensus         4 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~   73 (343)
                      ++|+.+++.++..++ -+..+|+.--..+...+.          +++++.+++.+...+    |.+..+|+.-...+...
T Consensus        47 ~eaL~~t~~~L~~nP-~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~----PKny~aW~hR~wlL~~l  121 (331)
T 3dss_A           47 ESVLELTSQILGANP-DFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN----PKSYGTWHHRCWLLSRL  121 (331)
T ss_dssp             HHHHHHHHHHHTTCT-TCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHCc-hhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhC----CCCHHHHHHHHHHHhcc
Confidence            355666666665432 122334443333333222          455555555555443    22235555544444444


Q ss_pred             C--cHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccC-HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 044084           74 G--RAFEILKFFRDMKEKGILEDPSVYASLICSFASIAE-VKVAEELFKEAEEKGMLRDLEVFLKLVLMYIE  142 (343)
Q Consensus        74 ~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  142 (343)
                      +  .+++++++++++.+.... |...|+.-.-.+...|. ++++++.++.+.+..+. |...|+.....+..
T Consensus       122 ~~~~~~~EL~~~~k~l~~dpr-Ny~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~p~-N~SAW~~R~~ll~~  191 (331)
T 3dss_A          122 PEPNWARELELCARFLEADER-NFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFS-NYSSWHYRSCLLPQ  191 (331)
T ss_dssp             SSCCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCSC-CHHHHHHHHHHHHH
T ss_pred             CcccHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHH
Confidence            4  255666666666555322 44555544444444454 45555666655555443 55555555444443

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.81  E-value=3.1e-07  Score=63.84  Aligned_cols=99  Identities=7%  Similarity=-0.008  Sum_probs=50.7

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLM  139 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  139 (343)
                      ...+..+...+...|++++|...+++..... +.+...+..+...+...|++++|...+++..+.... +...+..+...
T Consensus        12 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~   89 (131)
T 2vyi_A           12 AERLKTEGNEQMKVENFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICIDPA-YSKAYGRMGLA   89 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcCcc-CHHHHHHHHHH
Confidence            3445555555555555555555555555432 123444445555555555555555555555544321 34455555555


Q ss_pred             HHhcCcHhHHHHHHHHHHhcC
Q 044084          140 YIEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus       140 ~~~~~~~~~a~~~~~~~~~~~  160 (343)
                      +...|++++|...|++..+..
T Consensus        90 ~~~~~~~~~A~~~~~~~~~~~  110 (131)
T 2vyi_A           90 LSSLNKHVEAVAYYKKALELD  110 (131)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHhCCHHHHHHHHHHHHhcC
Confidence            555555555555555554443

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=98.77  E-value=3.3e-08  Score=79.28  Aligned_cols=195  Identities=9%  Similarity=-0.033  Sum_probs=130.2

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHH
Q 044084           21 DSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYAS  100 (343)
Q Consensus        21 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  100 (343)
                      +...+..+...+.+.|++++|...|++.....    |.+...|..+..++...|++++|+..+++..+... .+...+..
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~----p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~   77 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRN----PLVAVYYTNRALCYLKMQQPEQALADCRRALELDG-QSVKAHFF   77 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCT-TCHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC----CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC-CCHHHHHH
Confidence            55678888999999999999999999998765    33368899999999999999999999999988642 35678888


Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCc
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRA  180 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  180 (343)
                      +..++...|++++|...|++..+..+. +...+...+....+   ..++.. +........+.+......+ ..+. .|+
T Consensus        78 lg~~~~~~g~~~~A~~~~~~al~l~p~-~~~~~~~~~~~~~~---~~~~~~-~~~~~~~~~~~~~~i~~~l-~~l~-~~~  150 (281)
T 2c2l_A           78 LGQCQLEMESYDEAIANLQRAYSLAKE-QRLNFGDDIPSALR---IAKKKR-WNSIEERRIHQESELHSYL-TRLI-AAE  150 (281)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHH-TTCCCCSHHHHHHH---HHHHHH-HHHHHHTCCCCCCHHHHHH-HHHH-HHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCcc-chhhHHHHHHHHHH---HHHHHH-HHHHHHHHHhhhHHHHHHH-HHHH-HHH
Confidence            999999999999999999998875421 11111111111111   111112 1222223333333333333 3332 688


Q ss_pred             HHHHHHHHHHHHHcCCCCCHhhHH-HHHHHHHcc-CChhHHHHHHHHHHHc
Q 044084          181 YWAAVKVYEQLISQGCIPGQVTYA-SIINAYCRI-GLYSKAEKVFIEMQQK  229 (343)
Q Consensus       181 ~~~a~~~~~~~~~~~~~p~~~~~~-~ll~~~~~~-~~~~~a~~~~~~~~~~  229 (343)
                      +++|.+.++...+.  .|+..... .+...+.+. +.++++.++|....+.
T Consensus       151 ~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~~~  199 (281)
T 2c2l_A          151 RERELEECQRNHEG--HEDDGHIRAQQACIEAKHDKYMADMDELFSQVDEK  199 (281)
T ss_dssp             HHHHHTTTSGGGTT--TSCHHHHTHHHHHHHHHHHHHHHHHHHHHHHSSCT
T ss_pred             HHHHHHHHHhhhcc--ccchhhhhhHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence            99999988887765  45544333 333333443 6688899999877653

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=98.76  E-value=1.7e-07  Score=67.18  Aligned_cols=101  Identities=8%  Similarity=0.022  Sum_probs=59.7

Q ss_pred             CchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHH
Q 044084           57 PSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKL  136 (343)
Q Consensus        57 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  136 (343)
                      |.+...+..+...+...|++++|+..|++...... .+...|..+..++...|++++|...|++..+..+. +...+..+
T Consensus        18 p~~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~-~~~~~~~l   95 (148)
T 2vgx_A           18 SDTLEQLYSLAFNQYQSGXYEDAHXVFQALCVLDH-YDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDIX-EPRFPFHA   95 (148)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CTHHHHHH
T ss_pred             HhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHcCc-ccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC-CchHHHHH
Confidence            33345555566666666666666666666655432 24555555666666666666666666666655432 45556666


Q ss_pred             HHHHHhcCcHhHHHHHHHHHHhc
Q 044084          137 VLMYIEEGMVEKTLEVVESMKNA  159 (343)
Q Consensus       137 ~~~~~~~~~~~~a~~~~~~~~~~  159 (343)
                      ..+|...|++++|...|++..+.
T Consensus        96 g~~~~~~g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A           96 AECLLQXGELAEAESGLFLAQEL  118 (148)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHH
Confidence            66666666666666666665543

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.76  E-value=2.8e-07  Score=65.52  Aligned_cols=103  Identities=10%  Similarity=-0.003  Sum_probs=64.1

Q ss_pred             CCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHH
Q 044084           56 TPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLK  135 (343)
Q Consensus        56 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  135 (343)
                      +|.+...+..+...+.+.|++++|+..|++....+. .+...|..+..++...|++++|...|++..+..+. ++..+..
T Consensus        14 ~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~   91 (142)
T 2xcb_A           14 SEDTLEQLYALGFNQYQAGKWDDAQKIFQALCMLDH-YDARYFLGLGACRQSLGLYEQALQSYSYGALMDIN-EPRFPFH   91 (142)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CTHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC-CcHHHHH
Confidence            344445555666666666777777777766665532 24555666666666667777777777666665533 5556666


Q ss_pred             HHHHHHhcCcHhHHHHHHHHHHhcC
Q 044084          136 LVLMYIEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus       136 l~~~~~~~~~~~~a~~~~~~~~~~~  160 (343)
                      +..+|...|++++|...|+......
T Consensus        92 lg~~~~~~g~~~~A~~~~~~al~~~  116 (142)
T 2xcb_A           92 AAECHLQLGDLDGAESGFYSARALA  116 (142)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            6666777777777777776665443

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=98.76  E-value=3.6e-07  Score=75.26  Aligned_cols=132  Identities=14%  Similarity=0.037  Sum_probs=85.2

Q ss_pred             CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCc--------------hhhHHHHHHHHhcCCcHHHHHHHHHHHHHc
Q 044084          129 DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNIS--------------DCISCVIVNGFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       129 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--------------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  194 (343)
                      +...+..+...|.+.|++++|+..|++.........              ...|..+..++.+.|++++|...+++..+.
T Consensus       146 ~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  225 (336)
T 1p5q_A          146 QSTIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALEL  225 (336)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            456677777777788888888888887776554221              355666666777777777777777776665


Q ss_pred             CCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHH-HHHHHHHh
Q 044084          195 GCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDA-MRLVAKMK  262 (343)
Q Consensus       195 ~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a-~~~~~~m~  262 (343)
                      . +.+...+..+..+|...|++++|...|+...+.. +.+...+..+..++...|+.+++ ...++.|.
T Consensus       226 ~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~~  292 (336)
T 1p5q_A          226 D-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQLY-PNNKAAKTQLAVCQQRIRRQLAREKKLYANMF  292 (336)
T ss_dssp             C-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             C-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3 3345566666666777777777777777766654 33455666666666666666666 33444443

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=98.74  E-value=5.4e-07  Score=62.45  Aligned_cols=97  Identities=13%  Similarity=0.114  Sum_probs=56.8

Q ss_pred             HHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 044084           61 HMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMY  140 (343)
Q Consensus        61 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  140 (343)
                      ..|..+...+.+.|++++|+..|++..+.. +.+...|..+..++.+.|++++|...+++..+..+. +...+..+..++
T Consensus         5 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~   82 (126)
T 3upv_A            5 EEARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPN-FVRAYIRKATAQ   82 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHH
Confidence            445555566666666666666666665543 124455555666666666666666666666655432 455666666666


Q ss_pred             HhcCcHhHHHHHHHHHHhc
Q 044084          141 IEEGMVEKTLEVVESMKNA  159 (343)
Q Consensus       141 ~~~~~~~~a~~~~~~~~~~  159 (343)
                      ...|++++|...|++..+.
T Consensus        83 ~~~~~~~~A~~~~~~al~~  101 (126)
T 3upv_A           83 IAVKEYASALETLDAARTK  101 (126)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHHhCHHHHHHHHHHHHHh
Confidence            6666666666666665543

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=98.73  E-value=1.2e-07  Score=67.92  Aligned_cols=98  Identities=10%  Similarity=-0.058  Sum_probs=67.9

Q ss_pred             hHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHH
Q 044084           95 PSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNG  174 (343)
Q Consensus        95 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  174 (343)
                      ...+..+...+...|++++|...|++.....+. +...|..+..+|...|++++|+..|++....++ .+...+..+..+
T Consensus        21 ~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p-~~~~~~~~lg~~   98 (148)
T 2vgx_A           21 LEQLYSLAFNQYQSGXYEDAHXVFQALCVLDHY-DSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDI-XEPRFPFHAAEC   98 (148)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHHcCcc-cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCchHHHHHHHH
Confidence            344555666677777777777777777766543 677777777777777777777777777766654 344566667777


Q ss_pred             HhcCCcHHHHHHHHHHHHHc
Q 044084          175 FSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       175 ~~~~~~~~~a~~~~~~~~~~  194 (343)
                      +...|++++|...|++..+.
T Consensus        99 ~~~~g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A           99 LLQXGELAEAESGLFLAQEL  118 (148)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHH
Confidence            77777777777777776654

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=98.72  E-value=3.1e-05  Score=67.09  Aligned_cols=101  Identities=11%  Similarity=0.169  Sum_probs=68.9

Q ss_pred             hhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCc-HHHHHH
Q 044084            3 SQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGR-AFEILK   81 (343)
Q Consensus         3 ~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~-~~~a~~   81 (343)
                      .+.|..+|+.+...  -|.              |+++.+..+|++....-  |+   ...|...+....+.+. .+....
T Consensus        11 i~~aR~vyer~l~~--~P~--------------~~~e~~~~iferal~~~--ps---~~LW~~Y~~f~~~~~~~~~~i~~   69 (493)
T 2uy1_A           11 LSSPSAIMEHARRL--YMS--------------KDYRSLESLFGRCLKKS--YN---LDLWMLYIEYVRKVSQKKFKLYE   69 (493)
T ss_dssp             -CCHHHHHHHHHHH--HHT--------------TCHHHHHHHHHHHSTTC--CC---HHHHHHHHHHHHHHC----CTHH
T ss_pred             hHHHHHHHHHHHHH--CCC--------------CCHHHHHHHHHHHhccC--CC---HHHHHHHHHHHHHhCchHHHHHH
Confidence            45566666666553  122              88999999999987743  33   6789988888777663 456777


Q ss_pred             HHHHHHhc-CCCC-ChHhHHHHHHHHh----cccCHHHHHHHHHHHHHc
Q 044084           82 FFRDMKEK-GILE-DPSVYASLICSFA----SIAEVKVAEELFKEAEEK  124 (343)
Q Consensus        82 ~~~~~~~~-~~~~-~~~~~~~l~~~~~----~~~~~~~a~~~~~~~~~~  124 (343)
                      +|+..... |..| +...|...+..+.    ..++.+.+..+|++.+..
T Consensus        70 ~fe~al~~vg~d~~s~~iW~~Yi~f~~~~~~~~~~~~~vR~iy~rAL~~  118 (493)
T 2uy1_A           70 VYEFTLGQFENYWDSYGLYKEYIEEEGKIEDEQTRIEKIRNGYMRALQT  118 (493)
T ss_dssp             HHHHHHHHSTTCTTCHHHHHHHHHHTSSCSSHHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHcCCCcccHHHHHHHHHHHHhchhhhHHHHHHHHHHHHHHhC
Confidence            88877664 4333 5677877776654    346788899999998873

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.71  E-value=2.3e-07  Score=73.04  Aligned_cols=127  Identities=9%  Similarity=-0.016  Sum_probs=53.6

Q ss_pred             HHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHh
Q 044084           65 ILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLR--DLEVFLKLVLMYIE  142 (343)
Q Consensus        65 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~  142 (343)
                      .+...+...|++++|.++|+.+...+  |+......+...+.+.+++++|+..|+...... .|  ....+..+..++..
T Consensus       107 ayA~~L~~~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~-d~~~~~~a~~~LG~al~~  183 (282)
T 4f3v_A          107 GFAACEAAQGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP-DKFLAGAAGVAHGVAAAN  183 (282)
T ss_dssp             HHHHHHHHHTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS-CHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC-CcccHHHHHHHHHHHHHH
Confidence            34444455555555555555444322  222122233334445555555555554322211 00  01234444455555


Q ss_pred             cCcHhHHHHHHHHHHhcCCCCc--hhhHHHHHHHHhcCCcHHHHHHHHHHHHHc
Q 044084          143 EGMVEKTLEVVESMKNAELNIS--DCISCVIVNGFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       143 ~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  194 (343)
                      .|++++|+..|++.......|.  .........++.+.|+.++|...|+++...
T Consensus       184 LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~  237 (282)
T 4f3v_A          184 LALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTT  237 (282)
T ss_dssp             TTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            5555555555555442221021  122333344444455555555555555444

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=98.71  E-value=5e-08  Score=73.80  Aligned_cols=148  Identities=11%  Similarity=-0.004  Sum_probs=72.2

Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCC-CC--------------h
Q 044084           31 AFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGIL-ED--------------P   95 (343)
Q Consensus        31 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~-~~--------------~   95 (343)
                      .....|+++++.+.|+......    +.....+..+...+...|++++|+..|++....... |+              .
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~   88 (198)
T 2fbn_A           13 GRENLYFQGAKKSIYDYTDEEK----VQSAFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEI   88 (198)
T ss_dssp             ---------CCCSGGGCCHHHH----HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHH
T ss_pred             hhhhhhhccccCchhhCCHHHH----HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHH
Confidence            3444455555555543221111    111345666677777777888888887777664211 10              1


Q ss_pred             HhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHH
Q 044084           96 SVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGF  175 (343)
Q Consensus        96 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  175 (343)
                      ..+..+..++...|++++|...+++..+... .+...+..+..+|...|++++|+..|++..+..+ .+...+..+..++
T Consensus        89 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~  166 (198)
T 2fbn_A           89 SCNLNLATCYNKNKDYPKAIDHASKVLKIDK-NNVKALYKLGVANMYFGFLEEAKENLYKAASLNP-NNLDIRNSYELCV  166 (198)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhCc-ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCC-CcHHHHHHHHHHH
Confidence            3445555555555666666666665555432 2455555555556666666666666655554433 2333444444444


Q ss_pred             hcCCcHHHH
Q 044084          176 SKRRAYWAA  184 (343)
Q Consensus       176 ~~~~~~~~a  184 (343)
                      ...++..++
T Consensus       167 ~~~~~~~~~  175 (198)
T 2fbn_A          167 NKLKEARKK  175 (198)
T ss_dssp             HHHHHHHC-
T ss_pred             HHHHHHHHH
Confidence            444444333

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.70  E-value=2.9e-07  Score=72.50  Aligned_cols=188  Identities=11%  Similarity=-0.037  Sum_probs=126.0

Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHH-------HHHhhccCcHHHHHHHHHHHHhcCCCCCh-----------
Q 044084           34 KIGDSEKVAALFLECESRKLDLTPSSTHMYKIL-------CDSLGKSGRAFEILKFFRDMKEKGILEDP-----------   95 (343)
Q Consensus        34 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~l-------i~~~~~~~~~~~a~~~~~~~~~~~~~~~~-----------   95 (343)
                      ..++...|.+.|.++....    |.....|..+       ...+...++..+++..++.-..  +.|+.           
T Consensus        18 ~~~d~~~A~~~F~~a~~~d----P~~~Daw~g~~a~g~~~~~~L~~~~r~~~a~~~~~~~l~--l~p~~l~a~~~~~g~y   91 (282)
T 4f3v_A           18 LPMSEARSLDLFTEITNYD----ESACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQ--ISMSTLNARIAIGGLY   91 (282)
T ss_dssp             TTTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTT--CCGGGGCCEEECCTTT
T ss_pred             cCCCHHHHHHHHHHHHHhC----hhhhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhc--CChhhhhhhhccCCcc
Confidence            5799999999999998876    3336889888       4555555555566555554433  22221           


Q ss_pred             -----------HhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCc
Q 044084           96 -----------SVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNIS  164 (343)
Q Consensus        96 -----------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  164 (343)
                                 .....+...+...|++++|.++|+.+...+  |+......+...+.+.+++++|+..|+...... .|.
T Consensus        92 ~~~~~~v~~r~dl~LayA~~L~~~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~-d~~  168 (282)
T 4f3v_A           92 GDITYPVTSPLAITMGFAACEAAQGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP-DKF  168 (282)
T ss_dssp             CCCEEECSSHHHHHHHHHHHHHHHTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS-CHH
T ss_pred             cccccccCCHhHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC-Ccc
Confidence                       122335566778888888888888777654  333366666677888888888888887554322 111


Q ss_pred             --hhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCC--HhhHHHHHHHHHccCChhHHHHHHHHHHHcC
Q 044084          165 --DCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPG--QVTYASIINAYCRIGLYSKAEKVFIEMQQKG  230 (343)
Q Consensus       165 --~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~--~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  230 (343)
                        ...+..+..++...|++++|+..|++.......|.  .........++.+.|+.++|..+|+++....
T Consensus       169 ~~~~a~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~  238 (282)
T 4f3v_A          169 LAGAAGVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTH  238 (282)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             cHHHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence              23566677788888888888888888774432143  2344555666777888888888888888764

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=98.68  E-value=5.8e-07  Score=63.24  Aligned_cols=97  Identities=9%  Similarity=-0.007  Sum_probs=57.8

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLM  139 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  139 (343)
                      ...|..+...+...|++++|+..|++...... .+...+..+..++...|+++.|...+++..+..+. +...+..+..+
T Consensus         9 ~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~~~   86 (137)
T 3q49_B            9 AQELKEQGNRLFVGRKYPEAAACYGRAITRNP-LVAVYYTNRALCYLKMQQPEQALADCRRALELDGQ-SVKAHFFLGQC   86 (137)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHhhCc-CcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCch-hHHHHHHHHHH
Confidence            45556666666666666666666666655432 23455555666666666666666666666655432 45566666666


Q ss_pred             HHhcCcHhHHHHHHHHHHh
Q 044084          140 YIEEGMVEKTLEVVESMKN  158 (343)
Q Consensus       140 ~~~~~~~~~a~~~~~~~~~  158 (343)
                      +...|++++|+..|++...
T Consensus        87 ~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           87 QLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhhHHHHHHHHHHHHH
Confidence            6666666666666666544

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=98.67  E-value=5.3e-08  Score=73.69  Aligned_cols=124  Identities=7%  Similarity=0.003  Sum_probs=67.8

Q ss_pred             HHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCc---------------hhhHHHHHHHHhcCCcHHHHHHHHHHHHHc
Q 044084          130 LEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNIS---------------DCISCVIVNGFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       130 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---------------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  194 (343)
                      ...+..+...+...|++++|+..|++.........               ...+..+..++...|++++|...+++..+.
T Consensus        38 ~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~  117 (198)
T 2fbn_A           38 AFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKI  117 (198)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            33455555566666666666666666554322111               134555566666666666666666666655


Q ss_pred             CCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHH
Q 044084          195 GCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAM  255 (343)
Q Consensus       195 ~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  255 (343)
                      . +.+...+..+..+|...|++++|...|+...+.. +.+...+..+..++...++..++.
T Consensus       118 ~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~~~  176 (198)
T 2fbn_A          118 D-KNNVKALYKLGVANMYFGFLEEAKENLYKAASLN-PNNLDIRNSYELCVNKLKEARKKD  176 (198)
T ss_dssp             S-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHC--
T ss_pred             C-cccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHHHHHHHH
Confidence            2 2344555566666666666666666666666553 234445555555555555444443

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=98.67  E-value=2.5e-06  Score=57.82  Aligned_cols=98  Identities=10%  Similarity=-0.043  Sum_probs=52.3

Q ss_pred             HHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 044084           61 HMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMY  140 (343)
Q Consensus        61 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  140 (343)
                      ..+..+...+...|++++|...|++..... +.+...+..+...+...|++++|...+++..+..+. +...+..+...+
T Consensus         5 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~a~~~   82 (118)
T 1elw_A            5 NELKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPD-WGKGYSRKAAAL   82 (118)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCcc-cHHHHHHHHHHH
Confidence            344555555555555555555555555442 123444555555555555555555555555554322 455555555555


Q ss_pred             HhcCcHhHHHHHHHHHHhcC
Q 044084          141 IEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus       141 ~~~~~~~~a~~~~~~~~~~~  160 (343)
                      ...|++++|.+.+++..+.+
T Consensus        83 ~~~~~~~~A~~~~~~~~~~~  102 (118)
T 1elw_A           83 EFLNRFEEAKRTYEEGLKHE  102 (118)
T ss_dssp             HHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHhhHHHHHHHHHHHHHcC
Confidence            55666666666555555443

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=98.65  E-value=8.4e-05  Score=60.25  Aligned_cols=231  Identities=8%  Similarity=0.005  Sum_probs=153.3

Q ss_pred             hhHHHHHHH---HHhcCCH-HHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCc----------HHHHHHHHHHHHh
Q 044084           23 GCYCQIMEA---FYKIGDS-EKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGR----------AFEILKFFRDMKE   88 (343)
Q Consensus        23 ~~~~~l~~~---~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~----------~~~a~~~~~~~~~   88 (343)
                      ..|..+...   ..+.|.+ ++|+++++.+...+    |.+..+|+.--..+...+.          +++++.+++.+..
T Consensus        27 ~~y~~~~~~~~~~~~~~e~s~eaL~~t~~~L~~n----P~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~  102 (331)
T 3dss_A           27 KLYQSATQAVFQKRQAGELDESVLELTSQILGAN----PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLR  102 (331)
T ss_dssp             HHHHHHHHHHHHHHHTTCCSHHHHHHHHHHHTTC----TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHC----chhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHH
Confidence            345444443   2345555 48899999997766    3345677765444443333          6788889988888


Q ss_pred             cCCCCChHhHHHHHHHHhccc--CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCc-HhHHHHHHHHHHhcCCCCch
Q 044084           89 KGILEDPSVYASLICSFASIA--EVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGM-VEKTLEVVESMKNAELNISD  165 (343)
Q Consensus        89 ~~~~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~  165 (343)
                      ...+ +..+|+.-...+.+.+  ++++++.+++.+.+..+. |..+|+.-.......|. ++++++.++++.+.++ -|.
T Consensus       103 ~~PK-ny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~dpr-Ny~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~p-~N~  179 (331)
T 3dss_A          103 VNPK-SYGTWHHRCWLLSRLPEPNWARELELCARFLEADER-NFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNF-SNY  179 (331)
T ss_dssp             HCTT-CHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCS-CCH
T ss_pred             hCCC-CHHHHHHHHHHHhccCcccHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHCC-CCH
Confidence            6543 6777777666666666  488999999999988764 88888888888888888 5899999999988876 566


Q ss_pred             hhHHHHHHHHhcC--------------CcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHcc-----------CChhHHH
Q 044084          166 CISCVIVNGFSKR--------------RAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRI-----------GLYSKAE  220 (343)
Q Consensus       166 ~~~~~l~~~~~~~--------------~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~-----------~~~~~a~  220 (343)
                      ..|+.....+...              +.++++++.+.+..... +-|...|+-+-..+.+.           +.++++.
T Consensus       180 SAW~~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~-P~d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l~~el  258 (331)
T 3dss_A          180 SSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTD-PNDQSAWFYHRWLLGAGSGRCELSVEKSTVLQSEL  258 (331)
T ss_dssp             HHHHHHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHSSSCGGGCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccCccccchHHHHHHHHHH
Confidence            6777655444433              45778888888887763 34556665444444443           3467778


Q ss_pred             HHHHHHHHcCCCcChhhHHHHH-----HHHHccCChHHHHHHHHHHhhC
Q 044084          221 KVFIEMQQKGFDKCVVAYSSMV-----AMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~l~-----~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                      +.++++.+..  ||. .|..+.     ...-..|..+++...+.++++.
T Consensus       259 ~~~~elle~~--pd~-~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~~  304 (331)
T 3dss_A          259 ESCKELQELE--PEN-KWCLLTIILLMRALDPLLYEKETLQYFSTLKAV  304 (331)
T ss_dssp             HHHHHHHHHC--TTC-HHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhC--ccc-chHHHHHHHHHHhhcccccHHHHHHHHHHHHHh
Confidence            8888888764  443 233211     1222345666777777777754

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.65  E-value=6.9e-06  Score=70.03  Aligned_cols=200  Identities=9%  Similarity=-0.016  Sum_probs=111.4

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCCc-------------hHHHHHHHHHHhhccCcHHHHHHHHHHHHhcC-CCCC
Q 044084           29 MEAFYKIGDSEKVAALFLECESRKLDLTPS-------------STHMYKILCDSLGKSGRAFEILKFFRDMKEKG-ILED   94 (343)
Q Consensus        29 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-------------~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~-~~~~   94 (343)
                      ...+.+.|++++|.+.|..+.+........             ...++..+...|...|++++|.+.+.++...- ..++
T Consensus        11 a~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~   90 (434)
T 4b4t_Q           11 ARRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFAK   90 (434)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence            344566677777777777776654332210             01345667777777777777777777665421 1111


Q ss_pred             h----HhHHHHHHHHhcccCHHHHHHHHHHHHH----cCCCC-CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCC----
Q 044084           95 P----SVYASLICSFASIAEVKVAEELFKEAEE----KGMLR-DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAEL----  161 (343)
Q Consensus        95 ~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~----~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----  161 (343)
                      .    .+.+.+-..+...|+.+.+..++.....    .+..+ -..++..+...|...|++++|..++++....-.    
T Consensus        91 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~  170 (434)
T 4b4t_Q           91 SKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDD  170 (434)
T ss_dssp             HHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSC
T ss_pred             hHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhccc
Confidence            1    1122223333455667777777666543    22222 245666677777777777777777776543211    


Q ss_pred             -CCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHc----CCCCC--HhhHHHHHHHHHccCChhHHHHHHHHHHH
Q 044084          162 -NISDCISCVIVNGFSKRRAYWAAVKVYEQLISQ----GCIPG--QVTYASIINAYCRIGLYSKAEKVFIEMQQ  228 (343)
Q Consensus       162 -~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~p~--~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  228 (343)
                       +....++..++..|...|++++|..++++....    +.+|.  ...+..+...+...|++++|...|.+..+
T Consensus       171 ~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~~  244 (434)
T 4b4t_Q          171 KPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFESFE  244 (434)
T ss_dssp             STHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence             111235666677777777777777777765542    11111  13344455556666777777766655543

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=98.65  E-value=1.4e-06  Score=60.40  Aligned_cols=96  Identities=5%  Similarity=-0.089  Sum_probs=58.9

Q ss_pred             hHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHh
Q 044084           97 VYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFS  176 (343)
Q Consensus        97 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  176 (343)
                      .+..+...+.+.|++++|...|++..+..+. +...|..+..+|.+.|++++|+..+++..+.++ .+...|..+..++.
T Consensus         6 ~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~   83 (126)
T 3upv_A            6 EARLEGKEYFTKSDWPNAVKAYTEMIKRAPE-DARGYSNRAAALAKLMSFPEAIADCNKAIEKDP-NFVRAYIRKATAQI   83 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHH
Confidence            4455555666666666666666666665432 566666666666666666666666666665543 34445556666666


Q ss_pred             cCCcHHHHHHHHHHHHHc
Q 044084          177 KRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       177 ~~~~~~~a~~~~~~~~~~  194 (343)
                      ..|++++|...|++..+.
T Consensus        84 ~~~~~~~A~~~~~~al~~  101 (126)
T 3upv_A           84 AVKEYASALETLDAARTK  101 (126)
T ss_dssp             HTTCHHHHHHHHHHHHHH
T ss_pred             HHhCHHHHHHHHHHHHHh
Confidence            666666666666665544

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.64  E-value=3.8e-06  Score=59.70  Aligned_cols=99  Identities=13%  Similarity=0.038  Sum_probs=66.9

Q ss_pred             hHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCC----hHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHH
Q 044084           59 STHMYKILCDSLGKSGRAFEILKFFRDMKEKGILED----PSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFL  134 (343)
Q Consensus        59 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  134 (343)
                      ....+..+...+...|++++|++.|++..+.  .|+    ...+..+...+...|++++|...+++..+.... +...+.
T Consensus        27 ~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~  103 (148)
T 2dba_A           27 SVEQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKDGG-DVKALY  103 (148)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSC-CHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCcc-CHHHHH
Confidence            3566667777777777777777777777664  333    455666666677777777777777776665432 566666


Q ss_pred             HHHHHHHhcCcHhHHHHHHHHHHhcC
Q 044084          135 KLVLMYIEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus       135 ~l~~~~~~~~~~~~a~~~~~~~~~~~  160 (343)
                      .+..++...|++++|...|++.....
T Consensus       104 ~~a~~~~~~~~~~~A~~~~~~al~~~  129 (148)
T 2dba_A          104 RRSQALEKLGRLDQAVLDLQRCVSLE  129 (148)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHcC
Confidence            77777777777777777777766554

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=98.64  E-value=2.5e-06  Score=57.83  Aligned_cols=97  Identities=11%  Similarity=0.001  Sum_probs=57.2

Q ss_pred             HhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHH
Q 044084           96 SVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGF  175 (343)
Q Consensus        96 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  175 (343)
                      ..+..+...+...|++++|...+++..+..+. +...+..+...+...|++++|...+++..+..+ .+...+..+..++
T Consensus         5 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~~   82 (118)
T 1elw_A            5 NELKEKGNKALSVGNIDDALQCYSEAIKLDPH-NHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKP-DWGKGYSRKAAAL   82 (118)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCc-ccHHHHHHHHHHH
Confidence            34555555666666666666666666655432 555666666666666666666666666655443 2344555555666


Q ss_pred             hcCCcHHHHHHHHHHHHHc
Q 044084          176 SKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       176 ~~~~~~~~a~~~~~~~~~~  194 (343)
                      ...|++++|.+.+++..+.
T Consensus        83 ~~~~~~~~A~~~~~~~~~~  101 (118)
T 1elw_A           83 EFLNRFEEAKRTYEEGLKH  101 (118)
T ss_dssp             HHTTCHHHHHHHHHHHHTT
T ss_pred             HHHhhHHHHHHHHHHHHHc
Confidence            6666666666666665544

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.64  E-value=4.9e-06  Score=70.92  Aligned_cols=198  Identities=8%  Similarity=0.004  Sum_probs=142.2

Q ss_pred             HHHHhhccCcHHHHHHHHHHHHhcCCCCCh----------------HhHHHHHHHHhcccCHHHHHHHHHHHHHcCCC-C
Q 044084           66 LCDSLGKSGRAFEILKFFRDMKEKGILEDP----------------SVYASLICSFASIAEVKVAEELFKEAEEKGML-R  128 (343)
Q Consensus        66 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~----------------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~  128 (343)
                      -.+.+.+.|++++|++.|.++.+.......                ..+..+...|...|++++|.+.+..+.+.-.. +
T Consensus        10 ~a~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~   89 (434)
T 4b4t_Q           10 EARRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFA   89 (434)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSC
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence            356778899999999999999886432211                23677889999999999999999887763211 1


Q ss_pred             CH----HHHHHHHHHHHhcCcHhHHHHHHHHHHhc----CCC-CchhhHHHHHHHHhcCCcHHHHHHHHHHHHHc--CC-
Q 044084          129 DL----EVFLKLVLMYIEEGMVEKTLEVVESMKNA----ELN-ISDCISCVIVNGFSKRRAYWAAVKVYEQLISQ--GC-  196 (343)
Q Consensus       129 ~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~-  196 (343)
                      +.    .+.+.+...+...|++++|..+++.....    +.. ....++..+...+...|++++|..+++++...  +. 
T Consensus        90 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~  169 (434)
T 4b4t_Q           90 KSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLD  169 (434)
T ss_dssp             HHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSS
T ss_pred             chHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcc
Confidence            22    23344444555678899999999887542    221 22446778899999999999999999988654  11 


Q ss_pred             -CC-CHhhHHHHHHHHHccCChhHHHHHHHHHHHc----CCCcC--hhhHHHHHHHHHccCChHHHHHHHHHHhh
Q 044084          197 -IP-GQVTYASIINAYCRIGLYSKAEKVFIEMQQK----GFDKC--VVAYSSMVAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       197 -~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~----~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                       .+ ...++..++..|...|++++|..+++.....    +.++.  ...+..+...+...|++++|...|.+..+
T Consensus       170 ~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~~  244 (434)
T 4b4t_Q          170 DKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFESFE  244 (434)
T ss_dssp             CSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHH
T ss_pred             cchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence             11 2356788889999999999999999887653    21111  24566777788889999999888877653

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=98.62  E-value=1.3e-06  Score=60.73  Aligned_cols=58  Identities=10%  Similarity=0.016  Sum_probs=22.4

Q ss_pred             HHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHH
Q 044084           63 YKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEA  121 (343)
Q Consensus        63 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  121 (343)
                      +..+...+.+.|++++|++.|++..+... -+...|..+..++...|++++|+..+++.
T Consensus        11 ~~~lG~~~~~~~~~~~A~~~y~~Al~~~p-~~~~~~~nlg~~~~~~~~~~~A~~~~~~a   68 (127)
T 4gcn_A           11 EKDLGNAAYKQKDFEKAHVHYDKAIELDP-SNITFYNNKAAVYFEEKKFAECVQFCEKA   68 (127)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHhHHHHHHHhhhHHHHHHHHHHH
Confidence            33344444444444444444444433321 12333333333344444444444444333

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.61  E-value=9.7e-07  Score=62.68  Aligned_cols=96  Identities=11%  Similarity=-0.024  Sum_probs=65.6

Q ss_pred             hHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHh
Q 044084           97 VYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFS  176 (343)
Q Consensus        97 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  176 (343)
                      .+..+...+.+.|++++|...|++.....+. +...|..+..+|...|++++|+..|++....++ .+...+..+..++.
T Consensus        20 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~   97 (142)
T 2xcb_A           20 QLYALGFNQYQAGKWDDAQKIFQALCMLDHY-DARYFLGLGACRQSLGLYEQALQSYSYGALMDI-NEPRFPFHAAECHL   97 (142)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccHHHHHHHHHHHHHhCCc-cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCcHHHHHHHHHHH
Confidence            3444556666777777777777777766543 666777777777777777777777777766654 34455666677777


Q ss_pred             cCCcHHHHHHHHHHHHHc
Q 044084          177 KRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       177 ~~~~~~~a~~~~~~~~~~  194 (343)
                      ..|++++|...|++..+.
T Consensus        98 ~~g~~~~A~~~~~~al~~  115 (142)
T 2xcb_A           98 QLGDLDGAESGFYSARAL  115 (142)
T ss_dssp             HTTCHHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHh
Confidence            777777777777776654

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.61  E-value=1.2e-06  Score=58.85  Aligned_cols=95  Identities=8%  Similarity=-0.088  Sum_probs=42.6

Q ss_pred             HHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCC--chhhHHHHHHHH
Q 044084           98 YASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNI--SDCISCVIVNGF  175 (343)
Q Consensus        98 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~  175 (343)
                      +..+...+...|++++|...+++..+.... +...+..+...+...|++++|...|++..+... .  +...+..+..++
T Consensus         9 ~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~~~l~~~~   86 (112)
T 2kck_A            9 YYLEGVLQYDAGNYTESIDLFEKAIQLDPE-ESKYWLMKGKALYNLERYEEAVDCYNYVINVIE-DEYNKDVWAAKADAL   86 (112)
T ss_dssp             GGGHHHHHHSSCCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSC-CTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHhCcC-CHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCc-ccchHHHHHHHHHHH
Confidence            333444444444444444444444443321 344444444444445555555555544444332 1  233444444444


Q ss_pred             hcC-CcHHHHHHHHHHHHHc
Q 044084          176 SKR-RAYWAAVKVYEQLISQ  194 (343)
Q Consensus       176 ~~~-~~~~~a~~~~~~~~~~  194 (343)
                      ... |++++|.+.+++....
T Consensus        87 ~~~~~~~~~A~~~~~~~~~~  106 (112)
T 2kck_A           87 RYIEGKEVEAEIAEARAKLE  106 (112)
T ss_dssp             TTCSSCSHHHHHHHHHHGGG
T ss_pred             HHHhCCHHHHHHHHHHHhhc
Confidence            444 4444444444444443

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.59  E-value=2.4e-06  Score=62.22  Aligned_cols=99  Identities=11%  Similarity=0.024  Sum_probs=63.9

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLM  139 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  139 (343)
                      ...|..+...+...|++++|++.|++..+... -+...|..+..++.+.|++++|...+++..+.... +...|..+..+
T Consensus        11 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~   88 (164)
T 3sz7_A           11 SDKLKSEGNAAMARKEYSKAIDLYTQALSIAP-ANPIYLSNRAAAYSASGQHEKAAEDAELATVVDPK-YSKAWSRLGLA   88 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-cCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-CHHHHHHHHHH
Confidence            45566666666666777777777766666532 24556666666666677777777777766665532 56666667777


Q ss_pred             HHhcCcHhHHHHHHHHHHhcC
Q 044084          140 YIEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus       140 ~~~~~~~~~a~~~~~~~~~~~  160 (343)
                      |...|++++|+..|++..+..
T Consensus        89 ~~~~g~~~~A~~~~~~al~~~  109 (164)
T 3sz7_A           89 RFDMADYKGAKEAYEKGIEAE  109 (164)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHccCHHHHHHHHHHHHHhC
Confidence            777777777777777666544

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.57  E-value=1.9e-06  Score=57.86  Aligned_cols=97  Identities=10%  Similarity=-0.004  Sum_probs=62.3

Q ss_pred             hhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCc--ChhhHHHHHH
Q 044084          166 CISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDK--CVVAYSSMVA  243 (343)
Q Consensus       166 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~  243 (343)
                      ..+..+...+...|++++|...+++..+.. +.+...+..+..++...|++++|...++...+.. +.  +...+..+..
T Consensus         7 ~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~l~~   84 (112)
T 2kck_A            7 EEYYLEGVLQYDAGNYTESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYVINVI-EDEYNKDVWAAKAD   84 (112)
T ss_dssp             TGGGGHHHHHHSSCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-CCTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccchHHHHHHHHH
Confidence            345556666666677777777776666553 2344556666666667777777777777766653 23  4566666777


Q ss_pred             HHHcc-CChHHHHHHHHHHhhC
Q 044084          244 MYGKT-GRIRDAMRLVAKMKPK  264 (343)
Q Consensus       244 ~~~~~-~~~~~a~~~~~~m~~~  264 (343)
                      ++... |++++|.+.+++....
T Consensus        85 ~~~~~~~~~~~A~~~~~~~~~~  106 (112)
T 2kck_A           85 ALRYIEGKEVEAEIAEARAKLE  106 (112)
T ss_dssp             HHTTCSSCSHHHHHHHHHHGGG
T ss_pred             HHHHHhCCHHHHHHHHHHHhhc
Confidence            77777 7777777777776654

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=98.57  E-value=2.2e-06  Score=59.54  Aligned_cols=56  Identities=14%  Similarity=0.149  Sum_probs=23.2

Q ss_pred             HHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHH
Q 044084          100 SLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESM  156 (343)
Q Consensus       100 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  156 (343)
                      .+...+.+.|++++|+..|++..+..+. +..+|..+..+|...|++++|++.+++.
T Consensus        13 ~lG~~~~~~~~~~~A~~~y~~Al~~~p~-~~~~~~nlg~~~~~~~~~~~A~~~~~~a   68 (127)
T 4gcn_A           13 DLGNAAYKQKDFEKAHVHYDKAIELDPS-NITFYNNKAAVYFEEKKFAECVQFCEKA   68 (127)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHhHHHHHHHhhhHHHHHHHHHHH
Confidence            3334444444444444444444443321 3344444444444444444444444443

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=98.56  E-value=1.5e-06  Score=60.29  Aligned_cols=97  Identities=15%  Similarity=0.123  Sum_probs=41.5

Q ss_pred             HHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCC--CC----HHHHH
Q 044084           61 HMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGML--RD----LEVFL  134 (343)
Q Consensus        61 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~----~~~~~  134 (343)
                      ..|..+...+...|++++|...|++..... +.+...+..+...+...|++++|...+++..+....  ++    ..++.
T Consensus         5 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (131)
T 1elr_A            5 LKEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYA   83 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHH
Confidence            344444444445555555555555444432 113333444444444444444444444444432211  01    33344


Q ss_pred             HHHHHHHhcCcHhHHHHHHHHHHh
Q 044084          135 KLVLMYIEEGMVEKTLEVVESMKN  158 (343)
Q Consensus       135 ~l~~~~~~~~~~~~a~~~~~~~~~  158 (343)
                      .+...+...|++++|.+.|++..+
T Consensus        84 ~la~~~~~~~~~~~A~~~~~~~~~  107 (131)
T 1elr_A           84 RIGNSYFKEEKYKDAIHFYNKSLA  107 (131)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHH
Confidence            444444444444444444444433

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=98.55  E-value=3.5e-06  Score=59.13  Aligned_cols=97  Identities=11%  Similarity=-0.017  Sum_probs=49.3

Q ss_pred             hHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHH
Q 044084           95 PSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNG  174 (343)
Q Consensus        95 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  174 (343)
                      ...+..+...+...|+++.|...|.+..+..+. +...+..+..++...|++++|...+++..+.++ .+...+..+..+
T Consensus         9 ~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~l~~~   86 (137)
T 3q49_B            9 AQELKEQGNRLFVGRKYPEAAACYGRAITRNPL-VAVYYTNRALCYLKMQQPEQALADCRRALELDG-QSVKAHFFLGQC   86 (137)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHhhCcC-cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCc-hhHHHHHHHHHH
Confidence            344445555555555555555555555554322 445555555555555555555555555554433 233344445555


Q ss_pred             HhcCCcHHHHHHHHHHHHH
Q 044084          175 FSKRRAYWAAVKVYEQLIS  193 (343)
Q Consensus       175 ~~~~~~~~~a~~~~~~~~~  193 (343)
                      +...|++++|...|++..+
T Consensus        87 ~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           87 QLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhhHHHHHHHHHHHHH
Confidence            5555555555555555443

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=98.53  E-value=1.4e-06  Score=60.50  Aligned_cols=62  Identities=10%  Similarity=-0.020  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHH
Q 044084          131 EVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLIS  193 (343)
Q Consensus       131 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  193 (343)
                      ..+..+...+...|++++|...|++.....+ .+...+..+...+...|++++|...+++...
T Consensus         5 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~   66 (131)
T 1elr_A            5 LKEKELGNDAYKKKDFDTALKHYDKAKELDP-TNMTYITNQAAVYFEKGDYNKCRELCEKAIE   66 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhcCC-ccHHHHHHHHHHHHHhccHHHHHHHHHHHHh
Confidence            3444455555555555555555555544432 2333444444455555555555555554443

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.52  E-value=3.3e-06  Score=61.51  Aligned_cols=99  Identities=16%  Similarity=0.018  Sum_probs=72.8

Q ss_pred             ChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHH
Q 044084           94 DPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVN  173 (343)
Q Consensus        94 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  173 (343)
                      +...+..+...+.+.|++++|...|++..+.... +...|..+..+|...|++++|+..|++..+... .+...|..+..
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~   87 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSKAIDLYTQALSIAPA-NPIYLSNRAAAYSASGQHEKAAEDAELATVVDP-KYSKAWSRLGL   87 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCc-CHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCC-CCHHHHHHHHH
Confidence            3445666777777788888888888887776543 677777777888888888888888887777654 34566777777


Q ss_pred             HHhcCCcHHHHHHHHHHHHHc
Q 044084          174 GFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       174 ~~~~~~~~~~a~~~~~~~~~~  194 (343)
                      ++...|++++|...|++..+.
T Consensus        88 ~~~~~g~~~~A~~~~~~al~~  108 (164)
T 3sz7_A           88 ARFDMADYKGAKEAYEKGIEA  108 (164)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHccCHHHHHHHHHHHHHh
Confidence            777788888888887777765

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.51  E-value=1.8e-06  Score=59.32  Aligned_cols=89  Identities=18%  Similarity=0.046  Sum_probs=39.3

Q ss_pred             HHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcH
Q 044084           67 CDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMV  146 (343)
Q Consensus        67 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  146 (343)
                      ...+.+.|++++|+..|++..+... .+...|..+..++...|++++|...+++..+..+. +...+..+..++...|++
T Consensus        24 g~~~~~~g~~~~A~~~~~~al~~~P-~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~-~~~~~~~la~~~~~~g~~  101 (121)
T 1hxi_A           24 GLSMLKLANLAEAALAFEAVCQKEP-EREEAWRSLGLTQAENEKDGLAIIALNHARMLDPK-DIAVHAALAVSHTNEHNA  101 (121)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCH
Confidence            3344444444444444444444321 13334444444444444444444444444443322 344444444444444444


Q ss_pred             hHHHHHHHHHH
Q 044084          147 EKTLEVVESMK  157 (343)
Q Consensus       147 ~~a~~~~~~~~  157 (343)
                      ++|+..|++..
T Consensus       102 ~~A~~~~~~al  112 (121)
T 1hxi_A          102 NAALASLRAWL  112 (121)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            44444444444

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.51  E-value=7.4e-06  Score=58.15  Aligned_cols=96  Identities=11%  Similarity=-0.052  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCc---hhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHH
Q 044084          131 EVFLKLVLMYIEEGMVEKTLEVVESMKNAELNIS---DCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASII  207 (343)
Q Consensus       131 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll  207 (343)
                      ..+..+...+...|++++|...|++..+.... +   ...+..+..++...|++++|...+++..+.. +.+...+..+.
T Consensus        29 ~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a  106 (148)
T 2dba_A           29 EQLRKEGNELFKCGDYGGALAAYTQALGLDAT-PQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKD-GGDVKALYRRS  106 (148)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHHHHHTSCCC-HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-SCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHHccc-chHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-ccCHHHHHHHH
Confidence            33444444444444444444444444333210 1   2233333444444444444444444443331 11233333344


Q ss_pred             HHHHccCChhHHHHHHHHHHH
Q 044084          208 NAYCRIGLYSKAEKVFIEMQQ  228 (343)
Q Consensus       208 ~~~~~~~~~~~a~~~~~~~~~  228 (343)
                      .++...|++++|...|+...+
T Consensus       107 ~~~~~~~~~~~A~~~~~~al~  127 (148)
T 2dba_A          107 QALEKLGRLDQAVLDLQRCVS  127 (148)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHH
Confidence            444444444444444444443

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.48  E-value=1.7e-06  Score=62.45  Aligned_cols=132  Identities=15%  Similarity=0.007  Sum_probs=70.7

Q ss_pred             HHHHHHHHHHhcCcHhHHHHHHHHHHhcCCC-Cc----hhhHHHHHHHHhcCCcHHHHHHHHHHHHHc----CCCC-CHh
Q 044084          132 VFLKLVLMYIEEGMVEKTLEVVESMKNAELN-IS----DCISCVIVNGFSKRRAYWAAVKVYEQLISQ----GCIP-GQV  201 (343)
Q Consensus       132 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~p-~~~  201 (343)
                      ++..+...+...|++++|...+++..+.... .+    ..++..+...+...|++++|...+++..+.    +..+ ...
T Consensus        11 ~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~   90 (164)
T 3ro3_A           11 AFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQ   90 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHH
Confidence            4455555555556666666655554432110 00    124455555566666666666666655432    1000 123


Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHHHHc----CCC-cChhhHHHHHHHHHccCChHHHHHHHHHHhh
Q 044084          202 TYASIINAYCRIGLYSKAEKVFIEMQQK----GFD-KCVVAYSSMVAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       202 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                      .+..+...+...|++++|...++...+.    +.+ .....+..+...+...|++++|.+.+++..+
T Consensus        91 ~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~  157 (164)
T 3ro3_A           91 SCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLE  157 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            4555566666677777777766665532    111 1134566666777777777777777766553

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.46  E-value=2.9e-06  Score=58.33  Aligned_cols=95  Identities=12%  Similarity=0.014  Sum_probs=71.1

Q ss_pred             HHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhc
Q 044084           98 YASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSK  177 (343)
Q Consensus        98 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  177 (343)
                      +..+...+.+.|++++|...+++..+..+. +...|..+..++...|++++|+..|++..+..+ .+...+..+..++..
T Consensus        20 ~~~~g~~~~~~g~~~~A~~~~~~al~~~P~-~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P-~~~~~~~~la~~~~~   97 (121)
T 1hxi_A           20 PMEEGLSMLKLANLAEAALAFEAVCQKEPE-REEAWRSLGLTQAENEKDGLAIIALNHARMLDP-KDIAVHAALAVSHTN   97 (121)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHH
Confidence            445556677788888888888888876543 677788888888888888888888888777665 355567777778888


Q ss_pred             CCcHHHHHHHHHHHHHc
Q 044084          178 RRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       178 ~~~~~~a~~~~~~~~~~  194 (343)
                      .|++++|...+++..+.
T Consensus        98 ~g~~~~A~~~~~~al~~  114 (121)
T 1hxi_A           98 EHNANAALASLRAWLLS  114 (121)
T ss_dssp             HHHHHHHHHHHHHHHC-
T ss_pred             cCCHHHHHHHHHHHHHh
Confidence            88888888888877654

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=98.41  E-value=5.5e-06  Score=71.22  Aligned_cols=123  Identities=11%  Similarity=-0.020  Sum_probs=64.1

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCC--------------hHhHHHHHHHHhcccCHHHHHHHHHHHHHcC
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEKGILED--------------PSVYASLICSFASIAEVKVAEELFKEAEEKG  125 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~--------------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  125 (343)
                      ...|..+...+.+.|++++|+..|++..+......              ...|..+..++.+.|++++|...+++..+..
T Consensus       268 a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~  347 (457)
T 1kt0_A          268 AAIVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD  347 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC
Confidence            45666777777777777777777777766421111              2344445555555555555555555555543


Q ss_pred             CCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHH
Q 044084          126 MLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAA  184 (343)
Q Consensus       126 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  184 (343)
                      .. +...|..+..+|...|++++|+..|++..+..+ .+...+..+..++...++.+++
T Consensus       348 p~-~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~P-~~~~a~~~l~~~~~~~~~~~~a  404 (457)
T 1kt0_A          348 SA-NEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNP-QNKAARLQISMCQKKAKEHNER  404 (457)
T ss_dssp             TT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-----CHHHHHHHHHHHHHHHHHH
T ss_pred             Cc-cHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHHHHHHH
Confidence            22 445555555555555555555555555544432 2333444444444444444433

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=98.40  E-value=4.4e-07  Score=78.42  Aligned_cols=124  Identities=12%  Similarity=0.036  Sum_probs=94.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHH
Q 044084           25 YCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICS  104 (343)
Q Consensus        25 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  104 (343)
                      +..+...+.+.|++++|.+.|++..+..    |.+..+|..+..++.+.|++++|++.+++..+... .+...+..+..+
T Consensus         9 ~~~lg~~~~~~g~~~~A~~~~~~Al~~~----p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p-~~~~~~~~lg~~   83 (477)
T 1wao_1            9 LKTQANDYFKAKDYENAIKFYSQAIELN----PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDK-KYIKGYYRRAAS   83 (477)
T ss_dssp             SSSSSSSTTTTTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHhC----CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC-CCHHHHHHHHHH
Confidence            4444556678899999999999987764    33368899999999999999999999999988742 356788888889


Q ss_pred             HhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH--HHhcCcHhHHHHHHH
Q 044084          105 FASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLM--YIEEGMVEKTLEVVE  154 (343)
Q Consensus       105 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~~a~~~~~  154 (343)
                      +...|++++|...+++..+.... +...+..+..+  +.+.|++++|++.++
T Consensus        84 ~~~~g~~~eA~~~~~~al~~~p~-~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           84 NMALGKFRAALRDYETVVKVKPH-DKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHSTT-CTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            99999999999999998886543 44455555555  888899999999988

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.39  E-value=3.4e-06  Score=60.86  Aligned_cols=95  Identities=14%  Similarity=0.051  Sum_probs=41.1

Q ss_pred             HHHHHHHHhhccCcHHHHHHHHHHHHhcCCC-CC----hHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCC-C----CHH
Q 044084           62 MYKILCDSLGKSGRAFEILKFFRDMKEKGIL-ED----PSVYASLICSFASIAEVKVAEELFKEAEEKGML-R----DLE  131 (343)
Q Consensus        62 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~----~~~  131 (343)
                      ++..+...+...|++++|+..+++..+.... ++    ..++..+...+...|++++|...+++..+.... .    ...
T Consensus        11 ~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~   90 (164)
T 3ro3_A           11 AFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQ   90 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHH
Confidence            4444555555555555555555554432100 00    123344444444555555555555444331100 0    123


Q ss_pred             HHHHHHHHHHhcCcHhHHHHHHHHH
Q 044084          132 VFLKLVLMYIEEGMVEKTLEVVESM  156 (343)
Q Consensus       132 ~~~~l~~~~~~~~~~~~a~~~~~~~  156 (343)
                      ++..+...+...|++++|.+.+++.
T Consensus        91 ~~~~l~~~~~~~~~~~~A~~~~~~a  115 (164)
T 3ro3_A           91 SCYSLGNTYTLLQDYEKAIDYHLKH  115 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            3444444555555555555555443

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=98.39  E-value=6.1e-06  Score=70.93  Aligned_cols=125  Identities=10%  Similarity=-0.012  Sum_probs=71.6

Q ss_pred             CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCc--------------hhhHHHHHHHHhcCCcHHHHHHHHHHHHHc
Q 044084          129 DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNIS--------------DCISCVIVNGFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       129 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--------------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  194 (343)
                      ....+..+...+.+.|++++|+..|++..+......              ...|..+..+|.+.|++++|+..+++..+.
T Consensus       267 ~a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  346 (457)
T 1kt0_A          267 QAAIVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGL  346 (457)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            345667777777788888888888887766443211              245555556666666666666666665554


Q ss_pred             CCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHH
Q 044084          195 GCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAM  255 (343)
Q Consensus       195 ~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  255 (343)
                      . +.+...|..+..+|...|++++|...|+...+.. +.+...+..+..++.+.++.+++.
T Consensus       347 ~-p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~-P~~~~a~~~l~~~~~~~~~~~~a~  405 (457)
T 1kt0_A          347 D-SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVN-PQNKAARLQISMCQKKAKEHNERD  405 (457)
T ss_dssp             S-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-----CHHHHHHHHHHHHHHHHHHH
T ss_pred             C-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHH
Confidence            3 2344555555566666666666666666655543 223445555555555555555443

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.37  E-value=3e-05  Score=53.58  Aligned_cols=91  Identities=16%  Similarity=0.090  Sum_probs=38.6

Q ss_pred             HHHhhccCcHHHHHHHHHHHHhcCCCCCh---HhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHH
Q 044084           67 CDSLGKSGRAFEILKFFRDMKEKGILEDP---SVYASLICSFASIAEVKVAEELFKEAEEKGMLRD---LEVFLKLVLMY  140 (343)
Q Consensus        67 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~  140 (343)
                      ...+...|++++|.+.|++..+.... +.   ..+..+..++...|++++|...++++.+..+. +   ...+..+..++
T Consensus         9 a~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~~~~la~~~   86 (129)
T 2xev_A            9 AFDALKNGKYDDASQLFLSFLELYPN-GVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPT-HDKAAGGLLKLGLSQ   86 (129)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCSS-STTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-STTHHHHHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHHCCC-CcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCC-CcccHHHHHHHHHHH
Confidence            33344444444444444444433211 11   23333444444444444444444444443321 1   33344444444


Q ss_pred             HhcCcHhHHHHHHHHHHhc
Q 044084          141 IEEGMVEKTLEVVESMKNA  159 (343)
Q Consensus       141 ~~~~~~~~a~~~~~~~~~~  159 (343)
                      ...|++++|...|+++...
T Consensus        87 ~~~g~~~~A~~~~~~~~~~  105 (129)
T 2xev_A           87 YGEGKNTEAQQTLQQVATQ  105 (129)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHH
Confidence            4455555555555444443

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.36  E-value=1.9e-05  Score=54.58  Aligned_cols=93  Identities=10%  Similarity=-0.096  Sum_probs=49.3

Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCCCCH---HHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCc--hhhHHHHHHHH
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGMLRDL---EVFLKLVLMYIEEGMVEKTLEVVESMKNAELNIS--DCISCVIVNGF  175 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~  175 (343)
                      +...+...|++++|...|+.+.+..+. +.   ..+..+..++...|++++|...|++.....+...  ...+..+..++
T Consensus         8 ~a~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~la~~~   86 (129)
T 2xev_A            8 VAFDALKNGKYDDASQLFLSFLELYPN-GVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPTHDKAAGGLLKLGLSQ   86 (129)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCSS-STTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHHCCC-CcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHH
Confidence            344455556666666666666554322 22   3555555566666666666666666555432110  23344455555


Q ss_pred             hcCCcHHHHHHHHHHHHHc
Q 044084          176 SKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       176 ~~~~~~~~a~~~~~~~~~~  194 (343)
                      ...|++++|...|+++.+.
T Consensus        87 ~~~g~~~~A~~~~~~~~~~  105 (129)
T 2xev_A           87 YGEGKNTEAQQTLQQVATQ  105 (129)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHH
Confidence            5556666666665555554

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=98.35  E-value=2.7e-06  Score=73.46  Aligned_cols=124  Identities=13%  Similarity=0.044  Sum_probs=99.1

Q ss_pred             HHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 044084           63 YKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIE  142 (343)
Q Consensus        63 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  142 (343)
                      +..+...+.+.|++++|++.|++..+... .+..+|..+..++.+.|++++|...+++..+.... +...+..+..+|..
T Consensus         9 ~~~lg~~~~~~g~~~~A~~~~~~Al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~-~~~~~~~lg~~~~~   86 (477)
T 1wao_1            9 LKTQANDYFKAKDYENAIKFYSQAIELNP-SNAIYYGNRSLAYLRTECYGYALGDATRAIELDKK-YIKGYYRRAASNMA   86 (477)
T ss_dssp             SSSSSSSTTTTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTT-CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHH
Confidence            44455667789999999999999988742 25778999999999999999999999999997643 78899999999999


Q ss_pred             cCcHhHHHHHHHHHHhcCCCCchhhHHHHHHH--HhcCCcHHHHHHHHH
Q 044084          143 EGMVEKTLEVVESMKNAELNISDCISCVIVNG--FSKRRAYWAAVKVYE  189 (343)
Q Consensus       143 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~~a~~~~~  189 (343)
                      .|++++|++.|++..+..+ .+...+..+..+  +...|++++|.+.++
T Consensus        87 ~g~~~eA~~~~~~al~~~p-~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           87 LGKFRAALRDYETVVKVKP-HDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HTCHHHHHHHHHHHHHHST-TCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             cCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            9999999999999988764 234455555555  788899999999988

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=98.31  E-value=1.6e-05  Score=66.29  Aligned_cols=124  Identities=12%  Similarity=-0.004  Sum_probs=62.8

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhCCC------------CCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCC
Q 044084           24 CYCQIMEAFYKIGDSEKVAALFLECESRKL------------DLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGI   91 (343)
Q Consensus        24 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~------------~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~   91 (343)
                      .+..+...+.+.|++++|...|++..+...            ..+|....+|..+..++.+.|++++|++.+++..+...
T Consensus       225 ~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p  304 (370)
T 1ihg_A          225 DLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEIDP  304 (370)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCT
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhCc
Confidence            356666777777888888777777654100            01122234455555555555555555555555554321


Q ss_pred             CCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHH
Q 044084           92 LEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKT  149 (343)
Q Consensus        92 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  149 (343)
                       .+...+..+..++...|++++|...|++..+.... +...+..+...+...++.+++
T Consensus       305 -~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~P~-~~~~~~~l~~~~~~~~~~~~a  360 (370)
T 1ihg_A          305 -SNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPE-DKAIQAELLKVKQKIKAQKDK  360 (370)
T ss_dssp             -TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHHHHHH
T ss_pred             -hhHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHHHHH
Confidence             13344444555555555555555555555544322 344444444444444444333

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=98.30  E-value=3.6e-06  Score=57.43  Aligned_cols=86  Identities=8%  Similarity=0.017  Sum_probs=37.4

Q ss_pred             CCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHH
Q 044084           36 GDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAE  115 (343)
Q Consensus        36 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  115 (343)
                      |++++|...|++..+.+.. +|.+..+|..+...+...|++++|++.|++..+.... +...+..+..++...|++++|.
T Consensus         4 g~~~~A~~~~~~al~~~~~-~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~A~   81 (117)
T 3k9i_A            4 GLEAQAVPYYEKAIASGLQ-GKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPN-HQALRVFYAMVLYNLGRYEQGV   81 (117)
T ss_dssp             ---CCCHHHHHHHHSSCCC-HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCC-CccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-chHHHHHHHHHHHHcCCHHHHH
Confidence            4444455555544443210 1222344444555555555555555555554443211 2334444444444555555555


Q ss_pred             HHHHHHHH
Q 044084          116 ELFKEAEE  123 (343)
Q Consensus       116 ~~~~~~~~  123 (343)
                      ..+++..+
T Consensus        82 ~~~~~al~   89 (117)
T 3k9i_A           82 ELLLKIIA   89 (117)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            55544444

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=98.27  E-value=0.00012  Score=64.49  Aligned_cols=173  Identities=7%  Similarity=-0.050  Sum_probs=112.8

Q ss_pred             HHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccC----------HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC-
Q 044084           76 AFEILKFFRDMKEKGILEDPSVYASLICSFASIAE----------VKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEG-  144 (343)
Q Consensus        76 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-  144 (343)
                      .++|++.++++...+.. +...|+.--.++...++          ++++...++.+.+..++ +..+|+.-...+.+.+ 
T Consensus        45 ~eeal~~~~~~l~~nP~-~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~pK-~y~aW~hR~w~l~~l~~  122 (567)
T 1dce_A           45 DESVLELTSQILGANPD-FATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPK-SYGTWHHRCWLLSRLPE  122 (567)
T ss_dssp             SHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHTCSS
T ss_pred             CHHHHHHHHHHHHHCch-hHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHccc
Confidence            45667777776665322 34445554444444444          67777777777776654 6777777777777777 


Q ss_pred             -cHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCC-cHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHcc---------
Q 044084          145 -MVEKTLEVVESMKNAELNISDCISCVIVNGFSKRR-AYWAAVKVYEQLISQGCIPGQVTYASIINAYCRI---------  213 (343)
Q Consensus       145 -~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~---------  213 (343)
                       +++++++.++++.+.++ -+..+|+.-...+...| .++++.+.++++.+.. +-+...|+.....+.+.         
T Consensus       123 ~~~~~el~~~~k~l~~d~-~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~-p~n~saW~~r~~ll~~l~~~~~~~~~  200 (567)
T 1dce_A          123 PNWARELELCARFLEADE-RNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSSWHYRSCLLPQLHPQPDSGPQ  200 (567)
T ss_dssp             CCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT-CCCHHHHHHHHHHHHHHSCCCCSSSC
T ss_pred             ccHHHHHHHHHHHHhhcc-ccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHC-CCCccHHHHHHHHHHhhccccccccc
Confidence             55777777777777665 45666666666666666 6777777777776654 33555666555554442         


Q ss_pred             -----CChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHH
Q 044084          214 -----GLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRD  253 (343)
Q Consensus       214 -----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  253 (343)
                           +.++++.+.++...... +-|...|+-+-..+.+.++.++
T Consensus       201 ~~~~~~~~~eel~~~~~ai~~~-P~~~saW~y~~~ll~~~~~~~~  244 (567)
T 1dce_A          201 GRLPENVLLKELELVQNAFFTD-PNDQSAWFYHRWLLGRAEPHDV  244 (567)
T ss_dssp             CSSCHHHHHHHHHHHHHHHHHC-SSCSHHHHHHHHHHSCCCCCSC
T ss_pred             ccccHHHHHHHHHHHHHHHhhC-CCCccHHHHHHHHHhcCCCccc
Confidence                 45688888888888765 5577888888777777776443

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=98.27  E-value=1.3e-05  Score=66.69  Aligned_cols=98  Identities=9%  Similarity=-0.027  Sum_probs=51.7

Q ss_pred             HHHHHHHHHHHhcCcHhHHHHHHHHHHhcC---------------CCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcC
Q 044084          131 EVFLKLVLMYIEEGMVEKTLEVVESMKNAE---------------LNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQG  195 (343)
Q Consensus       131 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---------------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  195 (343)
                      ..+..+...+.+.|++++|+..|++..+.-               -+.+..+|..+..+|.+.|++++|...+++..+..
T Consensus       224 ~~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~  303 (370)
T 1ihg_A          224 EDLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID  303 (370)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhC
Confidence            446677778888888888888888776521               00122334444444455555555555555544432


Q ss_pred             CCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHc
Q 044084          196 CIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       196 ~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  229 (343)
                       +.+...+..+..+|...|++++|...|+...+.
T Consensus       304 -p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l  336 (370)
T 1ihg_A          304 -PSNTKALYRRAQGWQGLKEYDQALADLKKAQEI  336 (370)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             -chhHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence             122334444444444555555555555544443

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=98.27  E-value=2.4e-05  Score=56.67  Aligned_cols=64  Identities=9%  Similarity=0.061  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHc
Q 044084          130 LEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       130 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  194 (343)
                      ..+|..+..+|.+.|++++|+..+++....++ .+...|..+..++...|++++|...|++....
T Consensus        63 ~~~~~nla~~~~~~~~~~~A~~~~~~al~~~p-~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  126 (162)
T 3rkv_A           63 IPLYANMSQCYLNIGDLHEAEETSSEVLKREE-TNEKALFRRAKARIAAWKLDEAEEDLKLLLRN  126 (162)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCcHHHHHHHHHHHHhcCC-cchHHHHHHHHHHHHHhcHHHHHHHHHHHHhc
Confidence            34455555555555555555555555555443 33444555555555555555555555555544

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=98.26  E-value=5.9e-06  Score=68.01  Aligned_cols=148  Identities=11%  Similarity=0.027  Sum_probs=74.1

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLM  139 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  139 (343)
                      ...+..+...+.+.|++++|+..|++....  .|+...       +...++.+++...+.          ..+|..+..+
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~-------~~~~~~~~~~~~~l~----------~~~~~nla~~  239 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDFM-------FQLYGKYQDMALAVK----------NPCHLNIAAC  239 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHHH-------HTCCHHHHHHHHHHH----------THHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccchh-------hhhcccHHHHHHHHH----------HHHHHHHHHH
Confidence            355667777888888888888888887664  233221       122233333322211          1366677777


Q ss_pred             HHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCC-HhhHHHHHHH-HHccCChh
Q 044084          140 YIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPG-QVTYASIINA-YCRIGLYS  217 (343)
Q Consensus       140 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~-~~~~~~ll~~-~~~~~~~~  217 (343)
                      |.+.|++++|+..+++..+... .+...|..+..+|...|++++|...|++..+.  .|+ ...+..+... ....+..+
T Consensus       240 ~~~~g~~~~A~~~~~~al~~~p-~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l--~p~~~~a~~~L~~l~~~~~~~~~  316 (338)
T 2if4_A          240 LIKLKRYDEAIGHCNIVLTEEE-KNPKALFRRGKAKAELGQMDSARDDFRKAQKY--APDDKAIRRELRALAEQEKALYQ  316 (338)
T ss_dssp             HHTTTCCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC--------------------------
T ss_pred             HHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHH
Confidence            7777888888888777776654 35566777777777788888888877776654  233 2333333333 22345566


Q ss_pred             HHHHHHHHHHHc
Q 044084          218 KAEKVFIEMQQK  229 (343)
Q Consensus       218 ~a~~~~~~~~~~  229 (343)
                      .+..+|..+...
T Consensus       317 ~a~~~~~~~l~~  328 (338)
T 2if4_A          317 KQKEMYKGIFKG  328 (338)
T ss_dssp             ------------
T ss_pred             HHHHHHHHhhCC
Confidence            677777776654

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=98.25  E-value=0.00012  Score=64.58  Aligned_cols=175  Identities=7%  Similarity=-0.049  Sum_probs=137.6

Q ss_pred             CCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCc----------HHHHHHHHHHHHhcCCCCChHhHHHHHHHH
Q 044084           36 GDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGR----------AFEILKFFRDMKEKGILEDPSVYASLICSF  105 (343)
Q Consensus        36 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~----------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  105 (343)
                      ...++|++.++.+...+.    ....+|+.--..+...++          ++++++.++.+.+...+ +..+|+.-...+
T Consensus        43 ~~~eeal~~~~~~l~~nP----~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~pK-~y~aW~hR~w~l  117 (567)
T 1dce_A           43 ELDESVLELTSQILGANP----DFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPK-SYGTWHHRCWLL  117 (567)
T ss_dssp             CCSHHHHHHHHHHHHHCT----TCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHCc----hhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCCC-CHHHHHHHHHHH
Confidence            345788999999988763    335788877777766666          89999999999987644 677888888888


Q ss_pred             hccc--CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcC----
Q 044084          106 ASIA--EVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEG-MVEKTLEVVESMKNAELNISDCISCVIVNGFSKR----  178 (343)
Q Consensus       106 ~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----  178 (343)
                      .+.+  +++++.+.++++.+.... +..+|+.-...+.+.| .++++++.++++.+.++ -+...|+.....+...    
T Consensus       118 ~~l~~~~~~~el~~~~k~l~~d~~-N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p-~n~saW~~r~~ll~~l~~~~  195 (567)
T 1dce_A          118 SRLPEPNWARELELCARFLEADER-NFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNF-SNYSSWHYRSCLLPQLHPQP  195 (567)
T ss_dssp             HTCSSCCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTC-CCHHHHHHHHHHHHHHSCCC
T ss_pred             HHcccccHHHHHHHHHHHHhhccc-cccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCC-CCccHHHHHHHHHHhhcccc
Confidence            8888  779999999999998765 8999999888888999 89999999999988876 5677777666555442    


Q ss_pred             ----------CcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhH
Q 044084          179 ----------RAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSK  218 (343)
Q Consensus       179 ----------~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~  218 (343)
                                +.++++.+.+++..... +-+...|.-.-..+.+.++.++
T Consensus       196 ~~~~~~~~~~~~~~eel~~~~~ai~~~-P~~~saW~y~~~ll~~~~~~~~  244 (567)
T 1dce_A          196 DSGPQGRLPENVLLKELELVQNAFFTD-PNDQSAWFYHRWLLGRAEPHDV  244 (567)
T ss_dssp             CSSSCCSSCHHHHHHHHHHHHHHHHHC-SSCSHHHHHHHHHHSCCCCCSC
T ss_pred             cccccccccHHHHHHHHHHHHHHHhhC-CCCccHHHHHHHHHhcCCCccc
Confidence                      56789999999988764 3456677777667766666443

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=98.25  E-value=2.6e-05  Score=56.49  Aligned_cols=64  Identities=14%  Similarity=0.191  Sum_probs=45.7

Q ss_pred             HhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcC
Q 044084           96 SVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus        96 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  160 (343)
                      ..|..+..++.+.|+++.|...+++..+..+. +...|..+..+|...|++++|...|++.....
T Consensus        64 ~~~~nla~~~~~~~~~~~A~~~~~~al~~~p~-~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~  127 (162)
T 3rkv_A           64 PLYANMSQCYLNIGDLHEAEETSSEVLKREET-NEKALFRRAKARIAAWKLDEAEEDLKLLLRNH  127 (162)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhcCcHHHHHHHHHHHHhcCCc-chHHHHHHHHHHHHHhcHHHHHHHHHHHHhcC
Confidence            45666667777777777777777777776532 56777777777777777777777777776654

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=98.22  E-value=3.3e-06  Score=57.58  Aligned_cols=84  Identities=13%  Similarity=0.220  Sum_probs=37.7

Q ss_pred             CcHHHHHHHHHHHHhcCC--CCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHH
Q 044084           74 GRAFEILKFFRDMKEKGI--LEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLE  151 (343)
Q Consensus        74 ~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  151 (343)
                      |++++|+..|++..+.+.  +.+...+..+..++...|++++|...+++..+..+. +..++..+..++...|++++|+.
T Consensus         4 g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~A~~   82 (117)
T 3k9i_A            4 GLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPN-HQALRVFYAMVLYNLGRYEQGVE   82 (117)
T ss_dssp             ---CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-chHHHHHHHHHHHHcCCHHHHHH
Confidence            445555555555544320  112233444444455555555555555555544332 34444445555555555555555


Q ss_pred             HHHHHHh
Q 044084          152 VVESMKN  158 (343)
Q Consensus       152 ~~~~~~~  158 (343)
                      .|++...
T Consensus        83 ~~~~al~   89 (117)
T 3k9i_A           83 LLLKIIA   89 (117)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            5554443

>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=98.17  E-value=0.0001  Score=51.77  Aligned_cols=112  Identities=10%  Similarity=0.015  Sum_probs=67.9

Q ss_pred             CCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhc----ccCH
Q 044084           36 GDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFAS----IAEV  111 (343)
Q Consensus        36 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~  111 (343)
                      +++++|.+.|++..+.+...      ..  |...|...+.+++|+++|++..+.|   +...+..|...|..    .++.
T Consensus         9 ~d~~~A~~~~~~aa~~g~~~------a~--lg~~y~~g~~~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~   77 (138)
T 1klx_A            9 KDLKKAIQYYVKACELNEMF------GC--LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDL   77 (138)
T ss_dssp             HHHHHHHHHHHHHHHTTCTT------HH--HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCH
T ss_pred             cCHHHHHHHHHHHHcCCCHh------hh--HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccH
Confidence            34566666666666655211      12  5555555556666666666666553   44555555555555    5667


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----cCcHhHHHHHHHHHHhcCC
Q 044084          112 KVAEELFKEAEEKGMLRDLEVFLKLVLMYIE----EGMVEKTLEVVESMKNAEL  161 (343)
Q Consensus       112 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~  161 (343)
                      ++|...|++..+.|   ++..+..|...|..    .+++++|.+.|++..+.|.
T Consensus        78 ~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  128 (138)
T 1klx_A           78 RKAAQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  128 (138)
T ss_dssp             HHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCCC
Confidence            77777777666654   45566666666666    6677777777777666654

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=98.16  E-value=4.7e-05  Score=54.21  Aligned_cols=96  Identities=13%  Similarity=-0.030  Sum_probs=51.5

Q ss_pred             HHHHHHHHhhccCcHHHHHHHHHHHHhcCCC-C-----C-----hHhHHHHHHHHhcccCHHHHHHHHHHHHHc------
Q 044084           62 MYKILCDSLGKSGRAFEILKFFRDMKEKGIL-E-----D-----PSVYASLICSFASIAEVKVAEELFKEAEEK------  124 (343)
Q Consensus        62 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~-~-----~-----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------  124 (343)
                      .+......+.+.|++++|+..|++..+.... |     +     ...|..+..++.+.|++++|+..+++.++.      
T Consensus        13 ~~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e   92 (159)
T 2hr2_A           13 LALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGE   92 (159)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhcccc
Confidence            3444555556666666666666666554211 0     1     114555555555555666555555555553      


Q ss_pred             -CCCCCHHHH----HHHHHHHHhcCcHhHHHHHHHHHHh
Q 044084          125 -GMLRDLEVF----LKLVLMYIEEGMVEKTLEVVESMKN  158 (343)
Q Consensus       125 -~~~~~~~~~----~~l~~~~~~~~~~~~a~~~~~~~~~  158 (343)
                       .+. +...|    .....++...|++++|+..|++..+
T Consensus        93 ~~pd-~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAle  130 (159)
T 2hr2_A           93 LNQD-EGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  130 (159)
T ss_dssp             TTST-HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CCCc-hHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHh
Confidence             321 34455    5556666666666666666665543

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=98.13  E-value=1.5e-05  Score=68.72  Aligned_cols=124  Identities=9%  Similarity=-0.000  Sum_probs=84.3

Q ss_pred             HHhcCcHhHHHHHHHHHHhcC---CC---C-chhhHHHHHHHHhcCCcHHHHHHHHHHHHHc-----C-CCCC-HhhHHH
Q 044084          140 YIEEGMVEKTLEVVESMKNAE---LN---I-SDCISCVIVNGFSKRRAYWAAVKVYEQLISQ-----G-CIPG-QVTYAS  205 (343)
Q Consensus       140 ~~~~~~~~~a~~~~~~~~~~~---~~---~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~-~~p~-~~~~~~  205 (343)
                      +...|++++|+.++++..+..   +-   | ...+++.+...|...|++++|..++++....     | -.|+ ..+++.
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            456788888888888765421   11   1 2346788888888888888888888876542     2 1222 356778


Q ss_pred             HHHHHHccCChhHHHHHHHHHHHc-----CC--CcChhhHHHHHHHHHccCChHHHHHHHHHHhh
Q 044084          206 IINAYCRIGLYSKAEKVFIEMQQK-----GF--DKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       206 ll~~~~~~~~~~~a~~~~~~~~~~-----~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                      |...|...|++++|+.++++..+.     |.  +....+.+.+-.++...+.+.+|..+|.++++
T Consensus       399 La~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~  463 (490)
T 3n71_A          399 AGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMRE  463 (490)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            888888888888888888876542     31  11233455666777777888888888888765

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=98.12  E-value=5.5e-05  Score=65.16  Aligned_cols=129  Identities=12%  Similarity=0.028  Sum_probs=90.6

Q ss_pred             HHhcCCcHHHHHHHHHHHHHcC---CC---C-CHhhHHHHHHHHHccCChhHHHHHHHHHHHc-----C--CCcChhhHH
Q 044084          174 GFSKRRAYWAAVKVYEQLISQG---CI---P-GQVTYASIINAYCRIGLYSKAEKVFIEMQQK-----G--FDKCVVAYS  239 (343)
Q Consensus       174 ~~~~~~~~~~a~~~~~~~~~~~---~~---p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~-----~--~~~~~~~~~  239 (343)
                      .+...|++++|..++++..+..   +.   | ...+++.+..+|...|++++|+.++++..+.     |  .+-...+++
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            4567899999999999877541   12   2 2467889999999999999999999987653     2  122346789


Q ss_pred             HHHHHHHccCChHHHHHHHHHHhhC---CCCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 044084          240 SMVAMYGKTGRIRDAMRLVAKMKPK---GCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFR  316 (343)
Q Consensus       240 ~l~~~~~~~~~~~~a~~~~~~m~~~---~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~  316 (343)
                      .|...|...|++++|..++++..+.   -+-||....               +.....+..++...|.+++|..+|++++
T Consensus       398 nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~---------------~~~~~~l~~~~~e~~~~~~ae~~~~~~~  462 (490)
T 3n71_A          398 RAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPIT---------------KDLEAMRMQTEMELRMFRQNEFMYHKMR  462 (490)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHH---------------HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHH---------------HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999887642   111221111               1112334455666777788888888876


Q ss_pred             h
Q 044084          317 M  317 (343)
Q Consensus       317 ~  317 (343)
                      +
T Consensus       463 ~  463 (490)
T 3n71_A          463 E  463 (490)
T ss_dssp             H
T ss_pred             H
Confidence            5

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=98.10  E-value=1.1e-05  Score=66.34  Aligned_cols=127  Identities=11%  Similarity=-0.010  Sum_probs=51.7

Q ss_pred             HHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCch------------------hhHHHHHHHHhcCCcHHHHHHHHHHHHHc
Q 044084          133 FLKLVLMYIEEGMVEKTLEVVESMKNAELNISD------------------CISCVIVNGFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       133 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~------------------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  194 (343)
                      +..+...+.+.|++++|...|++.....  |+.                  ..|..+..+|.+.|++++|...+++..+.
T Consensus       182 ~~~~g~~~~~~g~~~~A~~~y~~Al~~~--p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  259 (338)
T 2if4_A          182 RKMDGNSLFKEEKLEEAMQQYEMAIAYM--GDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNIVLTE  259 (338)
T ss_dssp             HHHHHHHTCSSSCCHHHHHHHHHHHHHS--CHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHh--ccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            4444555555555555655555554432  111                  14555566666666666666666666554


Q ss_pred             CCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHH-HHccCChHHHHHHHHHHhh
Q 044084          195 GCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAM-YGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       195 ~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~~~a~~~~~~m~~  263 (343)
                      . +.+...+..+..+|...|++++|...|+...+.. +.+...+..+... ....+..+.+...|.+|..
T Consensus       260 ~-p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~-p~~~~a~~~L~~l~~~~~~~~~~a~~~~~~~l~  327 (338)
T 2if4_A          260 E-EKNPKALFRRGKAKAELGQMDSARDDFRKAQKYA-PDDKAIRRELRALAEQEKALYQKQKEMYKGIFK  327 (338)
T ss_dssp             C-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC------------------------------------
T ss_pred             C-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            2 2244555566666666666666666666655432 1223333333333 1223344555555555554

>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=98.09  E-value=0.00017  Score=50.65  Aligned_cols=110  Identities=6%  Similarity=-0.108  Sum_probs=63.5

Q ss_pred             cHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHc----cCChhHHH
Q 044084          145 MVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCR----IGLYSKAE  220 (343)
Q Consensus       145 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~----~~~~~~a~  220 (343)
                      ++++|++.|++..+.+. +..  .  +...|...+.+++|.+.|++..+.|   +...+..+...|..    .+++++|.
T Consensus        10 d~~~A~~~~~~aa~~g~-~~a--~--lg~~y~~g~~~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~   81 (138)
T 1klx_A           10 DLKKAIQYYVKACELNE-MFG--C--LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKAA   81 (138)
T ss_dssp             HHHHHHHHHHHHHHTTC-TTH--H--HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHH
T ss_pred             CHHHHHHHHHHHHcCCC-Hhh--h--HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccHHHHH
Confidence            45566666666655553 222  1  4445555555566666666666553   34445555555555    56666666


Q ss_pred             HHHHHHHHcCCCcChhhHHHHHHHHHc----cCChHHHHHHHHHHhhCC
Q 044084          221 KVFIEMQQKGFDKCVVAYSSMVAMYGK----TGRIRDAMRLVAKMKPKG  265 (343)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~m~~~~  265 (343)
                      ..|+...+.|   ++..+..|...|..    .++.++|..+|++..+.|
T Consensus        82 ~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g  127 (138)
T 1klx_A           82 QYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  127 (138)
T ss_dssp             HHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCC
Confidence            6666666654   34555566666665    566677777776666654

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=98.06  E-value=0.00013  Score=51.99  Aligned_cols=95  Identities=9%  Similarity=-0.085  Sum_probs=58.6

Q ss_pred             HHHHHHHHhcccCHHHHHHHHHHHHHcCCCC------CH-----HHHHHHHHHHHhcCcHhHHHHHHHHHHhc-------
Q 044084           98 YASLICSFASIAEVKVAEELFKEAEEKGMLR------DL-----EVFLKLVLMYIEEGMVEKTLEVVESMKNA-------  159 (343)
Q Consensus        98 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~------~~-----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-------  159 (343)
                      +......+.+.|++++|...|++..+..+..      +.     ..|..+..++.+.|++++|+..+++..+.       
T Consensus        14 ~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~   93 (159)
T 2hr2_A           14 ALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGEL   93 (159)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCT
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccC
Confidence            4445566677788888888888877754321      22     26677777777777777777777766654       


Q ss_pred             CCCCchhhH----HHHHHHHhcCCcHHHHHHHHHHHHH
Q 044084          160 ELNISDCIS----CVIVNGFSKRRAYWAAVKVYEQLIS  193 (343)
Q Consensus       160 ~~~~~~~~~----~~l~~~~~~~~~~~~a~~~~~~~~~  193 (343)
                      ++ -+...|    .....++...|++++|+..|++..+
T Consensus        94 ~p-d~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAle  130 (159)
T 2hr2_A           94 NQ-DEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  130 (159)
T ss_dssp             TS-THHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CC-chHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHh
Confidence            32 233344    5555566666666666666665544

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.98  E-value=4.6e-05  Score=50.95  Aligned_cols=63  Identities=17%  Similarity=0.179  Sum_probs=35.7

Q ss_pred             hhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhC
Q 044084          201 VTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       201 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                      ..+..+...+...|++++|...|+...+.. +.+...+..+..++...|++++|...+++..+.
T Consensus         5 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~   67 (111)
T 2l6j_A            5 EKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRY   67 (111)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            344455555555666666666666555543 334555555666666666666666666665543

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.93  E-value=7.7e-05  Score=50.39  Aligned_cols=81  Identities=11%  Similarity=0.042  Sum_probs=60.6

Q ss_pred             hhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHH
Q 044084            4 QSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFF   83 (343)
Q Consensus         4 ~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~   83 (343)
                      ++|+..|++..+..+ .+...+..+...+.+.|++++|...|++..+..    |.....|..+..++...|++++|...|
T Consensus         2 ~~a~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~----p~~~~~~~~la~~~~~~g~~~~A~~~~   76 (115)
T 2kat_A            2 QAITERLEAMLAQGT-DNMLLRFTLGKTYAEHEQFDAALPHLRAALDFD----PTYSVAWKWLGKTLQGQGDRAGARQAW   76 (115)
T ss_dssp             CCHHHHHHHHHTTTC-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC----CCcHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            457777888777643 456777888888888888888888888877654    223567788888888888888888888


Q ss_pred             HHHHhc
Q 044084           84 RDMKEK   89 (343)
Q Consensus        84 ~~~~~~   89 (343)
                      ++..+.
T Consensus        77 ~~al~~   82 (115)
T 2kat_A           77 ESGLAA   82 (115)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            877654

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.91  E-value=0.00025  Score=45.26  Aligned_cols=61  Identities=16%  Similarity=0.217  Sum_probs=25.0

Q ss_pred             HHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHH
Q 044084           62 MYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEE  123 (343)
Q Consensus        62 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  123 (343)
                      .+..+...+...|++++|+..|++..+... .+...+..+...+...|++++|...+++..+
T Consensus        11 ~~~~la~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~   71 (91)
T 1na3_A           11 AWYNLGNAYYKQGDYDEAIEYYQKALELDP-NNAEAWYNLGNAYYKQGDYDEAIEYYQKALE   71 (91)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            333444444444444444444444433321 1233333344444444444444444444443

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.85  E-value=8.8e-05  Score=49.51  Aligned_cols=59  Identities=10%  Similarity=0.058  Sum_probs=22.9

Q ss_pred             HHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHH
Q 044084          133 FLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLI  192 (343)
Q Consensus       133 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  192 (343)
                      +..+...+...|++++|++.|++..+..+ .+...+..+..++...|++++|...+++..
T Consensus         7 ~~~~g~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al   65 (111)
T 2l6j_A            7 QKEQGNSLFKQGLYREAVHCYDQLITAQP-QNPVGYSNKAMALIKLGEYTQAIQMCQQGL   65 (111)
T ss_dssp             HHHHHHHHHTTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            33333344444444444444444333322 122333333334444444444444444433

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.83  E-value=0.00026  Score=45.12  Aligned_cols=63  Identities=16%  Similarity=0.209  Sum_probs=33.5

Q ss_pred             hHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcC
Q 044084           97 VYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus        97 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  160 (343)
                      .+..+...+...|++++|...+++..+.... +...+..+...+...|++++|...|++..+..
T Consensus        11 ~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~   73 (91)
T 1na3_A           11 AWYNLGNAYYKQGDYDEAIEYYQKALELDPN-NAEAWYNLGNAYYKQGDYDEAIEYYQKALELD   73 (91)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC
Confidence            3444445555555555555555555554322 44555555555555555555555555555443

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=97.81  E-value=0.00019  Score=51.02  Aligned_cols=69  Identities=13%  Similarity=-0.074  Sum_probs=31.3

Q ss_pred             cCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCH----------HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 044084           73 SGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEV----------KVAEELFKEAEEKGMLRDLEVFLKLVLMYIE  142 (343)
Q Consensus        73 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~----------~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  142 (343)
                      .+.+++|++.+++..+.... +...|..+..++...+++          ++|+..|++.++..+. +..+|..+..+|..
T Consensus        15 ~~~feeA~~~~~~Ai~l~P~-~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~-~~~A~~~LG~ay~~   92 (158)
T 1zu2_A           15 ILLFEQIRQDAENTYKSNPL-DADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPK-KDEAVWCIGNAYTS   92 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHH
T ss_pred             HhHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcC-cHHHHHHHHHHHHH
Confidence            34455555555555544321 444455444455444433          2444444444444322 34444444444444


Q ss_pred             c
Q 044084          143 E  143 (343)
Q Consensus       143 ~  143 (343)
                      .
T Consensus        93 l   93 (158)
T 1zu2_A           93 F   93 (158)
T ss_dssp             H
T ss_pred             h
Confidence            3

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.80  E-value=0.00036  Score=47.00  Aligned_cols=62  Identities=13%  Similarity=-0.079  Sum_probs=29.0

Q ss_pred             hHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHH
Q 044084           95 PSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMK  157 (343)
Q Consensus        95 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  157 (343)
                      ...+..+...+...|++++|...+++..+..+. +...|..+..+|...|++++|...|++..
T Consensus        19 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~la~~~~~~g~~~~A~~~~~~al   80 (115)
T 2kat_A           19 MLLRFTLGKTYAEHEQFDAALPHLRAALDFDPT-YSVAWKWLGKTLQGQGDRAGARQAWESGL   80 (115)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            334444444444445555555555444443321 34444444555555555555555554443

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=97.75  E-value=0.00027  Score=50.26  Aligned_cols=88  Identities=14%  Similarity=0.076  Sum_probs=52.9

Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcH----------HHHHHHHHHHHhcCCCCChHhHHHH
Q 044084           32 FYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRA----------FEILKFFRDMKEKGILEDPSVYASL  101 (343)
Q Consensus        32 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~----------~~a~~~~~~~~~~~~~~~~~~~~~l  101 (343)
                      ..+.+.+++|.+.++...+.+    |.+...|..+..++...+++          ++|+..|++.++.+.. +..+|..+
T Consensus        12 ~~r~~~feeA~~~~~~Ai~l~----P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~-~~~A~~~L   86 (158)
T 1zu2_A           12 FDRILLFEQIRQDAENTYKSN----PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPK-KDEAVWCI   86 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHH
T ss_pred             HHHHhHHHHHHHHHHHHHHHC----CCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcC-cHHHHHHH
Confidence            345566777777777776655    33356677677777666654          4777777777665322 45566667


Q ss_pred             HHHHhccc-----------CHHHHHHHHHHHHHc
Q 044084          102 ICSFASIA-----------EVKVAEELFKEAEEK  124 (343)
Q Consensus       102 ~~~~~~~~-----------~~~~a~~~~~~~~~~  124 (343)
                      ..+|...|           ++++|...|++..+.
T Consensus        87 G~ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl~l  120 (158)
T 1zu2_A           87 GNAYTSFAFLTPDETEAKHNFDLATQFFQQAVDE  120 (158)
T ss_dssp             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcccCcchhhhhccHHHHHHHHHHHHHh
Confidence            77766554           445555555544443

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.63  E-value=0.00028  Score=46.26  Aligned_cols=63  Identities=19%  Similarity=0.190  Sum_probs=34.4

Q ss_pred             HhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhh
Q 044084          200 QVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       200 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                      ...+..+..+|...|++++|...|+...+.. +.+...|..+..+|...|++++|...|++..+
T Consensus         7 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~   69 (100)
T 3ma5_A            7 PFTRYALAQEHLKHDNASRALALFEELVETD-PDYVGTYYHLGKLYERLDRTDDAIDTYAQGIE   69 (100)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            3444555555555555666655555555543 23344555555555556666666555555543

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.57  E-value=0.00069  Score=44.35  Aligned_cols=63  Identities=13%  Similarity=0.033  Sum_probs=30.5

Q ss_pred             CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHH
Q 044084          129 DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLI  192 (343)
Q Consensus       129 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  192 (343)
                      +...+..+...|...|++++|+..|++..+.++ .+...|..+..+|...|++++|.+.|++..
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~g~~~~A~~~~~~al   68 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETDP-DYVGTYYHLGKLYERLDRTDDAIDTYAQGI   68 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCTHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            344444555555555555555555555544433 233344445555555555555555554443

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=97.55  E-value=0.0038  Score=51.01  Aligned_cols=64  Identities=8%  Similarity=0.065  Sum_probs=32.7

Q ss_pred             CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHc
Q 044084          129 DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       129 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  194 (343)
                      ++.++..+...+...|++++|...+++....+  |+...|..+...+...|++++|.+.|++....
T Consensus       276 ~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL  339 (372)
T 3ly7_A          276 LSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNL  339 (372)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            44555555444444455555555555555443  34434444444555555555555555555544

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=97.42  E-value=0.011  Score=48.28  Aligned_cols=48  Identities=10%  Similarity=-0.034  Sum_probs=27.8

Q ss_pred             CCChHhHHHHHHHHhc--c---cCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 044084           92 LEDPSVYASLICSFAS--I---AEVKVAEELFKEAEEKGMLRDLEVFLKLVLMY  140 (343)
Q Consensus        92 ~~~~~~~~~l~~~~~~--~---~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  140 (343)
                      +.+...|...+++...  .   .+..+|..+|++..+..+. ....|..+..+|
T Consensus       191 p~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~lDP~-~a~A~A~la~a~  243 (372)
T 3ly7_A          191 PHRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQSSPE-FTYARAEKALVD  243 (372)
T ss_dssp             CSSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCC-CHHHHHHHHHHH
Confidence            4466677776655432  2   2357778888888876533 345555444444

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=97.33  E-value=0.0021  Score=54.46  Aligned_cols=93  Identities=11%  Similarity=-0.032  Sum_probs=61.9

Q ss_pred             ccCChhHHHHHHHHHHHc---CCCc----ChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhccc
Q 044084          212 RIGLYSKAEKVFIEMQQK---GFDK----CVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAK  284 (343)
Q Consensus       212 ~~~~~~~a~~~~~~~~~~---~~~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~  284 (343)
                      ..|++++|+.++++..+.   -+.|    ...+++.|..+|...|++++|..++++..+.            .....-..
T Consensus       310 ~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i------------~~~~lG~~  377 (433)
T 3qww_A          310 HYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKP------------YSKHYPVY  377 (433)
T ss_dssp             TTSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH------------HHHHSCSS
T ss_pred             hccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHH------------HHHHcCCC
Confidence            457899999999887653   1122    2467899999999999999999999988642            00111112


Q ss_pred             ChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 044084          285 NLRQLEKYTTVISAYNMAREFDMCVKFYNEFR  316 (343)
Q Consensus       285 ~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~  316 (343)
                      ..+-|..++.|...|...|++++|+.++++..
T Consensus       378 Hp~~a~~l~nLa~~~~~qg~~~eA~~~~~~Al  409 (433)
T 3qww_A          378 SLNVASMWLKLGRLYMGLENKAAGEKALKKAI  409 (433)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHhccCHHHHHHHHHHHH
Confidence            23333335566666667777777777777663

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=97.24  E-value=0.0019  Score=41.86  Aligned_cols=57  Identities=12%  Similarity=0.109  Sum_probs=32.3

Q ss_pred             HHHhcccCHHHHHHHHHHHHHcCCCCCHH-HHHHHHHHHHhcCcHhHHHHHHHHHHhcC
Q 044084          103 CSFASIAEVKVAEELFKEAEEKGMLRDLE-VFLKLVLMYIEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus       103 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  160 (343)
                      ..+.+.|++++|...+++..+.... +.. .+..+..+|...|++++|++.|++..+..
T Consensus         8 ~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~   65 (99)
T 2kc7_A            8 KELINQGDIENALQALEEFLQTEPV-GKDEAYYLMGNAYRKLGDWQKALNNYQSAIELN   65 (99)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHCSS-THHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            3444556666666666665554432 444 55556666666666666666666655544

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=97.22  E-value=0.003  Score=53.51  Aligned_cols=56  Identities=16%  Similarity=-0.045  Sum_probs=24.6

Q ss_pred             HHhcCCHHHHHHHHHHHHhCC---CCC-CCchHHHHHHHHHHhhccCcHHHHHHHHHHHH
Q 044084           32 FYKIGDSEKVAALFLECESRK---LDL-TPSSTHMYKILCDSLGKSGRAFEILKFFRDMK   87 (343)
Q Consensus        32 ~~~~~~~~~a~~~~~~~~~~~---~~~-~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~   87 (343)
                      +.+.|++++|+.++++..+..   ..+ .|....+++.|...|...|++++|+.++++.+
T Consensus       297 ~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L  356 (429)
T 3qwp_A          297 LKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTM  356 (429)
T ss_dssp             HHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHH
Confidence            334455555555555443321   111 11223444555555555555555555554443

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=97.22  E-value=0.0012  Score=56.01  Aligned_cols=87  Identities=6%  Similarity=-0.080  Sum_probs=68.4

Q ss_pred             cCCcHHHHHHHHHHHHHc---CCCCC----HhhHHHHHHHHHccCChhHHHHHHHHHHHc-----C--CCcChhhHHHHH
Q 044084          177 KRRAYWAAVKVYEQLISQ---GCIPG----QVTYASIINAYCRIGLYSKAEKVFIEMQQK-----G--FDKCVVAYSSMV  242 (343)
Q Consensus       177 ~~~~~~~a~~~~~~~~~~---~~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~-----~--~~~~~~~~~~l~  242 (343)
                      ..|++++|..++++..+.   -+.|+    ..+++.+..+|...|++++|+.++++..+.     |  .+-...+++.|.
T Consensus       310 ~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa  389 (433)
T 3qww_A          310 HYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLG  389 (433)
T ss_dssp             TTSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHH
Confidence            467899999999987653   12222    367889999999999999999999987653     2  112245789999


Q ss_pred             HHHHccCChHHHHHHHHHHhh
Q 044084          243 AMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       243 ~~~~~~~~~~~a~~~~~~m~~  263 (343)
                      ..|...|++++|..++++..+
T Consensus       390 ~~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          390 RLYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhccCHHHHHHHHHHHHH
Confidence            999999999999999988764

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=97.13  E-value=0.0017  Score=55.08  Aligned_cols=92  Identities=11%  Similarity=0.025  Sum_probs=69.6

Q ss_pred             HHHHhcCCcHHHHHHHHHHHHHcC---CCCC----HhhHHHHHHHHHccCChhHHHHHHHHHHHc-----C--CCcChhh
Q 044084          172 VNGFSKRRAYWAAVKVYEQLISQG---CIPG----QVTYASIINAYCRIGLYSKAEKVFIEMQQK-----G--FDKCVVA  237 (343)
Q Consensus       172 ~~~~~~~~~~~~a~~~~~~~~~~~---~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~-----~--~~~~~~~  237 (343)
                      +..+...|++++|..++++..+..   +.|+    ..+++.+..+|...|++++|+.++++..+.     |  .+....+
T Consensus       294 ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~  373 (429)
T 3qwp_A          294 IEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQ  373 (429)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHH
T ss_pred             HHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHH
Confidence            455667889999999999887541   2222    357888889999999999999999887653     2  1122457


Q ss_pred             HHHHHHHHHccCChHHHHHHHHHHhh
Q 044084          238 YSSMVAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       238 ~~~l~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                      ++.|...|...|++++|..++++..+
T Consensus       374 l~nLa~~~~~~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          374 VMKVGKLQLHQGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            88899999999999999998888764

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=97.05  E-value=0.075  Score=41.77  Aligned_cols=85  Identities=12%  Similarity=0.022  Sum_probs=60.9

Q ss_pred             HHHHHHHHHHHHHcCCCCC---HHHHHHHHHHHHhc-----CcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcC-CcH
Q 044084          111 VKVAEELFKEAEEKGMLRD---LEVFLKLVLMYIEE-----GMVEKTLEVVESMKNAELNISDCISCVIVNGFSKR-RAY  181 (343)
Q Consensus       111 ~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~-----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~  181 (343)
                      ...|...+++..+..  |+   ...|..+...|.+.     |+.++|.+.|++..+.++.-+..++....+.++.. |+.
T Consensus       179 l~~A~a~lerAleLD--P~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~  256 (301)
T 3u64_A          179 VHAAVMMLERACDLW--PSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNR  256 (301)
T ss_dssp             HHHHHHHHHHHHHHC--TTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCH
T ss_pred             HHHHHHHHHHHHHhC--CCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCH
Confidence            566777777777754  44   56788888888874     88888888888887766532355666777777774 888


Q ss_pred             HHHHHHHHHHHHcCCC
Q 044084          182 WAAVKVYEQLISQGCI  197 (343)
Q Consensus       182 ~~a~~~~~~~~~~~~~  197 (343)
                      +.+.+.+++.......
T Consensus       257 ~~a~~~L~kAL~a~p~  272 (301)
T 3u64_A          257 AGFDEALDRALAIDPE  272 (301)
T ss_dssp             HHHHHHHHHHHHCCGG
T ss_pred             HHHHHHHHHHHcCCCC
Confidence            8888888888876444

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=97.05  E-value=0.0018  Score=42.04  Aligned_cols=56  Identities=13%  Similarity=0.131  Sum_probs=26.7

Q ss_pred             HhhccCcHHHHHHHHHHHHhcCCCCChH-hHHHHHHHHhcccCHHHHHHHHHHHHHcC
Q 044084           69 SLGKSGRAFEILKFFRDMKEKGILEDPS-VYASLICSFASIAEVKVAEELFKEAEEKG  125 (343)
Q Consensus        69 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  125 (343)
                      .+...|++++|++.|++..+... .+.. .+..+..++...|++++|...|++..+..
T Consensus         9 ~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~   65 (99)
T 2kc7_A            9 ELINQGDIENALQALEEFLQTEP-VGKDEAYYLMGNAYRKLGDWQKALNNYQSAIELN   65 (99)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHCS-STHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHcCCHHHHHHHHHHHHHHCC-CcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            34444555555555555544321 1233 44444455555555555555555555443

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=97.03  E-value=0.013  Score=54.19  Aligned_cols=155  Identities=12%  Similarity=0.097  Sum_probs=99.4

Q ss_pred             HHHHHhcCCHHHHHH-HHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhc
Q 044084           29 MEAFYKIGDSEKVAA-LFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFAS  107 (343)
Q Consensus        29 ~~~~~~~~~~~~a~~-~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  107 (343)
                      .......+++++|.+ ++..     ++ +   ......++..+.+.|.++.|+++.+.         ..   .-......
T Consensus       606 ~~~~~~~~~~~~a~~~~l~~-----i~-~---~~~~~~~~~~l~~~~~~~~a~~~~~~---------~~---~~f~~~l~  664 (814)
T 3mkq_A          606 FQTLTLRGEIEEAIENVLPN-----VE-G---KDSLTKIARFLEGQEYYEEALNISPD---------QD---QKFELALK  664 (814)
T ss_dssp             HHHHHHTTCHHHHHHHTGGG-----CC-C---HHHHHHHHHHHHHTTCHHHHHHHCCC---------HH---HHHHHHHH
T ss_pred             HhHHHHhCCHHHHHHHHHhc-----CC-c---hHHHHHHHHHHHhCCChHHheecCCC---------cc---hheehhhh
Confidence            344456788888877 5422     11 0   12336777778888888888876532         11   11334567


Q ss_pred             ccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHH
Q 044084          108 IAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKV  187 (343)
Q Consensus       108 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  187 (343)
                      .|+++.|.++.+.+      .+...|..+...+.+.++++.|.+.|.++.+         |..+...+...|+.+...++
T Consensus       665 ~~~~~~A~~~~~~~------~~~~~W~~la~~al~~~~~~~A~~~y~~~~d---------~~~l~~l~~~~~~~~~~~~~  729 (814)
T 3mkq_A          665 VGQLTLARDLLTDE------SAEMKWRALGDASLQRFNFKLAIEAFTNAHD---------LESLFLLHSSFNNKEGLVTL  729 (814)
T ss_dssp             HTCHHHHHHHHTTC------CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTC---------HHHHHHHHHHTTCHHHHHHH
T ss_pred             cCCHHHHHHHHHhh------CcHhHHHHHHHHHHHcCCHHHHHHHHHHccC---------hhhhHHHHHHcCCHHHHHHH
Confidence            78999998875432      3788999999999999999999999998753         44455555557777766666


Q ss_pred             HHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHH
Q 044084          188 YEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIE  225 (343)
Q Consensus       188 ~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~  225 (343)
                      -+.....|      -++....+|.+.|++++|.+++.+
T Consensus       730 ~~~a~~~~------~~~~A~~~~~~~g~~~~a~~~~~~  761 (814)
T 3mkq_A          730 AKDAETTG------KFNLAFNAYWIAGDIQGAKDLLIK  761 (814)
T ss_dssp             HHHHHHTT------CHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHcC------chHHHHHHHHHcCCHHHHHHHHHH
Confidence            55555543      123334445556666666665543

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.99  E-value=0.031  Score=51.58  Aligned_cols=155  Identities=11%  Similarity=0.119  Sum_probs=102.1

Q ss_pred             HhhccCcHHHHHH-HHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHh
Q 044084           69 SLGKSGRAFEILK-FFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVE  147 (343)
Q Consensus        69 ~~~~~~~~~~a~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  147 (343)
                      .....+++++|.+ ++..+      |+......++..+.+.|..+.|.++.+         +..   .-.......|+++
T Consensus       608 ~~~~~~~~~~a~~~~l~~i------~~~~~~~~~~~~l~~~~~~~~a~~~~~---------~~~---~~f~~~l~~~~~~  669 (814)
T 3mkq_A          608 TLTLRGEIEEAIENVLPNV------EGKDSLTKIARFLEGQEYYEEALNISP---------DQD---QKFELALKVGQLT  669 (814)
T ss_dssp             HHHHTTCHHHHHHHTGGGC------CCHHHHHHHHHHHHHTTCHHHHHHHCC---------CHH---HHHHHHHHHTCHH
T ss_pred             HHHHhCCHHHHHHHHHhcC------CchHHHHHHHHHHHhCCChHHheecCC---------Ccc---hheehhhhcCCHH
Confidence            3345778888766 44211      112233667777788888888876653         211   1134467789999


Q ss_pred             HHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHH
Q 044084          148 KTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQ  227 (343)
Q Consensus       148 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  227 (343)
                      +|.++.+.+      .+...|..+...+.+.++++.|.+.|.++.+         |..+...+...|+.+...++-+...
T Consensus       670 ~A~~~~~~~------~~~~~W~~la~~al~~~~~~~A~~~y~~~~d---------~~~l~~l~~~~~~~~~~~~~~~~a~  734 (814)
T 3mkq_A          670 LARDLLTDE------SAEMKWRALGDASLQRFNFKLAIEAFTNAHD---------LESLFLLHSSFNNKEGLVTLAKDAE  734 (814)
T ss_dssp             HHHHHHTTC------CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTC---------HHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHhh------CcHhHHHHHHHHHHHcCCHHHHHHHHHHccC---------hhhhHHHHHHcCCHHHHHHHHHHHH
Confidence            999986544      4566899999999999999999999998754         3445555566777777666665555


Q ss_pred             HcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHh
Q 044084          228 QKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMK  262 (343)
Q Consensus       228 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~  262 (343)
                      ..|      -++....+|.+.|++++|.+++.++.
T Consensus       735 ~~~------~~~~A~~~~~~~g~~~~a~~~~~~~~  763 (814)
T 3mkq_A          735 TTG------KFNLAFNAYWIAGDIQGAKDLLIKSQ  763 (814)
T ss_dssp             HTT------CHHHHHHHHHHHTCHHHHHHHHHHTT
T ss_pred             HcC------chHHHHHHHHHcCCHHHHHHHHHHcC
Confidence            544      23444445666777777777766654

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=96.80  E-value=0.025  Score=36.19  Aligned_cols=49  Identities=4%  Similarity=-0.052  Sum_probs=26.2

Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcC
Q 044084          111 VKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus       111 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  160 (343)
                      .++|..++++..+..+. ++.....+...+.+.|++++|+..|+++.+..
T Consensus        25 ~~~A~~~l~~AL~~dp~-~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~   73 (93)
T 3bee_A           25 TDEVSLLLEQALQLEPY-NEAALSLIANDHFISFRFQEAIDTWVLLLDSN   73 (93)
T ss_dssp             CHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCC
T ss_pred             CHHHHHHHHHHHHHCcC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            45555555555554432 45555555555555555555555555555444

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=96.74  E-value=0.015  Score=40.89  Aligned_cols=83  Identities=18%  Similarity=0.165  Sum_probs=40.6

Q ss_pred             HHHHHHHHHHHhcCCCCChHhHHHHHHHHhccc---CHHHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHhcCcHhHHHHH
Q 044084           77 FEILKFFRDMKEKGILEDPSVYASLICSFASIA---EVKVAEELFKEAEEKG-MLRDLEVFLKLVLMYIEEGMVEKTLEV  152 (343)
Q Consensus        77 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~  152 (343)
                      ..+.+.|.+....|. ++..+...+..++++++   +.+++..+++...+.. +.-....+-.|.-+|.+.|++++|++.
T Consensus        15 ~~~~~~y~~e~~~~~-~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~~p~~~rd~lY~LAv~~~kl~~Y~~A~~y   93 (152)
T 1pc2_A           15 LKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKALKY   93 (152)
T ss_dssp             HHHHHHHHHHHHTTC-CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHHHHccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccchHHHHHHHHHHHHHccCHHHHHHH
Confidence            334444444444333 34444444444555554   4445555555555543 101234444455555566666666666


Q ss_pred             HHHHHhcC
Q 044084          153 VESMKNAE  160 (343)
Q Consensus       153 ~~~~~~~~  160 (343)
                      ++.+.+..
T Consensus        94 ~~~lL~ie  101 (152)
T 1pc2_A           94 VRGLLQTE  101 (152)
T ss_dssp             HHHHHHHC
T ss_pred             HHHHHhcC
Confidence            66655544

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=96.70  E-value=0.034  Score=35.54  Aligned_cols=67  Identities=9%  Similarity=0.029  Sum_probs=46.6

Q ss_pred             CCHHHHHHHHHHHHhcCc---HhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcC
Q 044084          128 RDLEVFLKLVLMYIEEGM---VEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQG  195 (343)
Q Consensus       128 ~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  195 (343)
                      .++..+..+..++...++   .++|..++++..+.++ -+......+...+...|++++|+..|+++.+..
T Consensus         4 ~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp-~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~   73 (93)
T 3bee_A            4 VTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEP-YNEAALSLIANDHFISFRFQEAIDTWVLLLDSN   73 (93)
T ss_dssp             CCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCC
T ss_pred             CCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCc-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            456666666666654444   5778888887777665 455566667777777888888888888877763

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=96.61  E-value=0.11  Score=37.53  Aligned_cols=130  Identities=10%  Similarity=0.040  Sum_probs=87.8

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcc
Q 044084           29 MEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASI  108 (343)
Q Consensus        29 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  108 (343)
                      .....+.|+++.|.++.+.+.      +   ...|..|.......|+++-|.+.|.+...         +..+.-.|.-.
T Consensus        12 F~LAL~lg~l~~A~e~a~~l~------~---~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D---------~~~L~~Ly~~t   73 (177)
T 3mkq_B           12 FDLALEYGNLDAALDEAKKLN------D---SITWERLIQEALAQGNASLAEMIYQTQHS---------FDKLSFLYLVT   73 (177)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHC------C---HHHHHHHHHHHHHTTCHHHHHHHHHHTTC---------HHHHHHHHHHH
T ss_pred             HHHHHhcCCHHHHHHHHHHhC------C---HHHHHHHHHHHHHcCChHHHHHHHHHhCC---------HHHHHHHHHHh
Confidence            455668899999998877651      1   46899999999999999999999987643         55565666777


Q ss_pred             cCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHH
Q 044084          109 AEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVY  188 (343)
Q Consensus       109 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  188 (343)
                      |+.+....+-+.....|-      ++.....+.-.|+++++.++|.+..+.   |-      -+......|..+.|.++.
T Consensus        74 g~~e~L~kla~iA~~~g~------~n~af~~~l~lGdv~~~i~lL~~~~r~---~e------A~~~A~t~g~~~~a~~~~  138 (177)
T 3mkq_B           74 GDVNKLSKMQNIAQTRED------FGSMLLNTFYNNSTKERSSIFAEGGSL---PL------AYAVAKANGDEAAASAFL  138 (177)
T ss_dssp             TCHHHHHHHHHHHHHTTC------HHHHHHHHHHHTCHHHHHHHHHHTTCH---HH------HHHHHHHTTCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHCcc------HHHHHHHHHHcCCHHHHHHHHHHCCCh---HH------HHHHHHHcCcHHHHHHHH
Confidence            888777766665555542      344455566778888888888654321   11      111122356677777777


Q ss_pred             HHH
Q 044084          189 EQL  191 (343)
Q Consensus       189 ~~~  191 (343)
                      +++
T Consensus       139 ~~~  141 (177)
T 3mkq_B          139 EQA  141 (177)
T ss_dssp             HHT
T ss_pred             HHh
Confidence            665

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=96.60  E-value=0.037  Score=38.88  Aligned_cols=86  Identities=13%  Similarity=0.144  Sum_probs=55.8

Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC---cHhHHHHHHHHHHhcCCCC--chhhHHHHHHHHhcCCcHHHH
Q 044084          110 EVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEG---MVEKTLEVVESMKNAELNI--SDCISCVIVNGFSKRRAYWAA  184 (343)
Q Consensus       110 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a  184 (343)
                      ....+.+-|.+....+. ++..+...+..++++.+   +.++++.+|+...+.+. |  ....+-.+.-++.+.|++++|
T Consensus        13 ~l~~~~~~y~~e~~~~~-~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~~-p~~~rd~lY~LAv~~~kl~~Y~~A   90 (152)
T 1pc2_A           13 DLLKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKGS-KEEQRDYVFYLAVGNYRLKEYEKA   90 (152)
T ss_dssp             HHHHHHHHHHHHHHTTC-CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSC-HHHHHHHHHHHHHHHHHTSCHHHH
T ss_pred             HHHHHHHHHHHHHccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCC-ccchHHHHHHHHHHHHHccCHHHH
Confidence            34455556666555554 57777777777777777   55677888877776652 2  233344555666777888888


Q ss_pred             HHHHHHHHHcCCCCC
Q 044084          185 VKVYEQLISQGCIPG  199 (343)
Q Consensus       185 ~~~~~~~~~~~~~p~  199 (343)
                      .+.++.+.+.  .|+
T Consensus        91 ~~y~~~lL~i--eP~  103 (152)
T 1pc2_A           91 LKYVRGLLQT--EPQ  103 (152)
T ss_dssp             HHHHHHHHHH--CTT
T ss_pred             HHHHHHHHhc--CCC
Confidence            8888777776  454

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=96.41  E-value=0.052  Score=42.66  Aligned_cols=89  Identities=8%  Similarity=-0.046  Sum_probs=62.0

Q ss_pred             hhhHHHHHHHHHhCCCCCC---hhhHHHHHHHHHh-----cCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhcc-
Q 044084            3 SQSKLHYYEKMKSAGIVLD---SGCYCQIMEAFYK-----IGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKS-   73 (343)
Q Consensus         3 ~~~A~~~~~~~~~~~~~~~---~~~~~~l~~~~~~-----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~-   73 (343)
                      ..+|...+++.++..  |+   ...|..+...|.+     .|+.++|.+.|++..+.+...+   ..++......++.. 
T Consensus       179 l~~A~a~lerAleLD--P~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~---id~~v~YA~~l~~~~  253 (301)
T 3u64_A          179 VHAAVMMLERACDLW--PSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHD---PDHHITYADALCIPL  253 (301)
T ss_dssp             HHHHHHHHHHHHHHC--TTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTC---SHHHHHHHHHTTTTT
T ss_pred             HHHHHHHHHHHHHhC--CCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCC---chHHHHHHHHHHHhc
Confidence            356777777777753  44   5577888888887     4888888888888877664322   45666677777774 


Q ss_pred             CcHHHHHHHHHHHHhcCCC--CChH
Q 044084           74 GRAFEILKFFRDMKEKGIL--EDPS   96 (343)
Q Consensus        74 ~~~~~a~~~~~~~~~~~~~--~~~~   96 (343)
                      |+.+++.+.+++.......  |+..
T Consensus       254 gd~~~a~~~L~kAL~a~p~~~P~~~  278 (301)
T 3u64_A          254 NNRAGFDEALDRALAIDPESVPHNK  278 (301)
T ss_dssp             TCHHHHHHHHHHHHHCCGGGCSSCH
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCChh
Confidence            8888888888888876554  4443

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=96.41  E-value=0.064  Score=35.06  Aligned_cols=66  Identities=11%  Similarity=-0.085  Sum_probs=35.1

Q ss_pred             CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcC------CCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHc
Q 044084          129 DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAE------LNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       129 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  194 (343)
                      +..-+..|...+.+.++++.|...|+...+..      ..+....+..+..++.+.|+++.|...+++..+.
T Consensus         4 sa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l   75 (104)
T 2v5f_A            4 TAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (104)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhc
Confidence            44445555666666666666666665544321      1123344555555555566666666665555544

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=96.39  E-value=0.12  Score=35.20  Aligned_cols=140  Identities=11%  Similarity=0.048  Sum_probs=82.3

Q ss_pred             hcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHH
Q 044084          106 ASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAV  185 (343)
Q Consensus       106 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  185 (343)
                      .-.|..++..++..+..+.   .+..-+|.++--....-+-+-..++++.+-..   .|.          ...|+.....
T Consensus        18 ildG~v~qGveii~k~~~s---sni~E~NW~ICNiiD~a~C~y~v~vLd~IGki---FDi----------s~C~NlKrVi   81 (172)
T 1wy6_A           18 LLDGYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGSY---FDL----------DKCQNLKSVV   81 (172)
T ss_dssp             HHTTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGG---SCG----------GGCSCTHHHH
T ss_pred             HHhhhHHHHHHHHHHHcCC---CCccccceeeeecchhhchhHHHHHHHHHhhh---cCc----------HhhhcHHHHH
Confidence            3446677777777776664   24555555555555555555555555555332   121          1122222222


Q ss_pred             HHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCC
Q 044084          186 KVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKG  265 (343)
Q Consensus       186 ~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~  265 (343)
                      .-+-.+     ..+...+...+......|+-++-.++...+... .+|++...-.+..+|.+.|+..++.+++.+.-+.|
T Consensus        82 ~C~~~~-----n~~se~vd~ALd~lv~~~KkDqLdki~~~~l~n-~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG  155 (172)
T 1wy6_A           82 ECGVIN-----NTLNEHVNKALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLLIEACKKG  155 (172)
T ss_dssp             HHHHHT-----TCCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHh-----cchHHHHHHHHHHHHHhccHhHHHHHHHHHhcc-CCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhh
Confidence            222221     123344556667777778888888887775443 35677777788888888888888888888888777


Q ss_pred             CC
Q 044084          266 CE  267 (343)
Q Consensus       266 ~~  267 (343)
                      ++
T Consensus       156 ~k  157 (172)
T 1wy6_A          156 EK  157 (172)
T ss_dssp             CH
T ss_pred             hH
Confidence            64

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=96.37  E-value=0.072  Score=37.07  Aligned_cols=56  Identities=14%  Similarity=0.110  Sum_probs=43.3

Q ss_pred             CChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchH
Q 044084          214 GLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNV  270 (343)
Q Consensus       214 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~  270 (343)
                      +++++|.++|+.+.+.+-.- ...|-.....-.++|++..|.+++.+.+..+.+|..
T Consensus        74 ~D~d~aR~vy~~a~~~hKkF-AKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k~~~  129 (161)
T 4h7y_A           74 QEPDDARDYFQMARANCKKF-AFVHISFAQFELSQGNVKKSKQLLQKAVERGAVPLE  129 (161)
T ss_dssp             HCGGGCHHHHHHHHHHCTTB-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBCHH
T ss_pred             cCHHHHHHHHHHHHHHhHHH-HHHHHHHHHHHHHcccHHHHHHHHHHHhccCCCcHH
Confidence            68888888888887653233 677777778888899999999999998887766544

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.31  E-value=0.43  Score=40.60  Aligned_cols=311  Identities=9%  Similarity=0.088  Sum_probs=168.4

Q ss_pred             chhhHHHHHHHHHhC-----CCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHh----hc
Q 044084            2 NSQSKLHYYEKMKSA-----GIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSL----GK   72 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~-----~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~----~~   72 (343)
                      ++++|++.+-.+.+.     +..-.......++..|.+.++++...+.+..+........    ..-..+++.+    ..
T Consensus        31 ~~~~a~e~ll~lEK~~r~~~d~~s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lskkr~qlk----~ai~~~V~~~~~~l~~  106 (445)
T 4b4t_P           31 DCNSALDQLLVLEKKTRQASDLASSKEVLAKIVDLLASRNKWDDLNEQLTLLSKKHGQLK----LSIQYMIQKVMEYLKS  106 (445)
T ss_dssp             HHHHHHHHHHHHHHHHSSSCSTTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHTTTTTSH----HHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhhhhH----HHHHHHHHHHHHHHhc
Confidence            567777776555432     2333456678889999999999998888776655433322    2233333322    22


Q ss_pred             cCcHH--HHHHHHHHHHh--cC-CCC---ChHhHHHHHHHHhcccCHHHHHHHHHHHHHc--CCCCC---HHHHHHHHHH
Q 044084           73 SGRAF--EILKFFRDMKE--KG-ILE---DPSVYASLICSFASIAEVKVAEELFKEAEEK--GMLRD---LEVFLKLVLM  139 (343)
Q Consensus        73 ~~~~~--~a~~~~~~~~~--~~-~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~---~~~~~~l~~~  139 (343)
                      ....+  .-..+.+.+..  .| +..   .......|...+...|++.+|..++..+...  |....   ...+...++.
T Consensus       107 ~~~~d~~~~~~~i~~l~~vte~kiflE~erarl~~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~rl  186 (445)
T 4b4t_P          107 SKSLDLNTRISVIETIRVVTENKIFVEVERARVTKDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMEL  186 (445)
T ss_dssp             HCTTHHHHHHHHHHCCSSSSSCCCCCCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHH
T ss_pred             CCchhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            22222  22222222111  11 111   1122355778888999999999999988653  22111   4567778899


Q ss_pred             HHhcCcHhHHHHHHHHHHh----cCCCCc--hhhHHHHHHHHhcCCcHHHHHHHHHHHHHc-CCCCCHhhHHHH----HH
Q 044084          140 YIEEGMVEKTLEVVESMKN----AELNIS--DCISCVIVNGFSKRRAYWAAVKVYEQLISQ-GCIPGQVTYASI----IN  208 (343)
Q Consensus       140 ~~~~~~~~~a~~~~~~~~~----~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~p~~~~~~~l----l~  208 (343)
                      |...+++..|..++.++..    ....|+  ...+...+..+...+++.+|.+.|.++... ....+...+..+    +.
T Consensus       187 ~l~~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~~~~~~~~~~~~e~~y~~a~~~y~e~~~~~~~~~d~~~~~~~L~~~v~  266 (445)
T 4b4t_P          187 SILKGDYSQATVLSRKILKKTFKNPKYESLKLEYYNLLVKISLHKREYLEVAQYLQEIYQTDAIKSDEAKWKPVLSHIVY  266 (445)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHhhcccCCcHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHH
Confidence            9999999999999988742    222222  234566777778889999998888877653 111122222211    11


Q ss_pred             HHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHcc--CChHHHHHHHHHHhhCC-C----CchHHHHHHHHHHHh
Q 044084          209 AYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKT--GRIRDAMRLVAKMKPKG-C----EPNVWIYNSLMDMHG  281 (343)
Q Consensus       209 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~a~~~~~~m~~~~-~----~p~~~~~~~l~~~~~  281 (343)
                      +..-.+..+.-..++........-++...|..++.+|...  .+++.+...|....... +    ......+..|.....
T Consensus       267 ~~iLa~~~~~~~~ll~~~~~~~~~~~l~~~~~L~k~f~~~~L~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~L~~~v~  346 (445)
T 4b4t_P          267 FLVLSPYGNLQNDLIHKIQNDNNLKKLESQESLVKLFTTNELMRWPIVQKTYEPVLNEDDLAFGGEANKHHWEDLQKRVI  346 (445)
T ss_dssp             HHHHSSCSSTTHHHHHSHHHHSSCHHHHHHHHHHHHHHHCCSSSHHHHHHHTCSSTTTCCSSCCCSCSSHHHHHHHHHHH
T ss_pred             HHHhCCCCchHHHHHHHHhhcccccccHHHHHHHHHHHhchHhhhHHHHHHHHHHhcccchhhhcchhhHHHHHHHHHHH
Confidence            1111222222223333333322235677888888888654  35666666665544321 1    011223344433333


Q ss_pred             cccChhHHHh------HHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 044084          282 RAKNLRQLEK------YTTVISAYNMAREFDMCVKFYNEFRMNG  319 (343)
Q Consensus       282 ~~~~~~~a~~------~~~l~~~~~~~g~~~~a~~~~~~m~~~~  319 (343)
                      .++- ..+.+      +..+...+.-  ..+++...+.+|...|
T Consensus       347 ehnl-~~i~k~Ys~I~l~~la~lL~l--~~~evE~~ls~mI~~g  387 (445)
T 4b4t_P          347 EHNL-RVISEYYSRITLLRLNELLDL--TESQTETYISDLVNQG  387 (445)
T ss_dssp             HHHH-HHHHHHEEEEEHHHHHHHHTS--CHHHHHHHHHHHHHHT
T ss_pred             HHHH-HHHHHHhceeeHHHHHHHhCc--CHHHHHHHHHHHHHCC
Confidence            2221 11111      4444444322  5678888888886654

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=96.30  E-value=0.07  Score=34.85  Aligned_cols=61  Identities=13%  Similarity=0.012  Sum_probs=27.6

Q ss_pred             HHHHHHHhhccCcHHHHHHHHHHHHhcC------CCCChHhHHHHHHHHhcccCHHHHHHHHHHHHH
Q 044084           63 YKILCDSLGKSGRAFEILKFFRDMKEKG------ILEDPSVYASLICSFASIAEVKVAEELFKEAEE  123 (343)
Q Consensus        63 ~~~li~~~~~~~~~~~a~~~~~~~~~~~------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  123 (343)
                      +..|...+.+.+++..|..+|+...+.-      ..+....+..+..++.+.|+++.|...++++.+
T Consensus         8 c~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~   74 (104)
T 2v5f_A            8 CFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLE   74 (104)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHh
Confidence            3445555555555555555555544320      011223344444444444444444444444444

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=96.07  E-value=0.11  Score=36.19  Aligned_cols=54  Identities=9%  Similarity=-0.040  Sum_probs=32.7

Q ss_pred             CcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCc
Q 044084          179 RAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDK  233 (343)
Q Consensus       179 ~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~  233 (343)
                      +++++|.++|+.+.+.+-.. ...|......=.+.|+++.|.+++......+.+|
T Consensus        74 ~D~d~aR~vy~~a~~~hKkF-AKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k~  127 (161)
T 4h7y_A           74 QEPDDARDYFQMARANCKKF-AFVHISFAQFELSQGNVKKSKQLLQKAVERGAVP  127 (161)
T ss_dssp             HCGGGCHHHHHHHHHHCTTB-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBC
T ss_pred             cCHHHHHHHHHHHHHHhHHH-HHHHHHHHHHHHHcccHHHHHHHHHHHhccCCCc
Confidence            56677777777776542222 4444444444556777777777777777766443

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=96.01  E-value=0.27  Score=35.50  Aligned_cols=129  Identities=9%  Similarity=-0.003  Sum_probs=78.2

Q ss_pred             HHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHH
Q 044084          103 CSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYW  182 (343)
Q Consensus       103 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  182 (343)
                      ......|+++.|.++.+.+      -+...|..|.......|+++-|.+.|.+...         +..+.-.|...|+.+
T Consensus        13 ~LAL~lg~l~~A~e~a~~l------~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D---------~~~L~~Ly~~tg~~e   77 (177)
T 3mkq_B           13 DLALEYGNLDAALDEAKKL------NDSITWERLIQEALAQGNASLAEMIYQTQHS---------FDKLSFLYLVTGDVN   77 (177)
T ss_dssp             HHHHHTTCHHHHHHHHHHH------CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC---------HHHHHHHHHHHTCHH
T ss_pred             HHHHhcCCHHHHHHHHHHh------CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC---------HHHHHHHHHHhCCHH
Confidence            3445667888887776654      2677888888888888888888888877653         334444555567776


Q ss_pred             HHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHH
Q 044084          183 AAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKM  261 (343)
Q Consensus       183 ~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m  261 (343)
                      ...++-+.....|      -++.....+.-.|+++++.++|.+..+   -|.      -+......|..+.|.++.+++
T Consensus        78 ~L~kla~iA~~~g------~~n~af~~~l~lGdv~~~i~lL~~~~r---~~e------A~~~A~t~g~~~~a~~~~~~~  141 (177)
T 3mkq_B           78 KLSKMQNIAQTRE------DFGSMLLNTFYNNSTKERSSIFAEGGS---LPL------AYAVAKANGDEAAASAFLEQA  141 (177)
T ss_dssp             HHHHHHHHHHHTT------CHHHHHHHHHHHTCHHHHHHHHHHTTC---HHH------HHHHHHHTTCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHCc------cHHHHHHHHHHcCCHHHHHHHHHHCCC---hHH------HHHHHHHcCcHHHHHHHHHHh
Confidence            6666655555443      244555556667888888877744222   111      111112245566666666655

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=95.97  E-value=6.2e-06  Score=68.80  Aligned_cols=252  Identities=12%  Similarity=0.179  Sum_probs=142.2

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHH
Q 044084           21 DSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYAS  100 (343)
Q Consensus        21 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  100 (343)
                      .+..|..|..+..+.+...+|.+-|-+   .+   +|   ..|..+|.+..+.|.+++-++.+...++..-  ++..=+.
T Consensus        53 ~p~VWs~LgkAqL~~~~v~eAIdsyIk---A~---Dp---s~y~eVi~~A~~~~~~edLv~yL~MaRk~~k--e~~IDte  121 (624)
T 3lvg_A           53 EPAVWSQLAKAQLQKGMVKEAIDSYIK---AD---DP---SSYMEVVQAANTSGNWEELVKYLQMARKKAR--ESYVETE  121 (624)
T ss_dssp             CCCCSSSHHHHTTTSSSCTTTTTSSCC---CS---CC---CSSSHHHHHTTTSSCCTTHHHHHHTTSTTCC--STTTTHH
T ss_pred             CccHHHHHHHHHHccCchHHHHHHHHh---CC---Ch---HHHHHHHHHHHhCCCHHHHHHHHHHHHHHhc--ccccHHH
Confidence            345677788888888877777765521   11   12   2478888888888888888888776655432  3344456


Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcC--------------------
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAE--------------------  160 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--------------------  160 (343)
                      |+-+|++.++..+.++.+.       .|+..-...+.+-|...|.++.|.-+|..+....                    
T Consensus       122 Li~ayAk~~rL~elEefl~-------~~N~A~iq~VGDrcf~e~lYeAAKilys~isN~akLAstLV~L~~yq~AVdaAr  194 (624)
T 3lvg_A          122 LIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGAR  194 (624)
T ss_dssp             HHHHHHTSCSSSTTTSTTS-------CCSSSCTHHHHHHHHHSCCSTTSSTTGGGSCCCTTTSSSSSSCSGGGSSTTTTT
T ss_pred             HHHHHHhhCcHHHHHHHHc-------CCCcccHHHHHHHHHHccCHHHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHHH
Confidence            7888888887655443322       2555555667777777777777777765543211                    


Q ss_pred             CCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHH
Q 044084          161 LNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSS  240 (343)
Q Consensus       161 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  240 (343)
                      -..++.||-.+-.+|...+++.-|.-.--.+.-.   ||  -...++..|-..|.+++.+.+++.-.... ......|+.
T Consensus       195 KAns~ktWKeV~~ACvd~~EfrLAqicGLniIvh---ad--eL~elv~~YE~~G~f~ELIsLlEaglglE-rAHmGmFTE  268 (624)
T 3lvg_A          195 KANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVH---AD--ELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTE  268 (624)
T ss_dssp             TCCSSCSHHHHTHHHHHSCTTTTTTHHHHHHHCC---SS--CCSGGGSSSSTTCCCTTSTTTHHHHTTST-TCCHHHHHH
T ss_pred             hcCChhHHHHHHHHHhCchHHHHHHHhcchhccc---HH--HHHHHHHHHHhCCCHHHHHHHHHHHhCCC-chhHHHHHH
Confidence            0123445666666666666555443332222211   11  12234555666667777666666655322 345666777


Q ss_pred             HHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHHH
Q 044084          241 MVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCV  309 (343)
Q Consensus       241 l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~  309 (343)
                      |.-.|++- +.++..+.++..-.+ +.  .   --++++|.+..-      |..++-.|.+-.+++.|.
T Consensus       269 LaILYsKY-~PeKlmEHlklf~sr-iN--i---pKviracE~ahL------W~ElvfLY~~ydE~DnA~  324 (624)
T 3lvg_A          269 LAILYSKF-KPQKMREHLELFWSR-VN--I---PKVLRAAEQAHL------WAELVFLYDKYEEYDNAI  324 (624)
T ss_dssp             HHHHHHSS-CTTHHHHHHTTSSSS-SC--C---TTTHHHHTTTTC------HHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHhc-CHHHHHHHHHHHHHh-cc--H---HHHHHHHHHHhh------HHHHHHHHhcchhHHHHH
Confidence            77666655 345555544433322 11  0   013344433333      455566666666666554

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=95.41  E-value=0.14  Score=34.62  Aligned_cols=26  Identities=23%  Similarity=0.167  Sum_probs=13.1

Q ss_pred             HHHHHHHhcCcHhHHHHHHHHHHhcC
Q 044084          135 KLVLMYIEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus       135 ~l~~~~~~~~~~~~a~~~~~~~~~~~  160 (343)
                      .|.-++.+.|++++|++.++.+.+..
T Consensus        79 ~LAvg~yklg~Y~~A~~~~~~lL~~e  104 (126)
T 1nzn_A           79 YLAVGNYRLKEYEKALKYVRGLLQTE  104 (126)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHHhC
Confidence            34444555555555555555554443

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=95.16  E-value=0.46  Score=32.45  Aligned_cols=140  Identities=14%  Similarity=0.092  Sum_probs=99.0

Q ss_pred             hccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHH
Q 044084           71 GKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTL  150 (343)
Q Consensus        71 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  150 (343)
                      .-.|..++..+++.+.....   +..-||.+|--....-+-+-..++++.+-+.   .|.          ..+|+.....
T Consensus        18 ildG~v~qGveii~k~~~ss---ni~E~NW~ICNiiD~a~C~y~v~vLd~IGki---FDi----------s~C~NlKrVi   81 (172)
T 1wy6_A           18 LLDGYIDEGVKIVLEITKSS---TKSEYNWFICNLLESIDCRYMFQVLDKIGSY---FDL----------DKCQNLKSVV   81 (172)
T ss_dssp             HHTTCHHHHHHHHHHHHHHS---CHHHHTHHHHHHHHHCCHHHHHHHHHHHGGG---SCG----------GGCSCTHHHH
T ss_pred             HHhhhHHHHHHHHHHHcCCC---CccccceeeeecchhhchhHHHHHHHHHhhh---cCc----------HhhhcHHHHH
Confidence            44688888999999887752   5666777776666666766666666655432   232          2445555555


Q ss_pred             HHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcC
Q 044084          151 EVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKG  230 (343)
Q Consensus       151 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  230 (343)
                      ..+-.+-     .+......-++.+...|.-++..+++..+... .+|++.....+..+|.+.|+..++.+++.+.-+.|
T Consensus        82 ~C~~~~n-----~~se~vd~ALd~lv~~~KkDqLdki~~~~l~n-~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG  155 (172)
T 1wy6_A           82 ECGVINN-----TLNEHVNKALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLLIEACKKG  155 (172)
T ss_dssp             HHHHHTT-----CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHhc-----chHHHHHHHHHHHHHhccHhHHHHHHHHHhcc-CCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhh
Confidence            5554432     23345666778888899999999999986543 36788888889999999999999999999988888


Q ss_pred             CC
Q 044084          231 FD  232 (343)
Q Consensus       231 ~~  232 (343)
                      ++
T Consensus       156 ~k  157 (172)
T 1wy6_A          156 EK  157 (172)
T ss_dssp             CH
T ss_pred             hH
Confidence            54

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=94.67  E-value=0.82  Score=41.51  Aligned_cols=128  Identities=13%  Similarity=0.126  Sum_probs=77.8

Q ss_pred             HHHHHHHHhhccCc-HHHHHHHHHHHHhcCCCCChHhH--HHHHHHHhccc-CHHHHHHHHHHHHHc------CCC-CCH
Q 044084           62 MYKILCDSLGKSGR-AFEILKFFRDMKEKGILEDPSVY--ASLICSFASIA-EVKVAEELFKEAEEK------GML-RDL  130 (343)
Q Consensus        62 ~~~~li~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~--~~l~~~~~~~~-~~~~a~~~~~~~~~~------~~~-~~~  130 (343)
                      .-..++..+...++ .+.|..+|+++....  |...++  ..++..+...+ +--+|.+++.+..+.      ... .+.
T Consensus       250 L~~~Ll~~~~~t~~~~~~a~~~le~L~~~~--p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~~~  327 (754)
T 4gns_B          250 LMYSLKSFIAITPSLVDFTIDYLKGLTKKD--PIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPRDA  327 (754)
T ss_dssp             HHHHHHHHHHTCGGGHHHHHHHHHHHHHHC--GGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSCCH
T ss_pred             HHHHHHHHHcccccHHHHHHHHHHHHHhhC--CchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhccccc
Confidence            33445555555666 578999999988763  333222  23333333332 223344444443321      111 121


Q ss_pred             ----------HHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHH
Q 044084          131 ----------EVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLI  192 (343)
Q Consensus       131 ----------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  192 (343)
                                .....-.+.+...|+++.|+++-++....-+ .+-.+|..|..+|...|+++.|+-.++.+.
T Consensus       328 ~~~~~~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~~aP-seF~tW~~La~vYi~l~d~e~ALLtLNScP  398 (754)
T 4gns_B          328 DSARLMNCMSDLLNIQTNFLLNRGDYELALGVSNTSTELAL-DSFESWYNLARCHIKKEEYEKALFAINSMP  398 (754)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCS-SCHHHHHHHHHHHHHTTCHHHHHHHHHHSC
T ss_pred             ccccccCcchHHHHHHHHHHhccCcHHHHHHHHHHHHhcCc-hhhHHHHHHHHHHHHhccHHHHHHHHhcCC
Confidence                      1222224556678999999999998877654 456789999999999999999998888763

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=94.62  E-value=0.63  Score=31.39  Aligned_cols=67  Identities=9%  Similarity=0.072  Sum_probs=28.5

Q ss_pred             CCHHHHHHHHHHHHhcCcHhH---HHHHHHHHHhcCCC-CchhhHHHHHHHHhcCCcHHHHHHHHHHHHHc
Q 044084          128 RDLEVFLKLVLMYIEEGMVEK---TLEVVESMKNAELN-ISDCISCVIVNGFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       128 ~~~~~~~~l~~~~~~~~~~~~---a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  194 (343)
                      ++..+-..+..++.+..+...   ++.+++.+...+.+ -.....-.+.-++.+.|+++.|.+.++.+.+.
T Consensus        33 ~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~~p~~~Rd~lY~LAvg~yklg~Y~~A~~~~~~lL~~  103 (126)
T 1nzn_A           33 VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKALKYVRGLLQT  103 (126)
T ss_dssp             CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHh
Confidence            344444444444444444333   44444444443210 01111223334444555555555555555544

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=94.51  E-value=0.57  Score=42.52  Aligned_cols=45  Identities=4%  Similarity=0.019  Sum_probs=39.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHhccc
Q 044084          292 YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLS  338 (343)
Q Consensus       292 ~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~g  338 (343)
                      |..+.....|.+++++|.+.|+..+..  +-++..+.-|++.|.+.+
T Consensus       616 WEiLGlla~RL~h~~EA~~a~~~~l~~--RFs~ka~~kLLeiY~~~~  660 (754)
T 4gns_B          616 WELLGLIMLRTWHWEDAVACLRTSIVA--RFDPVSCQQLLKIYLQPP  660 (754)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHSS--SCCHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHh--ccCHHHHHHHHHHHHhcC
Confidence            999999999999999999999999875  458888888999998765

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=94.39  E-value=0.3  Score=40.71  Aligned_cols=56  Identities=14%  Similarity=0.033  Sum_probs=28.9

Q ss_pred             HHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHH
Q 044084          171 IVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQ  227 (343)
Q Consensus       171 l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  227 (343)
                      ++..+...|++.++...+..+.... +.+...+..+|.++.+.|+..+|.+.|+.+.
T Consensus       177 ~~~~~l~~g~~~~a~~~l~~~~~~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r  232 (388)
T 2ff4_A          177 KAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVK  232 (388)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4444455555555555555554432 3344455555555555555555555555443

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=94.23  E-value=4.9e-05  Score=63.55  Aligned_cols=191  Identities=11%  Similarity=0.043  Sum_probs=102.5

Q ss_pred             HHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHH
Q 044084          130 LEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINA  209 (343)
Q Consensus       130 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~  209 (343)
                      +.+|..|..++.+.+++.+|++.|-+.      -|...|..+|.+..+.|.+++-.+.+....+..  -+...=+.|+-+
T Consensus        54 p~VWs~LgkAqL~~~~v~eAIdsyIkA------~Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~~--ke~~IDteLi~a  125 (624)
T 3lvg_A           54 PAVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFA  125 (624)
T ss_dssp             CCCSSSHHHHTTTSSSCTTTTTSSCCC------SCCCSSSHHHHHTTTSSCCTTHHHHHHTTSTTC--CSTTTTHHHHHH
T ss_pred             ccHHHHHHHHHHccCchHHHHHHHHhC------CChHHHHHHHHHHHhCCCHHHHHHHHHHHHHHh--cccccHHHHHHH
Confidence            334555555555555555554433221      122245555555555555555555555444432  222333455555


Q ss_pred             HHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhC--------------------CCCch
Q 044084          210 YCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK--------------------GCEPN  269 (343)
Q Consensus       210 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~--------------------~~~p~  269 (343)
                      |++.++..+-++++.       .||..-...+.+-|...|.++.|.-+|..+...                    .-.-+
T Consensus       126 yAk~~rL~elEefl~-------~~N~A~iq~VGDrcf~e~lYeAAKilys~isN~akLAstLV~L~~yq~AVdaArKAns  198 (624)
T 3lvg_A          126 LAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANS  198 (624)
T ss_dssp             HHTSCSSSTTTSTTS-------CCSSSCTHHHHHHHHHSCCSTTSSTTGGGSCCCTTTSSSSSSCSGGGSSTTTTTTCCS
T ss_pred             HHhhCcHHHHHHHHc-------CCCcccHHHHHHHHHHccCHHHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            555555444333221       233333344444444444444443333322110                    00236


Q ss_pred             HHHHHHHHHHHhcccChhHHHh-----------HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHhc
Q 044084          270 VWIYNSLMDMHGRAKNLRQLEK-----------YTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSK  336 (343)
Q Consensus       270 ~~~~~~l~~~~~~~~~~~~a~~-----------~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~  336 (343)
                      +.||..+-.+|...+.+.-|..           ...++.-|-..|.+++-+.+++.-... -+.-...|+-|.-.|+|
T Consensus       199 ~ktWKeV~~ACvd~~EfrLAqicGLniIvhadeL~elv~~YE~~G~f~ELIsLlEaglgl-ErAHmGmFTELaILYsK  275 (624)
T 3lvg_A          199 TRTWKEVCFACVDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSK  275 (624)
T ss_dssp             SCSHHHHTHHHHHSCTTTTTTHHHHHHHCCSSCCSGGGSSSSTTCCCTTSTTTHHHHTTS-TTCCHHHHHHHHHHHHS
T ss_pred             hhHHHHHHHHHhCchHHHHHHHhcchhcccHHHHHHHHHHHHhCCCHHHHHHHHHHHhCC-CchhHHHHHHHHHHHHh
Confidence            7789999999999998888766           666777788888888888888876532 13344556666666665

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=94.05  E-value=0.25  Score=41.20  Aligned_cols=72  Identities=14%  Similarity=0.101  Sum_probs=60.4

Q ss_pred             HHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhh-----CCCCchHHHHHH
Q 044084          203 YASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKP-----KGCEPNVWIYNS  275 (343)
Q Consensus       203 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~-----~~~~p~~~~~~~  275 (343)
                      ...++.++...|+++++...+..+.... +.+...|..+|.++.+.|+..+|++.|++..+     .|+.|...+-..
T Consensus       174 ~~~~~~~~l~~g~~~~a~~~l~~~~~~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~l  250 (388)
T 2ff4_A          174 HTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRAL  250 (388)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence            3456777888999999999999988775 66888999999999999999999999988754     489998876433

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=94.00  E-value=2.5  Score=35.88  Aligned_cols=187  Identities=11%  Similarity=0.039  Sum_probs=91.5

Q ss_pred             cCcHHHHHHHHHHHHhc-----CCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH----Hhc
Q 044084           73 SGRAFEILKFFRDMKEK-----GILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMY----IEE  143 (343)
Q Consensus        73 ~~~~~~a~~~~~~~~~~-----~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~----~~~  143 (343)
                      .|+++.|++.+-.+.+.     +..........++..|...++++...+.+..+.+..-. .......+++.+    ...
T Consensus        29 ~~~~~~a~e~ll~lEK~~r~~~d~~s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lskkr~q-lk~ai~~~V~~~~~~l~~~  107 (445)
T 4b4t_P           29 QNDCNSALDQLLVLEKKTRQASDLASSKEVLAKIVDLLASRNKWDDLNEQLTLLSKKHGQ-LKLSIQYMIQKVMEYLKSS  107 (445)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSSCSTTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHTTTTT-SHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhhh-hHHHHHHHHHHHHHHHhcC
Confidence            36788888777665432     23334556677788888888888877776655542211 122223333322    222


Q ss_pred             CcHhHHHH--HHHHHHhcCCCCc--------hhhHHHHHHHHhcCCcHHHHHHHHHHHHHc--CCCCC---HhhHHHHHH
Q 044084          144 GMVEKTLE--VVESMKNAELNIS--------DCISCVIVNGFSKRRAYWAAVKVYEQLISQ--GCIPG---QVTYASIIN  208 (343)
Q Consensus       144 ~~~~~a~~--~~~~~~~~~~~~~--------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~p~---~~~~~~ll~  208 (343)
                      ...+....  +.+..  ..+...        ......|...+...|++.+|.+++..+...  |..+.   ...+...++
T Consensus       108 ~~~d~~~~~~~i~~l--~~vte~kiflE~erarl~~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~r  185 (445)
T 4b4t_P          108 KSLDLNTRISVIETI--RVVTENKIFVEVERARVTKDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQME  185 (445)
T ss_dssp             CTTHHHHHHHHHHCC--SSSSSCCCCCCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHH
T ss_pred             CchhHHHHHHHHHHH--HHHhccchHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            22221111  11111  011110        011234555666667777777776666543  21111   123444556


Q ss_pred             HHHccCChhHHHHHHHHHHHc----CCCcC--hhhHHHHHHHHHccCChHHHHHHHHHHh
Q 044084          209 AYCRIGLYSKAEKVFIEMQQK----GFDKC--VVAYSSMVAMYGKTGRIRDAMRLVAKMK  262 (343)
Q Consensus       209 ~~~~~~~~~~a~~~~~~~~~~----~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~m~  262 (343)
                      .|...+++..|..++..+...    ..+|+  ...+..++..+...+++.+|...|.++.
T Consensus       186 l~l~~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~~~~~~~~~~~~e~~y~~a~~~y~e~~  245 (445)
T 4b4t_P          186 LSILKGDYSQATVLSRKILKKTFKNPKYESLKLEYYNLLVKISLHKREYLEVAQYLQEIY  245 (445)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHhhcccCCcHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            666666666666666655321    11121  1234455555556666666665555543

>2wpv_A GET4, UPF0363 protein YOR164C; golgi-ER trafficking, tail-anchored protein, protein binding GET4; 1.99A {Saccharomyces cerevisiae} PDB: 3lku_A

Probab=93.96  E-value=1.9  Score=34.41  Aligned_cols=167  Identities=9%  Similarity=0.043  Sum_probs=106.8

Q ss_pred             HHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHH----HHHHHHHcCCCCCHhhHHHH
Q 044084          131 EVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVK----VYEQLISQGCIPGQVTYASI  206 (343)
Q Consensus       131 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~----~~~~~~~~~~~p~~~~~~~l  206 (343)
                      ..|.++..-|.+.+++++|++++..-..               .+.+.|+...|-+    +++-..+.+.+++......+
T Consensus        34 Q~~Rtl~~Ry~~~~~~~eAidlL~~ga~---------------~ll~~~Q~~sa~DLa~llvev~~~~~~~~~~~~~~rl   98 (312)
T 2wpv_A           34 QTLRTIANRYVRSKSYEHAIELISQGAL---------------SFLKAKQGGSGTDLIFYLLEVYDLAEVKVDDISVARL   98 (312)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH---------------HHHHTTCHHHHHHHHHHHHHHHHHTTCCCSHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHH---------------HHHHCCCcchHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            4556666777888888888887655321               1233455444433    34555556777887777777


Q ss_pred             HHHHHccCChh-HHHHHHHHHHH----cC--CCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHH
Q 044084          207 INAYCRIGLYS-KAEKVFIEMQQ----KG--FDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDM  279 (343)
Q Consensus       207 l~~~~~~~~~~-~a~~~~~~~~~----~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~  279 (343)
                      +..+......+ .-.++++.+.+    .|  ..-++..+..+...|.+.|++.+|...|-.-    -.-|...+..++.-
T Consensus        99 ~~l~~~~p~~~~~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~~a~~~~~e~~~~~A~~H~i~~----~~~s~~~~a~~l~~  174 (312)
T 2wpv_A           99 VRLIAELDPSEPNLKDVITGMNNWSIKFSEYKFGDPYLHNTIGSKLLEGDFVYEAERYFMLG----THDSMIKYVDLLWD  174 (312)
T ss_dssp             HHHHTTCCTTCTTHHHHHHHHHHHHHHTSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHHTS----CHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCCCchHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHhC----CCccHHHHHHHHHH
Confidence            77765533211 22344444442    22  1236788889999999999999998877521    12256777777776


Q ss_pred             Hhcc---cChhHHHh-HHHHHHHHHhcCCHHHHHHHHHHHH
Q 044084          280 HGRA---KNLRQLEK-YTTVISAYNMAREFDMCVKFYNEFR  316 (343)
Q Consensus       280 ~~~~---~~~~~a~~-~~~l~~~~~~~g~~~~a~~~~~~m~  316 (343)
                      +...   |...++-- ....+-.|.-.|+...|..+++...
T Consensus       175 w~~~~~~~~~~e~dlf~~RaVL~yL~l~n~~~A~~~~~~f~  215 (312)
T 2wpv_A          175 WLCQVDDIEDSTVAEFFSRLVFNYLFISNISFAHESKDIFL  215 (312)
T ss_dssp             HHHHTTCCCHHHHHHHHHHHHHHHHHTTBHHHHHHHHHHHH
T ss_pred             HHHhcCCCCcchHHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            6665   65555444 4555667778899999999998875

>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=93.55  E-value=0.66  Score=29.70  Aligned_cols=62  Identities=15%  Similarity=0.267  Sum_probs=36.4

Q ss_pred             cHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHH
Q 044084          180 AYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMV  242 (343)
Q Consensus       180 ~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  242 (343)
                      +.-++.+-++.+....+.|++....+.+++|-+.+++..|.++|+.++..- .....+|..++
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~-~~~~~iY~~~l   86 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVI   86 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh-cCchhhHHHHH
Confidence            455566666666666666666666666666666666666666666665442 12233455444

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=93.23  E-value=3.3  Score=40.03  Aligned_cols=83  Identities=14%  Similarity=0.053  Sum_probs=42.8

Q ss_pred             HHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCc----hhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHH
Q 044084          131 EVFLKLVLMYIEEGMVEKTLEVVESMKNAELNIS----DCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASI  206 (343)
Q Consensus       131 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l  206 (343)
                      ..|..++..+.+.+.++.+.++-....+...+-+    ...|..++.++...|++++|...+-.+.....  -...+..+
T Consensus       900 ~YY~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~~~~~~~l~~~iFk~~L~l~~ye~Ay~aL~~~pd~~~--r~~cLr~L  977 (1139)
T 4fhn_B          900 CYYLHLSKKLFEESAYIDALEFSLLADASKETDDEDLSIAITHETLKTACAAGKFDAAHVALMVLSTTPL--KKSCLLDF  977 (1139)
T ss_dssp             HHHHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHCCSGGGGHHHHHHHHSSS--CHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhccCCChhhHHHHHHHHHHHHHhhCCHHHHHHHHHhCCCHHH--HHHHHHHH
Confidence            4455666666666666666665554443221111    11355666666666666666666665554422  22344445


Q ss_pred             HHHHHccCC
Q 044084          207 INAYCRIGL  215 (343)
Q Consensus       207 l~~~~~~~~  215 (343)
                      +...|..|.
T Consensus       978 V~~lce~~~  986 (1139)
T 4fhn_B          978 VNQLTKQGK  986 (1139)
T ss_dssp             HHHHHHHCC
T ss_pred             HHHHHhCCC
Confidence            554444443

>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=92.91  E-value=1.1  Score=28.61  Aligned_cols=46  Identities=9%  Similarity=0.044  Sum_probs=21.4

Q ss_pred             HHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhh
Q 044084          218 KAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       218 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                      +..+-++.+...++.|++....+.+++|.+.+++..|.++|+-++.
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~   73 (109)
T 1v54_E           28 ELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKD   73 (109)
T ss_dssp             HHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            3334444444444444444444444444444455444444444443

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=91.69  E-value=3.9  Score=39.53  Aligned_cols=146  Identities=8%  Similarity=0.009  Sum_probs=83.2

Q ss_pred             HHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCC-----------------
Q 044084          136 LVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIP-----------------  198 (343)
Q Consensus       136 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-----------------  198 (343)
                      ++..+...+..+-+.++..-..     .+...--.+..++...|++++|...|.+... |+..                 
T Consensus       818 l~~~l~~~~~~~~~~~l~~~~~-----~~~~~~yl~g~~~L~~ge~~~A~~~F~kaa~-~~~~~~~l~~~~~~~~~~~~~  891 (1139)
T 4fhn_B          818 LVEKLFLFKQYNACMQLIGWLN-----SDPIAVYLKALIYLKSKEAVKAVRCFKTTSL-VLYSHTSQFAVLREFQEIAEK  891 (1139)
T ss_dssp             HHHHHHHHSCTTHHHHHHHHSC-----CCHHHHHHHHHHHHHTTCHHHHHHHHHTCCC-SCTTCCCSCSSHHHHHHHHHT
T ss_pred             HHHHHHHhhhHHHHHHHhhhcc-----CCcHHHHHHHHHHHhcCCHHHHHHHHHHHhh-hhcccchhhhhhccccccccc
Confidence            3344445555555544332221     1222223455667778888888888866421 1100                 


Q ss_pred             ------CHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcC----hhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCc
Q 044084          199 ------GQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKC----VVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEP  268 (343)
Q Consensus       199 ------~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p  268 (343)
                            -..-|..++..+.+.+.++.+.++-....+..-+.+    ...|..+.+.+...|++++|...+..+.....+ 
T Consensus       892 ~~~~~~l~~YY~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~~~~~~~l~~~iFk~~L~l~~ye~Ay~aL~~~pd~~~r-  970 (1139)
T 4fhn_B          892 YHHQNLLSCYYLHLSKKLFEESAYIDALEFSLLADASKETDDEDLSIAITHETLKTACAAGKFDAAHVALMVLSTTPLK-  970 (1139)
T ss_dssp             TTSCCSSHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHCCSGGGGHHHHHHHHSSSC-
T ss_pred             ccccccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccCCChhhHHHHHHHHHHHHHhhCCHHHHHHHHHhCCCHHHH-
Confidence                  112256677777778888887777666555421111    125777888888888888888887777654333 


Q ss_pred             hHHHHHHHHHHHhcccChhHH
Q 044084          269 NVWIYNSLMDMHGRAKNLRQL  289 (343)
Q Consensus       269 ~~~~~~~l~~~~~~~~~~~~a  289 (343)
                       ...+..|+..++..|..+.-
T Consensus       971 -~~cLr~LV~~lce~~~~~~L  990 (1139)
T 4fhn_B          971 -KSCLLDFVNQLTKQGKINQL  990 (1139)
T ss_dssp             -HHHHHHHHHHHHHHCCHHHH
T ss_pred             -HHHHHHHHHHHHhCCChhhh
Confidence             34455566666655555443

>2y69_E Cytochrome C oxidase subunit 5A; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}

Probab=91.68  E-value=1.3  Score=30.02  Aligned_cols=50  Identities=16%  Similarity=0.296  Sum_probs=26.8

Q ss_pred             cHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHc
Q 044084          180 AYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       180 ~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  229 (343)
                      +.-+..+-++.+....+.|++......+++|-+.+++..|.++|+.++..
T Consensus        68 D~wElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K  117 (152)
T 2y69_E           68 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK  117 (152)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHh
Confidence            34444455555555555555555555555555555555555555555443

>3lpz_A GET4 (YOR164C homolog); protein targeting, tail-anchored protein biogenesis, GET PAT GET5 binding, protein transport; 1.98A {Chaetomium thermophilum}

Probab=91.65  E-value=4.5  Score=32.62  Aligned_cols=167  Identities=8%  Similarity=0.050  Sum_probs=102.6

Q ss_pred             HHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHH----HHHHHHHcCCCCCHhhHHHHH
Q 044084          132 VFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVK----VYEQLISQGCIPGQVTYASII  207 (343)
Q Consensus       132 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~----~~~~~~~~~~~p~~~~~~~ll  207 (343)
                      .|.++..-|.+.+++++|++++..-..               .+.+.|+...+-+    +++-+.+.++++|......++
T Consensus        37 ~~RTi~~Ry~~~k~y~eAidLL~~GA~---------------~ll~~~Q~~sg~DL~~llvevy~~~~~~~~~~~~~rL~  101 (336)
T 3lpz_A           37 ETRLVAARYSKQGNWAAAVDILASVSQ---------------TLLRSGQGGSGGDLAVLLVDTFRQAGQRVDGASRGKLL  101 (336)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHH---------------HHHHTTCHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHH
T ss_pred             HHHHHHHHHHhhcCHHHHHHHHHHHHH---------------HHHHCCCcchHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            455566667778888888887654321               1223344433333    334445566777777777777


Q ss_pred             HHHHccCChh-HHHHHHHHHHH----cC--CCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHH
Q 044084          208 NAYCRIGLYS-KAEKVFIEMQQ----KG--FDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMH  280 (343)
Q Consensus       208 ~~~~~~~~~~-~a~~~~~~~~~----~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~  280 (343)
                      ..+.....-+ .-..+.+.+.+    .|  ..-|+.....+...|.+.+++.+|...|-  .  |-.+....+..++.-+
T Consensus       102 ~L~~~~~~~~p~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~ig~~~~~e~~~~~Ae~H~i--l--g~~~s~~~~a~mL~ew  177 (336)
T 3lpz_A          102 GCLRLFQPGEPVRKRFVKEMIDWSKKFGDYPAGDPELHHVVGTLYVEEGEFEAAEKHLV--L--GTKESPEVLARMEYEW  177 (336)
T ss_dssp             HHHTTSCTTCHHHHHHHHHHHHHHHHHSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHT--T--SCTTHHHHHHHHHHHH
T ss_pred             HHHHhCCCCCcHHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHccCCHHHHHHHHH--h--cCCchHHHHHHHHHHH
Confidence            6665544311 11223333332    12  22367778889999999999999988873  2  3455657777766666


Q ss_pred             hcccChhHHHh-HHHHHHHHHhcCCHHHHHHHHHHHHh
Q 044084          281 GRAKNLRQLEK-YTTVISAYNMAREFDMCVKFYNEFRM  317 (343)
Q Consensus       281 ~~~~~~~~a~~-~~~l~~~~~~~g~~~~a~~~~~~m~~  317 (343)
                      ...+...++-- ....+--|...++...|..+++.+.+
T Consensus       178 ~~~~~~~e~dlfiaRaVL~yL~l~n~~~A~~~~~~f~~  215 (336)
T 3lpz_A          178 YKQDESHTAPLYCARAVLPYLLVANVRAANTAYRIFTS  215 (336)
T ss_dssp             HHTSCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHhcCCccHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            55554333332 66677778889999999998877754

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=91.20  E-value=2.8  Score=35.42  Aligned_cols=63  Identities=8%  Similarity=0.089  Sum_probs=35.3

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHH
Q 044084           24 CYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMK   87 (343)
Q Consensus        24 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~   87 (343)
                      +...+...|.+.|+++.|.+.|.++......+. .....+-.+++.+...+++..+...+.+..
T Consensus       133 ~~~~la~~~~~~Gd~~~A~~~~~~~~~~~~~~~-~kid~~l~~irl~l~~~d~~~~~~~~~ka~  195 (429)
T 4b4t_R          133 AWINLGEYYAQIGDKDNAEKTLGKSLSKAISTG-AKIDVMLTIARLGFFYNDQLYVKEKLEAVN  195 (429)
T ss_dssp             CCHHHHHHHHHHCCCTTHHHHHHHHHHHHTCCC-SHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhcCChH-HHHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            455566666666666666666666654332222 224555556666666666666666665553

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=91.05  E-value=4.4  Score=31.41  Aligned_cols=54  Identities=13%  Similarity=0.156  Sum_probs=27.1

Q ss_pred             HhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHc
Q 044084          175 FSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       175 ~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  229 (343)
                      ..+.|++++++.....-.+.. +-|...=..++..+|-.|+++.|.+-++...+.
T Consensus         7 ll~~g~L~~al~~~~~~VR~~-P~da~~R~~LfqLLcv~G~w~RA~~QL~~~a~l   60 (273)
T 1zbp_A            7 ALSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIKL   60 (273)
T ss_dssp             HTTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh
Confidence            344555555555555544442 233333344555555555555555555555543

>2y69_E Cytochrome C oxidase subunit 5A; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}

Probab=91.02  E-value=2.6  Score=28.67  Aligned_cols=47  Identities=11%  Similarity=0.115  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHc
Q 044084          148 KTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       148 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  194 (343)
                      +..+-+..+...++.|+.....+.+++|.+.+++..|..+|+-++.+
T Consensus        71 ElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K  117 (152)
T 2y69_E           71 ELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK  117 (152)
T ss_dssp             HHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHh
Confidence            33344444444444555555555555555555555555555554443

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=89.56  E-value=4.9  Score=33.92  Aligned_cols=97  Identities=8%  Similarity=-0.068  Sum_probs=57.8

Q ss_pred             HHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCC--chhhHHHHHHHHhcCCcHHHHHHHHHHHHHcC-CCCCHhhHHHH--
Q 044084          132 VFLKLVLMYIEEGMVEKTLEVVESMKNAELNI--SDCISCVIVNGFSKRRAYWAAVKVYEQLISQG-CIPGQVTYASI--  206 (343)
Q Consensus       132 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~p~~~~~~~l--  206 (343)
                      +...+...|.+.|+++.|.+.|.++......+  -...+-.+++.+...+++..+...+.+....- -.++....+.+  
T Consensus       133 ~~~~la~~~~~~Gd~~~A~~~~~~~~~~~~~~~~kid~~l~~irl~l~~~d~~~~~~~~~ka~~~~~~~~d~~~~~~lk~  212 (429)
T 4b4t_R          133 AWINLGEYYAQIGDKDNAEKTLGKSLSKAISTGAKIDVMLTIARLGFFYNDQLYVKEKLEAVNSMIEKGGDWERRNRYKT  212 (429)
T ss_dssp             CCHHHHHHHHHHCCCTTHHHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTCCCTHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhhhcCCCHHHHHHHHH
Confidence            55667777888888888888888776543322  23346667777777788888877777765431 01222111111  


Q ss_pred             --HHHHHccCChhHHHHHHHHHHH
Q 044084          207 --INAYCRIGLYSKAEKVFIEMQQ  228 (343)
Q Consensus       207 --l~~~~~~~~~~~a~~~~~~~~~  228 (343)
                        ...+...+++..|...|-+...
T Consensus       213 ~~gl~~l~~r~f~~Aa~~f~e~~~  236 (429)
T 4b4t_R          213 YYGIHCLAVRNFKEAAKLLVDSLA  236 (429)
T ss_dssp             HHHHGGGGTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhChHHHHHHHHHHHhc
Confidence              1112346777777777766554

>3o48_A Mitochondria fission 1 protein; tetratricopeptide repeat fold, TPR, scaffold, peroxisome, membrane fission, protein binding; 1.75A {Saccharomyces cerevisiae} PDB: 2pqr_A 2pqn_A 3uux_A

Probab=89.32  E-value=3.7  Score=27.89  Aligned_cols=68  Identities=9%  Similarity=0.087  Sum_probs=36.2

Q ss_pred             CChHhHHHHHHHHhcccC---HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcC
Q 044084           93 EDPSVYASLICSFASIAE---VKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus        93 ~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  160 (343)
                      |+..+--.+..++.++.+   ...+..+++.+.+.+..-....+-.|.-++.+.|++++|++..+.+.+..
T Consensus        38 vs~qt~F~yAw~Lv~S~~~~d~~~GI~LLe~l~~~~~~~~Rd~LYyLAvg~yklgdY~~Ar~y~d~lL~~e  108 (134)
T 3o48_A           38 ATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHE  108 (134)
T ss_dssp             SCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTC
T ss_pred             CChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcchhHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhC
Confidence            344433333334444433   34556666666655532234455555666666666666666666666554

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=88.22  E-value=2.4  Score=30.11  Aligned_cols=63  Identities=11%  Similarity=-0.084  Sum_probs=31.9

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCCCCch----HHHHHHHHHHhhccCcHHHHHHHHHHHH
Q 044084           25 YCQIMEAFYKIGDSEKVAALFLECESRK-LDLTPSS----THMYKILCDSLGKSGRAFEILKFFRDMK   87 (343)
Q Consensus        25 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~----~~~~~~li~~~~~~~~~~~a~~~~~~~~   87 (343)
                      +-.-++.+...|.++.|+-+.+.+.... ..++..+    ..++..+.+++...+++..|...|++.+
T Consensus        23 l~dqik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qAL   90 (167)
T 3ffl_A           23 VIDHVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMAL   90 (167)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHH
Confidence            3444555666666666666666554432 2222100    1234445556666666666666666643

>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha solenoid, regulatory PART LID, hydrolase, protein binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A

Probab=87.99  E-value=11  Score=31.42  Aligned_cols=289  Identities=13%  Similarity=0.073  Sum_probs=160.9

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhC-CCCCCCchHHHHHHHHHHhhccC-cHHHHHHHHHHHHhcCCCCChHhH--
Q 044084           23 GCYCQIMEAFYKIGDSEKVAALFLECESR-KLDLTPSSTHMYKILCDSLGKSG-RAFEILKFFRDMKEKGILEDPSVY--   98 (343)
Q Consensus        23 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~~~~li~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~--   98 (343)
                      .....|...|.+.|+.++..+++.....- +..+...+......++..+.... ..+.-.++..+..+.... +..+|  
T Consensus        20 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~kak~~k~v~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~-~~r~flr   98 (394)
T 3txn_A           20 QGILQQGELYKQEGKAKELADLIKVTRPFLSSISKAKAAKLVRSLVDMFLDMDAGTGIEVQLCKDCIEWAKQ-EKRTFLR   98 (394)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHTTTGGGGSCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHH-TTCHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHH-HHHHHHH
Confidence            45667889999999999999998776332 11122222455667788776643 344444444444332100 11223  


Q ss_pred             ----HHHHHHHhcccCHHHHHHHHHHHHHcCCCCC-----HHHHHHHHHHHHhcCcHhHHHHHHHHHHhcC--CCCchhh
Q 044084           99 ----ASLICSFASIAEVKVAEELFKEAEEKGMLRD-----LEVFLKLVLMYIEEGMVEKTLEVVESMKNAE--LNISDCI  167 (343)
Q Consensus        99 ----~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~  167 (343)
                          ..++..|...|++.+|..++..+.+.--..|     ..++-.-++.|...+++.++...+.......  +.+++..
T Consensus        99 ~~l~~kL~~l~~~~~~y~~a~~~i~~l~~~~~~~dd~~~llev~lle~~~~~~~~n~~k~k~~l~~a~~~~~ai~~~p~i  178 (394)
T 3txn_A           99 QSLEARLIALYFDTALYTEALALGAQLLRELKKLDDKNLLVEVQLLESKTYHALSNLPKARAALTSARTTANAIYCPPKV  178 (394)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSSCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHH
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHhccHHHHHHHHHHHHhhhccCCCCHHH
Confidence                2578899999999999999998887421212     4556677788999999999999998875422  2122222


Q ss_pred             HH----HHHHHHh-cCCcHHHHHHHHHHHHHc-C-C-CC---CHhhHHHHHHHHHccCChhHHHHHHH-HHHHcCCCcCh
Q 044084          168 SC----VIVNGFS-KRRAYWAAVKVYEQLISQ-G-C-IP---GQVTYASIINAYCRIGLYSKAEKVFI-EMQQKGFDKCV  235 (343)
Q Consensus       168 ~~----~l~~~~~-~~~~~~~a~~~~~~~~~~-~-~-~p---~~~~~~~ll~~~~~~~~~~~a~~~~~-~~~~~~~~~~~  235 (343)
                      ..    .-...+. ..+++..|...|-+..+. . . .|   +...|..+... .. ++..+...++. .....-..|..
T Consensus       179 ~a~i~~~~Gi~~l~~~rdyk~A~~~F~eaf~~f~~~~~~~~~~~lkYlvL~aL-l~-~~r~el~~~l~~~~~~~~~~pei  256 (394)
T 3txn_A          179 QGALDLQSGILHAADERDFKTAFSYFYEAFEGFDSVDSVKALTSLKYMLLCKI-ML-GQSDDVNQLVSGKLAITYSGRDI  256 (394)
T ss_dssp             HHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHH-HT-TCGGGHHHHHHSHHHHTTCSHHH
T ss_pred             HHHHHHHhhHHHHHhccCHHHHHHHHHHHHhcccccccHHHHHHHHHHHHHHH-Hc-CCHHHHHHHhccccccccCCccH
Confidence            11    1122345 789999998887776432 1 0 11   12233332222 22 33333333322 11111124666


Q ss_pred             hhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHH---HHHHHHHhcccChhHHHh------HHHHHHHHHhcCCHH
Q 044084          236 VAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIY---NSLMDMHGRAKNLRQLEK------YTTVISAYNMAREFD  306 (343)
Q Consensus       236 ~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~---~~l~~~~~~~~~~~~a~~------~~~l~~~~~~~g~~~  306 (343)
                      ..+..++.+| ..+++.+...++...... +..|....   ..+.+..... .+.....      +..+...+.-  ..+
T Consensus       257 ~~l~~L~~a~-~~~dl~~f~~iL~~~~~~-l~~D~~l~~h~~~L~~~Ir~~-~L~~i~~pYsrIsl~~iA~~l~l--s~~  331 (394)
T 3txn_A          257 DAMKSVAEAS-HKRSLADFQAALKEYKKE-LAEDVIVQAHLGTLYDTMLEQ-NLCRIIEPYSRVQVAHVAESIQL--PMP  331 (394)
T ss_dssp             HHHHHHHHHH-HTTCHHHHHHHHHHSTTT-TTTSHHHHHHHHHHHHHHHHH-HHHHHHTTCSEEEHHHHHHHHTC--CHH
T ss_pred             HHHHHHHHHH-HhCCHHHHHHHHHHHHHH-HhcChHHHHHHHHHHHHHHHH-HHHHHhHhhceeeHHHHHHHHCc--CHH
Confidence            6677777765 566787777777765432 44455432   1121111111 1111111      5555555543  678


Q ss_pred             HHHHHHHHHHhCC
Q 044084          307 MCVKFYNEFRMNG  319 (343)
Q Consensus       307 ~a~~~~~~m~~~~  319 (343)
                      ++...+-+|...|
T Consensus       332 evE~~L~~lI~dg  344 (394)
T 3txn_A          332 QVEKKLSQMILDK  344 (394)
T ss_dssp             HHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHCC
Confidence            8899999997765

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} PDB: 4b4t_N

Probab=87.52  E-value=19  Score=33.81  Aligned_cols=155  Identities=10%  Similarity=0.104  Sum_probs=91.2

Q ss_pred             HHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHH--HHHhcCcHhHHHHHHHHHHhcCCCCchhh--HHHHHHHHhcC
Q 044084          103 CSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVL--MYIEEGMVEKTLEVVESMKNAELNISDCI--SCVIVNGFSKR  178 (343)
Q Consensus       103 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~--~~~~~~~~~~a~~~~~~~~~~~~~~~~~~--~~~l~~~~~~~  178 (343)
                      ..+.-.|+.+....++..+.+..   +..+...+..  ++.-.|+.+.+..+++.+....- |....  -.++.-+|+..
T Consensus       498 li~vGTgn~~ai~~LL~~~~e~~---~e~vrR~aalgLGll~~g~~e~~~~li~~L~~~~d-p~vRygaa~alglAyaGT  573 (963)
T 4ady_A          498 LCMLGTGKPEAIHDMFTYSQETQ---HGNITRGLAVGLALINYGRQELADDLITKMLASDE-SLLRYGGAFTIALAYAGT  573 (963)
T ss_dssp             HHHTTCCCHHHHHHHHHHHHHCS---CHHHHHHHHHHHHHHTTTCGGGGHHHHHHHHHCSC-HHHHHHHHHHHHHHTTTS
T ss_pred             hhhcccCCHHHHHHHHHHHhccC---cHHHHHHHHHHHHhhhCCChHHHHHHHHHHHhCCC-HHHHHHHHHHHHHHhcCC
Confidence            34556677777777777766532   3333333333  34467888888888887765421 22221  12344567778


Q ss_pred             CcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCCh-HHHHHH
Q 044084          179 RAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRI-RDAMRL  257 (343)
Q Consensus       179 ~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~  257 (343)
                      |+.....+++..+.+.. ..+......+.-++...|+.+.+.++++.+.+.+ .|.+.--..+.-+....|.. .++..+
T Consensus       574 Gn~~aIq~LL~~~~~d~-~d~VRraAViaLGlI~~g~~e~v~rlv~~L~~~~-d~~VR~gAalALGli~aGn~~~~aid~  651 (963)
T 4ady_A          574 GNNSAVKRLLHVAVSDS-NDDVRRAAVIALGFVLLRDYTTVPRIVQLLSKSH-NAHVRCGTAFALGIACAGKGLQSAIDV  651 (963)
T ss_dssp             CCHHHHHHHHHHHHHCS-CHHHHHHHHHHHHHHTSSSCSSHHHHTTTGGGCS-CHHHHHHHHHHHHHHTSSSCCHHHHHH
T ss_pred             CCHHHHHHHHHHhccCC-cHHHHHHHHHHHHhhccCCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHHhccCCCcHHHHHH
Confidence            88888888888887652 2233322333334445677777777776666544 45555555555555555554 567778


Q ss_pred             HHHHhh
Q 044084          258 VAKMKP  263 (343)
Q Consensus       258 ~~~m~~  263 (343)
                      +..+..
T Consensus       652 L~~L~~  657 (963)
T 4ady_A          652 LDPLTK  657 (963)
T ss_dssp             HHHHHT
T ss_pred             HHHHcc
Confidence            888765

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} PDB: 4b4t_N

Probab=87.30  E-value=19  Score=33.73  Aligned_cols=11  Identities=0%  Similarity=0.220  Sum_probs=6.2

Q ss_pred             HHHHHHHHHHH
Q 044084          306 DMCVKFYNEFR  316 (343)
Q Consensus       306 ~~a~~~~~~m~  316 (343)
                      .+++.++..+.
T Consensus       646 ~~aid~L~~L~  656 (963)
T 4ady_A          646 QSAIDVLDPLT  656 (963)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHc
Confidence            45555666554

>3kea_A K1L; tropism, ANK repeat, viral protein; 2.30A {Vaccinia virus}

Probab=86.76  E-value=2.9  Score=32.87  Aligned_cols=203  Identities=5%  Similarity=-0.120  Sum_probs=99.5

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChH---hHHHHHH
Q 044084           27 QIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPS---VYASLIC  103 (343)
Q Consensus        27 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~---~~~~l~~  103 (343)
                      +.+...+..|+.+-+..+++.    +..++..+  -++ .+...+..|+.+-+    +.+.+.|..++..   -++ .+.
T Consensus        33 t~L~~A~~~g~~~~v~~Ll~~----g~~~~~~~--g~t-~L~~A~~~g~~~~v----~~Ll~~ga~~~~~d~~g~t-~L~  100 (285)
T 3kea_A           33 SASYYAIADNNVRLVCTLLNA----GALKNLLE--NEF-PLHQAATLEDTKIV----KILLFSGLDDSQFDDKGNT-ALY  100 (285)
T ss_dssp             CHHHHHHHTTCHHHHHHHHHT----TGGGSCCT--TCC-HHHHHTTSSSCHHH----HHHHHTTCCTTCCCTTSCC-HHH
T ss_pred             CHHHHHHHcCCHHHHHHHHhC----CCCCCCCC--CCC-HHHHHHHcCCHHHH----HHHHHCCCCCCCcCCCCCc-HHH
Confidence            345566678888776666554    43332211  122 33444566766544    4444556554432   223 334


Q ss_pred             HHhcccCHHHHHHHHHHHHHcCCCCCH---HHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCC-ch-hhHHHHHHHHhcC
Q 044084          104 SFASIAEVKVAEELFKEAEEKGMLRDL---EVFLKLVLMYIEEGMVEKTLEVVESMKNAELNI-SD-CISCVIVNGFSKR  178 (343)
Q Consensus       104 ~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~-~~~~~l~~~~~~~  178 (343)
                      ..+..|+.+-+.-++    +.|..++.   .-+.+.+...+..|+.+-+.    .+.+.+..+ +. .-.+ .+...+..
T Consensus       101 ~A~~~g~~~~v~~Ll----~~ga~~~~~~~~g~~t~L~~A~~~~~~~~v~----~Ll~~g~~~~~~~~g~t-~L~~A~~~  171 (285)
T 3kea_A          101 YAVDSGNMQTVKLFV----KKNWRLMFYGKTGWKTSFYHAVMLNDVSIVS----YFLSEIPSTFDLAILLS-CIHITIKN  171 (285)
T ss_dssp             HHHHTTCHHHHHHHH----HHCGGGGGCSSSGGGSHHHHHHHTTCHHHHH----HHHTTSCTTCCCSTHHH-HHHHHHHT
T ss_pred             HHHHcCCHHHHHHHH----hcCCCCCccCCCCCCCHHHHHHHcCCHHHHH----HHHhCCCccccccCCcc-HHHHHHHc
Confidence            445667766554444    44544332   12234455566677765444    444444333 21 2233 34445567


Q ss_pred             CcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHH
Q 044084          179 RAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLV  258 (343)
Q Consensus       179 ~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  258 (343)
                      |+.+-+.-+++.-..-.. .+..-.+..+...+..|+.    ++.+.+.+.|..++.....     -...|+.+-+.-++
T Consensus       172 g~~~~v~~Ll~~gad~n~-~~~~g~t~~L~~A~~~~~~----~~v~~Ll~~gad~~~~~~~-----a~~~~~~~iv~~Ll  241 (285)
T 3kea_A          172 GHVDMMILLLDYMTSTNT-NNSLLFIPDIKLAIDNKDI----EMLQALFKYDINIYSANLE-----NVLLDDAEIAKMII  241 (285)
T ss_dssp             TCHHHHHHHHHHHHHTCT-TCCCBCCTTHHHHHHHTCH----HHHHHHTTSCBCSTTTTGG-----GGTTTCHHHHHHHH
T ss_pred             ChHHHHHHHHHcCCCCCc-ccCCCCChHHHHHHHcCCH----HHHHHHHHcCCCCCCCChh-----hhhcCCHHHHHHHH
Confidence            888777666665333221 1212222223333445664    4555566777777665432     14466665555554


Q ss_pred             HH
Q 044084          259 AK  260 (343)
Q Consensus       259 ~~  260 (343)
                      +.
T Consensus       242 ~~  243 (285)
T 3kea_A          242 EK  243 (285)
T ss_dssp             HH
T ss_pred             Hc
Confidence            44

>1wdy_A 2-5A-dependent ribonuclease; hydrolase, RNA-binding; HET: 25A; 1.80A {Homo sapiens} SCOP: d.211.1.1

Probab=86.39  E-value=3.5  Score=31.95  Aligned_cols=49  Identities=14%  Similarity=0.015  Sum_probs=24.7

Q ss_pred             HccCChhHHHHHHHHHHHcCCCcChhh--HHHHHHHHHccCChHHHHHHHH
Q 044084          211 CRIGLYSKAEKVFIEMQQKGFDKCVVA--YSSMVAMYGKTGRIRDAMRLVA  259 (343)
Q Consensus       211 ~~~~~~~~a~~~~~~~~~~~~~~~~~~--~~~l~~~~~~~~~~~~a~~~~~  259 (343)
                      +..++.....++.+.+.+.|..++...  -.+.+...++.|+.+-+..+++
T Consensus       190 ~~~~~~~~~~~i~~~Ll~~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~  240 (285)
T 1wdy_A          190 LLSSDDSDVEAITHLLLDHGADVNVRGERGKTPLILAVEKKHLGLVQRLLE  240 (285)
T ss_dssp             HHCSCTTTHHHHHHHHHHTTCCSSCCCTTSCCHHHHHHHTTCHHHHHHHHH
T ss_pred             HHccccchHHHHHHHHHHcCCCCCCcCCCCCcHHHHHHHcCCHHHHHHHHh
Confidence            344555555666666677665554321  1122333445666655444443

>3lpz_A GET4 (YOR164C homolog); protein targeting, tail-anchored protein biogenesis, GET PAT GET5 binding, protein transport; 1.98A {Chaetomium thermophilum}

Probab=85.37  E-value=13  Score=29.96  Aligned_cols=169  Identities=14%  Similarity=0.116  Sum_probs=90.5

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH----HHHHHHhcCCCCChHhH
Q 044084           23 GCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK----FFRDMKEKGILEDPSVY   98 (343)
Q Consensus        23 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~----~~~~~~~~~~~~~~~~~   98 (343)
                      .+|.++..-|.+.+++++|.+++-.-                  ...+.+.|+...+-+    +++-+.+.++++|....
T Consensus        36 Q~~RTi~~Ry~~~k~y~eAidLL~~G------------------A~~ll~~~Q~~sg~DL~~llvevy~~~~~~~~~~~~   97 (336)
T 3lpz_A           36 QETRLVAARYSKQGNWAAAVDILASV------------------SQTLLRSGQGGSGGDLAVLLVDTFRQAGQRVDGASR   97 (336)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHH------------------HHHHHHTTCHHHHHHHHHHHHHHHHHHTCCCCHHHH
T ss_pred             HHHHHHHHHHHhhcCHHHHHHHHHHH------------------HHHHHHCCCcchHHHHHHHHHHHHHHcCCCCCHHHH
Confidence            35666666677777777777765331                  122233454444333    33555556777787777


Q ss_pred             HHHHHHHhcccCHH-HHHHHHHHHH----HcC--CCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHH
Q 044084           99 ASLICSFASIAEVK-VAEELFKEAE----EKG--MLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVI  171 (343)
Q Consensus        99 ~~l~~~~~~~~~~~-~a~~~~~~~~----~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  171 (343)
                      ..++..+.....-+ .-..+.++++    +.|  ..-|+.....+...|.+.+++.+|...|-    .+..++...+..+
T Consensus        98 ~rL~~L~~~~~~~~p~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~ig~~~~~e~~~~~Ae~H~i----lg~~~s~~~~a~m  173 (336)
T 3lpz_A           98 GKLLGCLRLFQPGEPVRKRFVKEMIDWSKKFGDYPAGDPELHHVVGTLYVEEGEFEAAEKHLV----LGTKESPEVLARM  173 (336)
T ss_dssp             HHHHHHHTTSCTTCHHHHHHHHHHHHHHHHHSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHT----TSCTTHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHccCCHHHHHHHHH----hcCCchHHHHHHH
Confidence            77777666554311 1122222222    333  22367788888888888888888877762    1322333445444


Q ss_pred             HHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHH
Q 044084          172 VNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQ  228 (343)
Q Consensus       172 ~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  228 (343)
                      +.-+...+...              .++...-..++. |...+++..|..+++...+
T Consensus       174 L~ew~~~~~~~--------------e~dlfiaRaVL~-yL~l~n~~~A~~~~~~f~~  215 (336)
T 3lpz_A          174 EYEWYKQDESH--------------TAPLYCARAVLP-YLLVANVRAANTAYRIFTS  215 (336)
T ss_dssp             HHHHHHTSCGG--------------GHHHHHHHHHHH-HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCc--------------cHHHHHHHHHHH-HHHhCCHHHHHHHHHHHHH
Confidence            33333222210              122233333443 4556788888777666553

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=85.02  E-value=5.6  Score=25.38  Aligned_cols=85  Identities=14%  Similarity=0.019  Sum_probs=48.5

Q ss_pred             CcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHH
Q 044084          179 RAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLV  258 (343)
Q Consensus       179 ~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  258 (343)
                      ...++|..+-+.+...+.  ...+--+-+..+.+.|++++|..+.+.+    ..||...|-+|..  .+.|..+++...+
T Consensus        20 H~HqEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~----c~pdlepw~ALce--~rlGl~s~le~rL   91 (115)
T 2uwj_G           20 HCHEEALCIAEWLERLGQ--DEAARLIRISSLANQGRYQEALAFAHGN----PWPALEPWFALCE--WHLGLGAALDRRL   91 (115)
T ss_dssp             TCHHHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHGGGTTC----CCGGGHHHHHHHH--HHTTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCC----CCchHHHHHHHHH--HhcccHHHHHHHH
Confidence            345666666666666542  2222222234566777777777665432    2567776666654  3677777777777


Q ss_pred             HHHhhCCCCchHHH
Q 044084          259 AKMKPKGCEPNVWI  272 (343)
Q Consensus       259 ~~m~~~~~~p~~~~  272 (343)
                      .++...| .|....
T Consensus        92 ~~la~sg-~p~~q~  104 (115)
T 2uwj_G           92 AGLGGSS-DPALAD  104 (115)
T ss_dssp             HHHHTCS-SHHHHH
T ss_pred             HHHHhCC-CHHHHH
Confidence            6666654 344333

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=85.00  E-value=8.4  Score=27.37  Aligned_cols=128  Identities=10%  Similarity=0.082  Sum_probs=63.9

Q ss_pred             cCCCCCHHH--HHHHHHHHHhcCcHhHHHHHHHHHHhcC-CCCch-------hhHHHHHHHHhcCCcHHHHHHHHHHHHH
Q 044084          124 KGMLRDLEV--FLKLVLMYIEEGMVEKTLEVVESMKNAE-LNISD-------CISCVIVNGFSKRRAYWAAVKVYEQLIS  193 (343)
Q Consensus       124 ~~~~~~~~~--~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~~~~  193 (343)
                      .|+.|....  +-.-++.+...+.++.|+-+.+.+.... ..++.       .++..+.+++...+++.+|...|++..+
T Consensus        12 ~~~~~~~~~~~l~dqik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qALq   91 (167)
T 3ffl_A           12 SGLVPRGSHMNVIDHVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMALQ   91 (167)
T ss_dssp             ---------CCHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cCCCCCccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHH
Confidence            344443333  3344666777788888887777654321 11221       1345566777788888888888888654


Q ss_pred             cC-CCCCH-hhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhC
Q 044084          194 QG-CIPGQ-VTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       194 ~~-~~p~~-~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                      .. .-+.. .+...+-    .......         ......+...--.+..+|.+.+++++|+.+++.+..+
T Consensus        92 ~~k~l~k~~s~~~~~~----~~ss~p~---------s~~~~~e~Elkykia~C~~~l~~~~~Ai~~Le~Ip~k  151 (167)
T 3ffl_A           92 QKKALSKTSKVRPSTG----NSASTPQ---------SQCLPSEIEVKYKLAECYTVLKQDKDAIAILDGIPSR  151 (167)
T ss_dssp             HHHCC---------------------------------CCCCHHHHHHHHHHHHHHTTCHHHHHHHHHTSCGG
T ss_pred             HHHHHhcCCCcccccc----ccCCCcc---------cccccchHHHHHHHHHHHHHHCCHHHHHHHHhcCCch
Confidence            31 11111 1111110    0000000         0112234455556888999999999999988876544

>3o48_A Mitochondria fission 1 protein; tetratricopeptide repeat fold, TPR, scaffold, peroxisome, membrane fission, protein binding; 1.75A {Saccharomyces cerevisiae} PDB: 2pqr_A 2pqn_A 3uux_A

Probab=84.79  E-value=7.3  Score=26.49  Aligned_cols=74  Identities=9%  Similarity=0.049  Sum_probs=44.4

Q ss_pred             CCCCCHHHHHHHHHHHHhcCc---HhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCH
Q 044084          125 GMLRDLEVFLKLVLMYIEEGM---VEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQ  200 (343)
Q Consensus       125 ~~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~  200 (343)
                      +..|+..+--.+..++.+..+   ..+++.+++.+.+.+..-....+--+.-++.+.|+++.|.+..+.+.+.  .|+.
T Consensus        35 ~~~vs~qt~F~yAw~Lv~S~~~~d~~~GI~LLe~l~~~~~~~~Rd~LYyLAvg~yklgdY~~Ar~y~d~lL~~--eP~N  111 (134)
T 3o48_A           35 GPTATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEH--ERNN  111 (134)
T ss_dssp             GGGSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHTT--CTTC
T ss_pred             CCCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcchhHHHHHHHHHHHHHhhhHHHHHHHHHHHHhh--CCCC
Confidence            334566666666666666654   3456677777665543122333445556677777777777777777765  4543

>3eiq_C Programmed cell death protein 4; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Mus musculus}

Probab=84.66  E-value=4.2  Score=33.21  Aligned_cols=73  Identities=16%  Similarity=0.231  Sum_probs=42.2

Q ss_pred             HHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCC--hHHHHHHHHHHhhCCCCchHHHHHHH
Q 044084          203 YASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGR--IRDAMRLVAKMKPKGCEPNVWIYNSL  276 (343)
Q Consensus       203 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~--~~~a~~~~~~m~~~~~~p~~~~~~~l  276 (343)
                      ...++.-|...|+.++|.+.++++..-.+. ...+...+..++-+.++  .+....++..+...|+-+.......+
T Consensus       220 i~~lL~EY~~s~D~~EA~~ci~EL~~p~fh-he~V~~av~~aLE~~~~~~re~~~~LL~~L~~~glls~~q~~~Gf  294 (358)
T 3eiq_C          220 IDMLLKEYLLSGDISEAEHCLKELEVPHFH-HELVYEAIVMVLESTGESAFKMILDLLKSLWKSSTITIDQMKRGY  294 (358)
T ss_dssp             HHHHHHHHHHHCCHHHHHHHHHHHCCTTCH-HHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHTTCSCHHHHHHHH
T ss_pred             HHHHHHHhccCCCHHHHHHHHHHccCCcch-HHHHHHHHHHHHccCchHHHHHHHHHHHHHHHCCCCCHHHHHHHH
Confidence            466777788888888888888777532211 12334444445444332  34566777777766665544443333

>2p58_C Putative type III secretion protein YSCG; type III secretion system, structure, needle protein, YSCE, YSCF, transport protein/chaperone complex; 1.80A {Yersinia pestis}

Probab=84.61  E-value=5.9  Score=25.32  Aligned_cols=86  Identities=10%  Similarity=0.031  Sum_probs=51.8

Q ss_pred             CcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHH
Q 044084          179 RAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLV  258 (343)
Q Consensus       179 ~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  258 (343)
                      ...++|..+-+.+...+.  ...+--+-+..+.+.|++++|..+.+.+    ..||...|-+|..  .+.|..+++...+
T Consensus        21 H~HqEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~----c~pdlepw~ALce--~rlGl~s~le~rL   92 (116)
T 2p58_C           21 HYHEEANCIAEWLHLKGE--EEAVQLIRLSSLMNRGDYASALQQGNKL----AYPDLEPWLALCE--YRLGLGSALESRL   92 (116)
T ss_dssp             TCHHHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHHHHTTS----CCGGGHHHHHHHH--HHHTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCC----CCchHHHHHHHHH--HhcccHHHHHHHH
Confidence            456777777777766542  2222222244567778888887765443    3577777766654  3677777777777


Q ss_pred             HHHhhCCCCchHHHH
Q 044084          259 AKMKPKGCEPNVWIY  273 (343)
Q Consensus       259 ~~m~~~~~~p~~~~~  273 (343)
                      .++...| .|....|
T Consensus        93 ~~la~sg-~p~~q~F  106 (116)
T 2p58_C           93 NRLARSQ-DPRIQTF  106 (116)
T ss_dssp             HHHTTCC-CHHHHHH
T ss_pred             HHHHhCC-CHHHHHH
Confidence            7776664 3444333

>1y8m_A FIS1; mitochondria, unknown function; NMR {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=83.17  E-value=9.2  Score=26.38  Aligned_cols=49  Identities=12%  Similarity=0.167  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcC
Q 044084          112 KVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus       112 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  160 (343)
                      .++..+++.+.+.+..-.....-.|.-++.+.|++++|++..+.+.+..
T Consensus        59 ~~GI~LLe~l~~~~~~~~RdcLYyLAvg~ykl~~Y~~Ar~y~d~lL~~e  107 (144)
T 1y8m_A           59 RLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHE  107 (144)
T ss_dssp             HHHHHHHHHHHHHCCSTHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHhcCccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHhcC
Confidence            3444555555544332223333344445555555555555555555443

>2nsz_A Programmed cell death protein 4; PDCD4, tumor suppressor, translation, antitumor protein; 1.15A {Mus musculus} SCOP: a.118.1.14 PDB: 2kzt_B 2hm8_A 2ggf_A

Probab=80.78  E-value=11  Score=25.54  Aligned_cols=63  Identities=11%  Similarity=0.160  Sum_probs=33.4

Q ss_pred             HHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCC--cHHHHHHHHHHHHHcCC
Q 044084          133 FLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRR--AYWAAVKVYEQLISQGC  196 (343)
Q Consensus       133 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~  196 (343)
                      ...++.-|...|+.++|.+.++++..... -...+...+..++-+.+  ..+.+.+++..+...|+
T Consensus        10 i~~ll~EY~~~~D~~Ea~~cl~eL~~p~f-~~e~V~~~i~~alE~~~~~~~e~~~~LL~~L~~~~~   74 (129)
T 2nsz_A           10 IDMLLKEYLLSGDISEAEHCLKELEVPHF-HHELVYEAIVMVLESTGESAFKMILDLLKSLWKSST   74 (129)
T ss_dssp             HHHHHHHHHHHCCHHHHHHHHHHHTCGGG-HHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHhCCCcc-HHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHCCC
Confidence            34566667777777777777777642211 11222333444444432  23556666666665554

>2p58_C Putative type III secretion protein YSCG; type III secretion system, structure, needle protein, YSCE, YSCF, transport protein/chaperone complex; 1.80A {Yersinia pestis}

Probab=80.75  E-value=8.8  Score=24.55  Aligned_cols=80  Identities=11%  Similarity=-0.041  Sum_probs=50.5

Q ss_pred             CCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHH
Q 044084           36 GDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAE  115 (343)
Q Consensus        36 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  115 (343)
                      ...++|..+-+.+...+.  .   ..+--+-+..+...|++++|..+.+.+    ..||...|-.|-  -.+.|..+.+.
T Consensus        21 H~HqEA~tIAdwL~~~~~--~---E~v~lIR~sSLmNrG~Yq~Al~l~~~~----c~pdlepw~ALc--e~rlGl~s~le   89 (116)
T 2p58_C           21 HYHEEANCIAEWLHLKGE--E---EAVQLIRLSSLMNRGDYASALQQGNKL----AYPDLEPWLALC--EYRLGLGSALE   89 (116)
T ss_dssp             TCHHHHHHHHHHHHHTTC--H---HHHHHHHHHHHHHTTCHHHHHHHHTTS----CCGGGHHHHHHH--HHHHTCHHHHH
T ss_pred             hHHHHHHHHHHHHHhCCc--H---HHHHHHHHHHHHcchhHHHHHHhcCCC----CCchHHHHHHHH--HHhcccHHHHH
Confidence            356777777777766553  1   222223345567788888888776544    367777776553  44777777777


Q ss_pred             HHHHHHHHcCC
Q 044084          116 ELFKEAEEKGM  126 (343)
Q Consensus       116 ~~~~~~~~~~~  126 (343)
                      .-+.++...|-
T Consensus        90 ~rL~~la~sg~  100 (116)
T 2p58_C           90 SRLNRLARSQD  100 (116)
T ss_dssp             HHHHHHTTCCC
T ss_pred             HHHHHHHhCCC
Confidence            77777766653

>3eu9_A Huntingtin-interacting protein 14; epigenetics, ankyrin repeats, methyllyine binding, huntingti interacting protein 14, acyltransferase, ANK repeat; HET: HIS; 1.99A {Homo sapiens}

Probab=80.67  E-value=3.1  Score=31.32  Aligned_cols=54  Identities=9%  Similarity=-0.001  Sum_probs=25.1

Q ss_pred             HHHHHccCChhHHHHHHHHHHHcCCCcChhhH--HHHHHHHHccCChHHHHHHHHHHhhC
Q 044084          207 INAYCRIGLYSKAEKVFIEMQQKGFDKCVVAY--SSMVAMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       207 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~--~~l~~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                      +...+..|+.+-+..+    .+.|..++....  .+-+....+.|+.+-+..+++...+.
T Consensus       181 L~~A~~~~~~~~v~~L----l~~g~~~~~~~~~g~t~l~~A~~~~~~~~v~~L~~~~~~~  236 (240)
T 3eu9_A          181 LHWAVLAGNTTVISLL----LEAGANVDAQNIKGESALDLAKQRKNVWMINHLQEARQAK  236 (240)
T ss_dssp             HHHHHHHTCHHHHHHH----HHHTCCTTCBCTTSCBHHHHHHHTTCHHHHHHHHHHC---
T ss_pred             HHHHHHcCCHHHHHHH----HHcCCCCCCcCCCCCCHHHHHHHcCcHHHHHHHHHhhhcc
Confidence            3444556676544433    344544442211  12334445667776666665554443

---

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	343
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.92
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.89
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.75
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.7
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	99.45
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	99.42
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.41
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.41
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.4
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	99.39
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.34
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	99.31
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	99.28
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	99.21
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.9
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.85
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.81
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.81
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.75
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.72
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.7
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.69
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	98.64
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.61
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.61
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	98.61
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.53
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.53
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.43
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.43
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.38
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	98.38
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.36
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	98.34
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	98.26
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.24
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	98.24
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	98.18
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	98.16
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.16
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	98.15
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	98.1
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	98.09
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	98.05
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	98.0
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.95
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.93
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.93
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.81
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	97.65
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.51
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	97.39
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.39
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	97.09
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	97.0
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	96.84
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	96.39
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	95.23
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	94.75
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	93.5
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	93.11
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	92.08
d1qsaa1	450	70 KDa soluble lytic transglycosylase (SLT70), sup	85.83

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.92  E-value=2.8e-21  Score=160.99  Aligned_cols=325  Identities=12%  Similarity=0.087  Sum_probs=251.6

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      ++++|++.++++.+..+ -+...+..+..+|.+.|++++|...|+++.+.+    |.+..+|..+...+.+.|++++|++
T Consensus        14 ~~~~A~~~~~~~l~~~p-~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~----p~~~~a~~~l~~~~~~~g~~~~A~~   88 (388)
T d1w3ba_          14 DFEAAERHCMQLWRQEP-DNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN----PLLAEAYSNLGNVYKERGQLQEAIE   88 (388)
T ss_dssp             CHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC----CCCHHHHHHHHHHhhhhcccccccc
Confidence            67899999999988653 367789999999999999999999999998765    3346889999999999999999999


Q ss_pred             HHHHHHhcCCCCChHhHHH----------------------------------HHHHHhcccCHHHHHHHHHHHHHcCCC
Q 044084           82 FFRDMKEKGILEDPSVYAS----------------------------------LICSFASIAEVKVAEELFKEAEEKGML  127 (343)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~----------------------------------l~~~~~~~~~~~~a~~~~~~~~~~~~~  127 (343)
                      .+......... +......                                  ........+....+...+.......+ 
T Consensus        89 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  166 (388)
T d1w3ba_          89 HYRHALRLKPD-FIDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAIETQP-  166 (388)
T ss_dssp             HHHHHHHHCTT-CHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHCT-
T ss_pred             ccccccccccc-cccccccccccccccccccccccccccccccccccccccccccccccccchhhhhHHHHHHhhccCc-
Confidence            99988775422 2221111                                  11222233344444555555544433 


Q ss_pred             CCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHH
Q 044084          128 RDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASII  207 (343)
Q Consensus       128 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll  207 (343)
                      .+...+..+...+...|++++|...+++..+..+ -+...+..+...+...|++++|...+++....+ +.+...+..+.
T Consensus       167 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~  244 (388)
T d1w3ba_         167 NFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDP-NFLDAYINLGNVLKEARIFDRAVAAYLRALSLS-PNHAVVHGNLA  244 (388)
T ss_dssp             TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             chhHHHHhhcccccccCcHHHHHHHHHHHHHhCc-ccHHHHHHHhhhhhccccHHHHHHHHHHhHHHh-hhHHHHHHHHH
Confidence            2567777888888888899999998888877654 355677888888888899999999888888764 34566777788


Q ss_pred             HHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChh
Q 044084          208 NAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLR  287 (343)
Q Consensus       208 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~  287 (343)
                      ..+.+.|++++|...|+...+.. +.+..++..+...+...|++++|...++..... .+.+...+..+...+...|+++
T Consensus       245 ~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~  322 (388)
T d1w3ba_         245 CVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRL-CPTHADSLNNLANIKREQGNIE  322 (388)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTTTCHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhcc-CCccchhhhHHHHHHHHCCCHH
Confidence            88888899999999998888764 445678888888888899999999888887765 3446677788888888888888


Q ss_pred             HHHh---------------HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCc-cHHHHHHHHHHHhcccc
Q 044084          288 QLEK---------------YTTVISAYNMAREFDMCVKFYNEFRMNGGVI-DRAMAGIMVGVFSKLSQ  339 (343)
Q Consensus       288 ~a~~---------------~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~l~~~~~~~g~  339 (343)
                      +|..               +..+..+|...|++++|+..|++.++.  .| +...|..+..+|.+.|+
T Consensus       323 ~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~lg~~~~~~~D  388 (388)
T d1w3ba_         323 EAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTFADAYSNMGNTLKEMQD  388 (388)
T ss_dssp             HHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTT--CTTCHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCC
Confidence            8876               777889999999999999999999885  45 45678999999988775

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=1.4e-19  Score=150.60  Aligned_cols=305  Identities=12%  Similarity=0.098  Sum_probs=244.6

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhc
Q 044084           28 IMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFAS  107 (343)
Q Consensus        28 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  107 (343)
                      +...+.+.|++++|.+.|+++.+..    |.+..++..+...+.+.|++++|+..|++..+... -+..++..+..++.+
T Consensus         5 la~~~~~~G~~~~A~~~~~~~l~~~----p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p-~~~~a~~~l~~~~~~   79 (388)
T d1w3ba_           5 LAHREYQAGDFEAAERHCMQLWRQE----PDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQNP-LLAEAYSNLGNVYKE   79 (388)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC----CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHhhh
Confidence            4567789999999999999998765    33467899999999999999999999999988743 256789999999999


Q ss_pred             ccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH----------------------------------HhcCcHhHHHHHH
Q 044084          108 IAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMY----------------------------------IEEGMVEKTLEVV  153 (343)
Q Consensus       108 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~----------------------------------~~~~~~~~a~~~~  153 (343)
                      .|++++|...+....+.... +...........                                  ...+....+...+
T Consensus        80 ~g~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (388)
T d1w3ba_          80 RGQLQEAIEHYRHALRLKPD-FIDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACY  158 (388)
T ss_dssp             HTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHH
T ss_pred             hccccccccccccccccccc-cccccccccccccccccccccccccccccccccccccccccccccccccchhhhhHHHH
Confidence            99999999999998876543 333333333222                                  2333344444444


Q ss_pred             HHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCc
Q 044084          154 ESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDK  233 (343)
Q Consensus       154 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~  233 (343)
                      .......+ .+...+..+...+...|+++.|...+++..+.. +-+...+..+...+...|++++|...++.....+ +.
T Consensus       159 ~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~  235 (388)
T d1w3ba_         159 LKAIETQP-NFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLS-PN  235 (388)
T ss_dssp             HHHHHHCT-TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TT
T ss_pred             HHhhccCc-chhHHHHhhcccccccCcHHHHHHHHHHHHHhC-cccHHHHHHHhhhhhccccHHHHHHHHHHhHHHh-hh
Confidence            44444433 345567778888999999999999999988764 3356678889999999999999999999998875 45


Q ss_pred             ChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHh---------------HHHHHHH
Q 044084          234 CVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEK---------------YTTVISA  298 (343)
Q Consensus       234 ~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~---------------~~~l~~~  298 (343)
                      +...+..+...+.+.|++++|...|++..+.. +-+..++..+...+...|++++|..               +..+...
T Consensus       236 ~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~  314 (388)
T d1w3ba_         236 HAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANI  314 (388)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccCCccchhhhHHHHH
Confidence            67788889999999999999999999998863 2356788899999999999999987               7788889


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHHHHHhcccccccC
Q 044084          299 YNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMVGVFSKLSQIEEL  343 (343)
Q Consensus       299 ~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~g~~~~a  343 (343)
                      +...|++++|++.|++..+... -+...+..+..+|.+.|++++|
T Consensus       315 ~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~g~~~~A  358 (388)
T d1w3ba_         315 KREQGNIEEAVRLYRKALEVFP-EFAAAHSNLASVLQQQGKLQEA  358 (388)
T ss_dssp             HHTTTCHHHHHHHHHHHTTSCT-TCHHHHHHHHHHHHTTTCCHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHH
Confidence            9999999999999999987542 2456788999999999999875

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=4.5e-15  Score=120.18  Aligned_cols=237  Identities=11%  Similarity=0.066  Sum_probs=187.5

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHH
Q 044084           21 DSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYAS  100 (343)
Q Consensus        21 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  100 (343)
                      +....-.....+.+.|++++|...|+++.+.+    |.+..+|..+..++...|++++|...|++..+.... +...+..
T Consensus        18 ~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~----P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~   92 (323)
T d1fcha_          18 DHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQD----PKHMEAWQYLGTTQAENEQELLAISALRRCLELKPD-NQTALMA   92 (323)
T ss_dssp             TCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSC----TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHH
T ss_pred             chHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC----CCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccccc-ccccccc
Confidence            33333356777889999999999999998865    344689999999999999999999999999886432 5677888


Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCCC--------------CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCC-Cch
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGMLR--------------DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELN-ISD  165 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~~--------------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~  165 (343)
                      +...+...|++++|.+.++.........              +.......+..+...+.+.+|.+.|.+.....+. .+.
T Consensus        93 la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~  172 (323)
T d1fcha_          93 LAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDP  172 (323)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCH
T ss_pred             ccccccccccccccccchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhccccc
Confidence            8899999999999999999988754220              0111112233445567788899999887765432 345


Q ss_pred             hhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHH
Q 044084          166 CISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMY  245 (343)
Q Consensus       166 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  245 (343)
                      .++..+...+...|++++|...|++..... +-+...|..+..+|...|++++|.+.|+...+.. +-+..+|..+..+|
T Consensus       173 ~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~  250 (323)
T d1fcha_         173 DVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALELQ-PGYIRSRYNLGISC  250 (323)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             ccchhhHHHHHHHHHHhhhhcccccccccc-cccccchhhhhhcccccccchhHHHHHHHHHHHh-hccHHHHHHHHHHH
Confidence            677888889999999999999999988764 3356788889999999999999999999998875 44677899999999


Q ss_pred             HccCChHHHHHHHHHHhhC
Q 044084          246 GKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       246 ~~~~~~~~a~~~~~~m~~~  264 (343)
                      .+.|++++|...|++.++.
T Consensus       251 ~~~g~~~~A~~~~~~al~l  269 (323)
T d1fcha_         251 INLGAHREAVEHFLEALNM  269 (323)
T ss_dssp             HHHTCHHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHh
Confidence            9999999999999998763

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=2.6e-14  Score=115.67  Aligned_cols=219  Identities=12%  Similarity=0.045  Sum_probs=178.7

Q ss_pred             chhhHHHHHHHHHhCCCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHH
Q 044084            2 NSQSKLHYYEKMKSAGIVLDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILK   81 (343)
Q Consensus         2 ~~~~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~   81 (343)
                      ++++|+..|+++++..+ -+..+|..+..++...|++++|...|.+..+..    |.+...|..+...+...|++++|.+
T Consensus        34 ~~~~A~~~~~~al~~~P-~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~----p~~~~~~~~la~~~~~~~~~~~A~~  108 (323)
T d1fcha_          34 DLPNAVLLFEAAVQQDP-KHMEAWQYLGTTQAENEQELLAISALRRCLELK----PDNQTALMALAVSFTNESLQRQACE  108 (323)
T ss_dssp             CHHHHHHHHHHHHHSCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCChHHHHHHHHhhhccc----ccccccccccccccccccccccccc
Confidence            67899999999999754 367889999999999999999999999988765    3346889999999999999999999


Q ss_pred             HHHHHHhcCCCCChHh----------------HHHHHHHHhcccCHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHhcC
Q 044084           82 FFRDMKEKGILEDPSV----------------YASLICSFASIAEVKVAEELFKEAEEKGML-RDLEVFLKLVLMYIEEG  144 (343)
Q Consensus        82 ~~~~~~~~~~~~~~~~----------------~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~  144 (343)
                      .+++.....  |+...                ....+..+...+.+.++...+.+..+..+. .+..++..+...+...|
T Consensus       109 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~~~~~  186 (323)
T d1fcha_         109 ILRDWLRYT--PAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSG  186 (323)
T ss_dssp             HHHHHHHTS--TTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTT
T ss_pred             chhhHHHhc--cchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHHH
Confidence            999987753  22111                111222334556778888888888775432 46788899999999999


Q ss_pred             cHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHH
Q 044084          145 MVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFI  224 (343)
Q Consensus       145 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~  224 (343)
                      ++++|+..|++.....+ -+..+|..+..++...|++++|.+.|++..+.. +-+..++..+..+|.+.|++++|...|+
T Consensus       187 ~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~  264 (323)
T d1fcha_         187 EYDKAVDCFTAALSVRP-NDYLLWNKLGATLANGNQSEEAVAAYRRALELQ-PGYIRSRYNLGISCINLGAHREAVEHFL  264 (323)
T ss_dssp             CHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHhhhhccccccccccc-ccccchhhhhhcccccccchhHHHHHHHHHHHh-hccHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            99999999999987765 456788899999999999999999999998863 3356678889999999999999999999


Q ss_pred             HHHHc
Q 044084          225 EMQQK  229 (343)
Q Consensus       225 ~~~~~  229 (343)
                      +..+.
T Consensus       265 ~al~l  269 (323)
T d1fcha_         265 EALNM  269 (323)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            98774

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=9.4e-11  Score=93.75  Aligned_cols=217  Identities=9%  Similarity=0.038  Sum_probs=170.2

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccC-cHHHHHHHHHHHHhcCCCCChHhHHH
Q 044084           22 SGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSG-RAFEILKFFRDMKEKGILEDPSVYAS  100 (343)
Q Consensus        22 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~  100 (343)
                      ...|+.+...+.+.+.+++|+++++++.+.+    |.+..+|+....++...| ++++|+..++...+.... +..+|..
T Consensus        43 ~~a~~~~~~~~~~~e~~~~Al~~~~~ai~ln----P~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p~-~~~a~~~  117 (315)
T d2h6fa1          43 RDVYDYFRAVLQRDERSERAFKLTRDAIELN----AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPK-NYQVWHH  117 (315)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTT-CHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHHC----CCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHh-hhhHHHH
Confidence            3466777788889999999999999998865    445689999998888876 589999999999887543 6788999


Q ss_pred             HHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCC-
Q 044084          101 LICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRR-  179 (343)
Q Consensus       101 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-  179 (343)
                      +...+.+.|++++|+..+.++.+..+. +..+|..+...+...|++++|++.++++.+.++ -+...|+.+...+...+ 
T Consensus       118 ~~~~~~~l~~~~eAl~~~~kal~~dp~-n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p-~n~~a~~~r~~~l~~~~~  195 (315)
T d2h6fa1         118 RRVLVEWLRDPSQELEFIADILNQDAK-NYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDV-RNNSVWNQRYFVISNTTG  195 (315)
T ss_dssp             HHHHHHHHTCCTTHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTC
T ss_pred             HhHHHHhhccHHHHHHHHhhhhhhhhc-chHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCC-ccHHHHHHHHHHHHHccc
Confidence            999999999999999999999998754 799999999999999999999999999999876 46667776665554443 


Q ss_pred             -----cHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCc-ChhhHHHHHHHHHc
Q 044084          180 -----AYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDK-CVVAYSSMVAMYGK  247 (343)
Q Consensus       180 -----~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~  247 (343)
                           .+++|.+.+.+..+.. +.+...|..+...+.. ...+++...++...+....+ +...+..++..|..
T Consensus       196 ~~~~~~~~~ai~~~~~al~~~-P~~~~~~~~l~~ll~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~y~~  267 (315)
T d2h6fa1         196 YNDRAVLEREVQYTLEMIKLV-PHNESAWNYLKGILQD-RGLSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYED  267 (315)
T ss_dssp             SCSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTT-TCGGGCHHHHHHHHHHTTTCCCHHHHHHHHHHHHH
T ss_pred             cchhhhhHHhHHHHHHHHHhC-CCchHHHHHHHHHHHh-cChHHHHHHHHHHHHhCCCcCCHHHHHHHHHHHHH
Confidence                 3678999998888774 3456667666655544 45678888888877654322 34455666666643

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.42  E-value=7e-11  Score=94.50  Aligned_cols=259  Identities=9%  Similarity=0.040  Sum_probs=190.1

Q ss_pred             CchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhccc-CHHHHHHHHHHHHHcCCCCCHHHHHH
Q 044084           57 PSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIA-EVKVAEELFKEAEEKGMLRDLEVFLK  135 (343)
Q Consensus        57 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~  135 (343)
                      |.-..+|+.+...+.+.+.+++|+++++++.+.++. +...|+....++...| ++++|...++...+..+. +..+|..
T Consensus        40 p~~~~a~~~~~~~~~~~e~~~~Al~~~~~ai~lnP~-~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p~-~~~a~~~  117 (315)
T d2h6fa1          40 DKFRDVYDYFRAVLQRDERSERAFKLTRDAIELNAA-NYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPK-NYQVWHH  117 (315)
T ss_dssp             HHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTT-CHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHCCC-ChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHh-hhhHHHH
Confidence            344678888888888999999999999999997432 5667888888887766 599999999999998765 7999999


Q ss_pred             HHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCC
Q 044084          136 LVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGL  215 (343)
Q Consensus       136 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~  215 (343)
                      +...+.+.|++++|++.++++.+..+ -+...|..+...+...|++++|.+.++++.+.. +-+...|+.+...+.+.+.
T Consensus       118 ~~~~~~~l~~~~eAl~~~~kal~~dp-~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~-p~n~~a~~~r~~~l~~~~~  195 (315)
T d2h6fa1         118 RRVLVEWLRDPSQELEFIADILNQDA-KNYHAWQHRQWVIQEFKLWDNELQYVDQLLKED-VRNNSVWNQRYFVISNTTG  195 (315)
T ss_dssp             HHHHHHHHTCCTTHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HhHHHHhhccHHHHHHHHhhhhhhhh-cchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHC-CccHHHHHHHHHHHHHccc
Confidence            99999999999999999999998876 577889999999999999999999999999875 3456677777666665554


Q ss_pred             ------hhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCC-chHHHHHHHHHHHhcc--cCh
Q 044084          216 ------YSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCE-PNVWIYNSLMDMHGRA--KNL  286 (343)
Q Consensus       216 ------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~-p~~~~~~~l~~~~~~~--~~~  286 (343)
                            +++|...+....+.. |.+...|+.+...+.. ...+++.+.++...+.... .+...+..+...|...  +..
T Consensus       196 ~~~~~~~~~ai~~~~~al~~~-P~~~~~~~~l~~ll~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~y~~~~~~~~  273 (315)
T d2h6fa1         196 YNDRAVLEREVQYTLEMIKLV-PHNESAWNYLKGILQD-RGLSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYEDMLENQC  273 (315)
T ss_dssp             SCSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTT-TCGGGCHHHHHHHHHHTTTCCCHHHHHHHHHHHHHHHHTTC
T ss_pred             cchhhhhHHhHHHHHHHHHhC-CCchHHHHHHHHHHHh-cChHHHHHHHHHHHHhCCCcCCHHHHHHHHHHHHHHHhcCH
Confidence                  578888888888875 4567778777666544 4467788888777654222 2345556666665432  222


Q ss_pred             hHHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHH-HHHHHHHH
Q 044084          287 RQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAM-AGIMVGVF  334 (343)
Q Consensus       287 ~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~-~~~l~~~~  334 (343)
                      +.+            ...+++|.+++..+... +.|-..- |+-+...+
T Consensus       274 ~~~------------~~~~~ka~~l~~~l~~~-~DpiR~~yw~~~~~~l  309 (315)
T d2h6fa1         274 DNK------------EDILNKALELCEILAKE-KDTIRKEYWRYIGRSL  309 (315)
T ss_dssp             SSH------------HHHHHHHHHHHHHHHHT-TCGGGHHHHHHHHHHH
T ss_pred             HHH------------HHHHHHHHHHHHHHHHh-cCHHHHHHHHHHHHHH
Confidence            211            22346677777665543 3343333 54444443

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.41  E-value=1.3e-10  Score=92.86  Aligned_cols=188  Identities=6%  Similarity=0.027  Sum_probs=137.9

Q ss_pred             cHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHH
Q 044084           75 RAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVE  154 (343)
Q Consensus        75 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  154 (343)
                      ..++|..+|++..+...+.+...|...+....+.|+++.|..+|+++.+........+|...+....+.|+.+.|.++|+
T Consensus        79 ~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~  158 (308)
T d2onda1          79 FSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFK  158 (308)
T ss_dssp             HHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHH
Confidence            45788888888876544445566777777888888888888888888876544345678888888888888888888888


Q ss_pred             HHHhcCCCCchhhHHHHHHH-HhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcC-CC
Q 044084          155 SMKNAELNISDCISCVIVNG-FSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKG-FD  232 (343)
Q Consensus       155 ~~~~~~~~~~~~~~~~l~~~-~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~-~~  232 (343)
                      ++.+..+ .+...|...... +...|+.+.|..+|+.+.... +.+...+...+....+.|+++.|..+|++..+.. .+
T Consensus       159 ~al~~~~-~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~-p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~  236 (308)
T d2onda1         159 KAREDAR-TRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLP  236 (308)
T ss_dssp             HHHTSTT-CCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSC
T ss_pred             HHHHhCC-CcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhh-hhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCC
Confidence            8877664 233334333332 344678888888888888762 4456778888888888889999999998877753 23


Q ss_pred             cC--hhhHHHHHHHHHccCChHHHHHHHHHHhhC
Q 044084          233 KC--VVAYSSMVAMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       233 ~~--~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                      |+  ...|...+..-...|+.+.+..+++++.+.
T Consensus       237 ~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~~  270 (308)
T d2onda1         237 PEKSGEIWARFLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             GGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            32  347888888778889999888888887653

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.41  E-value=1.5e-10  Score=92.44  Aligned_cols=213  Identities=9%  Similarity=0.027  Sum_probs=156.5

Q ss_pred             cCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHH
Q 044084          109 AEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVY  188 (343)
Q Consensus       109 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  188 (343)
                      +..+++..+|++..+...+.+...|...+....+.|+++.|..+|+++....+......|...+..+.+.|+.+.|.++|
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            35678888999888765555777888888889999999999999999887655444456888888888899999999999


Q ss_pred             HHHHHcCCCCCHhhHHHHHHH-HHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCC-C
Q 044084          189 EQLISQGCIPGQVTYASIINA-YCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKG-C  266 (343)
Q Consensus       189 ~~~~~~~~~p~~~~~~~ll~~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~-~  266 (343)
                      +++.+.+ +.+...|...... +...|+.+.|..+|+.+.+.. +.+...|..++..+...|+++.|..+|++..... .
T Consensus       158 ~~al~~~-~~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~-p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~  235 (308)
T d2onda1         158 KKAREDA-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSL  235 (308)
T ss_dssp             HHHHTST-TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSS
T ss_pred             HHHHHhC-CCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhh-hhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCC
Confidence            9988764 2233344333332 344688999999999988863 5567889999999999999999999999987753 3


Q ss_pred             Cch--HHHHHHHHHHHhcccChhHHHh-HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCcc
Q 044084          267 EPN--VWIYNSLMDMHGRAKNLRQLEK-YTTVISAYNMAREFDMCVKFYNEFRMNGGVID  323 (343)
Q Consensus       267 ~p~--~~~~~~l~~~~~~~~~~~~a~~-~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~  323 (343)
                      .|+  ...|...+..-...|+.+.+.. +..+...+......+....+..+..-..+.|.
T Consensus       236 ~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~ry~~~d~~~~  295 (308)
T d2onda1         236 PPEKSGEIWARFLAFESNIGDLASILKVEKRRFTAFREEYEGKETALLVDRYKFMDLYPC  295 (308)
T ss_dssp             CGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTTSSCHHHHHHTTTCBTTBCSS
T ss_pred             ChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCccccccchHHHHHHHHHhcccCcC
Confidence            443  4578888887788899888887 56666666655555555555554433344443

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=99.40  E-value=3.4e-10  Score=91.90  Aligned_cols=269  Identities=7%  Similarity=-0.082  Sum_probs=184.5

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCc-hHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCC-CCC----hH
Q 044084           23 GCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPS-STHMYKILCDSLGKSGRAFEILKFFRDMKEKGI-LED----PS   96 (343)
Q Consensus        23 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~-~~~----~~   96 (343)
                      .........+...|++++|.+++++..+.....++. ...++..+...+...|++++|+..|++..+... .++    ..
T Consensus        13 e~~~lrA~~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~   92 (366)
T d1hz4a_          13 EFNALRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALW   92 (366)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHH
Confidence            344555677889999999999999998765432211 134677888999999999999999998876421 111    23


Q ss_pred             hHHHHHHHHhcccCHHHHHHHHHHHHHc----CCCC---CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCC----Cch
Q 044084           97 VYASLICSFASIAEVKVAEELFKEAEEK----GMLR---DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELN----ISD  165 (343)
Q Consensus        97 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~----~~~  165 (343)
                      .+..+...+...|++..+...+......    +...   ....+..+...+...|+++.+...+.........    ...
T Consensus        93 ~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  172 (366)
T d1hz4a_          93 SLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQL  172 (366)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHH
Confidence            4555667788889999999998876642    1111   1345667788899999999999999988754322    223


Q ss_pred             hhHHHHHHHHhcCCcHHHHHHHHHHHHHc----CCCCC--HhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCc---Chh
Q 044084          166 CISCVIVNGFSKRRAYWAAVKVYEQLISQ----GCIPG--QVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDK---CVV  236 (343)
Q Consensus       166 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~p~--~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~  236 (343)
                      ..+......+...+++..+...+.+....    +..+.  ...+..+...+...|++++|...+....+.....   ...
T Consensus       173 ~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  252 (366)
T d1hz4a_         173 QCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQG  252 (366)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHH
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHH
Confidence            34555667777889999999888876653    11111  2345556677888999999999998876543222   234


Q ss_pred             hHHHHHHHHHccCChHHHHHHHHHHhh----CCCCchH-HHHHHHHHHHhcccChhHHHh
Q 044084          237 AYSSMVAMYGKTGRIRDAMRLVAKMKP----KGCEPNV-WIYNSLMDMHGRAKNLRQLEK  291 (343)
Q Consensus       237 ~~~~l~~~~~~~~~~~~a~~~~~~m~~----~~~~p~~-~~~~~l~~~~~~~~~~~~a~~  291 (343)
                      .+..+...+...|++++|...+++...    .+..|+. .++..+..+|.+.|++++|..
T Consensus       253 ~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  312 (366)
T d1hz4a_         253 QWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQR  312 (366)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHH
Confidence            566788899999999999999988763    2333332 344555555555555555544

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=99.39  E-value=1.7e-11  Score=95.39  Aligned_cols=223  Identities=10%  Similarity=-0.050  Sum_probs=126.2

Q ss_pred             HHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHH
Q 044084           39 EKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELF  118 (343)
Q Consensus        39 ~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  118 (343)
                      +.++.-+++........++....+|..+...|.+.|++++|++.|++..+.... +..+|..+..++.+.|++++|...|
T Consensus        16 e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~p~-~~~a~~~lg~~~~~~g~~~~A~~~~   94 (259)
T d1xnfa_          16 EVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPD-MPEVFNYLGIYLTQAGNFDAAYEAF   94 (259)
T ss_dssp             HHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccCCC-CHHHHhhhchHHHHHHHHHHhhhhh
Confidence            444455555554433233333456666777777777777777777777765322 5667777777777777787787777


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCC
Q 044084          119 KEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIP  198 (343)
Q Consensus       119 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p  198 (343)
                      +++.+..+. +..++..+..+|...|++++|...|+...+..+ .+......+..++...+..+....+........  +
T Consensus        95 ~~al~~~p~-~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~  170 (259)
T d1xnfa_          95 DSVLELDPT-YNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDP-NDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSD--K  170 (259)
T ss_dssp             HHHHHHCTT-CTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSC--C
T ss_pred             hHHHHHHhh-hhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhcc-ccHHHHHHHHHHHHHhhhHHHHHHHHHHhhccc--h
Confidence            777776543 566677777777777888888888877776554 233333333334444444444444444444432  2


Q ss_pred             CHhhHHHHHHHHHccCC----hhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchH
Q 044084          199 GQVTYASIINAYCRIGL----YSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNV  270 (343)
Q Consensus       199 ~~~~~~~ll~~~~~~~~----~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~  270 (343)
                      +...+. ++..+.....    .+.+...+....... +-...+|..+...|...|++++|...|++.+..  .|+.
T Consensus       171 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~  242 (259)
T d1xnfa_         171 EQWGWN-IVEFYLGNISEQTLMERLKADATDNTSLA-EHLSETNFYLGKYYLSLGDLDSATALFKLAVAN--NVHN  242 (259)
T ss_dssp             CSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHHH-HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CCTT
T ss_pred             hhhhhh-HHHHHHHHHHHHHHHHHHHHHHHHhhhcC-cccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHc--CCCC
Confidence            211221 2222221111    111111111111110 112345667788888888888888888888865  4543

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=99.34  E-value=5.6e-10  Score=90.60  Aligned_cols=263  Identities=13%  Similarity=-0.003  Sum_probs=181.6

Q ss_pred             CchhhHHHHHHHHHhCCCCCC----hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC--CchHHHHHHHHHHhhccC
Q 044084            1 TNSQSKLHYYEKMKSAGIVLD----SGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLT--PSSTHMYKILCDSLGKSG   74 (343)
Q Consensus         1 ~~~~~A~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~~~~li~~~~~~~   74 (343)
                      .++++|++++++..+.....+    ...+..+...+...|++++|...|++..+......  +.....+..+...+...|
T Consensus        26 g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~  105 (366)
T d1hz4a_          26 GNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFAQG  105 (366)
T ss_dssp             TCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHH
Confidence            367889999998887542211    23567778888999999999999998876543322  222345666777888889


Q ss_pred             cHHHHHHHHHHHHhc----CCCCC---hHhHHHHHHHHhcccCHHHHHHHHHHHHHcCC----CCCHHHHHHHHHHHHhc
Q 044084           75 RAFEILKFFRDMKEK----GILED---PSVYASLICSFASIAEVKVAEELFKEAEEKGM----LRDLEVFLKLVLMYIEE  143 (343)
Q Consensus        75 ~~~~a~~~~~~~~~~----~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----~~~~~~~~~l~~~~~~~  143 (343)
                      ++..+...+.+....    +..+.   ...+..+...+...|+++.+...+........    ......+..+...+...
T Consensus       106 ~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  185 (366)
T d1hz4a_         106 FLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLAR  185 (366)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHhh
Confidence            999999888876542    11111   12445566777888999999998888776432    22355666777788888


Q ss_pred             CcHhHHHHHHHHHHhcC----CCC--chhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCC---CHhhHHHHHHHHHccC
Q 044084          144 GMVEKTLEVVESMKNAE----LNI--SDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIP---GQVTYASIINAYCRIG  214 (343)
Q Consensus       144 ~~~~~a~~~~~~~~~~~----~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p---~~~~~~~ll~~~~~~~  214 (343)
                      ++...+...+.......    ..+  ....+......+...|+++.|...+..........   ....+..+..++...|
T Consensus       186 ~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g  265 (366)
T d1hz4a_         186 GDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLG  265 (366)
T ss_dssp             TCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTT
T ss_pred             hhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcC
Confidence            99998888887765421    111  12235556667788899999999888866543222   2234556777888899


Q ss_pred             ChhHHHHHHHHHHHc----CCCcC-hhhHHHHHHHHHccCChHHHHHHHHHHhh
Q 044084          215 LYSKAEKVFIEMQQK----GFDKC-VVAYSSMVAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       215 ~~~~a~~~~~~~~~~----~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                      ++++|...++.....    +..|+ ..++..+...|...|++++|.+.+++..+
T Consensus       266 ~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~  319 (366)
T d1hz4a_         266 EFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  319 (366)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            999999998887642    33333 45677788889999999999999888764

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=99.31  E-value=7.7e-10  Score=85.76  Aligned_cols=226  Identities=12%  Similarity=0.028  Sum_probs=144.6

Q ss_pred             ccCcHHHHHHHHHHHHhcCCCCC---hHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhH
Q 044084           72 KSGRAFEILKFFRDMKEKGILED---PSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEK  148 (343)
Q Consensus        72 ~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  148 (343)
                      ...+.+.++.-+++........+   ..+|..+..+|.+.|++++|...|++..+..+. ++.+|+.+..+|.+.|++++
T Consensus        11 ~~~~~e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~p~-~~~a~~~lg~~~~~~g~~~~   89 (259)
T d1xnfa_          11 PTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPD-MPEVFNYLGIYLTQAGNFDA   89 (259)
T ss_dssp             CCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHTTCHHH
T ss_pred             ccHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccCCC-CHHHHhhhchHHHHHHHHHH
Confidence            34566777777888776532111   235666778888999999999999999987654 78889999999999999999


Q ss_pred             HHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHH
Q 044084          149 TLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQ  228 (343)
Q Consensus       149 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  228 (343)
                      |+..|++..+..+ -+..++..+..++...|++++|.+.|+...+.. +.+......+...+.+.+..+....+......
T Consensus        90 A~~~~~~al~~~p-~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (259)
T d1xnfa_          90 AYEAFDSVLELDP-TYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD-PNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEK  167 (259)
T ss_dssp             HHHHHHHHHHHCT-TCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHh-hhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhc-cccHHHHHHHHHHHHHhhhHHHHHHHHHHhhc
Confidence            9999999988765 355678888888999999999999999988764 23344433344444555555555555555554


Q ss_pred             cCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHH
Q 044084          229 KGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMC  308 (343)
Q Consensus       229 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a  308 (343)
                      ..  ++...++ ++..+.........   +...... .......-....            ..|..+...|...|++++|
T Consensus       168 ~~--~~~~~~~-~~~~~~~~~~~~~~---~~~~~~~-~~~~~~~~~~~~------------~~~~~lg~~~~~~g~~~~A  228 (259)
T d1xnfa_         168 SD--KEQWGWN-IVEFYLGNISEQTL---MERLKAD-ATDNTSLAEHLS------------ETNFYLGKYYLSLGDLDSA  228 (259)
T ss_dssp             SC--CCSTHHH-HHHHHTTSSCHHHH---HHHHHHH-CCSHHHHHHHHH------------HHHHHHHHHHHHTTCHHHH
T ss_pred             cc--hhhhhhh-HHHHHHHHHHHHHH---HHHHHHH-HHHhhhcCcccH------------HHHHHHHHHHHHCCCHHHH
Confidence            32  2222222 22222222221111   1121111 011111111111            1155567788899999999


Q ss_pred             HHHHHHHHhCC
Q 044084          309 VKFYNEFRMNG  319 (343)
Q Consensus       309 ~~~~~~m~~~~  319 (343)
                      ++.|++.+...
T Consensus       229 ~~~~~~al~~~  239 (259)
T d1xnfa_         229 TALFKLAVANN  239 (259)
T ss_dssp             HHHHHHHHTTC
T ss_pred             HHHHHHHHHcC
Confidence            99999998754

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.28  E-value=9.3e-12  Score=100.85  Aligned_cols=227  Identities=7%  Similarity=0.009  Sum_probs=119.6

Q ss_pred             CHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccC--cHHHHHHHHHHHHhcCCCCChHhHH-HHHHHHhcccCHHH
Q 044084           37 DSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSG--RAFEILKFFRDMKEKGILEDPSVYA-SLICSFASIAEVKV  113 (343)
Q Consensus        37 ~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~-~l~~~~~~~~~~~~  113 (343)
                      ++++|+.+++...+.+    |.+...|..+..++...+  ++++|+..+++..+... ++...+. .....+...+..+.
T Consensus        88 ~~~~al~~~~~~l~~~----pk~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~-~~~~~~~~~~~~~~~~~~~~~~  162 (334)
T d1dcea1          88 LVKAELGFLESCLRVN----PKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADE-RNFHCWDYRRFVAAQAAVAPAE  162 (334)
T ss_dssp             HHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTCCCHHH
T ss_pred             HHHHHHHHHHHHHHhC----CCcHHHHHHhhHHHHHhccccHHHHHHHHHHHHhhCc-hhhhhhhhHHHHHHHhccccHH
Confidence            3556666666665543    222345555554444433  35666666666655432 2333332 23344455566666


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHH
Q 044084          114 AEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLIS  193 (343)
Q Consensus       114 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  193 (343)
                      |...++.+.+..+. +...|+.+...+.+.|++++|...+.......  |.   ...+...+...+..+.+...+.....
T Consensus       163 Al~~~~~~i~~~p~-~~~a~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~---~~~~~~~~~~l~~~~~a~~~~~~~l~  236 (334)
T d1dcea1         163 ELAFTDSLITRNFS-NYSSWHYRSCLLPQLHPQPDSGPQGRLPENVL--LK---ELELVQNAFFTDPNDQSAWFYHRWLL  236 (334)
T ss_dssp             HHHHHHTTTTTTCC-CHHHHHHHHHHHHHHSCCCCSSSCCSSCHHHH--HH---HHHHHHHHHHHCSSCSHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCC-CHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhH--HH---HHHHHHHHHHhcchhHHHHHHHHHHH
Confidence            66666666655443 56666666666666666655544443322221  11   01112222333444445555555544


Q ss_pred             cCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhCCCCch-HHH
Q 044084          194 QGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPKGCEPN-VWI  272 (343)
Q Consensus       194 ~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~~  272 (343)
                      .. +++...+..+...+...++.++|...+....+.. +.+..++..+...+...|++++|.+.+++..+.  .|+ ...
T Consensus       237 ~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~l--dP~~~~y  312 (334)
T d1dcea1         237 GR-AEPLFRCELSVEKSTVLQSELESCKELQELEPEN-KWCLLTIILLMRALDPLLYEKETLQYFSTLKAV--DPMRAAY  312 (334)
T ss_dssp             SC-CCCSSSCCCCHHHHHHHHHHHHHHHHHHHHCTTC-HHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHH--CGGGHHH
T ss_pred             hC-cchhhHHHHHHHHHHHHhhHHHHHHHHHHHHhhC-chHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--CcccHHH
Confidence            42 2334444455555666677777777776666554 334556666777777777777777777777764  453 333


Q ss_pred             HHHHHH
Q 044084          273 YNSLMD  278 (343)
Q Consensus       273 ~~~l~~  278 (343)
                      |..+..
T Consensus       313 ~~~L~~  318 (334)
T d1dcea1         313 LDDLRS  318 (334)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            444433

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.21  E-value=2.2e-10  Score=92.54  Aligned_cols=272  Identities=7%  Similarity=-0.038  Sum_probs=166.2

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHh---hcc-------CcHHHHHHHHHHHHhcCCCCChHh
Q 044084           28 IMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSL---GKS-------GRAFEILKFFRDMKEKGILEDPSV   97 (343)
Q Consensus        28 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~---~~~-------~~~~~a~~~~~~~~~~~~~~~~~~   97 (343)
                      ++....+.+..++|+++++.+.+.+    |.+...|+..-..+   ...       |++++|+..++...+...+ +...
T Consensus        35 ~~~~~~~~~~~~~al~~~~~~l~~~----P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~pk-~~~~  109 (334)
T d1dcea1          35 VFQKRQAGELDESVLELTSQILGAN----PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPK-SYGT  109 (334)
T ss_dssp             HHHHHHTTCCSHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHH
T ss_pred             HHHHHhcccccHHHHHHHHHHHHHC----CCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhCCC-cHHH
Confidence            3333333344578888888887655    23345665443332   222       2366777777777765422 4555


Q ss_pred             HHHHHHHHhccc--CHHHHHHHHHHHHHcCCCCCHHHHH-HHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHH
Q 044084           98 YASLICSFASIA--EVKVAEELFKEAEEKGMLRDLEVFL-KLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNG  174 (343)
Q Consensus        98 ~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~-~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  174 (343)
                      |..+..++...+  +++++...+..+.+..+. +...+. .....+...+.+++|+..++.....++ -+...|+.+...
T Consensus       110 ~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~-~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p-~~~~a~~~l~~~  187 (334)
T d1dcea1         110 WHHRCWLLSRLPEPNWARELELCARFLEADER-NFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNF-SNYSSWHYRSCL  187 (334)
T ss_dssp             HHHHHHHHHTCSSCCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTC-CCHHHHHHHHHH
T ss_pred             HHHhhHHHHHhccccHHHHHHHHHHHHhhCch-hhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCC-CCHHHHHHHHHH
Confidence            655555555544  477777788877776543 455543 444566667778888888877777665 456667777777


Q ss_pred             HhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHH
Q 044084          175 FSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDA  254 (343)
Q Consensus       175 ~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  254 (343)
                      +...|++++|...++...+.  .|+.   ......+...+..+++...+....... +++...+..+...+...|+.++|
T Consensus       188 ~~~~~~~~~A~~~~~~~~~~--~~~~---~~~~~~~~~l~~~~~a~~~~~~~l~~~-~~~~~~~~~l~~~~~~~~~~~~a  261 (334)
T d1dcea1         188 LPQLHPQPDSGPQGRLPENV--LLKE---LELVQNAFFTDPNDQSAWFYHRWLLGR-AEPLFRCELSVEKSTVLQSELES  261 (334)
T ss_dssp             HHHHSCCCCSSSCCSSCHHH--HHHH---HHHHHHHHHHCSSCSHHHHHHHHHHSC-CCCSSSCCCCHHHHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHhHHh--HHHH---HHHHHHHHHhcchhHHHHHHHHHHHhC-cchhhHHHHHHHHHHHHhhHHHH
Confidence            77777777666555544332  1221   122333455566667777777666654 44555666667777777888888


Q ss_pred             HHHHHHHhhCCCCchH-HHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHH-HHHHHHH
Q 044084          255 MRLVAKMKPKGCEPNV-WIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRA-MAGIMVG  332 (343)
Q Consensus       255 ~~~~~~m~~~~~~p~~-~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~-~~~~l~~  332 (343)
                      ...+.+..+.  .|+. .+                   +..+..++...|++++|++.+++..+.  .|+.. -|..|..
T Consensus       262 ~~~~~~~~~~--~p~~~~~-------------------~~~l~~~~~~~~~~~eA~~~~~~ai~l--dP~~~~y~~~L~~  318 (334)
T d1dcea1         262 CKELQELEPE--NKWCLLT-------------------IILLMRALDPLLYEKETLQYFSTLKAV--DPMRAAYLDDLRS  318 (334)
T ss_dssp             HHHHHHHCTT--CHHHHHH-------------------HHHHHHHHCTGGGHHHHHHHHHHHHHH--CGGGHHHHHHHHH
T ss_pred             HHHHHHHHhh--CchHHHH-------------------HHHHHHHHHHCCCHHHHHHHHHHHHHH--CcccHHHHHHHHH
Confidence            8888777764  3322 23                   334455666788889999999999884  56544 4555554


Q ss_pred             HHh
Q 044084          333 VFS  335 (343)
Q Consensus       333 ~~~  335 (343)
                      .+.
T Consensus       319 ~~~  321 (334)
T d1dcea1         319 KFL  321 (334)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            443

>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=98.90  E-value=1.5e-07  Score=68.83  Aligned_cols=123  Identities=9%  Similarity=0.047  Sum_probs=75.7

Q ss_pred             HHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcH
Q 044084           67 CDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMV  146 (343)
Q Consensus        67 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  146 (343)
                      ...+...|+++.|++.|.++    .+|+..+|..+..++...|++++|.+.|++.++..+. +...|..+..+|.+.|++
T Consensus        12 g~~~~~~~d~~~Al~~~~~i----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp~-~~~a~~~~g~~~~~~g~~   86 (192)
T d1hh8a_          12 GVLAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKH-LAVAYFQRGMLYYQTEKY   86 (192)
T ss_dssp             HHHHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHCCCHHHHHHHHHhc----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhh-hhhhHHHHHHHHHhhccH
Confidence            44556677777777777653    2455666667777777777777777777777776543 567777777777777777


Q ss_pred             hHHHHHHHHHHhcCCCCc---------------hhhHHHHHHHHhcCCcHHHHHHHHHHHHHc
Q 044084          147 EKTLEVVESMKNAELNIS---------------DCISCVIVNGFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       147 ~~a~~~~~~~~~~~~~~~---------------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  194 (343)
                      ++|+..|++.........               ..++..+..++...|++++|.+.+....+.
T Consensus        87 ~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~  149 (192)
T d1hh8a_          87 DLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSM  149 (192)
T ss_dssp             HHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            777777777654211000               112333444555555555555555555444

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.85  E-value=1.4e-07  Score=74.05  Aligned_cols=199  Identities=11%  Similarity=-0.035  Sum_probs=117.7

Q ss_pred             HHHHHhhccCcHHHHHHHHHHHHhc----CCCC-ChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCC-----CCHHHHH
Q 044084           65 ILCDSLGKSGRAFEILKFFRDMKEK----GILE-DPSVYASLICSFASIAEVKVAEELFKEAEEKGML-----RDLEVFL  134 (343)
Q Consensus        65 ~li~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-----~~~~~~~  134 (343)
                      .....|...+++++|.+.|.+..+.    +-.+ -..+|..+..+|.+.|++++|...+++..+....     ....++.
T Consensus        42 ~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~  121 (290)
T d1qqea_          42 QAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKF  121 (290)
T ss_dssp             HHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHH
Confidence            3355566777788888777776542    1111 1245677777777888888888877766542111     1144555


Q ss_pred             HHHHHHHh-cCcHhHHHHHHHHHHhc----CCCC-chhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCH------hh
Q 044084          135 KLVLMYIE-EGMVEKTLEVVESMKNA----ELNI-SDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQ------VT  202 (343)
Q Consensus       135 ~l~~~~~~-~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~------~~  202 (343)
                      .+...|.. .|++++|++.+++..+.    +.++ ...++..+...+...|++++|...|+++.........      ..
T Consensus       122 ~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~  201 (290)
T d1qqea_         122 ELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDY  201 (290)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHH
T ss_pred             HHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHH
Confidence            66666644 58888888888776432    1111 1234666778888888888888888887765311111      11


Q ss_pred             HHHHHHHHHccCChhHHHHHHHHHHHcCCC-cC---hhhHHHHHHHHHc--cCChHHHHHHHHHHhh
Q 044084          203 YASIINAYCRIGLYSKAEKVFIEMQQKGFD-KC---VVAYSSMVAMYGK--TGRIRDAMRLVAKMKP  263 (343)
Q Consensus       203 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~---~~~~~~l~~~~~~--~~~~~~a~~~~~~m~~  263 (343)
                      +...+..+...|+++.|...++...+.... ++   ......++.++-.  .+.+++|+..|+++.+
T Consensus       202 ~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l~~a~~~~d~e~~~eai~~y~~~~~  268 (290)
T d1qqea_         202 FLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFMR  268 (290)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSSC
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhh
Confidence            233444556678888888888877664311 11   2234556666544  2346777777766554

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.81  E-value=1.2e-07  Score=74.52  Aligned_cols=203  Identities=10%  Similarity=0.002  Sum_probs=138.1

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC--CCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCC---CC--ChH
Q 044084           24 CYCQIMEAFYKIGDSEKVAALFLECESRKLD--LTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGI---LE--DPS   96 (343)
Q Consensus        24 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~---~~--~~~   96 (343)
                      .|......|...|++++|.+.|.+..+....  ..+....+|..+..+|.+.|++++|++.+++......   .+  ...
T Consensus        39 ~y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~  118 (290)
T d1qqea_          39 LCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGAN  118 (290)
T ss_dssp             HHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHH
Confidence            5788888999999999999999987553111  1122356899999999999999999999998765311   11  133


Q ss_pred             hHHHHHHHHh-cccCHHHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchh----
Q 044084           97 VYASLICSFA-SIAEVKVAEELFKEAEEK----GMLR-DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDC----  166 (343)
Q Consensus        97 ~~~~l~~~~~-~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----  166 (343)
                      ++..+...+. ..|+++.|...+++..+.    +..+ -..++..+...+...|++++|++.|+++..........    
T Consensus       119 ~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~  198 (290)
T d1qqea_         119 FKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSL  198 (290)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGH
T ss_pred             HHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhH
Confidence            4555666664 469999999999987652    2111 14567888999999999999999999987654322211    


Q ss_pred             --hHHHHHHHHhcCCcHHHHHHHHHHHHHcCCC-CC---HhhHHHHHHHHHc--cCChhHHHHHHHHH
Q 044084          167 --ISCVIVNGFSKRRAYWAAVKVYEQLISQGCI-PG---QVTYASIINAYCR--IGLYSKAEKVFIEM  226 (343)
Q Consensus       167 --~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-p~---~~~~~~ll~~~~~--~~~~~~a~~~~~~~  226 (343)
                        .+...+.++...|+++.|...+++..+.... ++   ......++.++..  .+.+++|...|+.+
T Consensus       199 ~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l~~a~~~~d~e~~~eai~~y~~~  266 (290)
T d1qqea_         199 KDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNF  266 (290)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence              2344555677889999999999998765311 11   2234556666554  23466666666543

>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=98.81  E-value=4.5e-07  Score=66.24  Aligned_cols=88  Identities=13%  Similarity=-0.014  Sum_probs=57.0

Q ss_pred             HHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcH
Q 044084          102 ICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAY  181 (343)
Q Consensus       102 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  181 (343)
                      ...+...|+++.|.+.|.++    .+|+..+|..+..+|...|++++|++.|++..+.++ -+...|..+..++.+.|++
T Consensus        12 g~~~~~~~d~~~Al~~~~~i----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp-~~~~a~~~~g~~~~~~g~~   86 (192)
T d1hh8a_          12 GVLAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDK-HLAVAYFQRGMLYYQTEKY   86 (192)
T ss_dssp             HHHHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHCCCHHHHHHHHHhc----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhh-hhhhhHHHHHHHHHhhccH
Confidence            33445666777777666543    235666666777777777777777777777766654 3455666666777777777


Q ss_pred             HHHHHHHHHHHHc
Q 044084          182 WAAVKVYEQLISQ  194 (343)
Q Consensus       182 ~~a~~~~~~~~~~  194 (343)
                      ++|.+.|++....
T Consensus        87 ~~A~~~~~kAl~~   99 (192)
T d1hh8a_          87 DLAIKDLKEALIQ   99 (192)
T ss_dssp             HHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHh
Confidence            7777777666543

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.75  E-value=5.1e-07  Score=60.06  Aligned_cols=92  Identities=10%  Similarity=-0.038  Sum_probs=50.0

Q ss_pred             HHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcH
Q 044084           67 CDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMV  146 (343)
Q Consensus        67 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  146 (343)
                      ...+...|++++|+..|++..+... -+...|..+..++...|++++|...+....+..+. ++..|..+..++...|++
T Consensus        10 g~~~~~~g~~~eAi~~~~~al~~~p-~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~~g~~~~~~~~~   87 (117)
T d1elwa_          10 GNKALSVGNIDDALQCYSEAIKLDP-HNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPD-WGKGYSRKAAALEFLNRF   87 (117)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhcCC-cchhhhhcccccccccccccccchhhhhHHHhccc-hhhHHHHHHHHHHHccCH
Confidence            4444555555555555555555431 24445555555555555555555555555555432 555555555555555555


Q ss_pred             hHHHHHHHHHHhcC
Q 044084          147 EKTLEVVESMKNAE  160 (343)
Q Consensus       147 ~~a~~~~~~~~~~~  160 (343)
                      ++|+..|++..+..
T Consensus        88 ~~A~~~~~~a~~~~  101 (117)
T d1elwa_          88 EEAKRTYEEGLKHE  101 (117)
T ss_dssp             HHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhC
Confidence            55555555555443

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.72  E-value=4.9e-07  Score=63.88  Aligned_cols=93  Identities=12%  Similarity=0.024  Sum_probs=55.9

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhc
Q 044084           28 IMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFAS  107 (343)
Q Consensus        28 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  107 (343)
                      ....|.+.|++++|...|++..+.+    |.+...|..+..++...|++++|+..|++.++... -+..+|..+..++..
T Consensus        16 ~gn~~~~~~~y~~A~~~~~~al~~~----p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p-~~~~a~~~~g~~~~~   90 (159)
T d1a17a_          16 QANDYFKAKDYENAIKFYSQAIELN----PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDK-KYIKGYYRRAASNMA   90 (159)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHS----TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHhhhccccc----hhhhhhhhhhHHHHHhccccchHHHHHHHHHHHcc-cchHHHHHHHHHHHH
Confidence            3445566666666666666665543    22345666666666666666666666666665432 244556666666666


Q ss_pred             ccCHHHHHHHHHHHHHcC
Q 044084          108 IAEVKVAEELFKEAEEKG  125 (343)
Q Consensus       108 ~~~~~~a~~~~~~~~~~~  125 (343)
                      .|++++|...+++..+..
T Consensus        91 ~g~~~eA~~~~~~a~~~~  108 (159)
T d1a17a_          91 LGKFRAALRDYETVVKVK  108 (159)
T ss_dssp             TTCHHHHHHHHHHHHHHS
T ss_pred             cCCHHHHHHHHHHHHHcC
Confidence            666666666666666654

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.70  E-value=6.9e-07  Score=63.08  Aligned_cols=95  Identities=13%  Similarity=0.059  Sum_probs=61.7

Q ss_pred             HHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Q 044084           64 KILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEE  143 (343)
Q Consensus        64 ~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  143 (343)
                      ......+.+.|++++|+..|++..+... -+...|..+..++...|++++|...|++.++..+. +..+|..+..++...
T Consensus        14 ~~~gn~~~~~~~y~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p~-~~~a~~~~g~~~~~~   91 (159)
T d1a17a_          14 KTQANDYFKAKDYENAIKFYSQAIELNP-SNAIYYGNRSLAYLRTECYGYALGDATRAIELDKK-YIKGYYRRAASNMAL   91 (159)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCHHHHHHHhhhccccch-hhhhhhhhhHHHHHhccccchHHHHHHHHHHHccc-chHHHHHHHHHHHHc
Confidence            3345556667777777777777666542 24556666666677777777777777776665533 566666677777777


Q ss_pred             CcHhHHHHHHHHHHhcC
Q 044084          144 GMVEKTLEVVESMKNAE  160 (343)
Q Consensus       144 ~~~~~a~~~~~~~~~~~  160 (343)
                      |++++|...+++.....
T Consensus        92 g~~~eA~~~~~~a~~~~  108 (159)
T d1a17a_          92 GKFRAALRDYETVVKVK  108 (159)
T ss_dssp             TCHHHHHHHHHHHHHHS
T ss_pred             CCHHHHHHHHHHHHHcC
Confidence            77777777777666654

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.69  E-value=7.3e-07  Score=59.25  Aligned_cols=84  Identities=13%  Similarity=0.047  Sum_probs=31.3

Q ss_pred             cccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHH
Q 044084          107 SIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVK  186 (343)
Q Consensus       107 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  186 (343)
                      +.|++++|...|.+.++..+. +...|..+..+|...|++++|+..+....+.++ .+...|..+..++...|++++|+.
T Consensus        15 ~~g~~~eAi~~~~~al~~~p~-~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~~g~~~~~~~~~~~A~~   92 (117)
T d1elwa_          15 SVGNIDDALQCYSEAIKLDPH-NHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKP-DWGKGYSRKAAALEFLNRFEEAKR   92 (117)
T ss_dssp             HTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHhcCCc-chhhhhcccccccccccccccchhhhhHHHhcc-chhhHHHHHHHHHHHccCHHHHHH
Confidence            333333333333333333221 333333333333333333333333333333332 223333333333333333333333


Q ss_pred             HHHHHH
Q 044084          187 VYEQLI  192 (343)
Q Consensus       187 ~~~~~~  192 (343)
                      .|++..
T Consensus        93 ~~~~a~   98 (117)
T d1elwa_          93 TYEEGL   98 (117)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            333333

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=98.64  E-value=3.9e-05  Score=58.74  Aligned_cols=227  Identities=12%  Similarity=0.000  Sum_probs=150.1

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhc----cCcHHHHHHHHHHHHhcCCCCChH
Q 044084           21 DSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGK----SGRAFEILKFFRDMKEKGILEDPS   96 (343)
Q Consensus        21 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~   96 (343)
                      |+..+..|...+.+.+++++|.+.|++..+.|.      ..++..|...|..    ..++..|...+......+   +..
T Consensus         1 ~p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g~------~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~---~~~   71 (265)
T d1ouva_           1 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLKE------NSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSN   71 (265)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTC------HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCC------HHHHHHHHHHHHcCCCcchhHHHHHHhhccccccc---ccc
Confidence            355677778888889999999999999887663      3455556666654    567888998888877765   333


Q ss_pred             hHHHHHHHHh----cccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----cCcHhHHHHHHHHHHhcCCCCchhhH
Q 044084           97 VYASLICSFA----SIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIE----EGMVEKTLEVVESMKNAELNISDCIS  168 (343)
Q Consensus        97 ~~~~l~~~~~----~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~  168 (343)
                      ....+...+.    ...+.+.+...++...+.|.   ......+...+..    ......+...+......+   +...+
T Consensus        72 a~~~l~~~~~~~~~~~~~~~~a~~~~~~a~~~g~---~~a~~~l~~~~~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~  145 (265)
T d1ouva_          72 GCHLLGNLYYSGQGVSQNTNKALQYYSKACDLKY---AEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGC  145 (265)
T ss_dssp             HHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC---HHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHH
T ss_pred             hhhccccccccccccchhhHHHHHHHhhhhhhhh---hhHHHhhcccccCCCcccchhHHHHHHhhhhhccc---ccchh
Confidence            3333433333    24578888888888887763   2333334344433    334566666666655543   34456


Q ss_pred             HHHHHHHhc----CCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHc----cCChhHHHHHHHHHHHcCCCcChhhHHH
Q 044084          169 CVIVNGFSK----RRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCR----IGLYSKAEKVFIEMQQKGFDKCVVAYSS  240 (343)
Q Consensus       169 ~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~  240 (343)
                      ..+...+..    ..+...+...++...+.|   +......+...|..    ..++++|...|....+.|   ++..+..
T Consensus       146 ~~L~~~~~~~~~~~~~~~~~~~~~~~a~~~g---~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~~g---~~~a~~~  219 (265)
T d1ouva_         146 TILGSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGGGCFN  219 (265)
T ss_dssp             HHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHHHHHH
T ss_pred             hhhhhhhccCCCcccccccchhhhhcccccc---ccccccchhhhcccCcccccchhhhhhhHhhhhccc---CHHHHHH
Confidence            666666654    556778888888877765   44455555545543    467888999998888876   4556666


Q ss_pred             HHHHHHc----cCChHHHHHHHHHHhhCCCCc
Q 044084          241 MVAMYGK----TGRIRDAMRLVAKMKPKGCEP  268 (343)
Q Consensus       241 l~~~~~~----~~~~~~a~~~~~~m~~~~~~p  268 (343)
                      |...|..    ..+.++|.+.|++..+.|..+
T Consensus       220 LG~~y~~G~g~~~n~~~A~~~~~kAa~~g~~~  251 (265)
T d1ouva_         220 LGAMQYNGEGVTRNEKQAIENFKKGCKLGAKG  251 (265)
T ss_dssp             HHHHHHTTSSSSCCSTTHHHHHHHHHHHTCHH
T ss_pred             HHHHHHcCCCCccCHHHHHHHHHHHHHCcCHH
Confidence            7777664    347888999998888776543

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.61  E-value=1.7e-07  Score=69.15  Aligned_cols=99  Identities=11%  Similarity=-0.017  Sum_probs=64.2

Q ss_pred             CChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHH
Q 044084           93 EDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIV  172 (343)
Q Consensus        93 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  172 (343)
                      |+...+......+.+.|++++|...|.+.++..+. ++..|..+..+|.+.|++++|+..|++..+..+ -+..+|..+.
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~p~-~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~p-~~~~a~~~lg   79 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPL-VAVYYTNRALCYLKMQQPEQALADCRRALELDG-QSVKAHFFLG   79 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCT-TCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhCC-CcHHHHHHHH
Confidence            45555556666666777777777777766665543 566666677777777777777777777665543 2445566666


Q ss_pred             HHHhcCCcHHHHHHHHHHHHH
Q 044084          173 NGFSKRRAYWAAVKVYEQLIS  193 (343)
Q Consensus       173 ~~~~~~~~~~~a~~~~~~~~~  193 (343)
                      .+|...|++++|...|++...
T Consensus        80 ~~~~~l~~~~~A~~~~~~al~  100 (201)
T d2c2la1          80 QCQLEMESYDEAIANLQRAYS  100 (201)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHH
Confidence            666677777777766666554

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.61  E-value=5.5e-07  Score=66.26  Aligned_cols=98  Identities=9%  Similarity=-0.011  Sum_probs=72.5

Q ss_pred             HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 044084           60 THMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLM  139 (343)
Q Consensus        60 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  139 (343)
                      ...+......+.+.|++++|+..|++...... -+...|..+..+|.+.|+++.|...|+..++..+. +..+|..+..+
T Consensus         4 a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~p-~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~p~-~~~a~~~lg~~   81 (201)
T d2c2la1           4 AQELKEQGNRLFVGRKYPEAAACYGRAITRNP-LVAVYYTNRALCYLKMQQPEQALADCRRALELDGQ-SVKAHFFLGQC   81 (201)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCS-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTT-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhCCC-cHHHHHHHHHH
Confidence            45566677778888888888888887777642 35667777778888888888888888887765432 57777778888


Q ss_pred             HHhcCcHhHHHHHHHHHHhc
Q 044084          140 YIEEGMVEKTLEVVESMKNA  159 (343)
Q Consensus       140 ~~~~~~~~~a~~~~~~~~~~  159 (343)
                      |...|++++|+..|++..+.
T Consensus        82 ~~~l~~~~~A~~~~~~al~l  101 (201)
T d2c2la1          82 QLEMESYDEAIANLQRAYSL  101 (201)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHh
Confidence            88888888888888776543

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.61  E-value=5e-05  Score=59.76  Aligned_cols=277  Identities=10%  Similarity=0.110  Sum_probs=151.4

Q ss_pred             CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHH
Q 044084           20 LDSGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYA   99 (343)
Q Consensus        20 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~   99 (343)
                      |+..--..+++.|.+.|.++.|..+|..+.            -|..++..+.+.+++..|.+++.+.      -+..+|.
T Consensus        12 ~n~~d~~~i~~~c~~~~lye~A~~lY~~~~------------d~~rl~~~~v~l~~~~~avd~~~k~------~~~~~~k   73 (336)
T d1b89a_          12 PNNAHIQQVGDRCYDEKMYDAAKLLYNNVS------------NFGRLASTLVHLGEYQAAVDGARKA------NSTRTWK   73 (336)
T ss_dssp             C----------------CTTTHHHHHHHTT------------CHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHH
T ss_pred             CCcCCHHHHHHHHHHCCCHHHHHHHHHhCC------------CHHHHHHHHHhhccHHHHHHHHHHc------CCHHHHH
Confidence            455555667778888889988888887541            2777888888888888888877644      1566787


Q ss_pred             HHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCC
Q 044084          100 SLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRR  179 (343)
Q Consensus       100 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  179 (343)
                      .+...|.+......+     .+.......++.....++..|-..|.+++...+++....... .+...++-++..|++.+
T Consensus        74 ~~~~~l~~~~e~~la-----~i~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~~~-~~~~~~~~L~~lyak~~  147 (336)
T d1b89a_          74 EVCFACVDGKEFRLA-----QMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLER-AHMGMFTELAILYSKFK  147 (336)
T ss_dssp             HHHHHHHHTTCHHHH-----HHTTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSTT-CCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHhCcHHHHH-----HHHHHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcCCc-cchHHHHHHHHHHHHhC
Confidence            788887776665443     222233334666667788888888888888888887764432 55667778888887764


Q ss_pred             cHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHc--------CCCcChhhHHHHHHHHHccCCh
Q 044084          180 AYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQK--------GFDKCVVAYSSMVAMYGKTGRI  251 (343)
Q Consensus       180 ~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~--------~~~~~~~~~~~l~~~~~~~~~~  251 (343)
                       .++..+.+...   +..   .....+++.|.+.+-++++.-++..+...        ..+++..-...++..+.+.++.
T Consensus       148 -~~kl~e~l~~~---s~~---y~~~k~~~~c~~~~l~~elv~Ly~~~~~~~~A~~~~i~~~~~~~~~~~f~e~~~k~~N~  220 (336)
T d1b89a_         148 -PQKMREHLELF---WSR---VNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAWKEGQFKDIITKVANV  220 (336)
T ss_dssp             -HHHHHHHHHHH---STT---SCHHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHHHHSTTTTCCHHHHHHHHHHCSST
T ss_pred             -hHHHHHHHHhc---ccc---CCHHHHHHHHHHcCChHHHHHHHHhcCCHHHHHHHHHHcchhhhhHHHHHHHHHccCCh
Confidence             34434333332   111   11223344444444444444444332111        0134444555666666777776


Q ss_pred             HHHHHHHHHHhhCCCCchHHHHHHHHHHHhcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCccHHHHHHHH
Q 044084          252 RDAMRLVAKMKPKGCEPNVWIYNSLMDMHGRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGGVIDRAMAGIMV  331 (343)
Q Consensus       252 ~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~  331 (343)
                      +...++.....+.  .|+  ..+.++......-+.      ..++..+.+.+++.-....++.....|   +..+.++|.
T Consensus       221 e~~~~~i~~yL~~--~p~--~i~~lL~~v~~~~d~------~r~V~~~~k~~~l~li~p~Le~v~~~n---~~~vn~al~  287 (336)
T d1b89a_         221 ELYYRAIQFYLEF--KPL--LLNDLLMVLSPRLDH------TRAVNYFSKVKQLPLVKPYLRSVQNHN---NKSVNESLN  287 (336)
T ss_dssp             HHHHHHHHHHHHH--CGG--GHHHHHHHHGGGCCH------HHHHHHHHHTTCTTTTHHHHHHHHTTC---CHHHHHHHH
T ss_pred             HHHHHHHHHHHHc--CHH--HHHHHHHHhccCCCH------HHHHHHHHhcCCcHHHHHHHHHHHHcC---hHHHHHHHH
Confidence            6666665555542  232  234444444433333      334555556666666666666655544   234666666


Q ss_pred             HHHhccccc
Q 044084          332 GVFSKLSQI  340 (343)
Q Consensus       332 ~~~~~~g~~  340 (343)
                      +.|...+++
T Consensus       288 ~lyie~~d~  296 (336)
T d1b89a_         288 NLFITEEDY  296 (336)
T ss_dssp             HHHHHTTCH
T ss_pred             HHHhCcchh
Confidence            666666553

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=98.53  E-value=6.7e-07  Score=58.90  Aligned_cols=84  Identities=12%  Similarity=0.056  Sum_probs=36.5

Q ss_pred             HhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHH
Q 044084          105 FASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAA  184 (343)
Q Consensus       105 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  184 (343)
                      +.+.|++++|...|++..+..+. ++.+|..+..++.+.|++++|+..|++..+..+ .+...|..+..+|...|++++|
T Consensus        26 ~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~~~a~~~la~~y~~~g~~~~A  103 (112)
T d1hxia_          26 MLKLANLAEAALAFEAVCQKEPE-REEAWRSLGLTQAENEKDGLAIIALNHARMLDP-KDIAVHAALAVSHTNEHNANAA  103 (112)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhHHHHHHHhhhcccccc-cchhhhhhhhhhhhhhhHHHhhccccccccccc-ccccchHHHHHHHHHCCCHHHH
Confidence            33444444444444444443322 344444444444444444444444444444332 2333444444444444444444


Q ss_pred             HHHHHH
Q 044084          185 VKVYEQ  190 (343)
Q Consensus       185 ~~~~~~  190 (343)
                      .+.+++
T Consensus       104 ~~~l~~  109 (112)
T d1hxia_         104 LASLRA  109 (112)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            444443

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=98.53  E-value=9.1e-07  Score=58.25  Aligned_cols=89  Identities=17%  Similarity=0.019  Sum_probs=54.8

Q ss_pred             HHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCc
Q 044084           66 LCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGM  145 (343)
Q Consensus        66 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  145 (343)
                      +...+.+.|++++|+..|++....... +..+|..+..++.+.|++++|...+++..+..+. +..++..+...|...|+
T Consensus        22 ~g~~~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~a~~~la~~y~~~g~   99 (112)
T d1hxia_          22 EGLSMLKLANLAEAALAFEAVCQKEPE-REEAWRSLGLTQAENEKDGLAIIALNHARMLDPK-DIAVHAALAVSHTNEHN   99 (112)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHhhhcccccc-cchhhhhhhhhhhhhhhHHHhhcccccccccccc-cccchHHHHHHHHHCCC
Confidence            344555666666666666666655322 4556666666666666666666666666665433 56666666666666666


Q ss_pred             HhHHHHHHHHH
Q 044084          146 VEKTLEVVESM  156 (343)
Q Consensus       146 ~~~a~~~~~~~  156 (343)
                      +++|++.+++.
T Consensus       100 ~~~A~~~l~~~  110 (112)
T d1hxia_         100 ANAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            66666666654

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.43  E-value=1.7e-06  Score=57.69  Aligned_cols=23  Identities=22%  Similarity=0.294  Sum_probs=9.2

Q ss_pred             HHHHHhcCCcHHHHHHHHHHHHH
Q 044084          171 IVNGFSKRRAYWAAVKVYEQLIS  193 (343)
Q Consensus       171 l~~~~~~~~~~~~a~~~~~~~~~  193 (343)
                      +..+|.+.|++++|.+.|+++.+
T Consensus        78 Lg~~y~~~g~~~~A~~~~~~aL~  100 (122)
T d1nzna_          78 LAVGNYRLKEYEKALKYVRGLLQ  100 (122)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHH
Confidence            33333344444444444444333

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.43  E-value=1.4e-06  Score=58.12  Aligned_cols=94  Identities=12%  Similarity=0.055  Sum_probs=47.0

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccC---cHHHHHHHHHHHHhcCCCCC-hHhHHHHHH
Q 044084           28 IMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSG---RAFEILKFFRDMKEKGILED-PSVYASLIC  103 (343)
Q Consensus        28 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~---~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~  103 (343)
                      ++..+...+++++|.+.|+.....+    |.+..++..+..++.+.+   ++++|+++|+++...+..|+ ..++..+..
T Consensus         5 l~n~~~~~~~l~~Ae~~Y~~aL~~~----p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~   80 (122)
T d1nzna_           5 VLNELVSVEDLLKFEKKFQSEKAAG----SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAV   80 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHS----CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHH
T ss_pred             HHHHhcCHHHHHHHHHHHHHHHhhC----CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHH
Confidence            4445555555566666665555543    222345555555555433   23345555555554432222 124444555


Q ss_pred             HHhcccCHHHHHHHHHHHHHcC
Q 044084          104 SFASIAEVKVAEELFKEAEEKG  125 (343)
Q Consensus       104 ~~~~~~~~~~a~~~~~~~~~~~  125 (343)
                      +|.+.|++++|...|+++.+..
T Consensus        81 ~y~~~g~~~~A~~~~~~aL~~~  102 (122)
T d1nzna_          81 GNYRLKEYEKALKYVRGLLQTE  102 (122)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHhhhHHHHHHHHHHHHhC
Confidence            5555555666655555555543

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.38  E-value=1.7e-05  Score=56.33  Aligned_cols=62  Identities=10%  Similarity=-0.088  Sum_probs=32.2

Q ss_pred             HHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcC
Q 044084           98 YASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus        98 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  160 (343)
                      |+.+..+|.+.|++++|...++..++..+. ++.++..+..+|...|++++|+..|+...+.+
T Consensus        65 ~~nla~~y~k~~~~~~A~~~~~~al~~~p~-~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~  126 (170)
T d1p5qa1          65 HLNLAMCHLKLQAFSAAIESCNKALELDSN-NEKGLSRRGEAHLAVNDFELARADFQKVLQLY  126 (170)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHhhhhcccccchhhhhhhcccc-chhhhHHHHHHHHHhhhHHHHHHHHHHHHHhC
Confidence            333444455555555555555555554422 45555555555555555555555555555443

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.38  E-value=7.4e-07  Score=75.42  Aligned_cols=228  Identities=7%  Similarity=-0.111  Sum_probs=127.9

Q ss_pred             hHHHHHHHHHhCCCCCC-hhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHH
Q 044084            5 SKLHYYEKMKSAGIVLD-SGCYCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFF   83 (343)
Q Consensus         5 ~A~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~   83 (343)
                      +|.+.|++..+.  +|+ ...+..+..++...+++++|   |+++...+    |.....++..-.  .-...+..+.+.+
T Consensus         4 eA~q~~~qA~~l--~p~~a~a~~~la~~~~~~~~l~ea---ye~~i~~d----p~~a~~~~~e~~--Lw~~~y~~~ie~~   72 (497)
T d1ya0a1           4 QSAQYLRQAEVL--KADMTDSKLGPAEVWTSRQALQDL---YQKMLVTD----LEYALDKKVEQD--LWNHAFKNQITTL   72 (497)
T ss_dssp             HHHHHHHHHHHH--HGGGTCSSSCSSSSHHHHHHHHHH---HHHHHHHC----HHHHHHHTHHHH--HHHHHTHHHHHHH
T ss_pred             HHHHHHHHHHHc--CCCCHHHHhhHHHHHHHHchHHHH---HHHHHHcC----hhhHHHHhHHHH--HHHHHHHHHHHHH
Confidence            688899988875  454 55778888889988888876   66665433    211122221111  1112245677777


Q ss_pred             HHHHhcCCCCChHhHHHHHHH--HhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCC
Q 044084           84 RDMKEKGILEDPSVYASLICS--FASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAEL  161 (343)
Q Consensus        84 ~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  161 (343)
                      +...+....++..-....+..  ....+.++.+...+....+..+ ++...+..+...+.+.|+.++|...+........
T Consensus        73 r~~~k~~~~~~~~~~~~~~~~~l~~a~~~Y~~ai~~l~~~~~l~~-~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~  151 (497)
T d1ya0a1          73 QGQAKNRANPNRSEVQANLSLFLEAASGFYTQLLQELCTVFNVDL-PCRVKSSQLGIISNKQTHTSAIVKPQSSSCSYIC  151 (497)
T ss_dssp             HHHHSCSSCTTTTHHHHHHHHHHHHHHHHHHHHHHHHTC--------------------------------CCHHHHHHH
T ss_pred             HHhcccccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCh-hhHHHHHHhHHHHHhCCCHHHHHHHHHHHhCCCH
Confidence            777665434443322222222  2233455555555554444332 3566778888888899999999888877654321


Q ss_pred             CCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHH
Q 044084          162 NISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSM  241 (343)
Q Consensus       162 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  241 (343)
                         ..++..+...+...|++++|...|++..+.. +-+...|+.+...+...|+..+|...|.+..... +|-..++..|
T Consensus       152 ---~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l~-P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~-~~~~~a~~nL  226 (497)
T d1ya0a1         152 ---QHCLVHLGDIARYRNQTSQAESYYRHAAQLV-PSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVK-FPFPAASTNL  226 (497)
T ss_dssp             ---HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSS-BCCHHHHHHH
T ss_pred             ---HHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC-CCCHHHHHHH
Confidence               2467778888888999999999999988874 3445788889999999999999999999888775 5677788888


Q ss_pred             HHHHHccC
Q 044084          242 VAMYGKTG  249 (343)
Q Consensus       242 ~~~~~~~~  249 (343)
                      ...+.+..
T Consensus       227 ~~~~~~~~  234 (497)
T d1ya0a1         227 QKALSKAL  234 (497)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHhh
Confidence            77765543

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.36  E-value=2.4e-05  Score=55.55  Aligned_cols=120  Identities=8%  Similarity=-0.089  Sum_probs=92.3

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCC-c----------hHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCC
Q 044084           24 CYCQIMEAFYKIGDSEKVAALFLECESRKLDLTP-S----------STHMYKILCDSLGKSGRAFEILKFFRDMKEKGIL   92 (343)
Q Consensus        24 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~----------~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~   92 (343)
                      .+......+.+.|++++|...|.+.......... .          ...+|+.+..+|.+.|++++|+..++..+..+. 
T Consensus        15 ~l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~p-   93 (170)
T d1p5qa1          15 IVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELDS-   93 (170)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhccc-
Confidence            4555677899999999999999988654221111 0          135677788899999999999999999998753 


Q ss_pred             CChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCc
Q 044084           93 EDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGM  145 (343)
Q Consensus        93 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  145 (343)
                      .++.++..+..++...|+++.|...|+...+..+. +..+...+.....+.+.
T Consensus        94 ~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~P~-n~~~~~~l~~~~~~~~~  145 (170)
T d1p5qa1          94 NNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPN-NKAAKTQLAVCQQRIRR  145 (170)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSS-CHHHHHHHHHHHHHHHH
T ss_pred             cchhhhHHHHHHHHHhhhHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHH
Confidence            37788999999999999999999999999997643 66666666555544433

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=98.34  E-value=0.00027  Score=53.84  Aligned_cols=229  Identities=13%  Similarity=0.008  Sum_probs=155.8

Q ss_pred             HHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhc----ccCHHHHHHHHHHHHHcCCCCCHHHHHHH
Q 044084           61 HMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFAS----IAEVKVAEELFKEAEEKGMLRDLEVFLKL  136 (343)
Q Consensus        61 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  136 (343)
                      ..+..|...+.+.+++++|+++|++..+.|   +...+..|...|..    ..+...+...+....+.+   ++.....+
T Consensus         3 ~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g---~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~---~~~a~~~l   76 (265)
T d1ouva_           3 KELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCHLL   76 (265)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccc---ccchhhcc
Confidence            467777888888999999999999998876   55566666666665    568999999999888865   44555555


Q ss_pred             HHHHHh----cCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHH----hcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHH
Q 044084          137 VLMYIE----EGMVEKTLEVVESMKNAELNISDCISCVIVNGF----SKRRAYWAAVKVYEQLISQGCIPGQVTYASIIN  208 (343)
Q Consensus       137 ~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~----~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~  208 (343)
                      ...+..    ..+.+.|...++.....+.. ..  ...+...+    ........+...+......   .+...+..+..
T Consensus        77 ~~~~~~~~~~~~~~~~a~~~~~~a~~~g~~-~a--~~~l~~~~~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~L~~  150 (265)
T d1ouva_          77 GNLYYSGQGVSQNTNKALQYYSKACDLKYA-EG--CASLGGIYHDGKVVTRDFKKAVEYFTKACDL---NDGDGCTILGS  150 (265)
T ss_dssp             HHHHHHTSSSCCCHHHHHHHHHHHHHTTCH-HH--HHHHHHHHHHCSSSCCCHHHHHHHHHHHHHT---TCHHHHHHHHH
T ss_pred             ccccccccccchhhHHHHHHHhhhhhhhhh-hH--HHhhcccccCCCcccchhHHHHHHhhhhhcc---cccchhhhhhh
Confidence            555543    45678899999988877652 22  22222222    2355677788888877664   35566777777


Q ss_pred             HHHc----cCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHc----cCChHHHHHHHHHHhhCCCCchHHHHHHHHHHH
Q 044084          209 AYCR----IGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGK----TGRIRDAMRLVAKMKPKGCEPNVWIYNSLMDMH  280 (343)
Q Consensus       209 ~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~  280 (343)
                      .|..    ..+...+...+....+.|   +......+...|..    ..+.++|..+|.+..+.|   ++..+..|...|
T Consensus       151 ~~~~~~~~~~~~~~~~~~~~~a~~~g---~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~~g---~~~a~~~LG~~y  224 (265)
T d1ouva_         151 LYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGGGCFNLGAMQ  224 (265)
T ss_dssp             HHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHH
T ss_pred             hhccCCCcccccccchhhhhcccccc---ccccccchhhhcccCcccccchhhhhhhHhhhhccc---CHHHHHHHHHHH
Confidence            7765    456677788888877765   55666666666654    568999999999998876   344444454444


Q ss_pred             hcccChhHHHhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCc
Q 044084          281 GRAKNLRQLEKYTTVISAYNMAREFDMCVKFYNEFRMNGGVI  322 (343)
Q Consensus       281 ~~~~~~~~a~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p  322 (343)
                      .+ |.              ...++.++|.++|++....|..+
T Consensus       225 ~~-G~--------------g~~~n~~~A~~~~~kAa~~g~~~  251 (265)
T d1ouva_         225 YN-GE--------------GVTRNEKQAIENFKKGCKLGAKG  251 (265)
T ss_dssp             HT-TS--------------SSSCCSTTHHHHHHHHHHHTCHH
T ss_pred             Hc-CC--------------CCccCHHHHHHHHHHHHHCcCHH
Confidence            32 11              11336677888888877777543

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.26  E-value=1.2e-06  Score=74.03  Aligned_cols=170  Identities=8%  Similarity=-0.106  Sum_probs=94.9

Q ss_pred             HHHHHHHHHHHHhCCCCCCCchHHHHHHHHH-HhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHH
Q 044084           38 SEKVAALFLECESRKLDLTPSSTHMYKILCD-SLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEE  116 (343)
Q Consensus        38 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~-~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  116 (343)
                      +..+.+.++...+....++..  .....+.. .....+.++.++..+....... .++...+..+...+.+.|+.+.|..
T Consensus        65 y~~~ie~~r~~~k~~~~~~~~--~~~~~~~~~l~~a~~~Y~~ai~~l~~~~~l~-~~~~~~~~~lg~~~~~~~~~~~A~~  141 (497)
T d1ya0a1          65 FKNQITTLQGQAKNRANPNRS--EVQANLSLFLEAASGFYTQLLQELCTVFNVD-LPCRVKSSQLGIISNKQTHTSAIVK  141 (497)
T ss_dssp             THHHHHHHHHHHSCSSCTTTT--HHHHHHHHHHHHHHHHHHHHHHHHTC-------------------------------
T ss_pred             HHHHHHHHHHhcccccCccHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-hhhHHHHHHhHHHHHhCCCHHHHHH
Confidence            345566666655544333321  11111111 1122344555555554433322 2345567777778888899999988


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCC
Q 044084          117 LFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGC  196 (343)
Q Consensus       117 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  196 (343)
                      .+.......   ...++..+...+...|++++|...|++..+..+ -+...|+.+...+...|+..+|...|.+..... 
T Consensus       142 ~~~~al~~~---~~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l~P-~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~-  216 (497)
T d1ya0a1         142 PQSSSCSYI---CQHCLVHLGDIARYRNQTSQAESYYRHAAQLVP-SNGQPYNQLAILASSKGDHLTTIFYYCRSIAVK-  216 (497)
T ss_dssp             -CCHHHHHH---HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSS-
T ss_pred             HHHHHhCCC---HHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCC-CchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC-
Confidence            887766532   135677889999999999999999999988775 566789999999999999999999999998775 


Q ss_pred             CCCHhhHHHHHHHHHccCC
Q 044084          197 IPGQVTYASIINAYCRIGL  215 (343)
Q Consensus       197 ~p~~~~~~~ll~~~~~~~~  215 (343)
                      +|-..++..|...+.+..+
T Consensus       217 ~~~~~a~~nL~~~~~~~~~  235 (497)
T d1ya0a1         217 FPFPAASTNLQKALSKALE  235 (497)
T ss_dssp             BCCHHHHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHHHHHhhh
Confidence            5677888888887765443

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.24  E-value=1.8e-05  Score=53.22  Aligned_cols=54  Identities=17%  Similarity=0.183  Sum_probs=23.6

Q ss_pred             HHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHH
Q 044084          103 CSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMK  157 (343)
Q Consensus       103 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  157 (343)
                      ..+.+.|++++|...|.+.++..+. +..++..+..+|.+.|++++|++.++++.
T Consensus        12 ~~~~~~~~y~~Ai~~y~~al~~~p~-~~~~~~~~a~~~~~~~~~~~A~~~~~~al   65 (128)
T d1elra_          12 NDAYKKKDFDTALKHYDKAKELDPT-NMTYITNQAAVYFEKGDYNKCRELCEKAI   65 (128)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCcc-cHHHHHhHHHHHHHcCchHHHHHHHHHHH
Confidence            3344444444444444444443322 34444444444444444444444444433

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=98.24  E-value=3.6e-05  Score=53.48  Aligned_cols=112  Identities=10%  Similarity=0.060  Sum_probs=67.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCch-HHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHH
Q 044084           25 YCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSS-THMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLIC  103 (343)
Q Consensus        25 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  103 (343)
                      +..-...+.+.|++.+|...|.+....-....... ...+.                 ....+       ...+|..+..
T Consensus        20 ~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~-----------------~~~~~-------~~~~~~Nla~   75 (153)
T d2fbna1          20 IKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLD-----------------KKKNI-------EISCNLNLAT   75 (153)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHH-----------------HHHHH-------HHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHH-----------------hhhhH-------HHHHHhhHHH
Confidence            44455677788888888888887765322111000 00000                 00000       1234555666


Q ss_pred             HHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCC
Q 044084          104 SFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAEL  161 (343)
Q Consensus       104 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  161 (343)
                      +|.+.|++++|+..++...+..+. +..+|..+..++...|++++|+..|++..+.++
T Consensus        76 ~~~~l~~~~~Al~~~~~al~~~p~-~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l~P  132 (153)
T d2fbna1          76 CYNKNKDYPKAIDHASKVLKIDKN-NVKALYKLGVANMYFGFLEEAKENLYKAASLNP  132 (153)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHST
T ss_pred             HHHHhcccchhhhhhhccccccch-hhhhhHHhHHHHHHcCCHHHHHHHHHHHHHhCC
Confidence            777777777777777777776532 667777777777777777777777777776654

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=98.18  E-value=8.7e-05  Score=52.37  Aligned_cols=75  Identities=11%  Similarity=-0.010  Sum_probs=47.3

Q ss_pred             HHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHH
Q 044084           98 YASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNG  174 (343)
Q Consensus        98 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  174 (343)
                      |+.+..++.+.|++++|+..++...+..+. +...|..+..++...|++++|+..|+++.+.++ .+......+-..
T Consensus        67 ~~Nla~~~~~l~~~~~Ai~~~~~al~l~p~-~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~P-~n~~~~~~l~~~  141 (168)
T d1kt1a1          67 FLNLAMCYLKLREYTKAVECCDKALGLDSA-NEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNP-QNKAARLQIFMC  141 (168)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCT-TCHHHHHHHHHH
T ss_pred             HHhHHHHHHHhhhcccchhhhhhhhhcccc-hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHH
Confidence            445556666777777777777777765542 666777777777777777777777777766553 333344443333

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=98.16  E-value=9.1e-05  Score=51.35  Aligned_cols=118  Identities=8%  Similarity=-0.027  Sum_probs=84.5

Q ss_pred             HHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 044084           62 MYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYI  141 (343)
Q Consensus        62 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  141 (343)
                      .+..-...+.+.|++.+|+..|.+....-  |.....           . +...  ......    ....+|..+..+|.
T Consensus        19 ~~~~~G~~~f~~~~y~~A~~~Y~~al~~~--~~~~~~-----------~-~~~~--~~~~~~----~~~~~~~Nla~~~~   78 (153)
T d2fbna1          19 DIKEEGNEFFKKNEINEAIVKYKEALDFF--IHTEEW-----------D-DQIL--LDKKKN----IEISCNLNLATCYN   78 (153)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTT--TTCTTC-----------C-CHHH--HHHHHH----HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhC--cchhhh-----------h-hHHH--HHhhhh----HHHHHHhhHHHHHH
Confidence            44555667788899999999998887641  110000           0 0000  000000    12357788999999


Q ss_pred             hcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhh
Q 044084          142 EEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVT  202 (343)
Q Consensus       142 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~  202 (343)
                      +.|++++|++.++.....++ .+..+|..+..++...|++++|...|++..+..  |+...
T Consensus        79 ~l~~~~~Al~~~~~al~~~p-~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l~--P~n~~  136 (153)
T d2fbna1          79 KNKDYPKAIDHASKVLKIDK-NNVKALYKLGVANMYFGFLEEAKENLYKAASLN--PNNLD  136 (153)
T ss_dssp             HTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS--TTCHH
T ss_pred             Hhcccchhhhhhhccccccc-hhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHhC--CCCHH
Confidence            99999999999999998875 577899999999999999999999999999874  54433

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.16  E-value=1.7e-05  Score=53.31  Aligned_cols=95  Identities=16%  Similarity=0.144  Sum_probs=51.1

Q ss_pred             HHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCC-CC-----HHHHHHH
Q 044084           63 YKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGML-RD-----LEVFLKL  136 (343)
Q Consensus        63 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~-----~~~~~~l  136 (343)
                      +..+...+.+.|++++|++.|++.++.+. .+...+..+..+|.+.|+++.|...++++++.... +.     ..+|..+
T Consensus         7 ~k~~G~~~~~~~~y~~Ai~~y~~al~~~p-~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~l   85 (128)
T d1elra_           7 EKELGNDAYKKKDFDTALKHYDKAKELDP-TNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARI   85 (128)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCc-ccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHH
Confidence            34455555566666666666666555432 24455555556666666666666666655542211 00     1344555


Q ss_pred             HHHHHhcCcHhHHHHHHHHHHh
Q 044084          137 VLMYIEEGMVEKTLEVVESMKN  158 (343)
Q Consensus       137 ~~~~~~~~~~~~a~~~~~~~~~  158 (343)
                      ...+...+++++|++.|++...
T Consensus        86 g~~~~~~~~~~~A~~~~~kal~  107 (128)
T d1elra_          86 GNSYFKEEKYKDAIHFYNKSLA  107 (128)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHh
Confidence            5555666666666666665544

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.15  E-value=2.5e-05  Score=55.35  Aligned_cols=76  Identities=8%  Similarity=-0.002  Sum_probs=44.5

Q ss_pred             hHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHH
Q 044084           97 VYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNG  174 (343)
Q Consensus        97 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  174 (343)
                      .|..+..++.+.|++++|+..+.++++..+. ++.+|..+..+|...|++++|+..|++..+..+ .+......+..+
T Consensus        79 ~~~nla~~~~~~~~~~~Ai~~~~~al~~~p~-~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~p-~n~~~~~~l~~~  154 (169)
T d1ihga1          79 CVLNIGACKLKMSDWQGAVDSCLEALEIDPS-NTKALYRRAQGWQGLKEYDQALADLKKAQEIAP-EDKAIQAELLKV  154 (169)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHTTCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcccchhhhhhhhhhhhhhh-hhhHHHhHHHHHHHccCHHHHHHHHHHHHHhCC-CCHHHHHHHHHH
Confidence            4455555666666666666666666665432 566666666666666666666666666666543 233344444333

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.10  E-value=9e-05  Score=52.81  Aligned_cols=123  Identities=7%  Similarity=-0.021  Sum_probs=80.9

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHh
Q 044084           27 QIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFA  106 (343)
Q Consensus        27 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  106 (343)
                      .........|++++|.+.|.........+-..          .+ ..+.  -+...-..+...    ....+..+...+.
T Consensus        16 ~~g~~~~~~g~~e~A~~~~~~AL~l~rG~~l~----------~~-~~~~--w~~~~r~~l~~~----~~~a~~~la~~~~   78 (179)
T d2ff4a2          16 TAGVHAAAAGRFEQASRHLSAALREWRGPVLD----------DL-RDFQ--FVEPFATALVED----KVLAHTAKAEAEI   78 (179)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTTCCSSTTG----------GG-TTST--THHHHHHHHHHH----HHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhhCcccccc----------cC-cchH--HHHHHHHHHHHH----HHHHHHHHHHHHH
Confidence            34457788999999999999987643211100          00 0011  111111111111    2345667788888


Q ss_pred             cccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHH-----hcCCCCchhh
Q 044084          107 SIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMK-----NAELNISDCI  167 (343)
Q Consensus       107 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~-----~~~~~~~~~~  167 (343)
                      +.|++++|...++++.+..+. +...|..++.+|.+.|+.++|++.|+++.     +.|+.|+..+
T Consensus        79 ~~g~~~~Al~~~~~al~~~P~-~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          79 ACGRASAVIAELEALTFEHPY-REPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HCCCchHHHHHHHHHHHhCCc-cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            888888888888888887653 78888888888888888888888888864     3577777654

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=98.09  E-value=0.00014  Score=51.25  Aligned_cols=95  Identities=12%  Similarity=0.119  Sum_probs=63.8

Q ss_pred             HHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHH
Q 044084          130 LEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINA  209 (343)
Q Consensus       130 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~  209 (343)
                      ..+|+.+..+|.+.|++++|+..++.....++ .+..+|..+..++...|++++|...|.+..... +.+......+-..
T Consensus        64 ~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~p-~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~-P~n~~~~~~l~~~  141 (168)
T d1kt1a1          64 LAAFLNLAMCYLKLREYTKAVECCDKALGLDS-ANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVN-PQNKAARLQIFMC  141 (168)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHH
T ss_pred             HHHHHhHHHHHHHhhhcccchhhhhhhhhccc-chHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence            34566778888889999999999988887765 567778888888888999999999999888763 2333343433333


Q ss_pred             HHccCCh-hHHHHHHHHH
Q 044084          210 YCRIGLY-SKAEKVFIEM  226 (343)
Q Consensus       210 ~~~~~~~-~~a~~~~~~~  226 (343)
                      ....+.. +...+++..|
T Consensus       142 ~~~~~~~~e~~kk~~~~~  159 (168)
T d1kt1a1         142 QKKAKEHNERDRRTYANM  159 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhHHHHHHHHHHHH
Confidence            3333322 2333444443

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.05  E-value=4.6e-05  Score=53.96  Aligned_cols=82  Identities=7%  Similarity=0.023  Sum_probs=63.3

Q ss_pred             CHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHH
Q 044084          129 DLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIIN  208 (343)
Q Consensus       129 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~  208 (343)
                      ....+..+..+|.+.|++++|+..+++..+..+ .+..+|..+..++...|++++|...|++..+.. +.+......+..
T Consensus        76 ~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~p-~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~-p~n~~~~~~l~~  153 (169)
T d1ihga1          76 ALSCVLNIGACKLKMSDWQGAVDSCLEALEIDP-SNTKALYRRAQGWQGLKEYDQALADLKKAQEIA-PEDKAIQAELLK  153 (169)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhhcccchhhhhhhhhhhhhh-hhhhHHHhHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            456677788889999999999999999988775 567788889999999999999999999988873 234445555544


Q ss_pred             HHHc
Q 044084          209 AYCR  212 (343)
Q Consensus       209 ~~~~  212 (343)
                      +..+
T Consensus       154 ~~~~  157 (169)
T d1ihga1         154 VKQK  157 (169)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4433

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.00  E-value=0.00013  Score=51.89  Aligned_cols=126  Identities=11%  Similarity=0.108  Sum_probs=83.0

Q ss_pred             HHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 044084           62 MYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYI  141 (343)
Q Consensus        62 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  141 (343)
                      ............|++++|.+.|.+.+..-  +....        ......+-+...-..+..    .....+..+...+.
T Consensus        13 ~~~~~g~~~~~~g~~e~A~~~~~~AL~l~--rG~~l--------~~~~~~~w~~~~r~~l~~----~~~~a~~~la~~~~   78 (179)
T d2ff4a2          13 AEKTAGVHAAAAGRFEQASRHLSAALREW--RGPVL--------DDLRDFQFVEPFATALVE----DKVLAHTAKAEAEI   78 (179)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHTTC--CSSTT--------GGGTTSTTHHHHHHHHHH----HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhhC--ccccc--------ccCcchHHHHHHHHHHHH----HHHHHHHHHHHHHH
Confidence            34445567778899999999988887641  11100        000000111111111221    12456777888888


Q ss_pred             hcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHH-----cCCCCCHhh
Q 044084          142 EEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLIS-----QGCIPGQVT  202 (343)
Q Consensus       142 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~p~~~~  202 (343)
                      +.|++++|+..++++....+ -+...|..++.++...|+..+|++.|+++.+     .|+.|+..+
T Consensus        79 ~~g~~~~Al~~~~~al~~~P-~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          79 ACGRASAVIAELEALTFEHP-YREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HCCCchHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            89999999999998888776 5777888899999999999999988888743     477777654

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=97.95  E-value=1.3e-05  Score=61.24  Aligned_cols=122  Identities=11%  Similarity=-0.047  Sum_probs=63.0

Q ss_pred             hcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHH
Q 044084          106 ASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAV  185 (343)
Q Consensus       106 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  185 (343)
                      .+.|++++|...+++.++..+. +...+..+...++..|++++|...|+...+..+ -+...+..+...+...+..+++.
T Consensus         7 L~~G~l~eAl~~l~~al~~~P~-d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l~P-~~~~~~~~l~~ll~a~~~~~~a~   84 (264)
T d1zbpa1           7 LSEGQLQQALELLIEAIKASPK-DASLRSSFIELLCIDGDFERADEQLMQSIKLFP-EYLPGASQLRHLVKAAQARKDFA   84 (264)
T ss_dssp             TTTTCHHHHHHHHHHHHHTCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCG-GGHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHCCCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHhccccHHHH
Confidence            4556777777777777766543 667777777777777777777777777666543 12223333333332222222211


Q ss_pred             HHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHc
Q 044084          186 KVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       186 ~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  229 (343)
                      .-.......+-+++...+......+...|+.++|...++.+.+.
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            11100000011122223333445566667777777777776664

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.93  E-value=0.0001  Score=50.58  Aligned_cols=16  Identities=6%  Similarity=-0.276  Sum_probs=7.6

Q ss_pred             CcHHHHHHHHHHHHhc
Q 044084           74 GRAFEILKFFRDMKEK   89 (343)
Q Consensus        74 ~~~~~a~~~~~~~~~~   89 (343)
                      +.+++|++.|+...+.
T Consensus        11 ~~fe~A~~~~e~al~~   26 (145)
T d1zu2a1          11 LLFEQIRQDAENTYKS   26 (145)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHhh
Confidence            3444555555544443

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=97.93  E-value=1.7e-05  Score=60.47  Aligned_cols=122  Identities=14%  Similarity=-0.018  Sum_probs=63.5

Q ss_pred             hccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHH
Q 044084           71 GKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTL  150 (343)
Q Consensus        71 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  150 (343)
                      .+.|++++|+..+++.++... -|...+..+...++..|++++|...++...+..+. +...+..+...+...+..+++.
T Consensus         7 L~~G~l~eAl~~l~~al~~~P-~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l~P~-~~~~~~~l~~ll~a~~~~~~a~   84 (264)
T d1zbpa1           7 LSEGQLQQALELLIEAIKASP-KDASLRSSFIELLCIDGDFERADEQLMQSIKLFPE-YLPGASQLRHLVKAAQARKDFA   84 (264)
T ss_dssp             TTTTCHHHHHHHHHHHHHTCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGG-GHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHCCCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHhccccHHHH
Confidence            455677777777777666532 25566666777777777777777777776665432 3444444444333322222221


Q ss_pred             HHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHc
Q 044084          151 EVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       151 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  194 (343)
                      .-.......+.+++...+......+...|+.++|...++++.+.
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            11111011111122222333445556667777777777776655

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.81  E-value=0.00022  Score=48.76  Aligned_cols=42  Identities=12%  Similarity=-0.049  Sum_probs=27.9

Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHH
Q 044084           32 FYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAF   77 (343)
Q Consensus        32 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~   77 (343)
                      |-+.+.+++|.+.|+...+..    |.+..++..+..++...+++.
T Consensus         7 ~~r~~~fe~A~~~~e~al~~~----P~~~~~~~~~g~~l~~~~~~~   48 (145)
T d1zu2a1           7 FDRILLFEQIRQDAENTYKSN----PLDADNLTRWGGVLLELSQFH   48 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHC----TTCHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHccHHHHHHHHHHHHhhC----CcchHHHHHHHHHHHHhhhhh
Confidence            456677888888888877655    334567777777776554443

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.65  E-value=0.0076  Score=47.05  Aligned_cols=207  Identities=9%  Similarity=0.084  Sum_probs=129.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHH
Q 044084           25 YCQIMEAFYKIGDSEKVAALFLECESRKLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEKGILEDPSVYASLICS  104 (343)
Q Consensus        25 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  104 (343)
                      |..++..+.+.++++.|.+.+...   +   +   ..+|..+...+.+......+     .+.......++.....++..
T Consensus        43 ~~rl~~~~v~l~~~~~avd~~~k~---~---~---~~~~k~~~~~l~~~~e~~la-----~i~~~~~~~~~d~l~~~v~~  108 (336)
T d1b89a_          43 FGRLASTLVHLGEYQAAVDGARKA---N---S---TRTWKEVCFACVDGKEFRLA-----QMCGLHIVVHADELEELINY  108 (336)
T ss_dssp             HHHHHHHHHTTTCHHHHHHHHHHH---T---C---HHHHHHHHHHHHHTTCHHHH-----HHTTTTTTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHhhccHHHHHHHHHHc---C---C---HHHHHHHHHHHHhCcHHHHH-----HHHHHHhhcCHHHHHHHHHH
Confidence            556777788888888887777544   1   1   46888888888877766543     22233344566667788999


Q ss_pred             HhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHH
Q 044084          105 FASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAA  184 (343)
Q Consensus       105 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  184 (343)
                      |-..|.++....+++...... ..+...++.++..|++.+. ++..+.+....  + .-+   ..-++..|.+.+-+.++
T Consensus       109 ye~~~~~e~Li~~Le~~~~~~-~~~~~~~~~L~~lyak~~~-~kl~e~l~~~s--~-~y~---~~k~~~~c~~~~l~~el  180 (336)
T d1b89a_         109 YQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKFKP-QKMREHLELFW--S-RVN---IPKVLRAAEQAHLWAEL  180 (336)
T ss_dssp             HHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHTTCH-HHHHHHHHHHS--T-TSC---HHHHHHHHHTTTCHHHH
T ss_pred             HHHcCChHHHHHHHHHHHcCC-ccchHHHHHHHHHHHHhCh-HHHHHHHHhcc--c-cCC---HHHHHHHHHHcCChHHH
Confidence            999999999999999876432 3578889999999998653 44444443321  1 111   22334444445544444


Q ss_pred             HHHHHHH----------HHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHH
Q 044084          185 VKVYEQL----------ISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDA  254 (343)
Q Consensus       185 ~~~~~~~----------~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  254 (343)
                      .-++.++          .+.  +++.......+..+.+..+++...++.....+..  |  ...+.++......-+..+.
T Consensus       181 v~Ly~~~~~~~~A~~~~i~~--~~~~~~~~~f~e~~~k~~N~e~~~~~i~~yL~~~--p--~~i~~lL~~v~~~~d~~r~  254 (336)
T d1b89a_         181 VFLYDKYEEYDNAIITMMNH--PTDAWKEGQFKDIITKVANVELYYRAIQFYLEFK--P--LLLNDLLMVLSPRLDHTRA  254 (336)
T ss_dssp             HHHHHHTTCHHHHHHHHHHS--TTTTCCHHHHHHHHHHCSSTHHHHHHHHHHHHHC--G--GGHHHHHHHHGGGCCHHHH
T ss_pred             HHHHHhcCCHHHHHHHHHHc--chhhhhHHHHHHHHHccCChHHHHHHHHHHHHcC--H--HHHHHHHHHhccCCCHHHH
Confidence            4444432          222  3455555667777888888888777777766642  3  3445566555555555555


Q ss_pred             HHHHH
Q 044084          255 MRLVA  259 (343)
Q Consensus       255 ~~~~~  259 (343)
                      .+.++
T Consensus       255 V~~~~  259 (336)
T d1b89a_         255 VNYFS  259 (336)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55444

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=97.51  E-value=0.0015  Score=45.11  Aligned_cols=96  Identities=15%  Similarity=0.044  Sum_probs=48.6

Q ss_pred             HHHHH--HHHhhccCcHHHHHHHHHHHHhcCC-CCC----------hHhHHHHHHHHhcccCHHHHHHHHHHHHHc----
Q 044084           62 MYKIL--CDSLGKSGRAFEILKFFRDMKEKGI-LED----------PSVYASLICSFASIAEVKVAEELFKEAEEK----  124 (343)
Q Consensus        62 ~~~~l--i~~~~~~~~~~~a~~~~~~~~~~~~-~~~----------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----  124 (343)
                      +|..+  ...+...|++++|++.|++.++... .|+          ...|+.+..++...|++++|...+++..+.    
T Consensus         9 a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~   88 (156)
T d2hr2a1           9 AYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRR   88 (156)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhccccc
Confidence            44444  3344455666666666666654211 111          234555555556666666666555554431    


Q ss_pred             -CCCCC-----HHHHHHHHHHHHhcCcHhHHHHHHHHHH
Q 044084          125 -GMLRD-----LEVFLKLVLMYIEEGMVEKTLEVVESMK  157 (343)
Q Consensus       125 -~~~~~-----~~~~~~l~~~~~~~~~~~~a~~~~~~~~  157 (343)
                       ...++     ..+++.+..+|...|++++|++.|++..
T Consensus        89 ~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al  127 (156)
T d2hr2a1          89 GELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVV  127 (156)
T ss_dssp             CCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             ccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHH
Confidence             11111     1234555566666666666666666544

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.39  E-value=0.0012  Score=41.08  Aligned_cols=68  Identities=10%  Similarity=0.004  Sum_probs=42.1

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhC---CCCCCCchHHHHHHHHHHhhccCcHHHHHHHHHHHHhc
Q 044084           22 SGCYCQIMEAFYKIGDSEKVAALFLECESR---KLDLTPSSTHMYKILCDSLGKSGRAFEILKFFRDMKEK   89 (343)
Q Consensus        22 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~   89 (343)
                      ...+-.+...+.+.|++++|...|++..+.   ...+.+....+++.|..++.+.|++++|++.+++.++.
T Consensus         5 addc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l   75 (95)
T d1tjca_           5 AEDSFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (95)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHh
Confidence            334445666777777777777777665432   12222223456667777777777777777777777665

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=97.39  E-value=0.0026  Score=43.77  Aligned_cols=56  Identities=5%  Similarity=0.047  Sum_probs=27.2

Q ss_pred             HHHHHhcCcHhHHHHHHHHHHhcCCC-Cc----------hhhHHHHHHHHhcCCcHHHHHHHHHHHH
Q 044084          137 VLMYIEEGMVEKTLEVVESMKNAELN-IS----------DCISCVIVNGFSKRRAYWAAVKVYEQLI  192 (343)
Q Consensus       137 ~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----------~~~~~~l~~~~~~~~~~~~a~~~~~~~~  192 (343)
                      ...+...|++++|++.|++..+.... |+          ...|+.+..+|...|++++|...+++..
T Consensus        16 g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al   82 (156)
T d2hr2a1          16 AQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKAL   82 (156)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhh
Confidence            33445556666666666665542211 11          1234444555555555555555554443

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.09  E-value=0.0028  Score=39.34  Aligned_cols=19  Identities=0%  Similarity=-0.048  Sum_probs=7.4

Q ss_pred             HHHhhccCcHHHHHHHHHH
Q 044084           67 CDSLGKSGRAFEILKFFRD   85 (343)
Q Consensus        67 i~~~~~~~~~~~a~~~~~~   85 (343)
                      ...+.+.|++++|+..|++
T Consensus        12 G~~~~~~g~y~~A~~~~~~   30 (95)
T d1tjca_          12 GKVAYTEADYYHTELWMEQ   30 (95)
T ss_dssp             HHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHH
Confidence            3333333344444333333

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=97.00  E-value=0.02  Score=37.89  Aligned_cols=83  Identities=10%  Similarity=0.023  Sum_probs=46.6

Q ss_pred             cCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhc----ccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----cC
Q 044084           73 SGRAFEILKFFRDMKEKGILEDPSVYASLICSFAS----IAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIE----EG  144 (343)
Q Consensus        73 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~  144 (343)
                      ..+.++|++++++..+.|   ++.....|...|..    ..+.+.|..+|++..+.|   ++.....|...|..    ..
T Consensus        36 ~~~~~~a~~~~~~aa~~g---~~~a~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa~~g---~~~a~~~Lg~~y~~G~gv~~  109 (133)
T d1klxa_          36 QINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKAAQYYSKACGLN---DQDGCLILGYKQYAGKGVVK  109 (133)
T ss_dssp             TSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCC
T ss_pred             ccCHHHHHHHHhhhhccc---chhhhhhHHHhhhhccccchhhHHHHHHHhhhhccC---cchHHHHHHHHHHcCCccCC
Confidence            345566666666655554   33333334433332    345667777777766655   34455555555554    34


Q ss_pred             cHhHHHHHHHHHHhcCC
Q 044084          145 MVEKTLEVVESMKNAEL  161 (343)
Q Consensus       145 ~~~~a~~~~~~~~~~~~  161 (343)
                      +.++|.++|++..+.|.
T Consensus       110 d~~~A~~~~~~Aa~~G~  126 (133)
T d1klxa_         110 NEKQAVKTFEKACRLGS  126 (133)
T ss_dssp             CHHHHHHHHHHHHHTTC
T ss_pred             CHHHHHHHHHHHHHCCC
Confidence            66777777777666654

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=96.84  E-value=0.027  Score=37.14  Aligned_cols=110  Identities=13%  Similarity=-0.013  Sum_probs=62.0

Q ss_pred             cHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----cCcHhHHH
Q 044084           75 RAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIE----EGMVEKTL  150 (343)
Q Consensus        75 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~  150 (343)
                      ++++|+++|++..+.|   +......|.  .....+.+++...+++..+.|   ++..+..|...|..    ..+.++|.
T Consensus         8 d~~~A~~~~~kaa~~g---~~~a~~~l~--~~~~~~~~~a~~~~~~aa~~g---~~~a~~~Lg~~y~~g~~~~~d~~~A~   79 (133)
T d1klxa_           8 DLKKAIQYYVKACELN---EMFGCLSLV--SNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKAA   79 (133)
T ss_dssp             HHHHHHHHHHHHHHTT---CTTHHHHHH--TCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHH
T ss_pred             CHHHHHHHHHHHHHCC---Chhhhhhhc--cccccCHHHHHHHHhhhhccc---chhhhhhHHHhhhhccccchhhHHHH
Confidence            4566666666665554   122222222  223356677777777777665   44555556665554    34567777


Q ss_pred             HHHHHHHhcCCCCchhhHHHHHHHHhc----CCcHHHHHHHHHHHHHcC
Q 044084          151 EVVESMKNAELNISDCISCVIVNGFSK----RRAYWAAVKVYEQLISQG  195 (343)
Q Consensus       151 ~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~  195 (343)
                      ++|++..+.+. |.  ....|...|..    ..+.++|.++|++..+.|
T Consensus        80 ~~~~~aa~~g~-~~--a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~G  125 (133)
T d1klxa_          80 QYYSKACGLND-QD--GCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  125 (133)
T ss_dssp             HHHHHHHHTTC-HH--HHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHhhhhccCc-ch--HHHHHHHHHHcCCccCCCHHHHHHHHHHHHHCC
Confidence            77777776654 22  23334344433    356777777777777665

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=96.39  E-value=0.053  Score=34.74  Aligned_cols=139  Identities=12%  Similarity=0.068  Sum_probs=71.9

Q ss_pred             hcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhc-CCCCchhhHHHHHHHHhcCCcHHHH
Q 044084          106 ASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNA-ELNISDCISCVIVNGFSKRRAYWAA  184 (343)
Q Consensus       106 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a  184 (343)
                      .-.|..++..+++.+...+   .+..-||.++--....-+-+-..++++.+-.. ++.|- .-...++.++...+     
T Consensus        13 ildG~ve~Gveii~k~~~s---s~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~FDls~C-~Nlk~vv~C~~~~n-----   83 (161)
T d1wy6a1          13 LLDGYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDKC-QNLKSVVECGVINN-----   83 (161)
T ss_dssp             HHTTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGGC-SCTHHHHHHHHHTT-----
T ss_pred             HHhhhHHhHHHHHHHHccc---CCccccceeeeecccccchHHHHHHHHHHhhhcCchhh-hcHHHHHHHHHHhc-----
Confidence            3445666666666666554   24445555555444444555555555554332 11000 00111222222111     


Q ss_pred             HHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhhC
Q 044084          185 VKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKPK  264 (343)
Q Consensus       185 ~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  264 (343)
                                   .+...+...+.....+|+-++-.++.+.+.+.+ .+++...-.+..+|.+.|...++-+++.+.-+.
T Consensus        84 -------------~~se~vdlALd~lv~~~kkd~Ld~i~~~l~kn~-~i~~~~llkia~A~kkig~~re~nell~~ACe~  149 (161)
T d1wy6a1          84 -------------TLNEHVNKALDILVIQGKRDKLEEIGREILKNN-EVSASILVAIANALRRVGDERDATTLLIEACKK  149 (161)
T ss_dssp             -------------CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC--C-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             -------------chHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHH
Confidence                         122334445566666677777777766655544 556666666777777777777777777777666


Q ss_pred             CCC
Q 044084          265 GCE  267 (343)
Q Consensus       265 ~~~  267 (343)
                      |++
T Consensus       150 G~K  152 (161)
T d1wy6a1         150 GEK  152 (161)
T ss_dssp             TCH
T ss_pred             hHH
Confidence            654

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=95.23  E-value=0.19  Score=32.16  Aligned_cols=141  Identities=14%  Similarity=0.101  Sum_probs=95.7

Q ss_pred             hhccCcHHHHHHHHHHHHhcCCCCChHhHHHHHHHHhcccCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHH
Q 044084           70 LGKSGRAFEILKFFRDMKEKGILEDPSVYASLICSFASIAEVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKT  149 (343)
Q Consensus        70 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  149 (343)
                      +...|..++..+++.+.....   +..-||..+--....-+-+...++++.+-+.   .|.          ..+++....
T Consensus        12 ~ildG~ve~Gveii~k~~~ss---~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~---FDl----------s~C~Nlk~v   75 (161)
T d1wy6a1          12 FLLDGYIDEGVKIVLEITKSS---TKSEYNWFICNLLESIDCRYMFQVLDKIGSY---FDL----------DKCQNLKSV   75 (161)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS---CHHHHTHHHHHHHHHCCHHHHHHHHHHHGGG---SCG----------GGCSCTHHH
T ss_pred             HHHhhhHHhHHHHHHHHcccC---CccccceeeeecccccchHHHHHHHHHHhhh---cCc----------hhhhcHHHH
Confidence            345688888999998887752   5666777777777777777777777665442   221          233444444


Q ss_pred             HHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHc
Q 044084          150 LEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       150 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  229 (343)
                      ...+-.+-     .+......-++....+|.-++..++++.+.+.+ .|++...-.+..+|.+.|...++-+++.+.-+.
T Consensus        76 v~C~~~~n-----~~se~vdlALd~lv~~~kkd~Ld~i~~~l~kn~-~i~~~~llkia~A~kkig~~re~nell~~ACe~  149 (161)
T d1wy6a1          76 VECGVINN-----TLNEHVNKALDILVIQGKRDKLEEIGREILKNN-EVSASILVAIANALRRVGDERDATTLLIEACKK  149 (161)
T ss_dssp             HHHHHHTT-----CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC--C-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHhc-----chHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHH
Confidence            44333321     223345566777788888888888888877654 677778888888999999999998888888887


Q ss_pred             CCC
Q 044084          230 GFD  232 (343)
Q Consensus       230 ~~~  232 (343)
                      |++
T Consensus       150 G~K  152 (161)
T d1wy6a1         150 GEK  152 (161)
T ss_dssp             TCH
T ss_pred             hHH
Confidence            753

>d2pqrb1 a.118.8.1 (B:5-128) Mitochondria fission protein Fis1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.75  E-value=0.26  Score=31.54  Aligned_cols=51  Identities=12%  Similarity=0.166  Sum_probs=29.1

Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHhHHHHHHHHHHhcC
Q 044084          110 EVKVAEELFKEAEEKGMLRDLEVFLKLVLMYIEEGMVEKTLEVVESMKNAE  160 (343)
Q Consensus       110 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  160 (343)
                      +.+.+..+++.+.+.+..-....+-.|.-+|.+.|++++|.+.++.+.+..
T Consensus        53 d~~~gI~lLe~~~~~~p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~ie  103 (124)
T d2pqrb1          53 DERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHE  103 (124)
T ss_dssp             HHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHccC
Confidence            445666666666654422113455555666666666666666666666554

>d1v54e_ a.118.11.1 (E:) Cytochrome c oxidase subunit E {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cytochrome c oxidase subunit E
family: Cytochrome c oxidase subunit E
domain: Cytochrome c oxidase subunit E
species: Cow (Bos taurus) [TaxId: 9913]

Probab=93.50  E-value=0.33  Score=29.29  Aligned_cols=50  Identities=16%  Similarity=0.296  Sum_probs=30.4

Q ss_pred             cHHHHHHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHHc
Q 044084          180 AYWAAVKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQK  229 (343)
Q Consensus       180 ~~~~a~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  229 (343)
                      +.-++.+-++.+....+.|++....+.+++|-+.+++..|.++|+.++..
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K   70 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK   70 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            44555555555555556666666666666666666666666666665543

>d2pqrb1 a.118.8.1 (B:5-128) Mitochondria fission protein Fis1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.11  E-value=0.61  Score=29.76  Aligned_cols=67  Identities=9%  Similarity=0.052  Sum_probs=33.1

Q ss_pred             CCHHHHHHHHHHHHhcC---cHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHHHHHHHHHHHc
Q 044084          128 RDLEVFLKLVLMYIEEG---MVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAAVKVYEQLISQ  194 (343)
Q Consensus       128 ~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  194 (343)
                      +++.+--....++.+..   +.++++.+|+.+...+..-....+-.+.-+|.+.|+++.|.+.++.+.+.
T Consensus        33 ~s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~~~~~p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~i  102 (124)
T d2pqrb1          33 ATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEH  102 (124)
T ss_dssp             SCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             CCcchHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHcc
Confidence            44444444444554443   34456666665554332111123334455555666666666666666554

>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=92.08  E-value=0.69  Score=27.88  Aligned_cols=46  Identities=9%  Similarity=0.044  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHHcCCCcChhhHHHHHHHHHccCChHHHHHHHHHHhh
Q 044084          218 KAEKVFIEMQQKGFDKCVVAYSSMVAMYGKTGRIRDAMRLVAKMKP  263 (343)
Q Consensus       218 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  263 (343)
                      +..+-++.+...++.|++....+.+++|.+.+++..|.++|+-.+.
T Consensus        24 e~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~   69 (105)
T d1v54e_          24 ELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKD   69 (105)
T ss_dssp             HHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            4444444444445555555555555555555555555555554443

>d1qsaa1 a.118.5.1 (A:1-450) 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Bacterial muramidases
family: Bacterial muramidases
domain: 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain
species: Escherichia coli [TaxId: 562]

Probab=85.83  E-value=7.1  Score=31.06  Aligned_cols=116  Identities=8%  Similarity=-0.039  Sum_probs=62.1

Q ss_pred             cCHHHHHHHHHHHHHcCCCCCHHHHHHHHH----HHHhcCcHhHHHHHHHHHHhcCCCCchhhHHHHHHHHhcCCcHHHH
Q 044084          109 AEVKVAEELFKEAEEKGMLRDLEVFLKLVL----MYIEEGMVEKTLEVVESMKNAELNISDCISCVIVNGFSKRRAYWAA  184 (343)
Q Consensus       109 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~----~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  184 (343)
                      .+.+.+..++......... +..-+..+-.    .....+..+.+...+......+.  +.......+......+++..+
T Consensus       228 ~d~~~a~~~l~~~~~~~~~-~~~~~~~~~~~~a~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~w~~~~al~~~~~~~~  304 (450)
T d1qsaa1         228 QDAENARLMIPSLAQAQQL-NEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMRSQ--STSLIERRVRMALGTGDRRGL  304 (450)
T ss_dssp             HCHHHHHHHHHHHHHHTTC-CHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHHTCC--CHHHHHHHHHHHHHHTCHHHH
T ss_pred             cChhHHHHHHHhhhhcccc-cHHHHHHHHHHHHHHHHHcCchHHHHHHHHhhccccc--chHHHHHHHHHHHHcCChHHH
Confidence            4666777777666554322 2222222222    22234555666666666554443  222333344445556777777


Q ss_pred             HHHHHHHHHcCCCCCHhhHHHHHHHHHccCChhHHHHHHHHHHH
Q 044084          185 VKVYEQLISQGCIPGQVTYASIINAYCRIGLYSKAEKVFIEMQQ  228 (343)
Q Consensus       185 ~~~~~~~~~~~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  228 (343)
                      ...+..|.... .....-.-.+.+++...|+.+.|...|..+..
T Consensus       305 ~~~~~~l~~~~-~~~~r~~YW~gRa~~~~G~~~~A~~~~~~~a~  347 (450)
T d1qsaa1         305 NTWLARLPMEA-KEKDEWRYWQADLLLERGREAEAKEILHQLMQ  347 (450)
T ss_dssp             HHHHHHSCTTG-GGSHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHhcCccc-ccHHHHHHHHHHHHHHcCChhhHHHHHHHHhc
Confidence            77777664321 11223334556777777888888877777654