Citrus Sinensis ID: 039342

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------25
Protein Sequence
GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDLPQLATVVV
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHccccccccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHccccccccHHHHHHHHHHHHHccccccccccEEEEEc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHcccccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHccccccEEEEEEEEEc
Coil and Loop (DISEMBL)
GGLYKECQAILSRMsesgvarnsdSFNAVIEAFRQGGRFEEAIKAYVEMEKvrcdpnertLEAVLSVYCFAGLVDESKEQFQEIkssgilpsvMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGqmikgefddesNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEatkrglfpelfrhnklvwsvdvhrmwEGGAYTAISVWLNKMYEMFmmgedlpqlatvvv
Flexible Loop (DISEMBL)
GGLYKECQAILSRmsesgvarnsDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEatkrglfpelfrhnklvwsvdvhrmwEGGAYTAISVWLNKMYEMFMMGEDLPQLATVVV
Low Complexity Region (SEG)
GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDLPQLATVVV
Disordered region (IsUnstruct)
*************************FNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDLPQ******
Disordered Region (DISOPRED)
GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDLPQLATVVV
Disordered Region (DISEMBL)
GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDLPQLATVVV
Disordered Region (DISPRO)
*GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDLPQLATVVV
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDLPQLATVVV
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	248	2.2.26 [Sep-21-2011]
Q9S7Q2	862	Pentatricopeptide repeat-	yes	no	0.991	0.285	0.732	1e-107
Q9FLL3	527	Pentatricopeptide repeat-	no	no	0.822	0.387	0.264	8e-18
Q3E9F0	506	Pentatricopeptide repeat-	no	no	0.826	0.405	0.287	9e-18
Q9SH26	577	Pentatricopeptide repeat-	no	no	0.782	0.336	0.296	2e-16
Q9LQ14	629	Pentatricopeptide repeat-	no	no	0.822	0.324	0.268	4e-16
Q9SXD8	634	Pentatricopeptide repeat-	no	no	0.822	0.321	0.273	1e-15
Q9SIC9	918	Pentatricopeptide repeat-	no	no	0.790	0.213	0.263	7e-15
Q9CAN5	614	Pentatricopeptide repeat-	no	no	0.802	0.324	0.279	8e-15
Q9LQ16	632	Pentatricopeptide repeat-	no	no	0.814	0.319	0.275	1e-14
Q9C8T7	559	Pentatricopeptide repeat-	no	no	0.822	0.364	0.263	2e-14

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

 Score =  387 bits (994), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 181/247 (73%), Positives = 214/247 (86%), Gaps = 1/247 (0%)

Query: 1   GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERT 60
           GGL KE +AILSR+ +SG+ RN D+FNA IEA++QGG+FEEA+K YV+MEK RCDP+ERT
Sbjct: 505 GGLVKESEAILSRLVDSGIPRNRDTFNAQIEAYKQGGKFEEAVKTYVDMEKSRCDPDERT 564

Query: 61  LEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMH 120
           LEAVLSVY FA LVDE +EQF+E+K+S ILPS+MCYCM+LAVY K+ RWDD   LL+EM 
Sbjct: 565 LEAVLSVYSFARLVDECREQFEEMKASDILPSIMCYCMMLAVYGKTERWDDVNELLEEML 624

Query: 121 TNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR 180
           +NR+SNIHQV GQMIKG++DD+SNWQ+VEYV DKLN EG GLG+RFYNALL+ALW LG +
Sbjct: 625 SNRVSNIHQVIGQMIKGDYDDDSNWQIVEYVLDKLNSEGCGLGIRFYNALLDALWWLGQK 684

Query: 181 ERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDL 240
           ERAARVL+EATKRGLFPELFR NKLVWSVDVHRM EGG YTA+SVWLN + +M + G DL
Sbjct: 685 ERAARVLNEATKRGLFPELFRKNKLVWSVDVHRMSEGGMYTALSVWLNDINDMLLKG-DL 743

Query: 241 PQLATVV 247
           PQLA VV
Sbjct: 744 PQLAVVV 750

Involved in plastid gene expression.
Arabidopsis thaliana (taxid: 3702)

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

 Score = 90.9 bits (224), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 55/208 (26%), Positives = 107/208 (51%), Gaps = 4/208 (1%)

Query: 2   GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTL 61
           G +++  ++L  M++  +  +  +FNA+I+AF + G+F +A + Y EM ++   PN  T 
Sbjct: 226 GRWRDADSLLRGMTKRKIKPDVITFNALIDAFVKEGKFLDAEELYNEMIRMSIAPNIFTY 285

Query: 62  EAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHT 121
            ++++ +C  G VDE+++ F  +++ G  P V+ Y  L+  + K  + DDA  +  EM  
Sbjct: 286 TSLINGFCMEGCVDEARQMFYLMETKGCFPDVVAYTSLINGFCKCKKVDDAMKIFYEMSQ 345

Query: 122 NRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRE 181
             ++        +I+G F       + + VF  +   G    +R YN LL  L   G  +
Sbjct: 346 KGLTGNTITYTTLIQG-FGQVGKPNVAQEVFSHMVSRGVPPNIRTYNVLLHCLCYNGKVK 404

Query: 182 RAARVLDEATKR---GLFPELFRHNKLV 206
           +A  + ++  KR   G+ P ++ +N L+
Sbjct: 405 KALMIFEDMQKREMDGVAPNIWTYNVLL 432

Arabidopsis thaliana (taxid: 3702)

>sp|Q3E9F0|PP392_ARATH Pentatricopeptide repeat-containing protein At5g18475 OS=Arabidopsis thaliana GN=At5g18475 PE=2 SV=1

 Score = 90.5 bits (223), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 61/212 (28%), Positives = 103/212 (48%), Gaps = 7/212 (3%)

Query: 14  MSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGL 73
           +S+ G++ +  +FN +I  F + G  E A K    M+K  C+PN     A+++ +C  G 
Sbjct: 259 ISKEGISPDPVTFNVMINGFCRAGEVERAKKILDFMKKNGCNPNVYNYSALMNGFCKVGK 318

Query: 74  VDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQ 133
           + E+K+ F E+K +G+    + Y  L+  + ++   D+A  LL EM  +R      +T  
Sbjct: 319 IQEAKQTFDEVKKTGLKLDTVGYTTLMNCFCRNGETDEAMKLLGEMKASR-CRADTLTYN 377

Query: 134 MIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKR 193
           +I      E   +    + D+   EG  L    Y  +L AL C G  E+A + L   ++R
Sbjct: 378 VILRGLSSEGRSEEALQMLDQWGSEGVHLNKGSYRIILNALCCNGELEKAVKFLSVMSER 437

Query: 194 GLFPELFRHNKLVWSVDVHRMWEGGAYTAISV 225
           G++P     +   W+  V R+ E G YT I V
Sbjct: 438 GIWP-----HHATWNELVVRLCESG-YTEIGV 463

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SH26|PP102_ARATH Pentatricopeptide repeat-containing protein At1g63400 OS=Arabidopsis thaliana GN=At1g63400 PE=2 SV=1

 Score = 85.9 bits (211), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 59/199 (29%), Positives = 98/199 (49%), Gaps = 5/199 (2%)

Query: 10  ILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYC 69
           +LS M E  +  N  +FNA+I+AF + G+  EA K Y EM K   DP+  T  ++++ +C
Sbjct: 317 LLSDMIERKINPNVVTFNALIDAFVKEGKLVEAEKLYDEMIKRSIDPDIFTYSSLINGFC 376

Query: 70  FAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQ 129
               +DE+K  F+ + S    P+V+ Y  L+  + K+ R D+   L  EM    +     
Sbjct: 377 MHDRLDEAKHMFELMISKDCFPNVVTYNTLINGFCKAKRIDEGVELFREMSQRGLVGNTV 436

Query: 130 VTGQMIKGEFD--DESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVL 187
               +I G F   D  N QM   VF ++  +G    +  YN LL+ L   G  E+A  V 
Sbjct: 437 TYTTLIHGFFQARDCDNAQM---VFKQMVSDGVHPNIMTYNTLLDGLCKNGKLEKAMVVF 493

Query: 188 DEATKRGLFPELFRHNKLV 206
           +   +  + P ++ +N ++
Sbjct: 494 EYLQRSKMEPTIYTYNIMI 512

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LQ14|PPR96_ARATH Pentatricopeptide repeat-containing protein At1g62930, chloroplastic OS=Arabidopsis thaliana GN=At1g62930 PE=2 SV=2

 Score = 85.1 bits (209), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 55/205 (26%), Positives = 102/205 (49%), Gaps = 1/205 (0%)

Query: 2   GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTL 61
           G + +   +LS M E  +  N  +F+A+I+AF + G+  EA K Y EM K   DP+  T 
Sbjct: 304 GRWSDASRLLSDMIERKINPNVVTFSALIDAFVKEGKLVEAEKLYDEMIKRSIDPDIFTY 363

Query: 62  EAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHT 121
            ++++ +C    +DE+K  F+ + S    P+V+ Y  L+  + K+ R ++   L  EM  
Sbjct: 364 SSLINGFCMHDRLDEAKHMFELMISKDCFPNVVTYNTLIKGFCKAKRVEEGMELFREMSQ 423

Query: 122 NRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRE 181
             +         +I+G F    +  M + +F K+  +G    +  Y+ LL+ L   G  E
Sbjct: 424 RGLVGNTVTYNTLIQGLF-QAGDCDMAQKIFKKMVSDGVPPDIITYSILLDGLCKYGKLE 482

Query: 182 RAARVLDEATKRGLFPELFRHNKLV 206
           +A  V +   K  + P+++ +N ++
Sbjct: 483 KALVVFEYLQKSKMEPDIYTYNIMI 507

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SXD8|PPR90_ARATH Pentatricopeptide repeat-containing protein At1g62590 OS=Arabidopsis thaliana GN=At1g62590 PE=2 SV=1

 Score = 84.0 bits (206), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 56/205 (27%), Positives = 101/205 (49%), Gaps = 1/205 (0%)

Query: 2   GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTL 61
           G + +   +LS M E  +  N  +FNA+I+AF + G+F EA K Y +M K   DP+  T 
Sbjct: 309 GRWSDASQLLSDMIEKKINPNLVTFNALIDAFVKEGKFVEAEKLYDDMIKRSIDPDIFTY 368

Query: 62  EAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHT 121
            ++++ +C    +D++K+ F+ + S    P V+ Y  L+  + KS R +D   L  EM  
Sbjct: 369 NSLVNGFCMHDRLDKAKQMFEFMVSKDCFPDVVTYNTLIKGFCKSKRVEDGTELFREMSH 428

Query: 122 NRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRE 181
             +         +I+G F D  +    + VF ++  +G    +  Y+ LL+ L   G  E
Sbjct: 429 RGLVGDTVTYTTLIQGLFHD-GDCDNAQKVFKQMVSDGVPPDIMTYSILLDGLCNNGKLE 487

Query: 182 RAARVLDEATKRGLFPELFRHNKLV 206
           +A  V D   K  +  +++ +  ++
Sbjct: 488 KALEVFDYMQKSEIKLDIYIYTTMI 512

Arabidopsis thaliana (taxid: 3702)

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

 Score = 80.9 bits (198), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 52/197 (26%), Positives = 95/197 (48%), Gaps = 1/197 (0%)

Query: 10  ILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYC 69
           IL++M    +  N  S++ VI+ F + GRF+EA+  + EM  +    +  +   +LS+Y 
Sbjct: 396 ILAQMPVKRIMPNVVSYSTVIDGFAKAGRFDEALNLFGEMRYLGIALDRVSYNTLLSIYT 455

Query: 70  FAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQ 129
             G  +E+ +  +E+ S GI   V+ Y  LL  Y K  ++D+   +  EM    +     
Sbjct: 456 KVGRSEEALDILREMASVGIKKDVVTYNALLGGYGKQGKYDEVKKVFTEMKREHVLPNLL 515

Query: 130 VTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDE 189
               +I G +     ++    +F +    G    +  Y+AL++AL   GL   A  ++DE
Sbjct: 516 TYSTLIDG-YSKGGLYKEAMEIFREFKSAGLRADVVLYSALIDALCKNGLVGSAVSLIDE 574

Query: 190 ATKRGLFPELFRHNKLV 206
            TK G+ P +  +N ++
Sbjct: 575 MTKEGISPNVVTYNSII 591

Arabidopsis thaliana (taxid: 3702)

>sp|Q9CAN5|PPR98_ARATH Pentatricopeptide repeat-containing protein At1g63080, mitochondrial OS=Arabidopsis thaliana GN=At1g63080 PE=2 SV=1

 Score = 80.9 bits (198), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 57/204 (27%), Positives = 99/204 (48%), Gaps = 5/204 (2%)

Query: 2   GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTL 61
           G + +   +LS M E  +  N  +FN++I+AF + G+  EA K + EM +   DPN  T 
Sbjct: 289 GRWSDASRLLSDMLERKINPNVVTFNSLIDAFAKEGKLIEAEKLFDEMIQRSIDPNIVTY 348

Query: 62  EAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHT 121
            ++++ +C    +DE+++ F  + S   LP V+ Y  L+  + K+ +  D   L  +M  
Sbjct: 349 NSLINGFCMHDRLDEAQQIFTLMVSKDCLPDVVTYNTLINGFCKAKKVVDGMELFRDMSR 408

Query: 122 NRISNIHQVTGQMIKGEF--DDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGL 179
             +         +I G F   D  N QM   VF ++  +G    +  YN LL+ L   G 
Sbjct: 409 RGLVGNTVTYTTLIHGFFQASDCDNAQM---VFKQMVSDGVHPNIMTYNTLLDGLCKNGK 465

Query: 180 RERAARVLDEATKRGLFPELFRHN 203
            E+A  V +   K  + P+++ +N
Sbjct: 466 LEKAMVVFEYLQKSKMEPDIYTYN 489

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LQ16|PPR94_ARATH Pentatricopeptide repeat-containing protein At1g62910 OS=Arabidopsis thaliana GN=At1g62910 PE=2 SV=1

 Score = 80.1 bits (196), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 57/207 (27%), Positives = 100/207 (48%), Gaps = 5/207 (2%)

Query: 2   GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTL 61
           G + +   +LS M E  +  N  +F+A+I+AF + G+  EA K Y EM K   DP+  T 
Sbjct: 307 GRWSDASRLLSDMIERKINPNVVTFSALIDAFVKEGKLVEAEKLYDEMIKRSIDPDIFTY 366

Query: 62  EAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHT 121
            ++++ +C    +DE+K  F+ + S    P+V+ Y  L+  + K+ R ++   L  EM  
Sbjct: 367 SSLINGFCMHDRLDEAKHMFELMISKDCFPNVVTYSTLIKGFCKAKRVEEGMELFREMSQ 426

Query: 122 NRISNIHQVTGQMIKGEFD--DESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGL 179
             +         +I G F   D  N QM   VF ++   G    +  YN LL+ L   G 
Sbjct: 427 RGLVGNTVTYTTLIHGFFQARDCDNAQM---VFKQMVSVGVHPNILTYNILLDGLCKNGK 483

Query: 180 RERAARVLDEATKRGLFPELFRHNKLV 206
             +A  V +   +  + P+++ +N ++
Sbjct: 484 LAKAMVVFEYLQRSTMEPDIYTYNIMI 510

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C8T7|PP101_ARATH Pentatricopeptide repeat-containing protein At1g63330 OS=Arabidopsis thaliana GN=At1g63330 PE=2 SV=2

 Score = 79.3 bits (194), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 54/205 (26%), Positives = 100/205 (48%), Gaps = 1/205 (0%)

Query: 2   GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTL 61
           G + +   +LS M E  +  N  +FNA+I+AF + G+F EA K + +M K   DP+  T 
Sbjct: 234 GRWSDASQLLSDMIEKKINPNLVTFNALIDAFVKEGKFVEAEKLHDDMIKRSIDPDIFTY 293

Query: 62  EAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHT 121
            ++++ +C    +D++K+ F+ + S    P +  Y  L+  + KS R +D   L  EM  
Sbjct: 294 NSLINGFCMHDRLDKAKQMFEFMVSKDCFPDLDTYNTLIKGFCKSKRVEDGTELFREMSH 353

Query: 122 NRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRE 181
             +         +I+G F D  +    + VF ++  +G    +  Y+ LL+ L   G  E
Sbjct: 354 RGLVGDTVTYTTLIQGLFHD-GDCDNAQKVFKQMVSDGVPPDIMTYSILLDGLCNNGKLE 412

Query: 182 RAARVLDEATKRGLFPELFRHNKLV 206
           +A  V D   K  +  +++ +  ++
Sbjct: 413 KALEVFDYMQKSEIKLDIYIYTTMI 437

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	248
297733858	627	unnamed protein product [Vitis vinifera]	0.931	0.368	0.790	1e-115
225457182	869	PREDICTED: pentatricopeptide repeat-cont	0.963	0.275	0.790	1e-115
224135699	866	predicted protein [Populus trichocarpa]	0.959	0.274	0.794	1e-113
255540825	754	pentatricopeptide repeat-containing prot	0.991	0.326	0.773	1e-112
356513567	857	PREDICTED: pentatricopeptide repeat-cont	0.979	0.283	0.766	1e-111
449469490	864	PREDICTED: pentatricopeptide repeat-cont	0.963	0.276	0.762	1e-110
449487793	864	PREDICTED: pentatricopeptide repeat-cont	0.963	0.276	0.762	1e-110
356562783	859	PREDICTED: pentatricopeptide repeat-cont	0.979	0.282	0.762	1e-109
297842227	863	hypothetical protein ARALYDRAFT_476621 [	0.959	0.275	0.740	1e-108
15221411	862	plastid transcriptionally active 2 [Arab	0.991	0.285	0.732	1e-105

>gi|297733858|emb|CBI15105.3| unnamed protein product [Vitis vinifera]

 Score =  420 bits (1080), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 196/248 (79%), Positives = 223/248 (89%)

Query: 1   GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERT 60
           GGLYKE +AIL +M +SGVARN D+FN VIEAFRQGG+FEEAIKAYVEMEK RCDP+E+T
Sbjct: 268 GGLYKESEAILLKMGQSGVARNRDTFNGVIEAFRQGGQFEEAIKAYVEMEKARCDPDEQT 327

Query: 61  LEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMH 120
           LEAVLSVYCFAGLV+ES+EQF EIK+ GILPSVMCYCM+LAVYAK++RWDDA+ LLDEM 
Sbjct: 328 LEAVLSVYCFAGLVEESEEQFGEIKALGILPSVMCYCMMLAVYAKADRWDDAHQLLDEMF 387

Query: 121 TNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR 180
           TNR+SNIHQV GQMI+G++DD+SNWQMVEYVF+KL  EG  LG+RFYN LLEALW LG +
Sbjct: 388 TNRVSNIHQVIGQMIRGDYDDDSNWQMVEYVFEKLKSEGCSLGVRFYNTLLEALWWLGQK 447

Query: 181 ERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDL 240
           ERA RVL+EATKRGLFPELFR NKLVWSVDVHRMWEG A TAISVWLN M+EMF+ G+DL
Sbjct: 448 ERATRVLNEATKRGLFPELFRKNKLVWSVDVHRMWEGAACTAISVWLNNMHEMFISGDDL 507

Query: 241 PQLATVVV 248
           PQLA+ VV
Sbjct: 508 PQLASAVV 515

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225457182|ref|XP_002280557.1| PREDICTED: pentatricopeptide repeat-containing protein At1g74850, chloroplastic [Vitis vinifera]

 Score =  420 bits (1079), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 196/248 (79%), Positives = 223/248 (89%)

Query: 1   GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERT 60
           GGLYKE +AIL +M +SGVARN D+FN VIEAFRQGG+FEEAIKAYVEMEK RCDP+E+T
Sbjct: 510 GGLYKESEAILLKMGQSGVARNRDTFNGVIEAFRQGGQFEEAIKAYVEMEKARCDPDEQT 569

Query: 61  LEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMH 120
           LEAVLSVYCFAGLV+ES+EQF EIK+ GILPSVMCYCM+LAVYAK++RWDDA+ LLDEM 
Sbjct: 570 LEAVLSVYCFAGLVEESEEQFGEIKALGILPSVMCYCMMLAVYAKADRWDDAHQLLDEMF 629

Query: 121 TNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR 180
           TNR+SNIHQV GQMI+G++DD+SNWQMVEYVF+KL  EG  LG+RFYN LLEALW LG +
Sbjct: 630 TNRVSNIHQVIGQMIRGDYDDDSNWQMVEYVFEKLKSEGCSLGVRFYNTLLEALWWLGQK 689

Query: 181 ERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDL 240
           ERA RVL+EATKRGLFPELFR NKLVWSVDVHRMWEG A TAISVWLN M+EMF+ G+DL
Sbjct: 690 ERATRVLNEATKRGLFPELFRKNKLVWSVDVHRMWEGAACTAISVWLNNMHEMFISGDDL 749

Query: 241 PQLATVVV 248
           PQLA+ VV
Sbjct: 750 PQLASAVV 757

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224135699|ref|XP_002322139.1| predicted protein [Populus trichocarpa] gi|222869135|gb|EEF06266.1| predicted protein [Populus trichocarpa]

 Score =  414 bits (1064), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 197/248 (79%), Positives = 218/248 (87%)

Query: 1   GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERT 60
           GGLYKE +AIL +M + GVAR  DSFN VIE FRQGG+FEEAIKAYVEMEK R  P+ERT
Sbjct: 507 GGLYKETEAILLKMGDFGVARERDSFNGVIEGFRQGGQFEEAIKAYVEMEKSRLVPDERT 566

Query: 61  LEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMH 120
           LEAVLSVYC AGLVDES EQFQEIK+SGILP+VMCYCM+LAVYAKS+RW++AY LLDEM 
Sbjct: 567 LEAVLSVYCIAGLVDESVEQFQEIKASGILPNVMCYCMMLAVYAKSDRWNEAYELLDEML 626

Query: 121 TNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR 180
           TNR SNIHQV GQMIKG+FDD+SNWQMVEYVFDKLN EG GLGMRFYN LLEALW LG +
Sbjct: 627 TNRASNIHQVIGQMIKGDFDDDSNWQMVEYVFDKLNSEGCGLGMRFYNTLLEALWWLGQK 686

Query: 181 ERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDL 240
           ERA RVL EATKRG FPELFR +KLVWSVD+HRMWEG AYTAISVWLN MYE+FM  +D+
Sbjct: 687 ERAVRVLGEATKRGHFPELFRKSKLVWSVDIHRMWEGSAYTAISVWLNNMYEIFMNRQDI 746

Query: 241 PQLATVVV 248
           PQLA+V+V
Sbjct: 747 PQLASVIV 754

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255540825|ref|XP_002511477.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis] gi|223550592|gb|EEF52079.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis]

 Score =  409 bits (1050), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 191/247 (77%), Positives = 219/247 (88%)

Query: 1   GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERT 60
           GGLYKE +AI+ +M ESGVAR+ DSFN VIE +RQGG+FEEAIK YVE+EK R  P+ERT
Sbjct: 506 GGLYKESEAIMWKMGESGVARDRDSFNGVIEGYRQGGQFEEAIKTYVELEKARFQPDERT 565

Query: 61  LEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMH 120
            EAVLSVYC AGLVDES+EQF+EI++SGILPSVMCYCM++AVYA+SNRWDDAY +LDEM 
Sbjct: 566 FEAVLSVYCTAGLVDESEEQFREIRASGILPSVMCYCMMIAVYARSNRWDDAYEVLDEMV 625

Query: 121 TNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR 180
           TN++SNIHQV G+M+KG++DD SNWQMVEYVFDKLN EG GLGMRFYN LLEALW LG +
Sbjct: 626 TNKVSNIHQVVGKMMKGDYDDYSNWQMVEYVFDKLNSEGCGLGMRFYNTLLEALWWLGQK 685

Query: 181 ERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDL 240
           ERAARVL EA KRGLFPELFR +KLVWSVDVHRMWEGGA TAISVWLN M+EMF+ GEDL
Sbjct: 686 ERAARVLSEAIKRGLFPELFRKSKLVWSVDVHRMWEGGACTAISVWLNNMHEMFLKGEDL 745

Query: 241 PQLATVV 247
           P +A+VV
Sbjct: 746 PHVASVV 752

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356513567|ref|XP_003525484.1| PREDICTED: pentatricopeptide repeat-containing protein At1g74850, chloroplastic-like [Glycine max]

 Score =  407 bits (1046), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 190/248 (76%), Positives = 222/248 (89%)

Query: 1   GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERT 60
           GGLYKE +AILSRM+ESG+ R+  SFN VIEAFRQGG++EEA+K+YVEMEK  C+PNE T
Sbjct: 498 GGLYKEAEAILSRMNESGLKRDVHSFNGVIEAFRQGGQYEEAVKSYVEMEKANCEPNELT 557

Query: 61  LEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMH 120
           LEAVLS+YC AGLVDE +EQFQEIK+SGILPSVMCYCM+LA+YAK++R +DAY L+D M 
Sbjct: 558 LEAVLSIYCSAGLVDEGEEQFQEIKASGILPSVMCYCMMLALYAKNDRLNDAYNLIDAMI 617

Query: 121 TNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR 180
           T R+S+IHQV GQMIKG+FDDESNWQ+VEYVFDKLN EG GLGMRFYNALLEALWC+  R
Sbjct: 618 TMRVSDIHQVIGQMIKGDFDDESNWQIVEYVFDKLNSEGCGLGMRFYNALLEALWCMFQR 677

Query: 181 ERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDL 240
           ERAARVL+EA+KRGLFPELFR +KLVWSVDVHRM EGGA TA+SVWLN ++EM M G+DL
Sbjct: 678 ERAARVLNEASKRGLFPELFRKSKLVWSVDVHRMSEGGALTALSVWLNNVHEMSMTGDDL 737

Query: 241 PQLATVVV 248
           P++ATVVV
Sbjct: 738 PEVATVVV 745

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449469490|ref|XP_004152453.1| PREDICTED: pentatricopeptide repeat-containing protein At1g74850, chloroplastic-like [Cucumis sativus]

 Score =  402 bits (1034), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 189/248 (76%), Positives = 217/248 (87%)

Query: 1   GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERT 60
           GGLYKE +AILSRM E G++RN+ SF+ +IE +RQ G++EEAIKA+VEMEK+RC+ +E+T
Sbjct: 512 GGLYKEFEAILSRMREYGISRNAKSFSGIIEGYRQSGQYEEAIKAFVEMEKMRCELDEQT 571

Query: 61  LEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMH 120
           LE VL VYCFAGLVDESKEQF EIK+SGILPSV+CYCM+LAVYAK+ RWDDA  LLDEM 
Sbjct: 572 LEGVLGVYCFAGLVDESKEQFIEIKASGILPSVLCYCMMLAVYAKNGRWDDASELLDEMI 631

Query: 121 TNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR 180
             R+S+IHQV GQMIKG++DD+SNWQMVEYVFDKLN EG G GMRFYN LLEALW LG +
Sbjct: 632 KTRVSSIHQVIGQMIKGDYDDDSNWQMVEYVFDKLNAEGCGFGMRFYNTLLEALWWLGQK 691

Query: 181 ERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDL 240
            RAARVL EATKRGLFPELFR +KLVWSVDVHRMWEGGAYTA+S+W+NKM EM M GEDL
Sbjct: 692 GRAARVLTEATKRGLFPELFRQSKLVWSVDVHRMWEGGAYTAVSLWVNKMNEMLMDGEDL 751

Query: 241 PQLATVVV 248
           PQLA VVV
Sbjct: 752 PQLAAVVV 759

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449487793|ref|XP_004157803.1| PREDICTED: pentatricopeptide repeat-containing protein At1g74850, chloroplastic-like [Cucumis sativus]

 Score =  402 bits (1034), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 189/248 (76%), Positives = 217/248 (87%)

Query: 1   GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERT 60
           GGLYKE +AILSRM E G++RN+ SF+ +IE +RQ G++EEAIKA+VEMEK+RC+ +E+T
Sbjct: 512 GGLYKEFEAILSRMREYGISRNAKSFSGIIEGYRQSGQYEEAIKAFVEMEKMRCELDEQT 571

Query: 61  LEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMH 120
           LE VL VYCFAGLVDESKEQF EIK+SGILPSV+CYCM+LAVYAK+ RWDDA  LLDEM 
Sbjct: 572 LEGVLGVYCFAGLVDESKEQFIEIKASGILPSVLCYCMMLAVYAKNGRWDDASELLDEMI 631

Query: 121 TNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR 180
             R+S+IHQV GQMIKG++DD+SNWQMVEYVFDKLN EG G GMRFYN LLEALW LG +
Sbjct: 632 KTRVSSIHQVIGQMIKGDYDDDSNWQMVEYVFDKLNAEGCGFGMRFYNTLLEALWWLGQK 691

Query: 181 ERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDL 240
            RAARVL EATKRGLFPELFR +KLVWSVDVHRMWEGGAYTA+S+W+NKM EM M GEDL
Sbjct: 692 GRAARVLTEATKRGLFPELFRQSKLVWSVDVHRMWEGGAYTAVSLWVNKMNEMLMDGEDL 751

Query: 241 PQLATVVV 248
           PQLA VVV
Sbjct: 752 PQLAAVVV 759

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356562783|ref|XP_003549648.1| PREDICTED: pentatricopeptide repeat-containing protein At1g74850, chloroplastic-like [Glycine max]

 Score =  399 bits (1024), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 189/248 (76%), Positives = 219/248 (88%)

Query: 1   GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERT 60
           GGLYKE +AILSRM+ESG+ R+  SFN VI+AFRQGG++EEA+K+YVEMEK  C+PNE T
Sbjct: 500 GGLYKEAEAILSRMNESGLKRDVHSFNGVIKAFRQGGQYEEAVKSYVEMEKANCEPNELT 559

Query: 61  LEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMH 120
           LE VLSVYC AGLVDES+EQFQEIK+SGILPSVMCYC++LA+YAK++R +DAY L+DEM 
Sbjct: 560 LEVVLSVYCSAGLVDESEEQFQEIKASGILPSVMCYCLMLALYAKNDRLNDAYNLIDEMI 619

Query: 121 TNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR 180
           T R+S+IHQ  GQMIKG+FDDESNWQ+VEYVFDKLN EG GLGMRFYNALLEALW +  R
Sbjct: 620 TMRVSDIHQGIGQMIKGDFDDESNWQIVEYVFDKLNSEGCGLGMRFYNALLEALWWMFQR 679

Query: 181 ERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDL 240
           ERAARVL+EA+KRGLFPELFR +KLVWSVDVHRM EGGA TA+SVWLN M+EM   G DL
Sbjct: 680 ERAARVLNEASKRGLFPELFRKSKLVWSVDVHRMSEGGALTALSVWLNNMHEMSRTGNDL 739

Query: 241 PQLATVVV 248
           P+LATVVV
Sbjct: 740 PELATVVV 747

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297842227|ref|XP_002888995.1| hypothetical protein ARALYDRAFT_476621 [Arabidopsis lyrata subsp. lyrata] gi|297334836|gb|EFH65254.1| hypothetical protein ARALYDRAFT_476621 [Arabidopsis lyrata subsp. lyrata]

 Score =  395 bits (1016), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 183/247 (74%), Positives = 215/247 (87%)

Query: 1   GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERT 60
           GGL KE +AILSR+ +SG+ RN D+FNA IEA++QGG+FEEA+K YV+MEK RCDP+ERT
Sbjct: 505 GGLVKESEAILSRLVDSGIPRNRDTFNAQIEAYKQGGKFEEAVKTYVDMEKSRCDPDERT 564

Query: 61  LEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMH 120
           LEAVLSVY FA LVDE +EQF+E+K+S ILPS+MCYCM+LAVY K+ RWDD   LL+EM 
Sbjct: 565 LEAVLSVYSFARLVDECREQFEEMKASDILPSIMCYCMMLAVYGKTERWDDVNELLEEML 624

Query: 121 TNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR 180
           +NR+SNIHQV GQMIKG++DD+SNWQ+VEYV DKLN EG GLG+RFYNALL+ALW LG +
Sbjct: 625 SNRVSNIHQVIGQMIKGDYDDDSNWQIVEYVLDKLNSEGCGLGIRFYNALLDALWWLGQK 684

Query: 181 ERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDL 240
           ERAARVL+EATKRGLFPELFR NKLVWSVDVHRM EGG YTA+SVWLN M +M + GEDL
Sbjct: 685 ERAARVLNEATKRGLFPELFRKNKLVWSVDVHRMSEGGMYTALSVWLNDMNDMLLNGEDL 744

Query: 241 PQLATVV 247
           PQLA VV
Sbjct: 745 PQLAVVV 751

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15221411|ref|NP_177623.1| plastid transcriptionally active 2 [Arabidopsis thaliana] gi|75194055|sp|Q9S7Q2.1|PP124_ARATH RecName: Full=Pentatricopeptide repeat-containing protein At1g74850, chloroplastic; AltName: Full=Protein PLASTID TRANSCRIPTIONALLY ACTIVE 2; Flags: Precursor gi|5882738|gb|AAD55291.1|AC008263_22 Contains 3 PF|01535 DUF17 domains [Arabidopsis thaliana] gi|12323908|gb|AAG51934.1|AC013258_28 hypothetical protein; 81052-84129 [Arabidopsis thaliana] gi|332197518|gb|AEE35639.1| plastid transcriptionally active 2 [Arabidopsis thaliana]

 Score =  387 bits (994), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 181/247 (73%), Positives = 214/247 (86%), Gaps = 1/247 (0%)

Query: 1   GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERT 60
           GGL KE +AILSR+ +SG+ RN D+FNA IEA++QGG+FEEA+K YV+MEK RCDP+ERT
Sbjct: 505 GGLVKESEAILSRLVDSGIPRNRDTFNAQIEAYKQGGKFEEAVKTYVDMEKSRCDPDERT 564

Query: 61  LEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMH 120
           LEAVLSVY FA LVDE +EQF+E+K+S ILPS+MCYCM+LAVY K+ RWDD   LL+EM 
Sbjct: 565 LEAVLSVYSFARLVDECREQFEEMKASDILPSIMCYCMMLAVYGKTERWDDVNELLEEML 624

Query: 121 TNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR 180
           +NR+SNIHQV GQMIKG++DD+SNWQ+VEYV DKLN EG GLG+RFYNALL+ALW LG +
Sbjct: 625 SNRVSNIHQVIGQMIKGDYDDDSNWQIVEYVLDKLNSEGCGLGIRFYNALLDALWWLGQK 684

Query: 181 ERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDL 240
           ERAARVL+EATKRGLFPELFR NKLVWSVDVHRM EGG YTA+SVWLN + +M + G DL
Sbjct: 685 ERAARVLNEATKRGLFPELFRKNKLVWSVDVHRMSEGGMYTALSVWLNDINDMLLKG-DL 743

Query: 241 PQLATVV 247
           PQLA VV
Sbjct: 744 PQLAVVV 750

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	248
TAIR|locus:2027166	862	PTAC2 "plastid transcriptional	0.991	0.285	0.732	4.1e-97
TAIR|locus:1006230454	506	AT5G18475 "AT5G18475" [Arabido	0.862	0.422	0.292	1.1e-19
TAIR|locus:2163041	527	AT5G41170 [Arabidopsis thalian	0.822	0.387	0.264	9e-18
TAIR|locus:2203916	634	AT1G62590 [Arabidopsis thalian	0.818	0.320	0.281	2e-16
TAIR|locus:2015494	629	RPF3 "RNA processing factor 3"	0.822	0.324	0.268	3.3e-16
TAIR|locus:2031301	577	AT1G63400 [Arabidopsis thalian	0.802	0.344	0.296	5.9e-16
TAIR|locus:2061310	918	GUN1 "AT2G31400" [Arabidopsis	0.826	0.223	0.262	2.7e-15
TAIR|locus:2015228	614	AT1G63080 [Arabidopsis thalian	0.806	0.325	0.275	1e-14
TAIR|locus:2026192	630	RPF2 "rna processing factor 2"	0.822	0.323	0.253	1.1e-14
TAIR|locus:2015208	630	AT1G63130 [Arabidopsis thalian	0.818	0.322	0.271	2.9e-14

TAIR|locus:2027166 PTAC2 "plastid transcriptionally active 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 965 (344.8 bits), Expect = 4.1e-97, P = 4.1e-97
 Identities = 181/247 (73%), Positives = 214/247 (86%)

Query:     1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERT 60
             GGL KE +AILSR+ +SG+ RN D+FNA IEA++QGG+FEEA+K YV+MEK RCDP+ERT
Sbjct:   505 GGLVKESEAILSRLVDSGIPRNRDTFNAQIEAYKQGGKFEEAVKTYVDMEKSRCDPDERT 564

Query:    61 LEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMH 120
             LEAVLSVY FA LVDE +EQF+E+K+S ILPS+MCYCM+LAVY K+ RWDD   LL+EM 
Sbjct:   565 LEAVLSVYSFARLVDECREQFEEMKASDILPSIMCYCMMLAVYGKTERWDDVNELLEEML 624

Query:   121 TNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR 180
             +NR+SNIHQV GQMIKG++DD+SNWQ+VEYV DKLN EG GLG+RFYNALL+ALW LG +
Sbjct:   625 SNRVSNIHQVIGQMIKGDYDDDSNWQIVEYVLDKLNSEGCGLGIRFYNALLDALWWLGQK 684

Query:   181 ERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDL 240
             ERAARVL+EATKRGLFPELFR NKLVWSVDVHRM EGG YTA+SVWLN + +M + G DL
Sbjct:   685 ERAARVLNEATKRGLFPELFRKNKLVWSVDVHRMSEGGMYTALSVWLNDINDMLLKG-DL 743

Query:   241 PQLATVV 247
             PQLA VV
Sbjct:   744 PQLAVVV 750

GO:0009507 "chloroplast" evidence=IDA

GO:0009295 "nucleoid" evidence=IDA

GO:0009508 "plastid chromosome" evidence=IDA

GO:0042793 "transcription from plastid promoter" evidence=RCA;IMP

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA;IMP

GO:0006364 "rRNA processing" evidence=RCA

GO:0006399 "tRNA metabolic process" evidence=RCA

GO:0009658 "chloroplast organization" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0010103 "stomatal complex morphogenesis" evidence=RCA

GO:0010207 "photosystem II assembly" evidence=RCA

GO:0030154 "cell differentiation" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

GO:0035304 "regulation of protein dephosphorylation" evidence=RCA

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

TAIR|locus:1006230454 AT5G18475 "AT5G18475" [Arabidopsis thaliana (taxid:3702)]

 Score = 241 (89.9 bits), Expect = 1.1e-19, P = 1.1e-19
 Identities = 65/222 (29%), Positives = 107/222 (48%)

Query:     5 KECQAILSRM-SESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEA 63
             KE   +   M S+ G++ +  +FN +I  F + G  E A K    M+K  C+PN     A
Sbjct:   249 KEAVELFEDMISKEGISPDPVTFNVMINGFCRAGEVERAKKILDFMKKNGCNPNVYNYSA 308

Query:    64 VLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNR 123
             +++ +C  G + E+K+ F E+K +G+    + Y  L+  + ++   D+A  LL EM  +R
Sbjct:   309 LMNGFCKVGKIQEAKQTFDEVKKTGLKLDTVGYTTLMNCFCRNGETDEAMKLLGEMKASR 368

Query:   124 ISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERA 183
                   +T  +I      E   +    + D+   EG  L    Y  +L AL C G  E+A
Sbjct:   369 C-RADTLTYNVILRGLSSEGRSEEALQMLDQWGSEGVHLNKGSYRIILNALCCNGELEKA 427

Query:   184 ARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISV 225
              + L   ++RG++P    H+   W+  V R+ E G YT I V
Sbjct:   428 VKFLSVMSERGIWP----HHA-TWNELVVRLCESG-YTEIGV 463

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2163041 AT5G41170 [Arabidopsis thaliana (taxid:3702)]

 Score = 224 (83.9 bits), Expect = 9.0e-18, P = 9.0e-18
 Identities = 55/208 (26%), Positives = 107/208 (51%)

Query:     2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTL 61
             G +++  ++L  M++  +  +  +FNA+I+AF + G+F +A + Y EM ++   PN  T 
Sbjct:   226 GRWRDADSLLRGMTKRKIKPDVITFNALIDAFVKEGKFLDAEELYNEMIRMSIAPNIFTY 285

Query:    62 EAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHT 121
              ++++ +C  G VDE+++ F  +++ G  P V+ Y  L+  + K  + DDA  +  EM  
Sbjct:   286 TSLINGFCMEGCVDEARQMFYLMETKGCFPDVVAYTSLINGFCKCKKVDDAMKIFYEMSQ 345

Query:   122 NRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRE 181
               ++        +I+G F       + + VF  +   G    +R YN LL  L   G  +
Sbjct:   346 KGLTGNTITYTTLIQG-FGQVGKPNVAQEVFSHMVSRGVPPNIRTYNVLLHCLCYNGKVK 404

Query:   182 RAARVLDEATKR---GLFPELFRHNKLV 206
             +A  + ++  KR   G+ P ++ +N L+
Sbjct:   405 KALMIFEDMQKREMDGVAPNIWTYNVLL 432

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2203916 AT1G62590 [Arabidopsis thaliana (taxid:3702)]

 Score = 213 (80.0 bits), Expect = 2.0e-16, P = 2.0e-16
 Identities = 58/206 (28%), Positives = 104/206 (50%)

Query:     2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTL 61
             G + +   +LS M E  +  N  +FNA+I+AF + G+F EA K Y +M K   DP+  T 
Sbjct:   309 GRWSDASQLLSDMIEKKINPNLVTFNALIDAFVKEGKFVEAEKLYDDMIKRSIDPDIFTY 368

Query:    62 EAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEM-H 120
              ++++ +C    +D++K+ F+ + S    P V+ Y  L+  + KS R +D   L  EM H
Sbjct:   369 NSLVNGFCMHDRLDKAKQMFEFMVSKDCFPDVVTYNTLIKGFCKSKRVEDGTELFREMSH 428

Query:   121 TNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR 180
                + +    T  +I+G F D  +    + VF ++  +G    +  Y+ LL+ L   G  
Sbjct:   429 RGLVGDTVTYT-TLIQGLFHD-GDCDNAQKVFKQMVSDGVPPDIMTYSILLDGLCNNGKL 486

Query:   181 ERAARVLDEATKRGLFPELFRHNKLV 206
             E+A  V D   K  +  +++ +  ++
Sbjct:   487 EKALEVFDYMQKSEIKLDIYIYTTMI 512

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2015494 RPF3 "RNA processing factor 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 211 (79.3 bits), Expect = 3.3e-16, P = 3.3e-16
 Identities = 55/205 (26%), Positives = 102/205 (49%)

Query:     2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTL 61
             G + +   +LS M E  +  N  +F+A+I+AF + G+  EA K Y EM K   DP+  T 
Sbjct:   304 GRWSDASRLLSDMIERKINPNVVTFSALIDAFVKEGKLVEAEKLYDEMIKRSIDPDIFTY 363

Query:    62 EAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHT 121
              ++++ +C    +DE+K  F+ + S    P+V+ Y  L+  + K+ R ++   L  EM  
Sbjct:   364 SSLINGFCMHDRLDEAKHMFELMISKDCFPNVVTYNTLIKGFCKAKRVEEGMELFREMSQ 423

Query:   122 NRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRE 181
               +         +I+G F    +  M + +F K+  +G    +  Y+ LL+ L   G  E
Sbjct:   424 RGLVGNTVTYNTLIQGLFQ-AGDCDMAQKIFKKMVSDGVPPDIITYSILLDGLCKYGKLE 482

Query:   182 RAARVLDEATKRGLFPELFRHNKLV 206
             +A  V +   K  + P+++ +N ++
Sbjct:   483 KALVVFEYLQKSKMEPDIYTYNIMI 507

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0006397 "mRNA processing" evidence=IMP

TAIR|locus:2031301 AT1G63400 [Arabidopsis thaliana (taxid:3702)]

 Score = 208 (78.3 bits), Expect = 5.9e-16, P = 5.9e-16
 Identities = 61/206 (29%), Positives = 102/206 (49%)

Query:     4 YKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEA 63
             + +   +LS M E  +  N  +FNA+I+AF + G+  EA K Y EM K   DP+  T  +
Sbjct:   311 WSDASRLLSDMIERKINPNVVTFNALIDAFVKEGKLVEAEKLYDEMIKRSIDPDIFTYSS 370

Query:    64 VLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEM-HTN 122
             +++ +C    +DE+K  F+ + S    P+V+ Y  L+  + K+ R D+   L  EM    
Sbjct:   371 LINGFCMHDRLDEAKHMFELMISKDCFPNVVTYNTLINGFCKAKRIDEGVELFREMSQRG 430

Query:   123 RISNIHQVTGQMIKGEFD--DESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR 180
              + N    T  +I G F   D  N QMV   F ++  +G    +  YN LL+ L   G  
Sbjct:   431 LVGNTVTYT-TLIHGFFQARDCDNAQMV---FKQMVSDGVHPNIMTYNTLLDGLCKNGKL 486

Query:   181 ERAARVLDEATKRGLFPELFRHNKLV 206
             E+A  V +   +  + P ++ +N ++
Sbjct:   487 EKAMVVFEYLQRSKMEPTIYTYNIMI 512

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 205 (77.2 bits), Expect = 2.7e-15, P = 2.7e-15
 Identities = 54/206 (26%), Positives = 97/206 (47%)

Query:     1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERT 60
             GG       IL++M    +  N  S++ VI+ F + GRF+EA+  + EM  +    +  +
Sbjct:   387 GGQMDLAFEILAQMPVKRIMPNVVSYSTVIDGFAKAGRFDEALNLFGEMRYLGIALDRVS 446

Query:    61 LEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMH 120
                +LS+Y   G  +E+ +  +E+ S GI   V+ Y  LL  Y K  ++D+   +  EM 
Sbjct:   447 YNTLLSIYTKVGRSEEALDILREMASVGIKKDVVTYNALLGGYGKQGKYDEVKKVFTEMK 506

Query:   121 TNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR 180
                +         +I G +     ++    +F +    G    +  Y+AL++AL   GL 
Sbjct:   507 REHVLPNLLTYSTLIDG-YSKGGLYKEAMEIFREFKSAGLRADVVLYSALIDALCKNGLV 565

Query:   181 ERAARVLDEATKRGLFPELFRHNKLV 206
               A  ++DE TK G+ P +  +N ++
Sbjct:   566 GSAVSLIDEMTKEGISPNVVTYNSII 591

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:2015228 AT1G63080 [Arabidopsis thaliana (taxid:3702)]

 Score = 197 (74.4 bits), Expect = 1.0e-14, P = 1.0e-14
 Identities = 56/203 (27%), Positives = 100/203 (49%)

Query:     2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTL 61
             G + +   +LS M E  +  N  +FN++I+AF + G+  EA K + EM +   DPN  T 
Sbjct:   289 GRWSDASRLLSDMLERKINPNVVTFNSLIDAFAKEGKLIEAEKLFDEMIQRSIDPNIVTY 348

Query:    62 EAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEM-H 120
              ++++ +C    +DE+++ F  + S   LP V+ Y  L+  + K+ +  D   L  +M  
Sbjct:   349 NSLINGFCMHDRLDEAQQIFTLMVSKDCLPDVVTYNTLINGFCKAKKVVDGMELFRDMSR 408

Query:   121 TNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR 180
                + N    T  +I G F   S+    + VF ++  +G    +  YN LL+ L   G  
Sbjct:   409 RGLVGNTVTYT-TLIHGFFQ-ASDCDNAQMVFKQMVSDGVHPNIMTYNTLLDGLCKNGKL 466

Query:   181 ERAARVLDEATKRGLFPELFRHN 203
             E+A  V +   K  + P+++ +N
Sbjct:   467 EKAMVVFEYLQKSKMEPDIYTYN 489

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 197 (74.4 bits), Expect = 1.1e-14, P = 1.1e-14
 Identities = 52/205 (25%), Positives = 100/205 (48%)

Query:     2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTL 61
             G + +   +LS M E  +  +  +F+A+I+AF + G+  EA K Y EM K   DP+  T 
Sbjct:   305 GRWSDASRLLSDMIERKINPDVFTFSALIDAFVKEGKLVEAEKLYDEMVKRSIDPSIVTY 364

Query:    62 EAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHT 121
              ++++ +C    +DE+K+ F+ + S    P V+ Y  L+  + K  R ++   +  EM  
Sbjct:   365 SSLINGFCMHDRLDEAKQMFEFMVSKHCFPDVVTYNTLIKGFCKYKRVEEGMEVFREMSQ 424

Query:   122 NRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRE 181
               +         +I+G F    +  M + +F ++  +G    +  YN LL+ L   G  E
Sbjct:   425 RGLVGNTVTYNILIQGLFQ-AGDCDMAQEIFKEMVSDGVPPNIMTYNTLLDGLCKNGKLE 483

Query:   182 RAARVLDEATKRGLFPELFRHNKLV 206
             +A  V +   +  + P ++ +N ++
Sbjct:   484 KAMVVFEYLQRSKMEPTIYTYNIMI 508

GO:0005739 "mitochondrion" evidence=ISM;IDA

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

GO:0003723 "RNA binding" evidence=IDA

TAIR|locus:2015208 AT1G63130 [Arabidopsis thaliana (taxid:3702)]

 Score = 193 (73.0 bits), Expect = 2.9e-14, P = 2.9e-14
 Identities = 56/206 (27%), Positives = 100/206 (48%)

Query:     2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTL 61
             G + +   +LS M E  +  N  +F+A+I+AF + G+  EA K Y EM K   DP+  T 
Sbjct:   305 GRWSDASRLLSDMIERKINPNVVTFSALIDAFVKEGKLVEAEKLYDEMIKRSIDPDIFTY 364

Query:    62 EAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEM-H 120
              ++++ +C    +DE+K  F+ + S    P+V+ Y  L+  + K+ R D+   L  EM  
Sbjct:   365 SSLINGFCMHDRLDEAKHMFELMISKDCFPNVVTYNTLIKGFCKAKRVDEGMELFREMSQ 424

Query:   121 TNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR 180
                + N    T  +I G F         + VF ++  +G    +  Y+ LL+ L   G  
Sbjct:   425 RGLVGNTVTYT-TLIHGFFQARE-CDNAQIVFKQMVSDGVLPDIMTYSILLDGLCNNGKV 482

Query:   181 ERAARVLDEATKRGLFPELFRHNKLV 206
             E A  V +   +  + P+++ +N ++
Sbjct:   483 ETALVVFEYLQRSKMEPDIYTYNIMI 508

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9S7Q2	PP124_ARATH	No assigned EC number	0.7327	0.9919	0.2853	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00016182001 SubName- Full=Chromosome chr17 scaffold_12, whole genome shotgun sequence; (869 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	248
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	4e-09
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	3e-07
pfam13041	50	pfam13041, PPR_2, PPR repeat family	7e-06
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	1e-05
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	3e-05
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	5e-05
pfam13041	50	pfam13041, PPR_2, PPR repeat family	1e-04
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	4e-04
pfam12854	34	pfam12854, PPR_1, PPR repeat	4e-04
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	0.002
pfam13041	50	pfam13041, PPR_2, PPR repeat family	0.002
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	0.002
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	0.002

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

 Score = 56.4 bits (136), Expect = 4e-09
 Identities = 46/181 (25%), Positives = 81/181 (44%), Gaps = 16/181 (8%)

Query: 21  RNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ 80
           +N  S+NA+I  +   GR  +A++ +  M      PN  T  AVLS   ++GL ++  E 
Sbjct: 389 KNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEI 448

Query: 81  FQEI-KSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQ--VTGQMIKG 137
           FQ + ++  I P  M Y  ++ +  +    D+AY ++         N+    +T   I  
Sbjct: 449 FQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHK 508

Query: 138 EFDDESNWQMVEYVFDKLNCEGYGLG---MRFYNALLEALWCLGLRERAARVLDEATKRG 194
                 N ++     +KL    YG+G   +  Y  LL      G +  AA+V++   ++G
Sbjct: 509 ------NLELGRLAAEKL----YGMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKG 558

Query: 195 L 195
           L
Sbjct: 559 L 559

Length = 697

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

 Score = 50.6 bits (121), Expect = 3e-07
 Identities = 51/209 (24%), Positives = 79/209 (37%), Gaps = 38/209 (18%)

Query: 26  FNAVIEAFRQGGRFEEAIKAYVEM--EKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQE 83
           FNA+I A  Q G  + A     EM  E    DP+  T+ A++     AG VD +KE +Q 
Sbjct: 545 FNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQM 604

Query: 84  IKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEM--------------------HTNR 123
           I    I  +   Y + +   ++   WD A  + D+M                    H   
Sbjct: 605 IHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGD 664

Query: 124 I----SNIHQVTGQMIK----------GEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNA 169
           +      +     Q IK          G   +  NW+    +++ +        +   NA
Sbjct: 665 LDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNA 724

Query: 170 LLEALWCLGLR-ERAARVLDEATKRGLFP 197
           L+ AL C G +  +A  VL E  + GL P
Sbjct: 725 LITAL-CEGNQLPKALEVLSEMKRLGLCP 752

Length = 1060

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

 Score = 42.0 bits (100), Expect = 7e-06
 Identities = 14/48 (29%), Positives = 27/48 (56%)

Query: 22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYC 69
          +  ++N +I+ + + G+ EEA+K + EM+K    PN  T   ++   C
Sbjct: 2  DVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLC 49

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

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

 Score = 45.6 bits (108), Expect = 1e-05
 Identities = 23/106 (21%), Positives = 49/106 (46%)

Query: 14  MSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGL 73
           + E  +    + +   + +  Q G ++ A+  Y +M+K    P+E    A++ V   AG 
Sbjct: 605 IHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGD 664

Query: 74  VDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEM 119
           +D++ E  Q+ +  GI    + Y  L+   + +  W  A  L +++
Sbjct: 665 LDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDI 710

Length = 1060

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

 Score = 44.5 bits (105), Expect = 3e-05
 Identities = 28/111 (25%), Positives = 56/111 (50%), Gaps = 4/111 (3%)

Query: 2   GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTL 61
           G + E + + SRM      +++ S+ A+I  + + G  ++A++ Y  ME+    P+E T+
Sbjct: 337 GSWGEAEKVFSRME----TKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITI 392

Query: 62  EAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDA 112
            +VLS     G +D   +  +  +  G++  V+    L+ +Y+K    D A
Sbjct: 393 ASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKA 443

Length = 857

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

 Score = 43.7 bits (103), Expect = 5e-05
 Identities = 27/118 (22%), Positives = 59/118 (50%), Gaps = 3/118 (2%)

Query: 10  ILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYC 69
           IL    + G+   + S+++++ A      +++A++ Y +++ ++  P   T+ A+++  C
Sbjct: 671 ILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALC 730

Query: 70  FAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNI 127
               + ++ E   E+K  G+ P+ + Y +LL     S R DDA   LD +   +   I
Sbjct: 731 EGNQLPKALEVLSEMKRLGLCPNTITYSILLVA---SERKDDADVGLDLLSQAKEDGI 785

Length = 1060

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

 Score = 38.5 bits (91), Expect = 1e-04
 Identities = 11/35 (31%), Positives = 17/35 (48%)

Query: 91  PSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRIS 125
           P V+ Y  L+  Y K  + ++A  L +EM    I 
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIK 35

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

 Score = 41.0 bits (96), Expect = 4e-04
 Identities = 26/125 (20%), Positives = 56/125 (44%), Gaps = 5/125 (4%)

Query: 2   GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTL 61
           G  ++ + +   M E        ++N+++  +   G  EEA+  Y EM       ++ T 
Sbjct: 273 GDIEDARCVFDGMPEKTTV----AWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTF 328

Query: 62  EAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEM-H 120
             ++ ++    L++ +K+    +  +G    ++    L+ +Y+K  R +DA  + D M  
Sbjct: 329 SIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPR 388

Query: 121 TNRIS 125
            N IS
Sbjct: 389 KNLIS 393

Length = 697

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

 Score = 36.6 bits (86), Expect = 4e-04
 Identities = 13/33 (39%), Positives = 19/33 (57%)

Query: 87  SGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEM 119
            G+ P V+ Y  L+    ++ R D+A  LLDEM
Sbjct: 1   KGLKPDVVTYNTLIDGLCRAGRVDEAVELLDEM 33

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

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

 Score = 39.1 bits (91), Expect = 0.002
 Identities = 22/113 (19%), Positives = 48/113 (42%)

Query: 9   AILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVY 68
           +I   M + GV  +   F+A+++     G  ++A +   +  K        +  +++   
Sbjct: 635 SIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGAC 694

Query: 69  CFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHT 121
             A    ++ E +++IKS  + P+V     L+    + N+   A  +L EM  
Sbjct: 695 SNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKR 747

Length = 1060

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

 Score = 34.7 bits (81), Expect = 0.002
 Identities = 17/50 (34%), Positives = 27/50 (54%)

Query: 56  PNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAK 105
           P+  T   ++  YC  G V+E+ + F E+K  GI P+V  Y +L+    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 = 38.7 bits (90), Expect = 0.002
 Identities = 19/96 (19%), Positives = 49/96 (51%), Gaps = 1/96 (1%)

Query: 25  SFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEI 84
           S+N ++  +   G+   A++ +  M +   +P+E T  ++L     +G+V +  E F  +
Sbjct: 556 SWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSM 615

Query: 85  KSS-GILPSVMCYCMLLAVYAKSNRWDDAYGLLDEM 119
           +    I P++  Y  ++ +  ++ +  +AY  +++M
Sbjct: 616 EEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKM 651

Length = 857

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

 Score = 35.1 bits (82), Expect = 0.002
 Identities = 10/34 (29%), Positives = 22/34 (64%)

Query: 25 SFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNE 58
          ++N +I+   + GR EEA++ + EM++   +P+ 
Sbjct: 2  TYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	248
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.8
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.76
PF13041	50	PPR_2: PPR repeat family	99.67
PF13041	50	PPR_2: PPR repeat family	99.64
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.63
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.6
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.59
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.58
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.53
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.42
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.42
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.41
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.38
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.38
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.37
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.36
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.36
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.34
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.33
PRK12370	553	invasion protein regulator; Provisional	99.23
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.22
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.2
PF12854	34	PPR_1: PPR repeat	99.19
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.18
PF12854	34	PPR_1: PPR repeat	99.18
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.16
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.12
PRK12370	553	invasion protein regulator; Provisional	99.12
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.12
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.11
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.06
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.02
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.01
KOG1126	638	consensus DNA-binding cell division cycle control	98.96
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	98.96
PRK14574	822	hmsH outer membrane protein; Provisional	98.93
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	98.93
PRK14574	822	hmsH outer membrane protein; Provisional	98.92
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	98.91
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	98.87
KOG2003	840	consensus TPR repeat-containing protein [General f	98.86
KOG1126	638	consensus DNA-binding cell division cycle control	98.86
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.8
PRK11189	296	lipoprotein NlpI; Provisional	98.77
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.76
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.76
PRK11189	296	lipoprotein NlpI; Provisional	98.73
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.73
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.72
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	98.72
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	98.7
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.69
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	98.68
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.66
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	98.65
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.62
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	98.62
KOG2003	840	consensus TPR repeat-containing protein [General f	98.61
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.56
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	98.53
KOG1129	478	consensus TPR repeat-containing protein [General f	98.53
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	98.53
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	98.51
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.49
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	98.48
KOG2076	895	consensus RNA polymerase III transcription factor	98.48
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.47
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.46
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	98.46
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.44
KOG1129	478	consensus TPR repeat-containing protein [General f	98.44
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.43
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.41
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.39
KOG0547	606	consensus Translocase of outer mitochondrial membr	98.39
PRK15359	144	type III secretion system chaperone protein SscB;	98.36
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.34
KOG0495	913	consensus HAT repeat protein [RNA processing and m	98.29
KOG0547	606	consensus Translocase of outer mitochondrial membr	98.29
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.28
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.26
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.25
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	98.24
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	98.23
KOG0495	913	consensus HAT repeat protein [RNA processing and m	98.23
KOG2076	895	consensus RNA polymerase III transcription factor	98.22
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.21
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.14
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.13
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.12
KOG4340	459	consensus Uncharacterized conserved protein [Funct	98.12
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.06
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.04
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.04
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.01
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.0
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.0
PRK15359	144	type III secretion system chaperone protein SscB;	97.99
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	97.99
COG4783	484	Putative Zn-dependent protease, contains TPR repea	97.97
COG4783	484	Putative Zn-dependent protease, contains TPR repea	97.95
PRK04841	903	transcriptional regulator MalT; Provisional	97.95
KOG1915	677	consensus Cell cycle control protein (crooked neck	97.95
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	97.95
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.93
KOG1915	677	consensus Cell cycle control protein (crooked neck	97.91
KOG4340	459	consensus Uncharacterized conserved protein [Funct	97.89
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.87
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.86
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	97.86
KOG2376	652	consensus Signal recognition particle, subunit Srp	97.85
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.85
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	97.82
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.81
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	97.79
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	97.77
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.72
KOG3060	289	consensus Uncharacterized conserved protein [Funct	97.69
PRK04841	903	transcriptional regulator MalT; Provisional	97.67
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	97.67
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.66
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.66
PRK14720	906	transcript cleavage factor/unknown domain fusion p	97.62
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.61
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.59
KOG1128	777	consensus Uncharacterized conserved protein, conta	97.57
KOG3616	1636	consensus Selective LIM binding factor [Transcript	97.56
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.54
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.52
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.52
KOG1125	579	consensus TPR repeat-containing protein [General f	97.51
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.47
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.46
KOG3941	406	consensus Intermediate in Toll signal transduction	97.43
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.43
PLN02789	320	farnesyltranstransferase	97.41
PRK14720	906	transcript cleavage factor/unknown domain fusion p	97.36
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.36
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	97.35
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.31
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	97.31
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.28
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.21
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.21
KOG2376	652	consensus Signal recognition particle, subunit Srp	97.2
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	97.2
KOG3941	406	consensus Intermediate in Toll signal transduction	97.18
KOG3785	557	consensus Uncharacterized conserved protein [Funct	97.13
PRK10803	263	tol-pal system protein YbgF; Provisional	97.09
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.08
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	97.07
KOG2047	835	consensus mRNA splicing factor [RNA processing and	97.06
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	97.04
KOG3060	289	consensus Uncharacterized conserved protein [Funct	97.03
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.02
KOG2796	366	consensus Uncharacterized conserved protein [Funct	97.0
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	96.99
KOG3616	1636	consensus Selective LIM binding factor [Transcript	96.97
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	96.97
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	96.96
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	96.94
KOG1125	579	consensus TPR repeat-containing protein [General f	96.93
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	96.93
KOG2047	835	consensus mRNA splicing factor [RNA processing and	96.92
PF03704	146	BTAD: Bacterial transcriptional activator domain;	96.9
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	96.89
PLN02789	320	farnesyltranstransferase	96.83
PF12688	120	TPR_5: Tetratrico peptide repeat	96.82
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	96.82
KOG3785	557	consensus Uncharacterized conserved protein [Funct	96.77
PF12688	120	TPR_5: Tetratrico peptide repeat	96.74
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	96.73
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	96.71
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	96.64
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	96.63
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	96.61
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	96.58
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	96.52
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	96.49
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	96.49
PF13371	73	TPR_9: Tetratricopeptide repeat	96.45
PF13371	73	TPR_9: Tetratricopeptide repeat	96.42
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	96.33
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	96.32
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.31
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.3
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	96.28
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	96.26
KOG0553	304	consensus TPR repeat-containing protein [General f	96.21
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	96.14
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	96.05
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	96.0
PRK10803	263	tol-pal system protein YbgF; Provisional	95.98
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	95.96
KOG0553	304	consensus TPR repeat-containing protein [General f	95.88
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	95.85
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	95.79
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	95.77
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	95.6
KOG2796	366	consensus Uncharacterized conserved protein [Funct	95.53
COG3629	280	DnrI DNA-binding transcriptional activator of the	95.51
KOG2041	1189	consensus WD40 repeat protein [General function pr	95.47
KOG4570	418	consensus Uncharacterized conserved protein [Funct	95.4
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	95.36
PRK15331	165	chaperone protein SicA; Provisional	95.29
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	95.22
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	95.1
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	95.02
smart00299	140	CLH Clathrin heavy chain repeat homology.	94.98
smart00299	140	CLH Clathrin heavy chain repeat homology.	94.95
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	94.91
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	94.91
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	94.88
KOG4570	418	consensus Uncharacterized conserved protein [Funct	94.84
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	94.7
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	94.66
PRK15331	165	chaperone protein SicA; Provisional	94.32
PF13762	145	MNE1: Mitochondrial splicing apparatus component	94.31
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	94.24
COG3629	280	DnrI DNA-binding transcriptional activator of the	94.24
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	94.17
PF13512	142	TPR_18: Tetratricopeptide repeat	94.13
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	94.1
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	94.06
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	93.94
COG4105	254	ComL DNA uptake lipoprotein [General function pred	93.74
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	93.73
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	93.64
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	93.44
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	93.42
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	93.4
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	93.4
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	93.38
PF13929	292	mRNA_stabil: mRNA stabilisation	93.28
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	93.01
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	93.0
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	92.87
KOG4555	175	consensus TPR repeat-containing protein [Function	92.82
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	92.78
PF13929	292	mRNA_stabil: mRNA stabilisation	92.75
COG4700	251	Uncharacterized protein conserved in bacteria cont	92.71
PF07163	309	Pex26: Pex26 protein; InterPro: IPR010797 This fam	92.69
PF13428	44	TPR_14: Tetratricopeptide repeat	92.68
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	92.68
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	92.66
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	92.63
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	92.56
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	92.52
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	92.46
PF13512	142	TPR_18: Tetratricopeptide repeat	92.38
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	92.19
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	91.9
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	91.77
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	91.76
COG4700	251	Uncharacterized protein conserved in bacteria cont	91.16
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	91.15
KOG1550	552	consensus Extracellular protein SEL-1 and related	91.1
KOG2610	491	consensus Uncharacterized conserved protein [Funct	91.09
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	90.61
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	90.48
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	90.0
PF13428	44	TPR_14: Tetratricopeptide repeat	89.95
KOG2610	491	consensus Uncharacterized conserved protein [Funct	89.92
KOG4555	175	consensus TPR repeat-containing protein [Function	89.72
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	89.71
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	89.36
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	89.05
PF11848	48	DUF3368: Domain of unknown function (DUF3368); Int	88.99
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	88.91
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	88.84
KOG4077	149	consensus Cytochrome c oxidase, subunit Va/COX6 [E	88.58
COG3898	531	Uncharacterized membrane-bound protein [Function u	88.27
PF04097	613	Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic9	87.97
PF11848	48	DUF3368: Domain of unknown function (DUF3368); Int	87.87
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	87.49
PF13762	145	MNE1: Mitochondrial splicing apparatus component	87.44
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	87.12
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	87.09
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	87.02
COG3118	304	Thioredoxin domain-containing protein [Posttransla	86.9
COG1747	711	Uncharacterized N-terminal domain of the transcrip	86.83
PHA02875	413	ankyrin repeat protein; Provisional	86.2
COG3947	361	Response regulator containing CheY-like receiver a	84.65
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	84.63
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	84.34
COG4105	254	ComL DNA uptake lipoprotein [General function pred	83.97
COG4455	273	ImpE Protein of avirulence locus involved in tempe	83.76
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	83.54
PF11846	193	DUF3366: Domain of unknown function (DUF3366); Int	83.44
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	83.39
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	83.37
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	83.16
COG4455	273	ImpE Protein of avirulence locus involved in tempe	83.01
PF11846	193	DUF3366: Domain of unknown function (DUF3366); Int	82.87
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	81.79
PF11663	140	Toxin_YhaV: Toxin with endonuclease activity YhaV;	81.78
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	81.57
cd00280	200	TRFH Telomeric Repeat binding Factor or TTAGGG Rep	81.35
cd00280	200	TRFH Telomeric Repeat binding Factor or TTAGGG Rep	81.25
PF13431	34	TPR_17: Tetratricopeptide repeat	81.18
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	80.24
PF07163	309	Pex26: Pex26 protein; InterPro: IPR010797 This fam	80.17

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=1.1e-45  Score=322.29  Aligned_cols=237  Identities=20%  Similarity=0.261  Sum_probs=136.9

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHH--cCCCCCHHHHHHHHHHHHhcCChhHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEK--VRCDPNERTLEAVLSVYCFAGLVDESKE   79 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~--~~~~p~~~t~~~ll~~~~~~g~~~~a~~   79 (248)
                      |++++|.++|++|.+.|+.||..+||++|.+|++.|++++|.++|++|.+  .|+.||..||+++|.+|++.|++++|.+
T Consensus       521 G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~e  600 (1060)
T PLN03218        521 GQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKE  600 (1060)
T ss_pred             cCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHH
Confidence            44445555555555445555555555555555555555555555555533  3445555555555555555555555555


Q ss_pred             HHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcC
Q 039342           80 QFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEG  159 (248)
Q Consensus        80 ~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~  159 (248)
                      +|++|.+.|+.|+..+|+++|.+|++.|++++|.++|++|.+.|+.|+..+|+.++.+ +.+.|+++.|.+++++|.+.|
T Consensus       601 lf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a-~~k~G~~eeA~~l~~eM~k~G  679 (1060)
T PLN03218        601 VYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDV-AGHAGDLDKAFEILQDARKQG  679 (1060)
T ss_pred             HHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH-HHhCCCHHHHHHHHHHHHHcC
Confidence            5555555555555555555555555555555555555555555555555555555555 445555566666666666666


Q ss_pred             CCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHHHcCCC
Q 039342          160 YGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGED  239 (248)
Q Consensus       160 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~~~~~~  239 (248)
                      +.||..+|+++|.+|++.|++++|.++|++|.+.|+.||..+|+.+|     .+|++.|++++|.+++++|++.|+.|+.
T Consensus       680 ~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI-----~gy~k~G~~eeAlelf~eM~~~Gi~Pd~  754 (1060)
T PLN03218        680 IKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALI-----TALCEGNQLPKALEVLSEMKRLGLCPNT  754 (1060)
T ss_pred             CCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHH-----HHHHHCCCHHHHHHHHHHHHHcCCCCCH
Confidence            66666666666666666666666666666666666666666666666     6667777777777777777777777766


Q ss_pred             CCccc
Q 039342          240 LPQLA  244 (248)
Q Consensus       240 ~~~~~  244 (248)
                      .++..
T Consensus       755 ~Ty~s  759 (1060)
T PLN03218        755 ITYSI  759 (1060)
T ss_pred             HHHHH
Confidence            65543

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=2.1e-45  Score=320.48  Aligned_cols=235  Identities=18%  Similarity=0.285  Sum_probs=147.2

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|.++|++|.+.|+.||..+|+++|.+|++.|++++|.++|++|.+.|+.||..||+.+|.+|++.|++++|.++|
T Consensus       486 G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf  565 (1060)
T PLN03218        486 GKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVL  565 (1060)
T ss_pred             cCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            55566666666666666666666666666666666666666666666666666666666666666666666666666666


Q ss_pred             HHHHH--CCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcC
Q 039342           82 QEIKS--SGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEG  159 (248)
Q Consensus        82 ~~m~~--~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~  159 (248)
                      ++|.+  .|+.||..+|+++|.+|++.|++++|.++|++|.+.|+.|+..+|+.++.+ |.+.|++++|..+|++|.+.|
T Consensus       566 ~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~a-y~k~G~~deAl~lf~eM~~~G  644 (1060)
T PLN03218        566 AEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNS-CSQKGDWDFALSIYDDMKKKG  644 (1060)
T ss_pred             HHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHH-HHhcCCHHHHHHHHHHHHHcC
Confidence            66653  455566666666666666666666666666666666666666666666655 455556666666666666666


Q ss_pred             CCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHHHcCCC
Q 039342          160 YGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGED  239 (248)
Q Consensus       160 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~~~~~~  239 (248)
                      +.||..+|+++|++|++.|++++|.+++++|.+.|+.||..+|+.++     .+|++.|++++|.++|++|.+.|+.|+.
T Consensus       645 v~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~~pd~~tynsLI-----~ay~k~G~~eeA~~lf~eM~~~g~~Pdv  719 (1060)
T PLN03218        645 VKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLM-----GACSNAKNWKKALELYEDIKSIKLRPTV  719 (1060)
T ss_pred             CCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHH-----HHHHhCCCHHHHHHHHHHHHHcCCCCCH
Confidence            66666666666666666666666666666666666666666666666     6666667777777777777666666655


Q ss_pred             CCc
Q 039342          240 LPQ  242 (248)
Q Consensus       240 ~~~  242 (248)
                      .++
T Consensus       720 vty  722 (1060)
T PLN03218        720 STM  722 (1060)
T ss_pred             HHH
Confidence            444

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

Probab=100.00  E-value=7.3e-41  Score=287.77  Aligned_cols=216  Identities=17%  Similarity=0.299  Sum_probs=190.3

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      +|++++|.++|++|.+    +|+.+||++|.+|++.|++++|+++|++|.+.|+.||..||+++|.+|++.|++++|.++
T Consensus       272 ~g~~~~A~~vf~~m~~----~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i  347 (697)
T PLN03081        272 CGDIEDARCVFDGMPE----KTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQA  347 (697)
T ss_pred             CCCHHHHHHHHHhCCC----CChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccchHHHHHH
Confidence            5888999999998864    788899999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCC
Q 039342           81 FQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGY  160 (248)
Q Consensus        81 ~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~  160 (248)
                      +++|.+.|+.||..+|++||++|++.|++++|.++|++|.+    |+..+|+.++.+ |.+.|+.++|.++|++|.+.|+
T Consensus       348 ~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~----~d~~t~n~lI~~-y~~~G~~~~A~~lf~~M~~~g~  422 (697)
T PLN03081        348 HAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPR----KNLISWNALIAG-YGNHGRGTKAVEMFERMIAEGV  422 (697)
T ss_pred             HHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCC----CCeeeHHHHHHH-HHHcCCHHHHHHHHHHHHHhCC
Confidence            99999999999999999999999999999999999998853    677888888888 7788888999999999998899


Q ss_pred             CCCHHHHHHHHHHHHhcCchHHHHHHHHHHHH-CCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHH
Q 039342          161 GLGMRFYNALLEALWCLGLRERAARVLDEATK-RGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKM  230 (248)
Q Consensus       161 ~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m  230 (248)
                      .||..||+++|.+|++.|.+++|.++|+.|.+ .|+.|+..+|+.++     .+|++.|++++|.+++++|
T Consensus       423 ~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li-----~~l~r~G~~~eA~~~~~~~  488 (697)
T PLN03081        423 APNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMI-----ELLGREGLLDEAYAMIRRA  488 (697)
T ss_pred             CCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHH-----HHHHhcCCHHHHHHHHHHC
Confidence            99999999999999999999999999999875 68899988888888     7888888888888877654

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

Probab=100.00  E-value=2.2e-40  Score=284.79  Aligned_cols=173  Identities=17%  Similarity=0.186  Sum_probs=91.4

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccc
Q 039342           60 TLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEF  139 (248)
Q Consensus        60 t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~  139 (248)
                      +|++||.+|++.|++++|.++|++|.+    +|..+||+||.+|++.|++++|+++|++|.+.|+.|+..||+.++.+ |
T Consensus       261 ~~n~Li~~y~k~g~~~~A~~vf~~m~~----~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a-~  335 (697)
T PLN03081        261 VSCALIDMYSKCGDIEDARCVFDGMPE----KTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRI-F  335 (697)
T ss_pred             eHHHHHHHHHHCCCHHHHHHHHHhCCC----CChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH-H
Confidence            334444555555555555555555532    34555555555555555555555555555555555555555555555 4


Q ss_pred             cccchHHHHHHHHHHHHhcCCCC-------------------------------CHHHHHHHHHHHHhcCchHHHHHHHH
Q 039342          140 DDESNWQMVEYVFDKLNCEGYGL-------------------------------GMRFYNALLEALWCLGLRERAARVLD  188 (248)
Q Consensus       140 ~~~~~~~~a~~~~~~m~~~~~~p-------------------------------~~~~~~~li~~~~~~g~~~~a~~~~~  188 (248)
                      .+.+.++.+.+++..|.+.|+.|                               |..+||++|.+|++.|+.++|.++|+
T Consensus       336 ~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~~d~~t~n~lI~~y~~~G~~~~A~~lf~  415 (697)
T PLN03081        336 SRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFE  415 (697)
T ss_pred             HhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHcCCHHHHHHHHH
Confidence            44444555555555555555444                               44455555555555555555555555


Q ss_pred             HHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHH-HHHcCCCCCc
Q 039342          189 EATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYE-MFMMGEDLPQ  242 (248)
Q Consensus       189 ~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~-~~~~~~~~~~  242 (248)
                      +|.+.|+.||..||+.++     .+|++.|.++++.++|+.|.+ .|+.|+..+|
T Consensus       416 ~M~~~g~~Pd~~T~~~ll-----~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y  465 (697)
T PLN03081        416 RMIAEGVAPNHVTFLAVL-----SACRYSGLSEQGWEIFQSMSENHRIKPRAMHY  465 (697)
T ss_pred             HHHHhCCCCCHHHHHHHH-----HHHhcCCcHHHHHHHHHHHHHhcCCCCCccch
Confidence            555555555555555555     455555555555555555543 3555544443

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=7.8e-40  Score=287.24  Aligned_cols=241  Identities=14%  Similarity=0.127  Sum_probs=204.7

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      +|++++|+++|.+|.+.|+.||..||+++|.+|++.|+.+.+.+++..|.+.|+.||..+||++|.+|++.|++++|.++
T Consensus       266 ~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~v  345 (857)
T PLN03077        266 NGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKV  345 (857)
T ss_pred             CCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHH
Confidence            47788888888888888888888888888888888888888888888888888888888888888888888888888888


Q ss_pred             HHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCC
Q 039342           81 FQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGY  160 (248)
Q Consensus        81 ~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~  160 (248)
                      |++|.    .||..+||++|.+|++.|++++|+++|++|.+.|+.|+..+|..++.+ +...|+++.+.++++.|.+.|+
T Consensus       346 f~~m~----~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a-~~~~g~~~~a~~l~~~~~~~g~  420 (857)
T PLN03077        346 FSRME----TKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSA-CACLGDLDVGVKLHELAERKGL  420 (857)
T ss_pred             HhhCC----CCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHH-HhccchHHHHHHHHHHHHHhCC
Confidence            88886    368888999999999999999999999999999999999999999987 7788888999999999999999


Q ss_pred             CCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHC------------------------------CCCCCcchhhhHH----
Q 039342          161 GLGMRFYNALLEALWCLGLRERAARVLDEATKR------------------------------GLFPELFRHNKLV----  206 (248)
Q Consensus       161 ~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~------------------------------g~~p~~~t~~~li----  206 (248)
                      .|+..+||++|++|++.|++++|.++|++|.+.                              ++.||..||+.++    
T Consensus       421 ~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~~~~pd~~t~~~lL~a~~  500 (857)
T PLN03077        421 ISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLTLKPNSVTLIAALSACA  500 (857)
T ss_pred             CcchHHHHHHHHHHHHcCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHCCCHHHHHHHHHHHHhCCCCCHhHHHHHHHHHh
Confidence            888888888888888888888888887776542                              4567766666554    


Q ss_pred             --------------------------------------------------------hhhhhhccccchHHHHHHHHHHHH
Q 039342          207 --------------------------------------------------------WSVDVHRMWEGGAYTAISVWLNKM  230 (248)
Q Consensus       207 --------------------------------------------------------~~~~~~~~~~~g~~~~~~~~~~~m  230 (248)
                                                                              |+.++.+|++.|+.++|.++|++|
T Consensus       501 ~~g~l~~~~~i~~~~~~~g~~~~~~~~naLi~~y~k~G~~~~A~~~f~~~~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M  580 (857)
T PLN03077        501 RIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSHEKDVVSWNILLTGYVAHGKGSMAVELFNRM  580 (857)
T ss_pred             hhchHHHhHHHHHHHHHhCCCccceechHHHHHHHHcCCHHHHHHHHHhcCCChhhHHHHHHHHHHcCCHHHHHHHHHHH
Confidence                                                                    455668888999999999999999


Q ss_pred             HHHHHcCCCCCccccc
Q 039342          231 YEMFMMGEDLPQLATV  246 (248)
Q Consensus       231 ~~~~~~~~~~~~~~~i  246 (248)
                      .+.|+.||..|+...|
T Consensus       581 ~~~g~~Pd~~T~~~ll  596 (857)
T PLN03077        581 VESGVNPDEVTFISLL  596 (857)
T ss_pred             HHcCCCCCcccHHHHH
Confidence            9999999998886543

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=4.3e-39  Score=282.60  Aligned_cols=230  Identities=11%  Similarity=0.159  Sum_probs=186.6

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|+++|++|...|+.||..||+++|.+|++.+++..+.+++..|.+.|+.||..+||++|.+|++.|+++.|.++|
T Consensus       166 g~~~~A~~~f~~M~~~g~~Pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf  245 (857)
T PLN03077        166 GYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVF  245 (857)
T ss_pred             CCHHHHHHHHHHHHHcCCCCChhHHHHHHHHhCCccchhhHHHHHHHHHHcCCCcccchHhHHHHHHhcCCCHHHHHHHH
Confidence            56666777777776666667766666666666666666666666666666666677777777778888888888888888


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCC
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYG  161 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~  161 (248)
                      ++|.+    ||..+||++|.+|++.|++++|+++|++|.+.|+.|+..+|+.++.+ +...++++.+.+++..|.+.|+.
T Consensus       246 ~~m~~----~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a-~~~~g~~~~a~~l~~~~~~~g~~  320 (857)
T PLN03077        246 DRMPR----RDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISA-CELLGDERLGREMHGYVVKTGFA  320 (857)
T ss_pred             hcCCC----CCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHH-HHhcCChHHHHHHHHHHHHhCCc
Confidence            88763    67788888888888888888888888888888888998899888888 67778888888888888888888


Q ss_pred             CCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHHHcCCCCC
Q 039342          162 LGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDLP  241 (248)
Q Consensus       162 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~~~~~~~~  241 (248)
                      ||..+||++|.+|++.|++++|.++|++|.    .||..+|+.++     .+|++.|++++|.++|++|++.|+.|+..+
T Consensus       321 ~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~----~~d~~s~n~li-----~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t  391 (857)
T PLN03077        321 VDVSVCNSLIQMYLSLGSWGEAEKVFSRME----TKDAVSWTAMI-----SGYEKNGLPDKALETYALMEQDNVSPDEIT  391 (857)
T ss_pred             cchHHHHHHHHHHHhcCCHHHHHHHHhhCC----CCCeeeHHHHH-----HHHHhCCCHHHHHHHHHHHHHhCCCCCcee
Confidence            888888888888888888888888888885    47788888888     888999999999999999999999998887


Q ss_pred             cccc
Q 039342          242 QLAT  245 (248)
Q Consensus       242 ~~~~  245 (248)
                      +...
T Consensus       392 ~~~l  395 (857)
T PLN03077        392 IASV  395 (857)
T ss_pred             HHHH
Confidence            7554

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.80  E-value=6.3e-17  Score=131.12  Aligned_cols=230  Identities=14%  Similarity=0.134  Sum_probs=167.1

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH----HHHHHHHHHHHhcCChhHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNE----RTLEAVLSVYCFAGLVDES   77 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~----~t~~~ll~~~~~~g~~~~a   77 (248)
                      |++++|+++|+++.+.. +++..+++.+...+.+.|++++|.+.++.+.+.+-.++.    ..+..+...+.+.|++++|
T Consensus       121 g~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A  199 (389)
T PRK11788        121 GLLDRAEELFLQLVDEG-DFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDLDAA  199 (389)
T ss_pred             CCHHHHHHHHHHHHcCC-cchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCHHHH
Confidence            67788888888887642 245677888888888888888888888888765433221    2345566677788888888


Q ss_pred             HHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHh
Q 039342           78 KEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNC  157 (248)
Q Consensus        78 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  157 (248)
                      ...|+++.+.. +.+...+..+...+.+.|++++|.++|+++.+.+......++..+... +...|+++.|...++.+.+
T Consensus       200 ~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~-~~~~g~~~~A~~~l~~~~~  277 (389)
T PRK11788        200 RALLKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMEC-YQALGDEAEGLEFLRRALE  277 (389)
T ss_pred             HHHHHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHH-HHHcCCHHHHHHHHHHHHH
Confidence            88888887653 224567777888888888899999888888765422223344455444 6677888999998888877


Q ss_pred             cCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHHHcC
Q 039342          158 EGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMG  237 (248)
Q Consensus       158 ~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~~~~  237 (248)
                      ..  |+...+..+...+.+.|++++|..+++++.+.  .|+..+++.++...+.  ....|+.+++..++++|.+.++.|
T Consensus       278 ~~--p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~--~P~~~~~~~l~~~~~~--~~~~g~~~~a~~~~~~~~~~~~~~  351 (389)
T PRK11788        278 EY--PGADLLLALAQLLEEQEGPEAAQALLREQLRR--HPSLRGFHRLLDYHLA--EAEEGRAKESLLLLRDLVGEQLKR  351 (389)
T ss_pred             hC--CCchHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CcCHHHHHHHHHHhhh--ccCCccchhHHHHHHHHHHHHHhC
Confidence            63  56666788888999999999999999988765  6887777776632221  122567888888999999998888


Q ss_pred             CCC
Q 039342          238 EDL  240 (248)
Q Consensus       238 ~~~  240 (248)
                      ++.
T Consensus       352 ~p~  354 (389)
T PRK11788        352 KPR  354 (389)
T ss_pred             CCC
Confidence            665

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.76  E-value=5.5e-16  Score=125.63  Aligned_cols=223  Identities=14%  Similarity=0.135  Sum_probs=107.5

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHHHhcCChhHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN---ERTLEAVLSVYCFAGLVDESK   78 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~---~~t~~~ll~~~~~~g~~~~a~   78 (248)
                      |++++|.+.|.++.+.+. .+..+|..+...+...|++++|..+++.+.+.+..++   ...+..+...|.+.|++++|.
T Consensus        49 ~~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g~~~~A~  127 (389)
T PRK11788         49 EQPDKAIDLFIEMLKVDP-ETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAGLLDRAE  127 (389)
T ss_pred             CChHHHHHHHHHHHhcCc-ccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCCHHHHH
Confidence            445555555555554321 2334455555555555555555555555544321111   123444444555555555555


Q ss_pred             HHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC---------------------------------
Q 039342           79 EQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRIS---------------------------------  125 (248)
Q Consensus        79 ~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~---------------------------------  125 (248)
                      .+|+++.+.. +++..+++.+...+.+.|++++|.+.++.+.+.+..                                 
T Consensus       128 ~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a  206 (389)
T PRK11788        128 ELFLQLVDEG-DFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDLDAARALLKKA  206 (389)
T ss_pred             HHHHHHHcCC-cchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence            5555544321 123344444444444445555554444444433211                                 


Q ss_pred             ----chHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcch
Q 039342          126 ----NIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFR  201 (248)
Q Consensus       126 ----~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t  201 (248)
                          |+.......+...+...|+++.|..+++++.+.+......+++.+..+|...|++++|...++++.+.  .|+...
T Consensus       207 l~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~--~p~~~~  284 (389)
T PRK11788        207 LAADPQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRALEE--YPGADL  284 (389)
T ss_pred             HhHCcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCchH
Confidence                22221112222224445556666666666555432222345556666666666666666666666553  344433


Q ss_pred             hhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          202 HNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       202 ~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      +..+.     ..+.+.|++++|.++++++.+.
T Consensus       285 ~~~la-----~~~~~~g~~~~A~~~l~~~l~~  311 (389)
T PRK11788        285 LLALA-----QLLEEQEGPEAAQALLREQLRR  311 (389)
T ss_pred             HHHHH-----HHHHHhCCHHHHHHHHHHHHHh
Confidence            33333     5556666777777766666554

>PF13041 PPR_2: PPR repeat family

Probab=99.67  E-value=2.4e-16  Score=88.64  Aligned_cols=50  Identities=28%  Similarity=0.559  Sum_probs=35.9

Q ss_pred             CCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 039342           21 RNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCF   70 (248)
Q Consensus        21 ~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~   70 (248)
                      ||+.+||++|++|++.|++++|.++|++|++.|++||..||+++|++|++
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            66777777777777777777777777777777777777777777777654

>PF13041 PPR_2: PPR repeat family

Probab=99.64  E-value=7.9e-16  Score=86.49  Aligned_cols=50  Identities=34%  Similarity=0.596  Sum_probs=47.7

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHh
Q 039342           56 PNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAK  105 (248)
Q Consensus        56 p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~  105 (248)
                      ||..+||++|++|++.|++++|.++|++|.+.|+.||..||+++|++|++
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            89999999999999999999999999999999999999999999999975

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

Probab=99.63  E-value=2.3e-13  Score=120.99  Aligned_cols=217  Identities=14%  Similarity=0.054  Sum_probs=109.1

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|.++|+++.+.. +.+..++..+...+...|++++|.++++.+.+.+ +++...+..+...+.+.|++++|.+.|
T Consensus       649 ~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~  726 (899)
T TIGR02917       649 KNYAKAITSLKRALELK-PDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQH-PKAALGFELEGDLYLRQKDYPAAIQAY  726 (899)
T ss_pred             CCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCChHHHHHHHHHHHHCCCHHHHHHHH
Confidence            55666666666665432 1235556666666666666666666666655443 334445555555555555555555555


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCC
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYG  161 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~  161 (248)
                      +.+.+.+  |+..++..+...+.+.|++++|...++++.+..  |+.......+...+...|+++.|...|+.+.+... 
T Consensus       727 ~~~~~~~--~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~--~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p-  801 (899)
T TIGR02917       727 RKALKRA--PSSQNAIKLHRALLASGNTAEAVKTLEAWLKTH--PNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKAP-  801 (899)
T ss_pred             HHHHhhC--CCchHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhCC-
Confidence            5555432  333444445555555555555555555544432  22222222222223444444555555544444321 


Q ss_pred             CCHH---------------------------------HHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhh
Q 039342          162 LGMR---------------------------------FYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWS  208 (248)
Q Consensus       162 p~~~---------------------------------~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~  208 (248)
                      ++..                                 ++..+...+...|++++|.++++++.+.+-. +..++..+.  
T Consensus       802 ~~~~~~~~l~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~-~~~~~~~l~--  878 (899)
T TIGR02917       802 DNAVVLNNLAWLYLELKDPRALEYAEKALKLAPNIPAILDTLGWLLVEKGEADRALPLLRKAVNIAPE-AAAIRYHLA--  878 (899)
T ss_pred             CCHHHHHHHHHHHHhcCcHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-ChHHHHHHH--
Confidence            2333                                 3444455555566666666666666554321 444444444  


Q ss_pred             hhhhccccchHHHHHHHHHHHHH
Q 039342          209 VDVHRMWEGGAYTAISVWLNKMY  231 (248)
Q Consensus       209 ~~~~~~~~~g~~~~~~~~~~~m~  231 (248)
                         ..+.+.|+.++|..++++|.
T Consensus       879 ---~~~~~~g~~~~A~~~~~~~~  898 (899)
T TIGR02917       879 ---LALLATGRKAEARKELDKLL  898 (899)
T ss_pred             ---HHHHHcCCHHHHHHHHHHHh
Confidence               45555666666666666554

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

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

Probab=99.60  E-value=1.1e-12  Score=116.73  Aligned_cols=86  Identities=12%  Similarity=0.028  Sum_probs=38.9

Q ss_pred             cccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchH
Q 039342          140 DDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGA  219 (248)
Q Consensus       140 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~  219 (248)
                      ...|+++.|...++.+...+  |+..++..+..++.+.|++++|.+.++++.+.. +.+...+..+.     ..+...|+
T Consensus       714 ~~~g~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~-~~~~~~~~~la-----~~~~~~g~  785 (899)
T TIGR02917       714 LRQKDYPAAIQAYRKALKRA--PSSQNAIKLHRALLASGNTAEAVKTLEAWLKTH-PNDAVLRTALA-----ELYLAQKD  785 (899)
T ss_pred             HHCCCHHHHHHHHHHHHhhC--CCchHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHH-----HHHHHCcC
Confidence            33444444444444444432  222344444445555555555555555444321 11222222222     44455566


Q ss_pred             HHHHHHHHHHHHHH
Q 039342          220 YTAISVWLNKMYEM  233 (248)
Q Consensus       220 ~~~~~~~~~~m~~~  233 (248)
                      .++|...++++.+.
T Consensus       786 ~~~A~~~~~~~~~~  799 (899)
T TIGR02917       786 YDKAIKHYRTVVKK  799 (899)
T ss_pred             HHHHHHHHHHHHHh
Confidence            66666666666554

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.

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

Probab=99.59  E-value=6.2e-14  Score=117.15  Aligned_cols=217  Identities=17%  Similarity=0.095  Sum_probs=155.3

Q ss_pred             HHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCC
Q 039342            9 AILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSG   88 (248)
Q Consensus         9 ~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~   88 (248)
                      .++..+...|+.|+..||.++|.-||..|+.+.|- +|.-|+-...+.+...|+.++.+..++++.+.+.          
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk----------   79 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPK----------   79 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCC----------
Confidence            56778899999999999999999999999999998 9999988887777788888888888887777766          


Q ss_pred             CCcCHhhHHHHHHHHHhcCCHHH---HHHHHHHH----HHCCCCchHHhHHHHhccc-------------ccccchH---
Q 039342           89 ILPSVMCYCMLLAVYAKSNRWDD---AYGLLDEM----HTNRISNIHQVTGQMIKGE-------------FDDESNW---  145 (248)
Q Consensus        89 ~~p~~~~~~~li~~~~~~~~~~~---a~~~~~~m----~~~~~~~~~~~~~~~l~~~-------------~~~~~~~---  145 (248)
                       .|.+.||..|..+|..+|++..   +.+.+..+    ...|+-.....+...+..+             ....|.|   
T Consensus        80 -ep~aDtyt~Ll~ayr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~eglwaql  158 (1088)
T KOG4318|consen   80 -EPLADTYTNLLKAYRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVLEGLWAQL  158 (1088)
T ss_pred             -CCchhHHHHHHHHHHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHHHHHHHHH
Confidence             5777788888888888887544   22212111    1122211111111110000             0001111   


Q ss_pred             ---------------------------HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCC
Q 039342          146 ---------------------------QMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPE  198 (248)
Q Consensus       146 ---------------------------~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  198 (248)
                                                 .-.+++....+...-.|++.+|.+++..-...|+.+.|..++.+|++.|++.+
T Consensus       159 lkll~~~Pvsa~~~p~~vfLrqnv~~ntpvekLl~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfpir  238 (1088)
T KOG4318|consen  159 LKLLAKVPVSAWNAPFQVFLRQNVVDNTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIR  238 (1088)
T ss_pred             HHHHhhCCcccccchHHHHHHHhccCCchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCcc
Confidence                                       12222333333332269999999999999999999999999999999999999


Q ss_pred             cchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHHHcCCCCCcccc
Q 039342          199 LFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDLPQLAT  245 (248)
Q Consensus       199 ~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~~~~~~~~~~~~  245 (248)
                      .+-|-.|+     -|   .+...-++.++..|++.|+.|+..|+...
T Consensus       239 ~HyFwpLl-----~g---~~~~q~~e~vlrgmqe~gv~p~seT~ady  277 (1088)
T KOG4318|consen  239 AHYFWPLL-----LG---INAAQVFEFVLRGMQEKGVQPGSETQADY  277 (1088)
T ss_pred             cccchhhh-----hc---CccchHHHHHHHHHHHhcCCCCcchhHHH
Confidence            88888777     44   66667788899999999999999887643

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.58  E-value=1.1e-12  Score=102.03  Aligned_cols=167  Identities=15%  Similarity=0.208  Sum_probs=119.9

Q ss_pred             CCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHH
Q 039342           20 ARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCML   99 (248)
Q Consensus        20 ~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l   99 (248)
                      +.+..+|.+||.++|+-...+.|.+++++-.....+.+..+||.+|.+-.-..    ..+++.+|.+..+.||..|+|++
T Consensus       204 PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~----~K~Lv~EMisqkm~Pnl~TfNal  279 (625)
T KOG4422|consen  204 PKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSV----GKKLVAEMISQKMTPNLFTFNAL  279 (625)
T ss_pred             CCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhc----cHHHHHHHHHhhcCCchHhHHHH
Confidence            35678899999999998888899999888888888888888888887654332    27788888888888888888888


Q ss_pred             HHHHHhcCCHHH----HHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhc----CCCC----CHHHH
Q 039342          100 LAVYAKSNRWDD----AYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCE----GYGL----GMRFY  167 (248)
Q Consensus       100 i~~~~~~~~~~~----a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~----~~~p----~~~~~  167 (248)
                      +++.++.|+++.    |.+++.+|.+-|+.|...+|+.+|...+...+....+..+..++...    .++|    |...|
T Consensus       280 L~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~~FF  359 (625)
T KOG4422|consen  280 LSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDNKFF  359 (625)
T ss_pred             HHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchhHHH
Confidence            888888887654    56778888888888888888888887554444434444444443321    2222    34445


Q ss_pred             HHHHHHHHhcCchHHHHHHHHHH
Q 039342          168 NALLEALWCLGLRERAARVLDEA  190 (248)
Q Consensus       168 ~~li~~~~~~g~~~~a~~~~~~m  190 (248)
                      ...+..|.+..+.+.|.++-.-+
T Consensus       360 ~~AM~Ic~~l~d~~LA~~v~~ll  382 (625)
T KOG4422|consen  360 QSAMSICSSLRDLELAYQVHGLL  382 (625)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHH
Confidence            56666666666666666655443

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.53  E-value=2e-12  Score=100.60  Aligned_cols=179  Identities=16%  Similarity=0.204  Sum_probs=135.8

Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH--HHhcCChh-HHHHHHHHHHHCC------------
Q 039342           24 DSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSV--YCFAGLVD-ESKEQFQEIKSSG------------   88 (248)
Q Consensus        24 ~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~--~~~~g~~~-~a~~~~~~m~~~~------------   88 (248)
                      .+=|.|+.. ...|.+..+.-+|+.|++.|++.+...--.|+..  |....++- .-.+-|-.|...|            
T Consensus       117 ~~E~nL~km-IS~~EvKDs~ilY~~m~~e~~~vS~kvq~~L~~LV~~~Ns~~~~~~E~~~Fv~~~~~~E~S~~sWK~G~v  195 (625)
T KOG4422|consen  117 ETENNLLKM-ISSREVKDSCILYERMRSENVDVSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFGEDSTSSWKSGAV  195 (625)
T ss_pred             cchhHHHHH-HhhcccchhHHHHHHHHhcCCCCCHHHHHHHHHHHHhhcCCCCcchhHHHHhhccccccccccccccccH
Confidence            455555544 4567788888899999999988887666655543  22222221 1112222222211            


Q ss_pred             -------CCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCC
Q 039342           89 -------ILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYG  161 (248)
Q Consensus        89 -------~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~  161 (248)
                             .+-+..+|.+||.++|+-...+.|.+++++-.....+.+..+|+.+|...     .+....+++.+|....++
T Consensus       196 AdL~~E~~PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~-----S~~~~K~Lv~EMisqkm~  270 (625)
T KOG4422|consen  196 ADLLFETLPKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGAS-----SYSVGKKLVAEMISQKMT  270 (625)
T ss_pred             HHHHHhhcCCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHH-----HhhccHHHHHHHHHhhcC
Confidence                   12367899999999999999999999999999999999999999998752     233447899999999999


Q ss_pred             CCHHHHHHHHHHHHhcCchHH----HHHHHHHHHHCCCCCCcchhhhHHhh
Q 039342          162 LGMRFYNALLEALWCLGLRER----AARVLDEATKRGLFPELFRHNKLVWS  208 (248)
Q Consensus       162 p~~~~~~~li~~~~~~g~~~~----a~~~~~~m~~~g~~p~~~t~~~li~~  208 (248)
                      ||..|||+++++.++.|+++.    |.+++.+|++-|++|...+|..+|..
T Consensus       271 Pnl~TfNalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~  321 (625)
T KOG4422|consen  271 PNLFTFNALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKN  321 (625)
T ss_pred             CchHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHH
Confidence            999999999999999998775    56788899999999999999999943

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

Probab=99.42  E-value=2.7e-12  Score=99.47  Aligned_cols=214  Identities=19%  Similarity=0.168  Sum_probs=76.4

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |+++.|.+.++++...+.. ++..+..++.. ...+++++|.+++....+.  .++...+..++..+.+.++++++.+++
T Consensus        58 ~~~~~A~~ay~~l~~~~~~-~~~~~~~l~~l-~~~~~~~~A~~~~~~~~~~--~~~~~~l~~~l~~~~~~~~~~~~~~~l  133 (280)
T PF13429_consen   58 GDYDEAIEAYEKLLASDKA-NPQDYERLIQL-LQDGDPEEALKLAEKAYER--DGDPRYLLSALQLYYRLGDYDEAEELL  133 (280)
T ss_dssp             ----------------------------------------------------------------H-HHHTT-HHHHHHHH
T ss_pred             ccccccccccccccccccc-ccccccccccc-ccccccccccccccccccc--ccccchhhHHHHHHHHHhHHHHHHHHH
Confidence            4555666666666554332 44455555555 5666666666666554333  245555666666677777777777777


Q ss_pred             HHHHHC-CCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHh-HHHHhcccccccchHHHHHHHHHHHHhcC
Q 039342           82 QEIKSS-GILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQV-TGQMIKGEFDDESNWQMVEYVFDKLNCEG  159 (248)
Q Consensus        82 ~~m~~~-~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~m~~~~  159 (248)
                      +.+.+. ...++...|..+...+.+.|+.++|++.+++..+..  |+... ...++.. +...|+.+.+..+++......
T Consensus       134 ~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~--P~~~~~~~~l~~~-li~~~~~~~~~~~l~~~~~~~  210 (280)
T PF13429_consen  134 EKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKALELD--PDDPDARNALAWL-LIDMGDYDEAREALKRLLKAA  210 (280)
T ss_dssp             HHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH---TT-HHHHHHHHHH-HCTTCHHHHHHHHHHHHHHH-
T ss_pred             HHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHH-HHHCCChHHHHHHHHHHHHHC
Confidence            776543 233455666666677777777777777777766543  44333 3333333 555666666666666665553


Q ss_pred             CCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCC-cchhhhHHhhhhhhccccchHHHHHHHHHHHH
Q 039342          160 YGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPE-LFRHNKLVWSVDVHRMWEGGAYTAISVWLNKM  230 (248)
Q Consensus       160 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m  230 (248)
                       ..|...+..+..++...|+.++|..+|++..+.  .|+ ......     ....+...|+.++|.++..+.
T Consensus       211 -~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~--~p~d~~~~~~-----~a~~l~~~g~~~~A~~~~~~~  274 (280)
T PF13429_consen  211 -PDDPDLWDALAAAYLQLGRYEEALEYLEKALKL--NPDDPLWLLA-----YADALEQAGRKDEALRLRRQA  274 (280)
T ss_dssp             -HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHH--STT-HHHHHH-----HHHHHT---------------
T ss_pred             -cCHHHHHHHHHHHhccccccccccccccccccc--cccccccccc-----ccccccccccccccccccccc
Confidence             334455666677777777777777777776542  332 222222     225566677777776665544

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.42  E-value=2.7e-10  Score=98.02  Aligned_cols=78  Identities=19%  Similarity=0.187  Sum_probs=38.8

Q ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHH
Q 039342          148 VEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWL  227 (248)
Q Consensus       148 a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~  227 (248)
                      |...++...+.... +...+..+...+...|++++|...+++..+.  .|+..    .++..+...+.+.|++++|...+
T Consensus       269 A~~~~~~Al~l~P~-~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l--~P~~~----~a~~~La~~l~~~G~~~eA~~~l  341 (656)
T PRK15174        269 AAEHWRHALQFNSD-NVRIVTLYADALIRTGQNEKAIPLLQQSLAT--HPDLP----YVRAMYARALRQVGQYTAASDEF  341 (656)
T ss_pred             HHHHHHHHHhhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCH----HHHHHHHHHHHHCCCHHHHHHHH
Confidence            45555554443221 3445555566666666666666666665542  34321    11112224455556666666655


Q ss_pred             HHHHH
Q 039342          228 NKMYE  232 (248)
Q Consensus       228 ~~m~~  232 (248)
                      +.+.+
T Consensus       342 ~~al~  346 (656)
T PRK15174        342 VQLAR  346 (656)
T ss_pred             HHHHH
Confidence            55544

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.41  E-value=5e-10  Score=83.84  Aligned_cols=203  Identities=8%  Similarity=-0.023  Sum_probs=155.0

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHH
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLA  101 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~  101 (248)
                      ....+..+...+...|++++|.+.+++..+.. +.+...+..+...+...|++++|.+.+++..+.. +.+...+..+..
T Consensus        30 ~~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~  107 (234)
T TIGR02521        30 AAKIRVQLALGYLEQGDLEVAKENLDKALEHD-PDDYLAYLALALYYQQLGELEKAEDSFRRALTLN-PNNGDVLNNYGT  107 (234)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHH
Confidence            45678888999999999999999999987653 3456788889999999999999999999988764 235677888889


Q ss_pred             HHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchH
Q 039342          102 VYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRE  181 (248)
Q Consensus       102 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~  181 (248)
                      .+...|++++|...+++..+....+........+...+...|+++.|...++...+.... +...+..+...+...|+++
T Consensus       108 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~~~~~  186 (234)
T TIGR02521       108 FLCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQ-RPESLLELAELYYLRGQYK  186 (234)
T ss_pred             HHHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcC-ChHHHHHHHHHHHHcCCHH
Confidence            999999999999999999875433333222222333366778899999999988776432 4667888899999999999


Q ss_pred             HHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          182 RAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       182 ~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      +|...+++..+. .+.+...+..+.     ..+...|+.+++..+.+.+.+.
T Consensus       187 ~A~~~~~~~~~~-~~~~~~~~~~~~-----~~~~~~~~~~~a~~~~~~~~~~  232 (234)
T TIGR02521       187 DARAYLERYQQT-YNQTAESLWLGI-----RIARALGDVAAAQRYGAQLQKL  232 (234)
T ss_pred             HHHHHHHHHHHh-CCCCHHHHHHHH-----HHHHHHhhHHHHHHHHHHHHhh
Confidence            999999998875 222323332222     5566788999988887776553

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.

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.38  E-value=5.9e-10  Score=95.90  Aligned_cols=191  Identities=10%  Similarity=0.011  Sum_probs=124.0

Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHH-
Q 039342           33 FRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDD-  111 (248)
Q Consensus        33 ~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~-  111 (248)
                      +...|++++|...++.+.+..-.++...+..+..++.+.|++++|...+++..+.. +.+...+..+-..+...|++++ 
T Consensus       187 l~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~-p~~~~~~~~Lg~~l~~~G~~~eA  265 (656)
T PRK15174        187 FLNKSRLPEDHDLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARG-LDGAALRRSLGLAYYQSGRSREA  265 (656)
T ss_pred             HHHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCchhh
Confidence            44555555555555555443322333344444556666667777777776666543 2245566667777777777764 


Q ss_pred             ---HHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHH
Q 039342          112 ---AYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLD  188 (248)
Q Consensus       112 ---a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~  188 (248)
                         |...|++..+..  |+.......+...+...|+++.|...++...+.... +...+..+..++.+.|++++|...++
T Consensus       266 ~~~A~~~~~~Al~l~--P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~P~-~~~a~~~La~~l~~~G~~~eA~~~l~  342 (656)
T PRK15174        266 KLQAAEHWRHALQFN--SDNVRIVTLYADALIRTGQNEKAIPLLQQSLATHPD-LPYVRAMYARALRQVGQYTAASDEFV  342 (656)
T ss_pred             HHHHHHHHHHHHhhC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence               677777766543  544433333344466778999999999998876433 45667778899999999999999999


Q ss_pred             HHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          189 EATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       189 ~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      .+.+.  .|+...+..    .....+...|+.++|...+++..+.
T Consensus       343 ~al~~--~P~~~~~~~----~~a~al~~~G~~deA~~~l~~al~~  381 (656)
T PRK15174        343 QLARE--KGVTSKWNR----YAAAALLQAGKTSEAESVFEHYIQA  381 (656)
T ss_pred             HHHHh--CccchHHHH----HHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            98865  455322211    1124567889999999999887665

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

Probab=99.38  E-value=4e-12  Score=98.50  Aligned_cols=227  Identities=15%  Similarity=0.122  Sum_probs=94.5

Q ss_pred             CCchHHHHHHHHHHHHcCCCC-CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHH
Q 039342            1 GGLYKECQAILSRMSESGVAR-NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKE   79 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~-~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~   79 (248)
                      .|++++|++++........+| +..-|..+-..+...++++.|.+.++++...+-. +...+..++.. ...+++++|.+
T Consensus        21 ~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~~~-~~~~~~~l~~l-~~~~~~~~A~~   98 (280)
T PF13429_consen   21 RGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASDKA-NPQDYERLIQL-LQDGDPEEALK   98 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccc-ccccccccccc
Confidence            378999999996654433234 4445555555666789999999999999876543 56677777777 79999999999


Q ss_pred             HHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcC
Q 039342           80 QFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEG  159 (248)
Q Consensus        80 ~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~  159 (248)
                      ++...-+.  .++...+...+..+.+.++++++.+++++.....-.+....+......++...|+++.|...++...+..
T Consensus        99 ~~~~~~~~--~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~  176 (280)
T PF13429_consen   99 LAEKAYER--DGDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKALELD  176 (280)
T ss_dssp             ---------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH-
T ss_pred             cccccccc--ccccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC
Confidence            99876554  3567778889999999999999999999987654445555555555555788999999999999988875


Q ss_pred             CCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHHHcCCC
Q 039342          160 YGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGED  239 (248)
Q Consensus       160 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~~~~~~  239 (248)
                      .. |....+.++..+...|+.+++.+++....+.. +.|...+..+.     .++...|+.++|..++++..+.  .|++
T Consensus       177 P~-~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la-----~~~~~lg~~~~Al~~~~~~~~~--~p~d  247 (280)
T PF13429_consen  177 PD-DPDARNALAWLLIDMGDYDEAREALKRLLKAA-PDDPDLWDALA-----AAYLQLGRYEEALEYLEKALKL--NPDD  247 (280)
T ss_dssp             TT--HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHH-----HHHHHHT-HHHHHHHHHHHHHH--STT-
T ss_pred             CC-CHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-cCHHHHHHHHH-----HHhccccccccccccccccccc--cccc
Confidence            33 57778899999999999999999998887653 34444444454     6778899999999999997664  5544


Q ss_pred             C
Q 039342          240 L  240 (248)
Q Consensus       240 ~  240 (248)
                      +
T Consensus       248 ~  248 (280)
T PF13429_consen  248 P  248 (280)
T ss_dssp             H
T ss_pred             c
Confidence            3

>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=99.37  E-value=1.1e-09  Score=93.96  Aligned_cols=224  Identities=13%  Similarity=0.017  Sum_probs=163.5

Q ss_pred             CchHHHHHHHHHHHHcC-CCC-CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCChhHHH
Q 039342            2 GLYKECQAILSRMSESG-VAR-NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN-ERTLEAVLSVYCFAGLVDESK   78 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g-~~~-~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~ll~~~~~~g~~~~a~   78 (248)
                      +++++|.+.|+...+.+ ..| ....|+.+-..+...|++++|...+++..+.  .|+ ...|..+...+...|++++|.
T Consensus       308 ~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l--~P~~~~~~~~la~~~~~~g~~~eA~  385 (615)
T TIGR00990       308 ESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIEL--DPRVTQSYIKRASMNLELGDPDKAE  385 (615)
T ss_pred             hhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHCCCHHHHH
Confidence            46889999999888754 233 4567888888888999999999999998765  344 567888888899999999999


Q ss_pred             HHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhc
Q 039342           79 EQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCE  158 (248)
Q Consensus        79 ~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  158 (248)
                      ..|++..+.. +.+..+|..+-..+...|++++|...|++..+..  |+.......+...+...|+++.|...++.....
T Consensus       386 ~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~--P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~  462 (615)
T TIGR00990       386 EDFDKALKLN-SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLD--PDFIFSHIQLGVTQYKEGSIASSMATFRRCKKN  462 (615)
T ss_pred             HHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--ccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            9999987753 2256788889999999999999999999988664  554444444444467788899999999988765


Q ss_pred             CCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCc--chhhhH-HhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          159 GYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPEL--FRHNKL-VWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       159 ~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~--~t~~~l-i~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      . +-+...++.+...+...|++++|.+.|++..+.  .|+.  ...+.. +.......+...|++++|..++++..+.
T Consensus       463 ~-P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l--~p~~~~~~~~~~~l~~~a~~~~~~~~~~~eA~~~~~kAl~l  537 (615)
T TIGR00990       463 F-PEAPDVYNYYGELLLDQNKFDEAIEKFDTAIEL--EKETKPMYMNVLPLINKALALFQWKQDFIEAENLCEKALII  537 (615)
T ss_pred             C-CCChHHHHHHHHHHHHccCHHHHHHHHHHHHhc--CCccccccccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhc
Confidence            3 225678888999999999999999999987754  2221  111111 1111111222357888887777765543

>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=99.36  E-value=1.2e-09  Score=93.76  Aligned_cols=219  Identities=12%  Similarity=0.003  Sum_probs=163.4

Q ss_pred             CchHHHHHHHHHHHHcCCCCC-HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARN-SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~-~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      |++++|+..|++..+..  |+ ...|..+-..+...|++++|...|++..+.. +-+...|..+...+...|++++|...
T Consensus       345 g~~~eA~~~~~kal~l~--P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~  421 (615)
T TIGR00990       345 GKHLEALADLSKSIELD--PRVTQSYIKRASMNLELGDPDKAEEDFDKALKLN-SEDPDIYYHRAQLHFIKGEFAQAGKD  421 (615)
T ss_pred             CCHHHHHHHHHHHHHcC--CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            78999999999987743  44 6688888899999999999999999987653 34578888999999999999999999


Q ss_pred             HHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCC
Q 039342           81 FQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGY  160 (248)
Q Consensus        81 ~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~  160 (248)
                      |++..+.. +.+...+..+...+.+.|++++|+..|++..+..  |+.......+...+...|+++.|...|+...+...
T Consensus       422 ~~kal~l~-P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~--P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p  498 (615)
T TIGR00990       422 YQKSIDLD-PDFIFSHIQLGVTQYKEGSIASSMATFRRCKKNF--PEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEK  498 (615)
T ss_pred             HHHHHHcC-ccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCC
Confidence            99988763 2256778888889999999999999999987643  54433333333336678899999999998776532


Q ss_pred             CCCH------HHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcc-hhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          161 GLGM------RFYNALLEALWCLGLRERAARVLDEATKRGLFPELF-RHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       161 ~p~~------~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~-t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      ..+.      ..++.....+...|++++|.+++++..+.  .|+.. .+..+.     ..+...|++++|.+++++..+.
T Consensus       499 ~~~~~~~~~~~l~~~a~~~~~~~~~~~eA~~~~~kAl~l--~p~~~~a~~~la-----~~~~~~g~~~eAi~~~e~A~~l  571 (615)
T TIGR00990       499 ETKPMYMNVLPLINKALALFQWKQDFIEAENLCEKALII--DPECDIAVATMA-----QLLLQQGDVDEALKLFERAAEL  571 (615)
T ss_pred             ccccccccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhc--CCCcHHHHHHHH-----HHHHHccCHHHHHHHHHHHHHH
Confidence            2111      11222233344569999999999987764  45432 233333     7778899999999988887654

>TIGR00540 hemY_coli hemY protein

Probab=99.36  E-value=3.3e-09  Score=86.54  Aligned_cols=225  Identities=10%  Similarity=-0.015  Sum_probs=134.0

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH---HhcCChhHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVY---CFAGLVDESK   78 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~---~~~g~~~~a~   78 (248)
                      |+++.|.+.++.+.+... -+...+..+...+.+.|++++|.+.+..+.+.++.+.......-..++   ...+..+.+.
T Consensus       167 ~~~~~Al~~l~~l~~~~P-~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~  245 (409)
T TIGR00540       167 NELHAARHGVDKLLEMAP-RHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDEAMADEGI  245 (409)
T ss_pred             CCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCH
Confidence            556666666666655431 244555566666666666666666666666555432221111111111   1111222222


Q ss_pred             HHHHHHHHCC---CCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHh--HHHHhcccccccchHHHHHHHHH
Q 039342           79 EQFQEIKSSG---ILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQV--TGQMIKGEFDDESNWQMVEYVFD  153 (248)
Q Consensus        79 ~~~~~m~~~~---~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~--~~~~l~~~~~~~~~~~~a~~~~~  153 (248)
                      +.+..+.+..   .+.+...+..+...+...|+.++|.+++++..+..  |+...  +..+........++.+.+...++
T Consensus       246 ~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~--pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e  323 (409)
T TIGR00540       246 DGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKL--GDDRAISLPLCLPIPRLKPEDNEKLEKLIE  323 (409)
T ss_pred             HHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhC--CCcccchhHHHHHhhhcCCCChHHHHHHHH
Confidence            2333332221   11266777778888889999999999999988764  33331  11222221223466677777777


Q ss_pred             HHHhcCC-CCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHH
Q 039342          154 KLNCEGY-GLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYE  232 (248)
Q Consensus       154 ~m~~~~~-~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~  232 (248)
                      ...+... .|+.....++-..+.+.|++++|.+.|+........|+...+..+.     ..+.+.|+.++|.+++++-..
T Consensus       324 ~~lk~~p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La-----~ll~~~g~~~~A~~~~~~~l~  398 (409)
T TIGR00540       324 KQAKNVDDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAA-----DAFDQAGDKAEAAAMRQDSLG  398 (409)
T ss_pred             HHHHhCCCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHH-----HHHHHcCCHHHHHHHHHHHHH
Confidence            7665422 2222556688899999999999999999655545578887777666     778899999999988887544


Q ss_pred             HH
Q 039342          233 MF  234 (248)
Q Consensus       233 ~~  234 (248)
                      .-
T Consensus       399 ~~  400 (409)
T TIGR00540       399 LM  400 (409)
T ss_pred             HH
Confidence            43

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.

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.34  E-value=4.5e-09  Score=85.44  Aligned_cols=213  Identities=12%  Similarity=0.007  Sum_probs=137.4

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHH--HHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFN--AVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKE   79 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~--~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~   79 (248)
                      |+++.|.+.|.++.+.  .|+...+.  .....+...|+++.|.+.++++.+.. +-+...+..+...|.+.|++++|.+
T Consensus       132 g~~~~A~~~l~~A~~~--~~~~~~~~~l~~a~l~l~~g~~~~Al~~l~~~~~~~-P~~~~al~ll~~~~~~~gdw~~a~~  208 (398)
T PRK10747        132 GDEARANQHLERAAEL--ADNDQLPVEITRVRIQLARNENHAARHGVDKLLEVA-PRHPEVLRLAEQAYIRTGAWSSLLD  208 (398)
T ss_pred             CCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHHhHHHHHH
Confidence            5666666666666542  23332222  22445566666666666666665544 3345556666667777777777776


Q ss_pred             HHHHHHHCCCC-----------------------------------------cCHhhHHHHHHHHHhcCCHHHHHHHHHH
Q 039342           80 QFQEIKSSGIL-----------------------------------------PSVMCYCMLLAVYAKSNRWDDAYGLLDE  118 (248)
Q Consensus        80 ~~~~m~~~~~~-----------------------------------------p~~~~~~~li~~~~~~~~~~~a~~~~~~  118 (248)
                      ++..+.+.+..                                         .++.....+..++...|+.++|.+++++
T Consensus       209 ~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~  288 (398)
T PRK10747        209 ILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQSRKTRHQVALQVAMAEHLIECDDHDTAQQIILD  288 (398)
T ss_pred             HHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHHHhCCHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            66666644322                                         1233444556666777888888888877


Q ss_pred             HHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCC
Q 039342          119 MHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPE  198 (248)
Q Consensus       119 m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  198 (248)
                      ..+..  |+.....  +.+ ....++.+.+....+...+... -|...+.++-+.+.+.+++++|.+.|+...+.  .|+
T Consensus       289 ~l~~~--~~~~l~~--l~~-~l~~~~~~~al~~~e~~lk~~P-~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~--~P~  360 (398)
T PRK10747        289 GLKRQ--YDERLVL--LIP-RLKTNNPEQLEKVLRQQIKQHG-DTPLLWSTLGQLLMKHGEWQEASLAFRAALKQ--RPD  360 (398)
T ss_pred             HHhcC--CCHHHHH--HHh-hccCCChHHHHHHHHHHHhhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCC
Confidence            76632  3332211  111 1233667788888887776543 25667888899999999999999999998875  688


Q ss_pred             cchhhhHHhhhhhhccccchHHHHHHHHHHHH
Q 039342          199 LFRHNKLVWSVDVHRMWEGGAYTAISVWLNKM  230 (248)
Q Consensus       199 ~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m  230 (248)
                      ..+|..+-     ..+.+.|+.+++...+++=
T Consensus       361 ~~~~~~La-----~~~~~~g~~~~A~~~~~~~  387 (398)
T PRK10747        361 AYDYAWLA-----DALDRLHKPEEAAAMRRDG  387 (398)
T ss_pred             HHHHHHHH-----HHHHHcCCHHHHHHHHHHH
Confidence            87777666     7788899999987777644

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.33  E-value=2e-09  Score=80.57  Aligned_cols=186  Identities=13%  Similarity=0.113  Sum_probs=148.2

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|.+.|++..+.. +.+...+..+...+...|++++|.+.+++..+.. +.+...+..+...+...|++++|.+.
T Consensus        44 ~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~  121 (234)
T TIGR02521        44 QGDLEVAKENLDKALEHD-PDDYLAYLALALYYQQLGELEKAEDSFRRALTLN-PNNGDVLNNYGTFLCQQGKYEQAMQQ  121 (234)
T ss_pred             CCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcccHHHHHHH
Confidence            378999999999987653 2357788889999999999999999999987764 34567788889999999999999999


Q ss_pred             HHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchH-HhHHHHhcccccccchHHHHHHHHHHHHhc
Q 039342           81 FQEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIH-QVTGQMIKGEFDDESNWQMVEYVFDKLNCE  158 (248)
Q Consensus        81 ~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  158 (248)
                      +++..+....| ....+..+...+...|++++|...+++..+..  |+. ..+..+. ..+...++++.|...+++..+.
T Consensus       122 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~la-~~~~~~~~~~~A~~~~~~~~~~  198 (234)
T TIGR02521       122 FEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQID--PQRPESLLELA-ELYYLRGQYKDARAYLERYQQT  198 (234)
T ss_pred             HHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--cCChHHHHHHH-HHHHHcCCHHHHHHHHHHHHHh
Confidence            99998653222 34567778888999999999999999987654  332 3333333 3366788899999999998876


Q ss_pred             CCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          159 GYGLGMRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       159 ~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                       ...+...+..+...+...|+.+.|..+.+.+..
T Consensus       199 -~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  231 (234)
T TIGR02521       199 -YNQTAESLWLGIRIARALGDVAAAQRYGAQLQK  231 (234)
T ss_pred             -CCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence             344667777888889999999999999887754

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=99.23  E-value=1.7e-08  Score=85.53  Aligned_cols=218  Identities=9%  Similarity=-0.025  Sum_probs=150.4

Q ss_pred             chHHHHHHHHHHHHcCCCCC-HHhHHHHHHHHH---------hcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC
Q 039342            3 LYKECQAILSRMSESGVARN-SDSFNAVIEAFR---------QGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAG   72 (248)
Q Consensus         3 ~~~~a~~~~~~m~~~g~~~~-~~~y~~li~~~~---------~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g   72 (248)
                      ++++|.+.|++..+.  .|+ ...|..+-.++.         ..+++++|...+++..+.+ +-+...+..+-..+...|
T Consensus       276 ~~~~A~~~~~~Al~l--dP~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~ld-P~~~~a~~~lg~~~~~~g  352 (553)
T PRK12370        276 SLQQALKLLTQCVNM--SPNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATELD-HNNPQALGLLGLINTIHS  352 (553)
T ss_pred             HHHHHHHHHHHHHhc--CCccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcc
Confidence            467899999988764  354 445555544333         2345889999999987764 346677888888889999


Q ss_pred             ChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHh-HHHHhcccccccchHHHHHHH
Q 039342           73 LVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQV-TGQMIKGEFDDESNWQMVEYV  151 (248)
Q Consensus        73 ~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~  151 (248)
                      ++++|...|++..+.+ +.+...+..+-..+...|++++|...+++..+..  |.... ....... +...|++++|...
T Consensus       353 ~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~--P~~~~~~~~~~~~-~~~~g~~eeA~~~  428 (553)
T PRK12370        353 EYIVGSLLFKQANLLS-PISADIKYYYGWNLFMAGQLEEALQTINECLKLD--PTRAAAGITKLWI-TYYHTGIDDAIRL  428 (553)
T ss_pred             CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CCChhhHHHHHHH-HHhccCHHHHHHH
Confidence            9999999999998764 2246678888889999999999999999988765  43322 1222222 2335678999999


Q ss_pred             HHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHH
Q 039342          152 FDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMY  231 (248)
Q Consensus       152 ~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~  231 (248)
                      +++.......-+...+..+-.++...|+.++|...+.++...  .|+..+....+    ...|...|  +++...++.+.
T Consensus       429 ~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~--~~~~~~~~~~l----~~~~~~~g--~~a~~~l~~ll  500 (553)
T PRK12370        429 GDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQ--EITGLIAVNLL----YAEYCQNS--ERALPTIREFL  500 (553)
T ss_pred             HHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhc--cchhHHHHHHH----HHHHhccH--HHHHHHHHHHH
Confidence            988776532224555677788888999999999999887554  44433332222    13445555  36666677766


Q ss_pred             HHHH
Q 039342          232 EMFM  235 (248)
Q Consensus       232 ~~~~  235 (248)
                      +..-
T Consensus       501 ~~~~  504 (553)
T PRK12370        501 ESEQ  504 (553)
T ss_pred             HHhh
Confidence            5433

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.22  E-value=1.8e-08  Score=89.59  Aligned_cols=182  Identities=9%  Similarity=-0.028  Sum_probs=79.5

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|...|+++...  +|+...+..+...+.+.|+.++|.+.++...+.+ +.+...+..+.....+.|++++|...+
T Consensus       523 Gr~eeAi~~~rka~~~--~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~-P~~~~l~~~La~~l~~~Gr~~eAl~~~  599 (987)
T PRK09782        523 EDYATALAAWQKISLH--DMSNEDLLAAANTAQAAGNGAARDRWLQQAEQRG-LGDNALYWWLHAQRYIPGQPELALNDL  599 (987)
T ss_pred             CCHHHHHHHHHHHhcc--CCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHhCCCHHHHHHHH
Confidence            4445555555544321  2222333334444444555555555555544332 111122222222233335555555555


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCC
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYG  161 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~  161 (248)
                      ++..+.  .|+...|..+-..+.+.|+.++|+..|++..+..  |+.......+...+...|++++|...++...+....
T Consensus       600 ~~AL~l--~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~--Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l~P~  675 (987)
T PRK09782        600 TRSLNI--APSANAYVARATIYRQRHNVPAAVSDLRAALELE--PNNSNYQAALGYALWDSGDIAQSREMLERAHKGLPD  675 (987)
T ss_pred             HHHHHh--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC
Confidence            554433  2344445555555555555555555555544332  333333333332244444455555555544443221


Q ss_pred             CCHHHHHHHHHHHHhcCchHHHHHHHHHHH
Q 039342          162 LGMRFYNALLEALWCLGLRERAARVLDEAT  191 (248)
Q Consensus       162 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  191 (248)
                       +...+..+-.++...|++++|...+++..
T Consensus       676 -~~~a~~nLA~al~~lGd~~eA~~~l~~Al  704 (987)
T PRK09782        676 -DPALIRQLAYVNQRLDDMAATQHYARLVI  704 (987)
T ss_pred             -CHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence             33444445555555555555555555544

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.20  E-value=2.8e-08  Score=80.83  Aligned_cols=186  Identities=10%  Similarity=0.125  Sum_probs=126.2

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHh-HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHH--HHHHHHHhcCChhHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDS-FNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLE--AVLSVYCFAGLVDES   77 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~-y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~--~ll~~~~~~g~~~~a   77 (248)
                      .|++++|++.+....+..  +++.. |-....+..+.|+++.|.+.+.++.+.  .|+...+.  .....+...|+++.|
T Consensus        97 eGd~~~A~k~l~~~~~~~--~~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~--~~~~~~~~~l~~a~l~l~~g~~~~A  172 (398)
T PRK10747         97 EGDYQQVEKLMTRNADHA--EQPVVNYLLAAEAAQQRGDEARANQHLERAAEL--ADNDQLPVEITRVRIQLARNENHAA  172 (398)
T ss_pred             CCCHHHHHHHHHHHHhcc--cchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHCCCHHHH
Confidence            489999998888766542  22333 333344457899999999999999764  56654443  336688999999999


Q ss_pred             HHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHH-------hHHHHhcccccccchHHHHHH
Q 039342           78 KEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQ-------VTGQMIKGEFDDESNWQMVEY  150 (248)
Q Consensus        78 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~~  150 (248)
                      ...++++.+.. +-+......+...|.+.|++++|.+++..+.+....++..       .+..++.. .....+.+....
T Consensus       173 l~~l~~~~~~~-P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~-~~~~~~~~~l~~  250 (398)
T PRK10747        173 RHGVDKLLEVA-PRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQ-AMADQGSEGLKR  250 (398)
T ss_pred             HHHHHHHHhcC-CCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHH-HHHhcCHHHHHH
Confidence            99999998875 2267889999999999999999999999999887654332       11222222 111222344444


Q ss_pred             HHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHC
Q 039342          151 VFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKR  193 (248)
Q Consensus       151 ~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  193 (248)
                      +++.+... .+.+......+...+...|+.++|.+++++..+.
T Consensus       251 ~w~~lp~~-~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~  292 (398)
T PRK10747        251 WWKNQSRK-TRHQVALQVAMAEHLIECDDHDTAQQIILDGLKR  292 (398)
T ss_pred             HHHhCCHH-HhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            44443222 2335566666777777777777777777666553

>PF12854 PPR_1: PPR repeat

Probab=99.19  E-value=3.4e-11  Score=61.16  Aligned_cols=32  Identities=28%  Similarity=0.626  Sum_probs=17.2

Q ss_pred             CCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHH
Q 039342           18 GVARNSDSFNAVIEAFRQGGRFEEAIKAYVEM   49 (248)
Q Consensus        18 g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m   49 (248)
                      |+.||..|||+||++||+.|++++|.++|++|
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M   33 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEM   33 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence            44555555555555555555555555555554

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.18  E-value=3.6e-08  Score=87.78  Aligned_cols=216  Identities=15%  Similarity=0.020  Sum_probs=151.0

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |+.++|...|.+....  .|+......+...+...|++++|...|+++...  +|+...+..+..++.+.|++++|...+
T Consensus       490 ~~~~eAi~a~~~Al~~--~Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~--~p~~~a~~~la~all~~Gd~~eA~~~l  565 (987)
T PRK09782        490 TLPGVALYAWLQAEQR--QPDAWQHRAVAYQAYQVEDYATALAAWQKISLH--DMSNEDLLAAANTAQAAGNGAARDRWL  565 (987)
T ss_pred             CCcHHHHHHHHHHHHh--CCchHHHHHHHHHHHHCCCHHHHHHHHHHHhcc--CCCcHHHHHHHHHHHHCCCHHHHHHHH
Confidence            4566788877766553  255444333444456889999999999887543  455555667777888899999999999


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCC
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYG  161 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~  161 (248)
                      ++..+.. +++...+..+.....+.|++++|...+++..+..  |+...+..+- ..+.+.|++++|...++........
T Consensus       566 ~qAL~l~-P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l~--P~~~a~~~LA-~~l~~lG~~deA~~~l~~AL~l~Pd  641 (987)
T PRK09782        566 QQAEQRG-LGDNALYWWLHAQRYIPGQPELALNDLTRSLNIA--PSANAYVARA-TIYRQRHNVPAAVSDLRAALELEPN  641 (987)
T ss_pred             HHHHhcC-CccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhC--CCHHHHHHHH-HHHHHCCCHHHHHHHHHHHHHhCCC
Confidence            9888754 2233333334444456699999999999887655  5544444443 3377788899999999988877533


Q ss_pred             CCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCc-chhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          162 LGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPEL-FRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       162 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                       +...++.+-.++...|+.++|.+.+++..+.  .|+. ..+..+-     ..+...|++++|...+++-.+.
T Consensus       642 -~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l--~P~~~~a~~nLA-----~al~~lGd~~eA~~~l~~Al~l  706 (987)
T PRK09782        642 -NSNYQAALGYALWDSGDIAQSREMLERAHKG--LPDDPALIRQLA-----YVNQRLDDMAATQHYARLVIDD  706 (987)
T ss_pred             -CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHH-----HHHHHCCCHHHHHHHHHHHHhc
Confidence             5667778888899999999999999987764  5542 2223333     5677889999998888877654

>PF12854 PPR_1: PPR repeat

Probab=99.18  E-value=3.4e-11  Score=61.14  Aligned_cols=32  Identities=41%  Similarity=0.762  Sum_probs=15.9

Q ss_pred             CCCCCHHHHHHHHHHHHhcCChhHHHHHHHHH
Q 039342           53 RCDPNERTLEAVLSVYCFAGLVDESKEQFQEI   84 (248)
Q Consensus        53 ~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m   84 (248)
                      |+.||..|||+||++||+.|++++|.++|++|
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            44455555555555555555555555554444

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

Probab=99.16  E-value=2.2e-07  Score=72.29  Aligned_cols=135  Identities=11%  Similarity=-0.032  Sum_probs=93.9

Q ss_pred             HhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHH-HHhcCCCCCHHHHHHHH
Q 039342           93 VMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDK-LNCEGYGLGMRFYNALL  171 (248)
Q Consensus        93 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~-m~~~~~~p~~~~~~~li  171 (248)
                      +..-.+++.-+.+.|+.++|.++..+-.+.+..|....   ++.  +...++.+.-.+..+. +...+..|  ..+.++-
T Consensus       263 p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L~~---~~~--~l~~~d~~~l~k~~e~~l~~h~~~p--~L~~tLG  335 (400)
T COG3071         263 PELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRLCR---LIP--RLRPGDPEPLIKAAEKWLKQHPEDP--LLLSTLG  335 (400)
T ss_pred             hhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhHHH---HHh--hcCCCCchHHHHHHHHHHHhCCCCh--hHHHHHH
Confidence            44455556666777777777777777777665555222   221  2233344444444433 33445555  7788899


Q ss_pred             HHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHHHcCCCCC
Q 039342          172 EALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDLP  241 (248)
Q Consensus       172 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~~~~~~~~  241 (248)
                      +.|.+.+.|.+|.+.|+...+  ..|+..+|+.+-     +.+.+.|+..++....++-.-.-.+|+.+.
T Consensus       336 ~L~~k~~~w~kA~~~leaAl~--~~~s~~~~~~la-----~~~~~~g~~~~A~~~r~e~L~~~~~~~~~s  398 (400)
T COG3071         336 RLALKNKLWGKASEALEAALK--LRPSASDYAELA-----DALDQLGEPEEAEQVRREALLLTRQPNLPS  398 (400)
T ss_pred             HHHHHhhHHHHHHHHHHHHHh--cCCChhhHHHHH-----HHHHHcCChHHHHHHHHHHHHHhcCCCCcc
Confidence            999999999999999996655  489999999998     788899999999998888776666665543

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.12  E-value=9.7e-08  Score=84.00  Aligned_cols=224  Identities=11%  Similarity=0.038  Sum_probs=157.9

Q ss_pred             HHHHHHHHHHHHc-CCCCCHH-hH----HHHHHHHHhcCCHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHhcCChhHH
Q 039342            5 KECQAILSRMSES-GVARNSD-SF----NAVIEAFRQGGRFEEAIKAYVEMEKVRCD-PNERTLEAVLSVYCFAGLVDES   77 (248)
Q Consensus         5 ~~a~~~~~~m~~~-g~~~~~~-~y----~~li~~~~~~~~~~~a~~~~~~m~~~~~~-p~~~t~~~ll~~~~~~g~~~~a   77 (248)
                      ++|++.++.+.+. ...|+.. .+    ...+..+...|++++|.+.|+.+.+.+-+ |+. .-..+..+|...|++++|
T Consensus       213 d~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l~~Ll~~g~~~eA~~~~~~ll~~~~~~P~~-a~~~la~~yl~~g~~e~A  291 (765)
T PRK10049        213 DRALAQYDALEALWHDNPDATADYQRARIDRLGALLARDRYKDVISEYQRLKAEGQIIPPW-AQRWVASAYLKLHQPEKA  291 (765)
T ss_pred             HHHHHHHHHHHhhcccCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhccCCCCCHH-HHHHHHHHHHhcCCcHHH
Confidence            6788888888753 2223221 11    11144556779999999999999887632 432 222257789999999999


Q ss_pred             HHHHHHHHHCCCCc---CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCC-----------CchHH--hHHHHhcccccc
Q 039342           78 KEQFQEIKSSGILP---SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRI-----------SNIHQ--VTGQMIKGEFDD  141 (248)
Q Consensus        78 ~~~~~~m~~~~~~p---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-----------~~~~~--~~~~~l~~~~~~  141 (248)
                      ..+|+++.+.....   ....+..+..++...|++++|...++++.+..-           .|+..  ....+....+..
T Consensus       292 ~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~  371 (765)
T PRK10049        292 QSILTELFYHPETIADLSDEELADLFYSLLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKY  371 (765)
T ss_pred             HHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHH
Confidence            99999987643111   134567777789999999999999999986531           12221  122233334667


Q ss_pred             cchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcch-hhhHHhhhhhhccccchHH
Q 039342          142 ESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFR-HNKLVWSVDVHRMWEGGAY  220 (248)
Q Consensus       142 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t-~~~li~~~~~~~~~~~g~~  220 (248)
                      .|++++|..+++++..... -+...+..+...+...|+.++|.+.+++....  .|+... +-...     ..+...|++
T Consensus       372 ~g~~~eA~~~l~~al~~~P-~n~~l~~~lA~l~~~~g~~~~A~~~l~~al~l--~Pd~~~l~~~~a-----~~al~~~~~  443 (765)
T PRK10049        372 SNDLPQAEMRARELAYNAP-GNQGLRIDYASVLQARGWPRAAENELKKAEVL--EPRNINLEVEQA-----WTALDLQEW  443 (765)
T ss_pred             cCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhh--CCCChHHHHHHH-----HHHHHhCCH
Confidence            7999999999999887643 35788889999999999999999999998774  576432 22222     356678899


Q ss_pred             HHHHHHHHHHHHHHHcCCC
Q 039342          221 TAISVWLNKMYEMFMMGED  239 (248)
Q Consensus       221 ~~~~~~~~~m~~~~~~~~~  239 (248)
                      ++|+.+++++.+.  .|+.
T Consensus       444 ~~A~~~~~~ll~~--~Pd~  460 (765)
T PRK10049        444 RQMDVLTDDVVAR--EPQD  460 (765)
T ss_pred             HHHHHHHHHHHHh--CCCC
Confidence            9999999999885  5543

>PRK12370 invasion protein regulator; Provisional

Probab=99.12  E-value=5.3e-08  Score=82.56  Aligned_cols=216  Identities=13%  Similarity=0.054  Sum_probs=149.1

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|...+++..+... -+...|..+-..+...|++++|...|++..+.+ +.+...+..+-.++...|++++|...+
T Consensus       318 ~~~~~A~~~~~~Al~ldP-~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~G~~~eAi~~~  395 (553)
T PRK12370        318 NAMIKAKEHAIKATELDH-NNPQALGLLGLINTIHSEYIVGSLLFKQANLLS-PISADIKYYYGWNLFMAGQLEEALQTI  395 (553)
T ss_pred             hHHHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            457899999999887542 367788888888899999999999999998765 345677888889999999999999999


Q ss_pred             HHHHHCCCCcCH-hhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCC
Q 039342           82 QEIKSSGILPSV-MCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGY  160 (248)
Q Consensus        82 ~~m~~~~~~p~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~  160 (248)
                      ++..+..  |+. ..+..+...+...|++++|...+++..+.. .|+.......+..++...|+.++|...+..+.....
T Consensus       396 ~~Al~l~--P~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~-~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~~~  472 (553)
T PRK12370        396 NECLKLD--PTRAAAGITKLWITYYHTGIDDAIRLGDELRSQH-LQDNPILLSMQVMFLSLKGKHELARKLTKEISTQEI  472 (553)
T ss_pred             HHHHhcC--CCChhhHHHHHHHHHhccCHHHHHHHHHHHHHhc-cccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhccc
Confidence            9998763  432 233444555677899999999999987653 244444444444446678999999999988755422


Q ss_pred             CCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHC-CCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          161 GLGMRFYNALLEALWCLGLRERAARVLDEATKR-GLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       161 ~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                       .+....+.+...|+..|  ++|...++.+.+. .-.|.......++       |.-.|+-+.+..+ +++.+.
T Consensus       473 -~~~~~~~~l~~~~~~~g--~~a~~~l~~ll~~~~~~~~~~~~~~~~-------~~~~g~~~~~~~~-~~~~~~  535 (553)
T PRK12370        473 -TGLIAVNLLYAEYCQNS--ERALPTIREFLESEQRIDNNPGLLPLV-------LVAHGEAIAEKMW-NKFKNE  535 (553)
T ss_pred             -hhHHHHHHHHHHHhccH--HHHHHHHHHHHHHhhHhhcCchHHHHH-------HHHHhhhHHHHHH-HHhhcc
Confidence             13344455666677777  4888877776542 2223222223333       3344555544444 666554

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.12  E-value=5.6e-08  Score=89.18  Aligned_cols=225  Identities=10%  Similarity=-0.018  Sum_probs=146.1

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|++.|++..+... -+...+..+...|.+.|++++|...+++..+.. +-+...+..+...+.+.++.++|...+
T Consensus       475 g~~~eA~~~~~~Al~~~P-~~~~~~~~LA~~~~~~G~~~~A~~~l~~al~~~-P~~~~~~~a~al~l~~~~~~~~Al~~l  552 (1157)
T PRK11447        475 GKWAQAAELQRQRLALDP-GSVWLTYRLAQDLRQAGQRSQADALMRRLAQQK-PNDPEQVYAYGLYLSGSDRDRAALAHL  552 (1157)
T ss_pred             CCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHhCCCHHHHHHHH
Confidence            788999999999887542 256778888889999999999999999987543 223333322223334444444444444


Q ss_pred             HHHHHC---------------------------------------CCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 039342           82 QEIKSS---------------------------------------GILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTN  122 (248)
Q Consensus        82 ~~m~~~---------------------------------------~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  122 (248)
                      +.+...                                       ..+++...+..+-..+.+.|+.++|+..|++..+.
T Consensus       553 ~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~~l~~~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~  632 (1157)
T PRK11447        553 NTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEALLRQQPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTR  632 (1157)
T ss_pred             HhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHHHHHhCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            332110                                       11234556677788888889999999999988775


Q ss_pred             CCCchH-HhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcch
Q 039342          123 RISNIH-QVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFR  201 (248)
Q Consensus       123 ~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t  201 (248)
                      .  |+. .....+... +...|++++|...++...+... .+..+...+..++...|++++|.++++.+....-......
T Consensus       633 ~--P~~~~a~~~la~~-~~~~g~~~eA~~~l~~ll~~~p-~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~~~~~~~~  708 (1157)
T PRK11447        633 E--PGNADARLGLIEV-DIAQGDLAAARAQLAKLPATAN-DSLNTQRRVALAWAALGDTAAAQRTFNRLIPQAKSQPPSM  708 (1157)
T ss_pred             C--CCCHHHHHHHHHH-HHHCCCHHHHHHHHHHHhccCC-CChHHHHHHHHHHHhCCCHHHHHHHHHHHhhhCccCCcch
Confidence            4  443 333344433 6677888999999987765422 2345566677788889999999999998876421111111


Q ss_pred             hhhHHhhhhhhccccchHHHHHHHHHHHHHH
Q 039342          202 HNKLVWSVDVHRMWEGGAYTAISVWLNKMYE  232 (248)
Q Consensus       202 ~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~  232 (248)
                      .+.++.......+...|+.++|...++.-..
T Consensus       709 ~~a~~~~~~a~~~~~~G~~~~A~~~y~~Al~  739 (1157)
T PRK11447        709 ESALVLRDAARFEAQTGQPQQALETYKDAMV  739 (1157)
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            1233333233566788899999888776643

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

Probab=99.11  E-value=5.9e-08  Score=73.53  Aligned_cols=225  Identities=13%  Similarity=0.093  Sum_probs=150.1

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHc-CCCCCH--HHHHHHHHHHHhcCChhHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKV-RCDPNE--RTLEAVLSVYCFAGLVDES   77 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~-~~~p~~--~t~~~ll~~~~~~g~~~~a   77 (248)
                      +++.++|.++|.+|.+... -+..+--+|-+.|-+.|.++.|+.+...+.++ +.+.+.  ...-.|-.-|.+.|-+|.|
T Consensus        48 s~Q~dKAvdlF~e~l~~d~-~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DRA  126 (389)
T COG2956          48 SNQPDKAVDLFLEMLQEDP-ETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDRA  126 (389)
T ss_pred             hcCcchHHHHHHHHHhcCc-hhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhHH
Confidence            3577999999999987332 24556667888899999999999999998764 222221  1223455668899999999


Q ss_pred             HHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhH---HHHhcccccccchHHHHHHHHHH
Q 039342           78 KEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVT---GQMIKGEFDDESNWQMVEYVFDK  154 (248)
Q Consensus        78 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~---~~~l~~~~~~~~~~~~a~~~~~~  154 (248)
                      +++|..+.+.+. .-......|+..|-...+|++|+++-+++.+.+-.+...-+   .+=+.-......+.+.|..++..
T Consensus       127 E~~f~~L~de~e-fa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~k  205 (389)
T COG2956         127 EDIFNQLVDEGE-FAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLKK  205 (389)
T ss_pred             HHHHHHHhcchh-hhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHH
Confidence            999999987542 24567788999999999999999999998877655443322   22122213445566777777776


Q ss_pred             HHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          155 LNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       155 m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      ..+.+.+ .+..--.+-+.....|++..|.+.++...+.+-.     |-..+-..+..+|...|+.++...++..+.+.
T Consensus       206 Alqa~~~-cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~-----yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~  278 (389)
T COG2956         206 ALQADKK-CVRASIILGRVELAKGDYQKAVEALERVLEQNPE-----YLSEVLEMLYECYAQLGKPAEGLNFLRRAMET  278 (389)
T ss_pred             HHhhCcc-ceehhhhhhHHHHhccchHHHHHHHHHHHHhChH-----HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHc
Confidence            6655332 1222223445667777888888887777665322     23333333337777777777777666666554

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.06  E-value=1.4e-07  Score=86.61  Aligned_cols=117  Identities=10%  Similarity=0.080  Sum_probs=86.7

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHH------------------
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEA------------------   63 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~------------------   63 (248)
                      |++++|++.|++..+... .+...+..+-..+...|++++|.+.|++..+.. +.+...+..                  
T Consensus       365 g~~~eA~~~~~~Al~~~P-~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~-p~~~~a~~~L~~l~~~~~~~~A~~~l~  442 (1157)
T PRK11447        365 NNLAQAERLYQQARQVDN-TDSYAVLGLGDVAMARKDYAAAERYYQQALRMD-PGNTNAVRGLANLYRQQSPEKALAFIA  442 (1157)
T ss_pred             CCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCHHHHHHHHH
Confidence            678889999998877542 356677778888899999999999998887543 122222222                  


Q ss_pred             ------------------------HHHHHHhcCChhHHHHHHHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHH
Q 039342           64 ------------------------VLSVYCFAGLVDESKEQFQEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDE  118 (248)
Q Consensus        64 ------------------------ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~  118 (248)
                                              +...+...|++++|.+.|++..+..  | +...+..+...|.+.|++++|...+++
T Consensus       443 ~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~--P~~~~~~~~LA~~~~~~G~~~~A~~~l~~  520 (1157)
T PRK11447        443 SLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLALD--PGSVWLTYRLAQDLRQAGQRSQADALMRR  520 (1157)
T ss_pred             hCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence                                    2233456788899999998887653  4 556777888899999999999999998


Q ss_pred             HHHC
Q 039342          119 MHTN  122 (248)
Q Consensus       119 m~~~  122 (248)
                      ..+.
T Consensus       521 al~~  524 (1157)
T PRK11447        521 LAQQ  524 (1157)
T ss_pred             HHHc
Confidence            8654

>TIGR00540 hemY_coli hemY protein

Probab=99.02  E-value=7.6e-07  Score=72.82  Aligned_cols=188  Identities=13%  Similarity=0.102  Sum_probs=129.5

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHH-hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHH--HHHHHHHHHHhcCChhHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSD-SFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNER--TLEAVLSVYCFAGLVDES   77 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~-~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~--t~~~ll~~~~~~g~~~~a   77 (248)
                      .|+++.|++.+....+..  |+.. .|-..-.+..+.|+.+.|.+.+.+..+..  |+..  ..-.....+...|+++.|
T Consensus        97 ~g~~~~A~~~l~~~~~~~--~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~--p~~~l~~~~~~a~l~l~~~~~~~A  172 (409)
T TIGR00540        97 EGDYAKAEKLIAKNADHA--AEPVLNLIKAAEAAQQRGDEARANQHLEEAAELA--GNDNILVEIARTRILLAQNELHAA  172 (409)
T ss_pred             CCCHHHHHHHHHHHhhcC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CcCchHHHHHHHHHHHHCCCHHHH
Confidence            489999999998877643  5433 33444566778899999999999986543  5443  334457888899999999


Q ss_pred             HHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhccc--ccccchHHHHHHHHHHH
Q 039342           78 KEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGE--FDDESNWQMVEYVFDKL  155 (248)
Q Consensus        78 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~--~~~~~~~~~a~~~~~~m  155 (248)
                      .+.++.+.+.. +-+..+...+...+...|++++|.+.+..+.+.+..+.......-....  ....+..+.....+..+
T Consensus       173 l~~l~~l~~~~-P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~  251 (409)
T TIGR00540       173 RHGVDKLLEMA-PRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDEAMADEGIDGLLNW  251 (409)
T ss_pred             HHHHHHHHHhC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHH
Confidence            99999999874 2266789999999999999999999999999887554333211111110  00111111112223222


Q ss_pred             HhcC---CCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHC
Q 039342          156 NCEG---YGLGMRFYNALLEALWCLGLRERAARVLDEATKR  193 (248)
Q Consensus       156 ~~~~---~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  193 (248)
                      .+..   .+.+...+..+...+...|+.+.|.+++++..+.
T Consensus       252 ~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~  292 (409)
T TIGR00540       252 WKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKK  292 (409)
T ss_pred             HHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhh
Confidence            2221   1236778888888899999999999999887765

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

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.01  E-value=2.3e-07  Score=81.64  Aligned_cols=191  Identities=13%  Similarity=0.013  Sum_probs=144.5

Q ss_pred             CchHHHHHHHHHHHHcCCC-CC-HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHHHhcCChhH
Q 039342            2 GLYKECQAILSRMSESGVA-RN-SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDP---NERTLEAVLSVYCFAGLVDE   76 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~-~~-~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p---~~~t~~~ll~~~~~~g~~~~   76 (248)
                      |++++|++.|+.+.+.+.+ |+ ...+  +-..|...|++++|...|++..+..-..   .......+..++...|++++
T Consensus       251 g~~~eA~~~~~~ll~~~~~~P~~a~~~--la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~e  328 (765)
T PRK10049        251 DRYKDVISEYQRLKAEGQIIPPWAQRW--VASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLESENYPG  328 (765)
T ss_pred             hhHHHHHHHHHHhhccCCCCCHHHHHH--HHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccHHH
Confidence            6789999999999887632 33 2233  4668999999999999999987543111   13456667778899999999


Q ss_pred             HHHHHHHHHHCCC-----------CcC---HhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhccccccc
Q 039342           77 SKEQFQEIKSSGI-----------LPS---VMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDE  142 (248)
Q Consensus        77 a~~~~~~m~~~~~-----------~p~---~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~  142 (248)
                      |.++++.+.+...           .|+   ...+..+...+...|+.++|+..++++....  |+.......+...+...
T Consensus       329 A~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~--P~n~~l~~~lA~l~~~~  406 (765)
T PRK10049        329 ALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNA--PGNQGLRIDYASVLQAR  406 (765)
T ss_pred             HHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHhc
Confidence            9999999986521           123   2345677788899999999999999997664  65555554444457788


Q ss_pred             chHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCc
Q 039342          143 SNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPEL  199 (248)
Q Consensus       143 ~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  199 (248)
                      |+++.|+..++....... -+...+......+...|++++|..+++++.+.  .|+.
T Consensus       407 g~~~~A~~~l~~al~l~P-d~~~l~~~~a~~al~~~~~~~A~~~~~~ll~~--~Pd~  460 (765)
T PRK10049        407 GWPRAAENELKKAEVLEP-RNINLEVEQAWTALDLQEWRQMDVLTDDVVAR--EPQD  460 (765)
T ss_pred             CCHHHHHHHHHHHHhhCC-CChHHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CCCC
Confidence            999999999998887652 23566667777899999999999999999874  5653

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

Probab=98.96  E-value=1.4e-07  Score=77.64  Aligned_cols=216  Identities=12%  Similarity=0.120  Sum_probs=135.5

Q ss_pred             hHHHHHHHHHHHHcCCCCCH-HhHHHHHHHHHhcCCHHHHHHHHHHHHHcC-----------------------------
Q 039342            4 YKECQAILSRMSESGVARNS-DSFNAVIEAFRQGGRFEEAIKAYVEMEKVR-----------------------------   53 (248)
Q Consensus         4 ~~~a~~~~~~m~~~g~~~~~-~~y~~li~~~~~~~~~~~a~~~~~~m~~~~-----------------------------   53 (248)
                      .++|...|..+.+.-  +|+ ....-+-.+|...+++++|.++|+..++..                             
T Consensus       335 ~~~A~~~~~klp~h~--~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~Ls~Laq~  412 (638)
T KOG1126|consen  335 CREALNLFEKLPSHH--YNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVALSYLAQD  412 (638)
T ss_pred             HHHHHHHHHhhHHhc--CCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhHHHHHHHHH
Confidence            345666666644322  222 334445556666667777777776665432                             


Q ss_pred             ----CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchH
Q 039342           54 ----CDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIH  128 (248)
Q Consensus        54 ----~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~  128 (248)
                          -+-.+.||.++-++|.-.++.+.|.+.|++..+.  .| ...+|+.+=.-++....+|.|..-|+.....  .|.+
T Consensus       413 Li~~~~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQl--dp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~--~~rh  488 (638)
T KOG1126|consen  413 LIDTDPNSPESWCALGNCFSLQKDHDTAIKCFKRAIQL--DPRFAYAYTLLGHESIATEEFDKAMKSFRKALGV--DPRH  488 (638)
T ss_pred             HHhhCCCCcHHHHHhcchhhhhhHHHHHHHHHHHhhcc--CCccchhhhhcCChhhhhHHHHhHHHHHHhhhcC--Cchh
Confidence                1345577888888888888888888888887764  34 5677777777777778888888888765432  2332


Q ss_pred             H-hHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHh
Q 039342          129 Q-VTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVW  207 (248)
Q Consensus       129 ~-~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~  207 (248)
                      . .|..+ --.+.+.+.++.|+..|+...+-+.. +.+....+...+-+.|+.|+|++++++...-  .|.    +.+-.
T Consensus       489 YnAwYGl-G~vy~Kqek~e~Ae~~fqkA~~INP~-nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~l--d~k----n~l~~  560 (638)
T KOG1126|consen  489 YNAWYGL-GTVYLKQEKLEFAEFHFQKAVEINPS-NSVILCHIGRIQHQLKRKDKALQLYEKAIHL--DPK----NPLCK  560 (638)
T ss_pred             hHHHHhh-hhheeccchhhHHHHHHHhhhcCCcc-chhHHhhhhHHHHHhhhhhHHHHHHHHHHhc--CCC----CchhH
Confidence            2 12222 22266777778888888776665443 5566667777778888888888888876542  222    11111


Q ss_pred             hhhhhccccchHHHHHHHHHHHHHHH
Q 039342          208 SVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       208 ~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      --..+.+...++.++|...|+++++-
T Consensus       561 ~~~~~il~~~~~~~eal~~LEeLk~~  586 (638)
T KOG1126|consen  561 YHRASILFSLGRYVEALQELEELKEL  586 (638)
T ss_pred             HHHHHHHHhhcchHHHHHHHHHHHHh
Confidence            11113445667778888888887765

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

Probab=98.96  E-value=1.8e-06  Score=71.18  Aligned_cols=230  Identities=15%  Similarity=0.180  Sum_probs=168.0

Q ss_pred             CchHHHHHHHHHHHHcCCCCC-HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARN-SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~-~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      |.+|.|.+.+++..+  +.|+ ...||.|-.++-..|++.+|.+.|++..... +--....+.|-..|...|.++.|..+
T Consensus       300 G~ldlAI~~Ykral~--~~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l~-p~hadam~NLgni~~E~~~~e~A~~l  376 (966)
T KOG4626|consen  300 GLLDLAIDTYKRALE--LQPNFPDAYNNLANALKDKGSVTEAVDCYNKALRLC-PNHADAMNNLGNIYREQGKIEEATRL  376 (966)
T ss_pred             ccHHHHHHHHHHHHh--cCCCchHHHhHHHHHHHhccchHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhccchHHHHH
Confidence            788999999998877  3465 6799999999999999999999999987642 22346788899999999999999999


Q ss_pred             HHHHHHCCCCcC-HhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcC
Q 039342           81 FQEIKSSGILPS-VMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEG  159 (248)
Q Consensus        81 ~~~m~~~~~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~  159 (248)
                      |....+.  .|. ...+|.|-..|-..|++++|+.-+++...  +.|+-.--..-+-..+...|+.+.|.+.+.+....+
T Consensus       377 y~~al~v--~p~~aaa~nNLa~i~kqqgnl~~Ai~~Ykealr--I~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~~n  452 (966)
T KOG4626|consen  377 YLKALEV--FPEFAAAHNNLASIYKQQGNLDDAIMCYKEALR--IKPTFADALSNMGNTYKEMGDVSAAIQCYTRAIQIN  452 (966)
T ss_pred             HHHHHhh--ChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHh--cCchHHHHHHhcchHHHHhhhHHHHHHHHHHHHhcC
Confidence            9888774  343 56789999999999999999999998774  457654433334444778888999999888776643


Q ss_pred             CCCC-HHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcc-hhhhHHhhhhhhcccc--chHHHHHHHHHHHHHHHHH
Q 039342          160 YGLG-MRFYNALLEALWCLGLRERAARVLDEATKRGLFPELF-RHNKLVWSVDVHRMWE--GGAYTAISVWLNKMYEMFM  235 (248)
Q Consensus       160 ~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~-t~~~li~~~~~~~~~~--~g~~~~~~~~~~~m~~~~~  235 (248)
                        |+ ...++.|-+.|-..|++.+|.+-|++..+  ++||.. .|..++.++-.-..+.  ..++++...+.++-.++..
T Consensus       453 --Pt~AeAhsNLasi~kDsGni~~AI~sY~~aLk--lkPDfpdA~cNllh~lq~vcdw~D~d~~~~kl~sivrdql~~~r  528 (966)
T KOG4626|consen  453 --PTFAEAHSNLASIYKDSGNIPEAIQSYRTALK--LKPDFPDAYCNLLHCLQIVCDWTDYDKRMKKLVSIVRDQLEKNR  528 (966)
T ss_pred             --cHHHHHHhhHHHHhhccCCcHHHHHHHHHHHc--cCCCCchhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHHhhhc
Confidence              43 56688899999999999999999998775  467653 2333432221111121  2344555555555554445


Q ss_pred             cCCCCCc
Q 039342          236 MGEDLPQ  242 (248)
Q Consensus       236 ~~~~~~~  242 (248)
                      -|.--|+
T Consensus       529 lpsvhP~  535 (966)
T KOG4626|consen  529 LPSVHPH  535 (966)
T ss_pred             CCccCcc
Confidence            5554443

>PRK14574 hmsH outer membrane protein; Provisional

Probab=98.93  E-value=5.9e-07  Score=78.70  Aligned_cols=160  Identities=13%  Similarity=0.071  Sum_probs=75.9

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCC-----CCcCHhhHHHHHHHH
Q 039342           29 VIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSG-----ILPSVMCYCMLLAVY  103 (248)
Q Consensus        29 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~-----~~p~~~~~~~li~~~  103 (248)
                      .+-++.+.|++.++.+.|+.+...+.+.-..+-..+.++|...+++++|..+++++....     ..++......|.-+|
T Consensus       298 rl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~  377 (822)
T PRK14574        298 RLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSL  377 (822)
T ss_pred             HHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHH
Confidence            344455555555555555555555544333344555555555555555555555553321     112223344555555


Q ss_pred             HhcCCHHHHHHHHHHHHHCCC-------------CchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHH
Q 039342          104 AKSNRWDDAYGLLDEMHTNRI-------------SNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNAL  170 (248)
Q Consensus       104 ~~~~~~~~a~~~~~~m~~~~~-------------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l  170 (248)
                      ..++++++|..+++++.+..-             .|+-.....+....+...|+...|++.++.+..... -|......+
T Consensus       378 ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~gdl~~Ae~~le~l~~~aP-~n~~l~~~~  456 (822)
T PRK14574        378 NESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVALNDLPTAQKKLEDLSSTAP-ANQNLRIAL  456 (822)
T ss_pred             HhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHH
Confidence            555555555555555544110             012222222333334444555555555555544322 245555555


Q ss_pred             HHHHHhcCchHHHHHHHHH
Q 039342          171 LEALWCLGLRERAARVLDE  189 (248)
Q Consensus       171 i~~~~~~g~~~~a~~~~~~  189 (248)
                      -+.+...|.+.+|.+.++.
T Consensus       457 A~v~~~Rg~p~~A~~~~k~  475 (822)
T PRK14574        457 ASIYLARDLPRKAEQELKA  475 (822)
T ss_pred             HHHHHhcCCHHHHHHHHHH
Confidence            5555555555555555543

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

Probab=98.93  E-value=2.9e-08  Score=84.17  Aligned_cols=86  Identities=17%  Similarity=0.135  Sum_probs=66.3

Q ss_pred             CcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHH
Q 039342           90 LPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNA  169 (248)
Q Consensus        90 ~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~  169 (248)
                      .|++.+|.+++..-..+|+.+.|..++.+|.+.|.+.+..-|+.++.+    .++...++.++..|.+.|+.|+..|+..
T Consensus       201 ~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfpir~HyFwpLl~g----~~~~q~~e~vlrgmqe~gv~p~seT~ad  276 (1088)
T KOG4318|consen  201 APTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIRAHYFWPLLLG----INAAQVFEFVLRGMQEKGVQPGSETQAD  276 (1088)
T ss_pred             CCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCcccccchhhhhc----CccchHHHHHHHHHHHhcCCCCcchhHH
Confidence            477888888888888888888888888888888887777777777765    4556777777888888888888888887


Q ss_pred             HHHHHHhcCc
Q 039342          170 LLEALWCLGL  179 (248)
Q Consensus       170 li~~~~~~g~  179 (248)
                      -+..+.+.|.
T Consensus       277 yvip~l~N~~  286 (1088)
T KOG4318|consen  277 YVIPQLSNGQ  286 (1088)
T ss_pred             HHHhhhcchh
Confidence            7777776544

>PRK14574 hmsH outer membrane protein; Provisional

Probab=98.92  E-value=2.2e-06  Score=75.26  Aligned_cols=194  Identities=10%  Similarity=0.005  Sum_probs=156.3

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcC-----CCCCHHHHHHHHHHHHhcCChhH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVR-----CDPNERTLEAVLSVYCFAGLVDE   76 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~-----~~p~~~t~~~ll~~~~~~g~~~~   76 (248)
                      |+..++.+.|+.+...|.+....+-..+-++|...+++++|..+|+......     ..++......|..+|...+++++
T Consensus       306 ~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~  385 (822)
T PRK14574        306 HQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDK  385 (822)
T ss_pred             hhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHH
Confidence            6789999999999998876667788899999999999999999999986543     23345556789999999999999


Q ss_pred             HHHHHHHHHHCCC-----------CcC---HhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhccccccc
Q 039342           77 SKEQFQEIKSSGI-----------LPS---VMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDE  142 (248)
Q Consensus        77 a~~~~~~m~~~~~-----------~p~---~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~  142 (248)
                      |..+++.+.+...           .|+   ...+..++..++..|++.+|++.++++....  |.+.-+...........
T Consensus       386 A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~gdl~~Ae~~le~l~~~a--P~n~~l~~~~A~v~~~R  463 (822)
T PRK14574        386 AYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVALNDLPTAQKKLEDLSSTA--PANQNLRIALASIYLAR  463 (822)
T ss_pred             HHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHhc
Confidence            9999999987311           122   1345567888899999999999999997664  77766666666668889


Q ss_pred             chHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcc
Q 039342          143 SNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELF  200 (248)
Q Consensus       143 ~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  200 (248)
                      |.+..|+..++........ +..+......++...++++.|..+.+.+.+.  .|+..
T Consensus       464 g~p~~A~~~~k~a~~l~P~-~~~~~~~~~~~al~l~e~~~A~~~~~~l~~~--~Pe~~  518 (822)
T PRK14574        464 DLPRKAEQELKAVESLAPR-SLILERAQAETAMALQEWHQMELLTDDVISR--SPEDI  518 (822)
T ss_pred             CCHHHHHHHHHHHhhhCCc-cHHHHHHHHHHHHhhhhHHHHHHHHHHHHhh--CCCch
Confidence            9999999999777666322 5677778888999999999999999988764  66643

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

Probab=98.91  E-value=2e-06  Score=65.44  Aligned_cols=186  Identities=14%  Similarity=0.106  Sum_probs=132.7

Q ss_pred             CchHHHHHHHHHHHHcCCCCCH------HhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChh
Q 039342            2 GLYKECQAILSRMSESGVARNS------DSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVD   75 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~------~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~   75 (248)
                      |.+|+|.++.+.+.++   ||.      ...-.|-.-|...|-++.|+.+|..+.+.+. .-......|+..|-...+|+
T Consensus        83 GEvDRAIRiHQ~L~~s---pdlT~~qr~lAl~qL~~Dym~aGl~DRAE~~f~~L~de~e-fa~~AlqqLl~IYQ~treW~  158 (389)
T COG2956          83 GEVDRAIRIHQTLLES---PDLTFEQRLLALQQLGRDYMAAGLLDRAEDIFNQLVDEGE-FAEGALQQLLNIYQATREWE  158 (389)
T ss_pred             chHHHHHHHHHHHhcC---CCCchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhcchh-hhHHHHHHHHHHHHHhhHHH
Confidence            6788888888877653   432      2344456667788888889888888877552 33456677888888888899


Q ss_pred             HHHHHHHHHHHCCCCcCH----hhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHH
Q 039342           76 ESKEQFQEIKSSGILPSV----MCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYV  151 (248)
Q Consensus        76 ~a~~~~~~m~~~~~~p~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  151 (248)
                      +|.++-+++.+.+-.+..    .-|--+-..+....+++.|...+++..+.+  |+..--+.++-......|+++.|.+.
T Consensus       159 KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~kAlqa~--~~cvRAsi~lG~v~~~~g~y~~AV~~  236 (389)
T COG2956         159 KAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLKKALQAD--KKCVRASIILGRVELAKGDYQKAVEA  236 (389)
T ss_pred             HHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhhC--ccceehhhhhhHHHHhccchHHHHHH
Confidence            988888888776544322    234455555556778888888888877665  44444444444445667888888888


Q ss_pred             HHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHC
Q 039342          152 FDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKR  193 (248)
Q Consensus       152 ~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  193 (248)
                      ++...+.+..--..+...|..+|...|+.++....+..+.+.
T Consensus       237 ~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~  278 (389)
T COG2956         237 LERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMET  278 (389)
T ss_pred             HHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHc
Confidence            888888876666777788888888888888888887776653

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

Probab=98.87  E-value=7e-06  Score=64.16  Aligned_cols=194  Identities=15%  Similarity=0.161  Sum_probs=146.0

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|+|.+|+++..+-.+.+-.| ...|-.-..+.-+.||.+.+-.++.+..+.--.++...+-+.-......|+.+.|..-
T Consensus        97 eG~~~qAEkl~~rnae~~e~p-~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~~aA~~~  175 (400)
T COG3071          97 EGDFQQAEKLLRRNAEHGEQP-VLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAAREN  175 (400)
T ss_pred             cCcHHHHHHHHHHhhhcCcch-HHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHHH
Confidence            489999999999987776543 5667777888888999999999999987653356667777778888999999999999


Q ss_pred             HHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchH-------HhHHHHhcccccccchHHHHHHHHH
Q 039342           81 FQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIH-------QVTGQMIKGEFDDESNWQMVEYVFD  153 (248)
Q Consensus        81 ~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~-------~~~~~~l~~~~~~~~~~~~a~~~~~  153 (248)
                      .+++.+.+.. ++........+|.+.|++.....++..|.+.+.-.+.       .++..++.. ....+..+.....++
T Consensus       176 v~~ll~~~pr-~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q-~~~~~~~~gL~~~W~  253 (400)
T COG3071         176 VDQLLEMTPR-HPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQ-ARDDNGSEGLKTWWK  253 (400)
T ss_pred             HHHHHHhCcC-ChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHH-HhccccchHHHHHHH
Confidence            9999887533 6788999999999999999999999999998875443       334445554 222222233334444


Q ss_pred             HHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCC
Q 039342          154 KLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPE  198 (248)
Q Consensus       154 ~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  198 (248)
                      ..... .+-++..-.+++.-+..+|+.++|.++..+-.+++..|+
T Consensus       254 ~~pr~-lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~  297 (400)
T COG3071         254 NQPRK-LRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPR  297 (400)
T ss_pred             hccHH-hhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChh
Confidence            43332 344556667788888888999999988888777766665

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

Probab=98.86  E-value=2.5e-06  Score=67.90  Aligned_cols=200  Identities=12%  Similarity=0.108  Sum_probs=146.5

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|.+.+.+.....-......||+=+ .+-+.|+.++|++.|-++..- +..+....-.+.+.|-...+...|.++
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            489999999999988654444444555443 356678999999999887432 234556677778888888899999988


Q ss_pred             HHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCC
Q 039342           81 FQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGY  160 (248)
Q Consensus        81 ~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~  160 (248)
                      +.+.... ++.|+...+.|-..|-+.|+-..|++.+-+--. -.+.+..+...+- ++|....-|+++...|+...  =+
T Consensus       581 ~~q~~sl-ip~dp~ilskl~dlydqegdksqafq~~ydsyr-yfp~nie~iewl~-ayyidtqf~ekai~y~ekaa--li  655 (840)
T KOG2003|consen  581 LMQANSL-IPNDPAILSKLADLYDQEGDKSQAFQCHYDSYR-YFPCNIETIEWLA-AYYIDTQFSEKAINYFEKAA--LI  655 (840)
T ss_pred             HHHhccc-CCCCHHHHHHHHHHhhcccchhhhhhhhhhccc-ccCcchHHHHHHH-HHHHhhHHHHHHHHHHHHHH--hc
Confidence            8766543 444788899999999999999999887654321 1233344444443 44777888899999988653  37


Q ss_pred             CCCHHHHHHHHHHHHh-cCchHHHHHHHHHHHHCCCCCCcchhhhHHhh
Q 039342          161 GLGMRFYNALLEALWC-LGLRERAARVLDEATKRGLFPELFRHNKLVWS  208 (248)
Q Consensus       161 ~p~~~~~~~li~~~~~-~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~  208 (248)
                      .|+..-|..+|..|.+ .|++.+|+++|++..++ ++-|..+...|+.-
T Consensus       656 qp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrk-fpedldclkflvri  703 (840)
T KOG2003|consen  656 QPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRK-FPEDLDCLKFLVRI  703 (840)
T ss_pred             CccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHh-CccchHHHHHHHHH
Confidence            8999999999887765 79999999999998765 56676666666633

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

Probab=98.86  E-value=1.8e-07  Score=77.11  Aligned_cols=195  Identities=15%  Similarity=0.068  Sum_probs=150.9

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHH--
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDP-NERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCM--   98 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~--   98 (248)
                      .+.+|.++-..|.-.++.+.|++.|++..+.  .| ...+|+.+-.-+.....+|.|...|+....    .|+..||+  
T Consensus       420 sPesWca~GNcfSLQkdh~~Aik~f~RAiQl--dp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~----~~~rhYnAwY  493 (638)
T KOG1126|consen  420 SPESWCALGNCFSLQKDHDTAIKCFKRAIQL--DPRFAYAYTLLGHESIATEEFDKAMKSFRKALG----VDPRHYNAWY  493 (638)
T ss_pred             CcHHHHHhcchhhhhhHHHHHHHHHHHhhcc--CCccchhhhhcCChhhhhHHHHhHHHHHHhhhc----CCchhhHHHH
Confidence            4678888888999999999999999998764  45 778999998889999999999999987664    45666665  


Q ss_pred             -HHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhc
Q 039342           99 -LLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCL  177 (248)
Q Consensus        99 -li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~  177 (248)
                       |--.|.+.++++.|+-.|+...+.+  |....+-.-+...+.+.+..++|.+++++......+ |+..--.-.+.+...
T Consensus       494 GlG~vy~Kqek~e~Ae~~fqkA~~IN--P~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~k-n~l~~~~~~~il~~~  570 (638)
T KOG1126|consen  494 GLGTVYLKQEKLEFAEFHFQKAVEIN--PSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPK-NPLCKYHRASILFSL  570 (638)
T ss_pred             hhhhheeccchhhHHHHHHHhhhcCC--ccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCC-CchhHHHHHHHHHhh
Confidence             4557889999999999999887654  777666665555577888899999999988776655 344444456777788


Q ss_pred             CchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHH
Q 039342          178 GLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMY  231 (248)
Q Consensus       178 g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~  231 (248)
                      ++.++|+..++++++  +.|+    +..+..++.+.|.+.|+.+.|..-|.-+.
T Consensus       571 ~~~~eal~~LEeLk~--~vP~----es~v~~llgki~k~~~~~~~Al~~f~~A~  618 (638)
T KOG1126|consen  571 GRYVEALQELEELKE--LVPQ----ESSVFALLGKIYKRLGNTDLALLHFSWAL  618 (638)
T ss_pred             cchHHHHHHHHHHHH--hCcc----hHHHHHHHHHHHHHHccchHHHHhhHHHh
Confidence            999999999999987  4776    44445555578888888887755444443

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.80  E-value=1.3e-08  Score=52.19  Aligned_cols=33  Identities=30%  Similarity=0.644  Sum_probs=25.2

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC
Q 039342           25 SFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN   57 (248)
Q Consensus        25 ~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~   57 (248)
                      +||++|.+|++.|++++|.++|++|.+.|++||
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            577777777777777777777777777777776

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.

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.77  E-value=5.4e-06  Score=64.78  Aligned_cols=182  Identities=13%  Similarity=0.065  Sum_probs=95.6

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |+.++|...|++..+... .+...|+.+-..+...|++++|.+.|+...+.. +-+..+|..+..++...|++++|.+.|
T Consensus        78 g~~~~A~~~~~~Al~l~P-~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~g~~~eA~~~~  155 (296)
T PRK11189         78 GLRALARNDFSQALALRP-DMADAYNYLGIYLTQAGNFDAAYEAFDSVLELD-PTYNYAYLNRGIALYYGGRYELAQDDL  155 (296)
T ss_pred             CCHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            566666666666655332 245666666667777777777777776665432 123455556666666667777777777


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhc-CC
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCE-GY  160 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~-~~  160 (248)
                      +...+.  .|+..........+...++.++|...|.+..... .|+... ..+... +  .++.... ..+..+.+. ..
T Consensus       156 ~~al~~--~P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~~~~-~~~~~~-~~~~~~-~--lg~~~~~-~~~~~~~~~~~~  227 (296)
T PRK11189        156 LAFYQD--DPNDPYRALWLYLAESKLDPKQAKENLKQRYEKL-DKEQWG-WNIVEF-Y--LGKISEE-TLMERLKAGATD  227 (296)
T ss_pred             HHHHHh--CCCCHHHHHHHHHHHccCCHHHHHHHHHHHHhhC-CccccH-HHHHHH-H--ccCCCHH-HHHHHHHhcCCC
Confidence            666653  2332211222222334556677777665543222 121111 111111 1  1111111 122333221 11


Q ss_pred             C----C-CHHHHHHHHHHHHhcCchHHHHHHHHHHHHC
Q 039342          161 G----L-GMRFYNALLEALWCLGLRERAARVLDEATKR  193 (248)
Q Consensus       161 ~----p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  193 (248)
                      .    | ....|..+-..+.+.|++++|...|++..+.
T Consensus       228 ~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~  265 (296)
T PRK11189        228 NTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALAN  265 (296)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            1    1 2346777778888888888888888887754

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

Probab=98.76  E-value=1.5e-07  Score=72.76  Aligned_cols=199  Identities=18%  Similarity=0.214  Sum_probs=122.9

Q ss_pred             CCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHH-HHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHH
Q 039342           20 ARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEA-VLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCM   98 (248)
Q Consensus        20 ~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~-ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~   98 (248)
                      .|.......+...+...++-+.+..-+++.......++..++.. .-..+...|+++.|.++++.-      .+......
T Consensus        63 ~~~l~av~~la~y~~~~~~~e~~l~~l~~~~~~~~~~~~~~~~~~~A~i~~~~~~~~~AL~~l~~~------~~lE~~al  136 (290)
T PF04733_consen   63 SPELQAVRLLAEYLSSPSDKESALEELKELLADQAGESNEIVQLLAATILFHEGDYEEALKLLHKG------GSLELLAL  136 (290)
T ss_dssp             SCCCHHHHHHHHHHCTSTTHHCHHHHHHHCCCTS---CHHHHHHHHHHHHCCCCHHHHHHCCCTTT------TCHHHHHH
T ss_pred             ChhHHHHHHHHHHHhCccchHHHHHHHHHHHHhccccccHHHHHHHHHHHHHcCCHHHHHHHHHcc------CcccHHHH
Confidence            45555554443333333445555555544433333333333333 335566789999998888642      36778888


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhccc---ccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHH
Q 039342           99 LLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGE---FDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALW  175 (248)
Q Consensus        99 li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~---~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  175 (248)
                      .+..|.+.++++.|.+.++.|.+.+   +..+...+..++   ......++.|..+|+++.+. ..+++.+.|.+..+..
T Consensus       137 ~Vqi~L~~~R~dlA~k~l~~~~~~~---eD~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~-~~~t~~~lng~A~~~l  212 (290)
T PF04733_consen  137 AVQILLKMNRPDLAEKELKNMQQID---EDSILTQLAEAWVNLATGGEKYQDAFYIFEELSDK-FGSTPKLLNGLAVCHL  212 (290)
T ss_dssp             HHHHHHHTT-HHHHHHHHHHHHCCS---CCHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCC-S--SHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcC---CcHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhc-cCCCHHHHHHHHHHHH
Confidence            9999999999999999999998764   333444443332   22334689999999998665 6678899999999999


Q ss_pred             hcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          176 CLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       176 ~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      ..|++++|.+++.+..+.  .|+  -..+++ +...-..-.++..+.+.+++.+++..
T Consensus       213 ~~~~~~eAe~~L~~al~~--~~~--~~d~La-Nliv~~~~~gk~~~~~~~~l~qL~~~  265 (290)
T PF04733_consen  213 QLGHYEEAEELLEEALEK--DPN--DPDTLA-NLIVCSLHLGKPTEAAERYLSQLKQS  265 (290)
T ss_dssp             HCT-HHHHHHHHHHHCCC---CC--HHHHHH-HHHHHHHHTT-TCHHHHHHHHHCHHH
T ss_pred             HhCCHHHHHHHHHHHHHh--ccC--CHHHHH-HHHHHHHHhCCChhHHHHHHHHHHHh
Confidence            999999999999986543  232  122222 22222222233336677788887765

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.

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.76  E-value=1.7e-08  Score=51.38  Aligned_cols=33  Identities=24%  Similarity=0.506  Sum_probs=20.2

Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC
Q 039342           24 DSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDP   56 (248)
Q Consensus        24 ~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p   56 (248)
                      .+||++|.+|++.|+++.|.++|++|++.|++|
T Consensus         2 ~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    2 HTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             cHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            356666666666666666666666666666555

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.73  E-value=2.3e-05  Score=61.24  Aligned_cols=220  Identities=10%  Similarity=-0.047  Sum_probs=144.5

Q ss_pred             chHHHHHHHHHHHHcC-CCCC--HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHH
Q 039342            3 LYKECQAILSRMSESG-VARN--SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKE   79 (248)
Q Consensus         3 ~~~~a~~~~~~m~~~g-~~~~--~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~   79 (248)
                      ..+.+..-+.++.... ..|+  ...|..+-..+...|++++|...|++..+.. +.+...|+.+-..+...|++++|.+
T Consensus        41 ~~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~~~~~g~~~~A~~  119 (296)
T PRK11189         41 QQEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALALR-PDMADAYNYLGIYLTQAGNFDAAYE  119 (296)
T ss_pred             HHHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            3456666777766432 2222  4567777788999999999999999987764 3467899999999999999999999


Q ss_pred             HHHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhc
Q 039342           80 QFQEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCE  158 (248)
Q Consensus        80 ~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  158 (248)
                      .|+...+.  .| +..+|..+-..+...|++++|.+.|++..+..  |+... ..+........++.++|...+......
T Consensus       120 ~~~~Al~l--~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~~--P~~~~-~~~~~~l~~~~~~~~~A~~~l~~~~~~  194 (296)
T PRK11189        120 AFDSVLEL--DPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQDD--PNDPY-RALWLYLAESKLDPKQAKENLKQRYEK  194 (296)
T ss_pred             HHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHH-HHHHHHHHHccCCHHHHHHHHHHHHhh
Confidence            99999875  35 46778888888999999999999999988754  44331 111111133456788999988665433


Q ss_pred             CCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCC-CCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          159 GYGLGMRFYNALLEALWCLGLRERAARVLDEATKRG-LFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       159 ~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      . .|+... ..+  .....|+.+.+ +.+..+.+.- -.|...--..-.|..+-..+.+.|+.++|...+++-.+.
T Consensus       195 ~-~~~~~~-~~~--~~~~lg~~~~~-~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~  265 (296)
T PRK11189        195 L-DKEQWG-WNI--VEFYLGKISEE-TLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALAN  265 (296)
T ss_pred             C-CccccH-HHH--HHHHccCCCHH-HHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            2 233221 122  22335555544 3455544321 111100001122333347788999999999999877654

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.73  E-value=2.4e-08  Score=50.84  Aligned_cols=33  Identities=36%  Similarity=0.481  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCC
Q 039342          165 RFYNALLEALWCLGLRERAARVLDEATKRGLFP  197 (248)
Q Consensus       165 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  197 (248)
                      .+|+++|++|++.|+++.|.++|++|++.|++|
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            589999999999999999999999999999988

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.72  E-value=3e-08  Score=50.79  Aligned_cols=34  Identities=32%  Similarity=0.554  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCc
Q 039342          166 FYNALLEALWCLGLRERAARVLDEATKRGLFPEL  199 (248)
Q Consensus       166 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  199 (248)
                      +||++|++|++.|++++|.++|++|.+.|+.||.
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            7999999999999999999999999999999984

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.

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=98.72  E-value=7.4e-06  Score=67.66  Aligned_cols=227  Identities=18%  Similarity=0.173  Sum_probs=155.5

Q ss_pred             CchHHHHHHHHHHHHc-----CC-CCCH-HhHHHHHHHHHhcCCHHHHHHHHHHHHHc---CCCCC----HHHHHHHHHH
Q 039342            2 GLYKECQAILSRMSES-----GV-ARNS-DSFNAVIEAFRQGGRFEEAIKAYVEMEKV---RCDPN----ERTLEAVLSV   67 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~-----g~-~~~~-~~y~~li~~~~~~~~~~~a~~~~~~m~~~---~~~p~----~~t~~~ll~~   67 (248)
                      |+++.|+.++.+..+.     |. .|.+ ...+.+-..|...+++.+|..+|+++..-   ..-++    ..+++.|-.+
T Consensus       213 g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h~~va~~l~nLa~l  292 (508)
T KOG1840|consen  213 GRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGEDHPAVAATLNNLAVL  292 (508)
T ss_pred             ccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHH
Confidence            7899999999976553     21 1232 23444666788899999999999998432   22222    3566777778


Q ss_pred             HHhcCChhHHHHHHHHHHH---C--CCC-cCH-hhHHHHHHHHHhcCCHHHHHHHHHHHHHC---CCCchH---HhHHHH
Q 039342           68 YCFAGLVDESKEQFQEIKS---S--GIL-PSV-MCYCMLLAVYAKSNRWDDAYGLLDEMHTN---RISNIH---QVTGQM  134 (248)
Q Consensus        68 ~~~~g~~~~a~~~~~~m~~---~--~~~-p~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~---~~~~~~---~~~~~~  134 (248)
                      |.+.|++++|...+++..+   .  |.. |.+ ..++.+...|...+++++|..+++...+.   -..+++   .-+..-
T Consensus       293 y~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g~~~~~~a~~~~n  372 (508)
T KOG1840|consen  293 YYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDAPGEDNVNLAKIYAN  372 (508)
T ss_pred             HhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhccccchHHHHHHHH
Confidence            9999999999988877643   1  222 233 35777888889999999999998865332   222222   222333


Q ss_pred             hcccccccchHHHHHHHHHHHHhc----CC--CC-CHHHHHHHHHHHHhcCchHHHHHHHHHHHH--CCCCCCcc----h
Q 039342          135 IKGEFDDESNWQMVEYVFDKLNCE----GY--GL-GMRFYNALLEALWCLGLRERAARVLDEATK--RGLFPELF----R  201 (248)
Q Consensus       135 l~~~~~~~~~~~~a~~~~~~m~~~----~~--~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~g~~p~~~----t  201 (248)
                      +...+...|++++|.++++...+.    +-  .+ ....++.+-..|.+.+...+|.++|.+...  .-+.|+..    +
T Consensus       373 l~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~~~~g~~~~~~~~~  452 (508)
T KOG1840|consen  373 LAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDIMKLCGPDHPDVTYT  452 (508)
T ss_pred             HHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHhCCCCCchHHH
Confidence            344477889999999999887543    11  22 245678888999999999999999987543  22334433    3


Q ss_pred             hhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          202 HNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       202 ~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      |..|.     ..|...|++++|+++.+.....
T Consensus       453 ~~nL~-----~~Y~~~g~~e~a~~~~~~~~~~  479 (508)
T KOG1840|consen  453 YLNLA-----ALYRAQGNYEAAEELEEKVLNA  479 (508)
T ss_pred             HHHHH-----HHHHHcccHHHHHHHHHHHHHH
Confidence            44444     7899999999999988877643

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

Probab=98.70  E-value=1.6e-06  Score=71.50  Aligned_cols=223  Identities=11%  Similarity=0.106  Sum_probs=118.3

Q ss_pred             CchHHHHHHHHHHHHcCCCCC-HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCChhHHHH
Q 039342            2 GLYKECQAILSRMSESGVARN-SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN-ERTLEAVLSVYCFAGLVDESKE   79 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~-~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~ll~~~~~~g~~~~a~~   79 (248)
                      |++.+|.+-|++...  +.|+ ...|-.|-..|...+.++.|...|.+....  .|+ ...|..+-..|...|.+|.|..
T Consensus       232 Gei~~aiq~y~eAvk--ldP~f~dAYiNLGnV~ke~~~~d~Avs~Y~rAl~l--rpn~A~a~gNla~iYyeqG~ldlAI~  307 (966)
T KOG4626|consen  232 GEIWLAIQHYEEAVK--LDPNFLDAYINLGNVYKEARIFDRAVSCYLRALNL--RPNHAVAHGNLACIYYEQGLLDLAID  307 (966)
T ss_pred             chHHHHHHHHHHhhc--CCCcchHHHhhHHHHHHHHhcchHHHHHHHHHHhc--CCcchhhccceEEEEeccccHHHHHH
Confidence            566667777766655  3344 456666666666667777766666665432  233 2445555555556666666666


Q ss_pred             HHHHHHHCCCCcC-HhhHHHHHHHHHhcCCHHHHHHHHHHHHHCC--------------------------------CCc
Q 039342           80 QFQEIKSSGILPS-VMCYCMLLAVYAKSNRWDDAYGLLDEMHTNR--------------------------------ISN  126 (248)
Q Consensus        80 ~~~~m~~~~~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~--------------------------------~~~  126 (248)
                      .+++..+.  .|+ ...|+.|-.++-..|++.+|.+.+.+...-.                                +.|
T Consensus       308 ~Ykral~~--~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l~p~hadam~NLgni~~E~~~~e~A~~ly~~al~v~p  385 (966)
T KOG4626|consen  308 TYKRALEL--QPNFPDAYNNLANALKDKGSVTEAVDCYNKALRLCPNHADAMNNLGNIYREQGKIEEATRLYLKALEVFP  385 (966)
T ss_pred             HHHHHHhc--CCCchHHHhHHHHHHHhccchHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhccchHHHHHHHHHHhhCh
Confidence            66555543  232 3455566666655566666655555543322                                112


Q ss_pred             hHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCC-HHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCc-chhhh
Q 039342          127 IHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLG-MRFYNALLEALWCLGLRERAARVLDEATKRGLFPEL-FRHNK  204 (248)
Q Consensus       127 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~t~~~  204 (248)
                      .-..-.+-+...+...|++++|...+++...  +.|+ ...|+.+-..|-..|+.+.|.+.+.+....  .|.. ..++.
T Consensus       386 ~~aaa~nNLa~i~kqqgnl~~Ai~~Ykealr--I~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~~--nPt~AeAhsN  461 (966)
T KOG4626|consen  386 EFAAAHNNLASIYKQQGNLDDAIMCYKEALR--IKPTFADALSNMGNTYKEMGDVSAAIQCYTRAIQI--NPTFAEAHSN  461 (966)
T ss_pred             hhhhhhhhHHHHHHhcccHHHHHHHHHHHHh--cCchHHHHHHhcchHHHHhhhHHHHHHHHHHHHhc--CcHHHHHHhh
Confidence            2221112222224555556666655555443  3343 344555666666666666666666655442  3321 12223


Q ss_pred             HHhhhhhhccccchHHHHHHHHHHHHHHHHHcCCCCC
Q 039342          205 LVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDLP  241 (248)
Q Consensus       205 li~~~~~~~~~~~g~~~~~~~~~~~m~~~~~~~~~~~  241 (248)
                      |-     ..|-..|++.+|..-+++-.+  +.||.+.
T Consensus       462 La-----si~kDsGni~~AI~sY~~aLk--lkPDfpd  491 (966)
T KOG4626|consen  462 LA-----SIYKDSGNIPEAIQSYRTALK--LKPDFPD  491 (966)
T ss_pred             HH-----HHhhccCCcHHHHHHHHHHHc--cCCCCch
Confidence            33     566777887777776665443  3666544

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

Probab=98.69  E-value=2.9e-05  Score=56.58  Aligned_cols=198  Identities=11%  Similarity=-0.032  Sum_probs=143.5

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCc-CHhhHHHHHHHH
Q 039342           25 SFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILP-SVMCYCMLLAVY  103 (248)
Q Consensus        25 ~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~  103 (248)
                      +.--|--+|...|+...|..-+++..+.. +-+..+|..+-..|-+.|+.+.|.+-|+...+.  .| +..+.|..=..+
T Consensus        37 arlqLal~YL~~gd~~~A~~nlekAL~~D-Ps~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl--~p~~GdVLNNYG~FL  113 (250)
T COG3063          37 ARLQLALGYLQQGDYAQAKKNLEKALEHD-PSYYLAHLVRAHYYQKLGENDLADESYRKALSL--APNNGDVLNNYGAFL  113 (250)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChhhHHHHHHHHHhc--CCCccchhhhhhHHH
Confidence            45556678889999999999999987764 345578888888899999999999999888765  34 556777888888


Q ss_pred             HhcCCHHHHHHHHHHHHHCCCCchH-HhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHH
Q 039342          104 AKSNRWDDAYGLLDEMHTNRISNIH-QVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRER  182 (248)
Q Consensus       104 ~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~  182 (248)
                      |..|++++|...|++-.....-+.. .++..+-. |..+.|+.+.++..|+.-.+.... ...+...+.+...+.|++-.
T Consensus       114 C~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~-Cal~~gq~~~A~~~l~raL~~dp~-~~~~~l~~a~~~~~~~~y~~  191 (250)
T COG3063         114 CAQGRPEEAMQQFERALADPAYGEPSDTLENLGL-CALKAGQFDQAEEYLKRALELDPQ-FPPALLELARLHYKAGDYAP  191 (250)
T ss_pred             HhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHH-HHhhcCCchhHHHHHHHHHHhCcC-CChHHHHHHHHHHhcccchH
Confidence            8899999999999988776544333 23333332 355678888999998888776543 34456677888888999999


Q ss_pred             HHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          183 AARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       183 a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      |..+++.....+. ++..+.-..|     +---..|+.+.+.++=..+.+.
T Consensus       192 Ar~~~~~~~~~~~-~~A~sL~L~i-----riak~~gd~~~a~~Y~~qL~r~  236 (250)
T COG3063         192 ARLYLERYQQRGG-AQAESLLLGI-----RIAKRLGDRAAAQRYQAQLQRL  236 (250)
T ss_pred             HHHHHHHHHhccc-ccHHHHHHHH-----HHHHHhccHHHHHHHHHHHHHh
Confidence            9999988877665 6655443333     4444567777777665555544

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

Probab=98.68  E-value=3.3e-05  Score=64.45  Aligned_cols=133  Identities=11%  Similarity=0.062  Sum_probs=70.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHH
Q 039342           96 YCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALW  175 (248)
Q Consensus        96 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  175 (248)
                      +.-+-..|...|+.++|+..+++..+..  |+..-+..+-...+...|+++.|....+...+.+.. |-..=+-....+.
T Consensus       197 ~~~lAqhyd~~g~~~~Al~~Id~aI~ht--Pt~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD~~-DRyiNsK~aKy~L  273 (517)
T PF12569_consen  197 LYFLAQHYDYLGDYEKALEYIDKAIEHT--PTLVELYMTKARILKHAGDLKEAAEAMDEARELDLA-DRYINSKCAKYLL  273 (517)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHhcC--CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCChh-hHHHHHHHHHHHH
Confidence            3444555666666666666666655443  444444443333355666666666666666655443 4444445556666


Q ss_pred             hcCchHHHHHHHHHHHHCCCCCCcchhhhH-Hh--hhhhhccccchHHHHHHHHHHHHH
Q 039342          176 CLGLRERAARVLDEATKRGLFPELFRHNKL-VW--SVDVHRMWEGGAYTAISVWLNKMY  231 (248)
Q Consensus       176 ~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l-i~--~~~~~~~~~~g~~~~~~~~~~~m~  231 (248)
                      +.|+.++|.+++....+.+..|-...+..- +|  .-.-.+|.+.|++..|.+.+....
T Consensus       274 Ra~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~r~~~~~~ALk~~~~v~  332 (517)
T PF12569_consen  274 RAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYLRQGDYGLALKRFHAVL  332 (517)
T ss_pred             HCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            667777777777666665553322221100 01  012355666666555555444433

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 [], [].

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

Probab=98.66  E-value=4.9e-05  Score=55.43  Aligned_cols=197  Identities=14%  Similarity=0.074  Sum_probs=153.2

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|+...|.+-+++..+... -+..+|..+-..|-+.|+.+.|.+-|++..+.. +-+-...|..-..+|..|++++|...
T Consensus        48 ~gd~~~A~~nlekAL~~DP-s~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~-p~~GdVLNNYG~FLC~qg~~~eA~q~  125 (250)
T COG3063          48 QGDYAQAKKNLEKALEHDP-SYYLAHLVRAHYYQKLGENDLADESYRKALSLA-PNNGDVLNNYGAFLCAQGRPEEAMQQ  125 (250)
T ss_pred             CCCHHHHHHHHHHHHHhCc-ccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcC-CCccchhhhhhHHHHhCCChHHHHHH
Confidence            4889999999999988542 357799999999999999999999999987653 23446778888889999999999999


Q ss_pred             HHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcC
Q 039342           81 FQEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEG  159 (248)
Q Consensus        81 ~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~  159 (248)
                      |++....-.-| -..+|..+.-+..+.|+.+.|...|++-.+..-.- ......+... ....|++-.|...++.....+
T Consensus       126 F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~~-~~~~l~~a~~-~~~~~~y~~Ar~~~~~~~~~~  203 (250)
T COG3063         126 FERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQF-PPALLELARL-HYKAGDYAPARLYLERYQQRG  203 (250)
T ss_pred             HHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcCC-ChHHHHHHHH-HHhcccchHHHHHHHHHHhcc
Confidence            99988763333 34688888888899999999999999987664221 1222233333 334677888998998888876


Q ss_pred             CCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhh
Q 039342          160 YGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNK  204 (248)
Q Consensus       160 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~  204 (248)
                      . ++....-..|+.--+.|+.+.+-++=..+.+.  .|...-|..
T Consensus       204 ~-~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r~--fP~s~e~q~  245 (250)
T COG3063         204 G-AQAESLLLGIRIAKRLGDRAAAQRYQAQLQRL--FPYSEEYQT  245 (250)
T ss_pred             c-ccHHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCcHHHHh
Confidence            6 89999999999999999999998887777654  565544443

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

Probab=98.65  E-value=4.5e-05  Score=61.23  Aligned_cols=207  Identities=12%  Similarity=0.058  Sum_probs=124.1

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCC-CcCH--hhHHHHHH
Q 039342           25 SFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGI-LPSV--MCYCMLLA  101 (248)
Q Consensus        25 ~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~-~p~~--~~~~~li~  101 (248)
                      ....+-..+...|++++|.+.+++..+.. +.+...+..+-..+...|++++|...+++..+... .|+.  ..|-.+..
T Consensus       116 ~~~~~a~~~~~~G~~~~A~~~~~~al~~~-p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~  194 (355)
T cd05804         116 LLGMLAFGLEEAGQYDRAEEAARRALELN-PDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLAL  194 (355)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHH
Confidence            33444556778899999999999987764 44566778888899999999999999988776422 2232  34557788


Q ss_pred             HHHhcCCHHHHHHHHHHHHHCCC-CchHHhH-HH-H-hc-----ccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 039342          102 VYAKSNRWDDAYGLLDEMHTNRI-SNIHQVT-GQ-M-IK-----GEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLE  172 (248)
Q Consensus       102 ~~~~~~~~~~a~~~~~~m~~~~~-~~~~~~~-~~-~-l~-----~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~  172 (248)
                      .+...|+.++|..++++...... .+..... .. . +.     +.......|+.+........ .+ ............
T Consensus       195 ~~~~~G~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~~~~w~~~~~~~~~~~-~~-~~~~~~~~~~a~  272 (355)
T cd05804         195 FYLERGDYEAALAIYDTHIAPSAESDPALDLLDAASLLWRLELAGHVDVGDRWEDLADYAAWHF-PD-HGLAFNDLHAAL  272 (355)
T ss_pred             HHHHCCCHHHHHHHHHHHhccccCCChHHHHhhHHHHHHHHHhcCCCChHHHHHHHHHHHHhhc-Cc-ccchHHHHHHHH
Confidence            88999999999999999754332 1111111 11 1 11     11111223333222211100 11 111122235677


Q ss_pred             HHHhcCchHHHHHHHHHHHHCCCCC---CcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHH
Q 039342          173 ALWCLGLRERAARVLDEATKRGLFP---ELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMF  234 (248)
Q Consensus       173 ~~~~~g~~~~a~~~~~~m~~~g~~p---~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~  234 (248)
                      ++...|+.+.|..+++.+......+   ........+..+..-.+...|+.++|.+.+..-...+
T Consensus       273 ~~~~~~~~~~a~~~L~~l~~~~~~~~~~~~~~~~~~~~~l~A~~~~~~g~~~~A~~~L~~al~~a  337 (355)
T cd05804         273 ALAGAGDKDALDKLLAALKGRASSADDNKQPARDVGLPLAEALYAFAEGNYATALELLGPVRDDL  337 (355)
T ss_pred             HHhcCCCHHHHHHHHHHHHHHHhccCchhhhHHhhhHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence            7888999999999999887633221   1111122222222244567888888888877766554

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.

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

Probab=98.62  E-value=1.3e-06  Score=56.22  Aligned_cols=82  Identities=16%  Similarity=0.175  Sum_probs=66.2

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHhcCC--------hhHHHHHHHHHHHCCCCcCHhh
Q 039342           25 SFNAVIEAFRQGGRFEEAIKAYVEMEKVRC-DPNERTLEAVLSVYCFAGL--------VDESKEQFQEIKSSGILPSVMC   95 (248)
Q Consensus        25 ~y~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~~~t~~~ll~~~~~~g~--------~~~a~~~~~~m~~~~~~p~~~~   95 (248)
                      |-...|..|...+++.....+|+.+++.|+ .|+..+|+.++.+-++...        .-..+.+|+.|...++.|+..+
T Consensus        27 t~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~et  106 (120)
T PF08579_consen   27 TQIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDET  106 (120)
T ss_pred             HHHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHH
Confidence            445567777777999999999999999999 8899999999988876542        4456778888888889999999


Q ss_pred             HHHHHHHHHhc
Q 039342           96 YCMLLAVYAKS  106 (248)
Q Consensus        96 ~~~li~~~~~~  106 (248)
                      |+.++..+.+.
T Consensus       107 Ynivl~~Llkg  117 (120)
T PF08579_consen  107 YNIVLGSLLKG  117 (120)
T ss_pred             HHHHHHHHHHh
Confidence            99988887653

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 [, , ].

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

Probab=98.62  E-value=2.2e-05  Score=65.41  Aligned_cols=84  Identities=21%  Similarity=0.230  Sum_probs=60.0

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH-h-----cCCh
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYC-F-----AGLV   74 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~-~-----~g~~   74 (248)
                      +|++++|++.+..-... +.-....+...-..+.+.|+.++|..+|..+.+.+  |+...|-..+..+. -     ....
T Consensus        17 ~g~~~~AL~~L~~~~~~-I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rN--Pdn~~Yy~~L~~~~g~~~~~~~~~~   93 (517)
T PF12569_consen   17 AGDYEEALEHLEKNEKQ-ILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRN--PDNYDYYRGLEEALGLQLQLSDEDV   93 (517)
T ss_pred             CCCHHHHHHHHHhhhhh-CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHhhhcccccccH
Confidence            58999999999775543 32345666677788889999999999999998875  66666655444443 2     2246


Q ss_pred             hHHHHHHHHHHHC
Q 039342           75 DESKEQFQEIKSS   87 (248)
Q Consensus        75 ~~a~~~~~~m~~~   87 (248)
                      +...++++++.+.
T Consensus        94 ~~~~~~y~~l~~~  106 (517)
T PF12569_consen   94 EKLLELYDELAEK  106 (517)
T ss_pred             HHHHHHHHHHHHh
Confidence            7778888887654

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 [], [].

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

Probab=98.61  E-value=1.4e-05  Score=63.90  Aligned_cols=172  Identities=13%  Similarity=0.125  Sum_probs=141.0

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|++.|-.+... ..-++....-+-..|--..+...|.+++.+..+ -++.|+.+.+-|-..|-+.|+-..|.+.+
T Consensus       538 ~~ldeald~f~klh~i-l~nn~evl~qianiye~led~aqaie~~~q~~s-lip~dp~ilskl~dlydqegdksqafq~~  615 (840)
T KOG2003|consen  538 GNLDEALDCFLKLHAI-LLNNAEVLVQIANIYELLEDPAQAIELLMQANS-LIPNDPAILSKLADLYDQEGDKSQAFQCH  615 (840)
T ss_pred             cCHHHHHHHHHHHHHH-HHhhHHHHHHHHHHHHHhhCHHHHHHHHHHhcc-cCCCCHHHHHHHHHHhhcccchhhhhhhh
Confidence            7899999999887542 124677788888889889999999999877643 36778899999999999999998888776


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCC
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYG  161 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~  161 (248)
                      =+--+. ++.+..+..=|-.-|....-+++++..|++..  -+.|+..-|..++.+++++.|+++.|..+++..... ++
T Consensus       616 ydsyry-fp~nie~iewl~ayyidtqf~ekai~y~ekaa--liqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrk-fp  691 (840)
T KOG2003|consen  616 YDSYRY-FPCNIETIEWLAAYYIDTQFSEKAINYFEKAA--LIQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRK-FP  691 (840)
T ss_pred             hhcccc-cCcchHHHHHHHHHHHhhHHHHHHHHHHHHHH--hcCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHh-Cc
Confidence            443222 34477888888888888999999999999754  467999999999999999999999999999998765 66


Q ss_pred             CCHHHHHHHHHHHHhcCc
Q 039342          162 LGMRFYNALLEALWCLGL  179 (248)
Q Consensus       162 p~~~~~~~li~~~~~~g~  179 (248)
                      -|......|++.+...|.
T Consensus       692 edldclkflvri~~dlgl  709 (840)
T KOG2003|consen  692 EDLDCLKFLVRIAGDLGL  709 (840)
T ss_pred             cchHHHHHHHHHhccccc
Confidence            788889999999887774

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

Probab=98.56  E-value=1e-06  Score=70.96  Aligned_cols=120  Identities=13%  Similarity=0.133  Sum_probs=96.0

Q ss_pred             CCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhh
Q 039342           18 GVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKV--RCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMC   95 (248)
Q Consensus        18 g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~--~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~   95 (248)
                      +.+.+......+++.+....+++.+..++-+++..  ....-..|.+++|+.|.+.|..+.+.++++.=...|+-||..+
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            44567778888888888888899999998888765  3333345667999999999999999999998888999999999


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcc
Q 039342           96 YCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKG  137 (248)
Q Consensus        96 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~  137 (248)
                      ||.||+.+.+.|++..|.++..+|...+...+..|....+.+
T Consensus       141 ~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~  182 (429)
T PF10037_consen  141 FNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYS  182 (429)
T ss_pred             HHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHH
Confidence            999999999999999999999988777665555555444443

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 [].

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

Probab=98.53  E-value=9.1e-05  Score=59.35  Aligned_cols=220  Identities=14%  Similarity=0.034  Sum_probs=141.6

Q ss_pred             HHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC--CCCHHHHHHH------------------
Q 039342            5 KECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRC--DPNERTLEAV------------------   64 (248)
Q Consensus         5 ~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~--~p~~~t~~~l------------------   64 (248)
                      +++.+-.....+.|.+-+...-+-.-.+.-...|+++|+.+|++..+...  --|..+|+.+                  
T Consensus       244 ~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~skLs~LA~~v~  323 (559)
T KOG1155|consen  244 EEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSKLSYLAQNVS  323 (559)
T ss_pred             HHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHHHHHHHHHHH
Confidence            34444444444555533322222222233345677777777777766531  0133444443                  


Q ss_pred             -------------HHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhH
Q 039342           65 -------------LSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVT  131 (248)
Q Consensus        65 -------------l~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~  131 (248)
                                   -+-|+-.++.++|...|++..+.+. -....|+.|=.-|....+...|.+-++...+.+ +.|-..|
T Consensus       324 ~idKyR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLNp-~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~-p~DyRAW  401 (559)
T KOG1155|consen  324 NIDKYRPETCCIIANYYSLRSEHEKAVMYFKRALKLNP-KYLSAWTLMGHEYVEMKNTHAAIESYRRAVDIN-PRDYRAW  401 (559)
T ss_pred             HhccCCccceeeehhHHHHHHhHHHHHHHHHHHHhcCc-chhHHHHHhhHHHHHhcccHHHHHHHHHHHhcC-chhHHHH
Confidence                         3445666788888888888877542 245678888888888888888988888877654 2334444


Q ss_pred             HHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhh
Q 039342          132 GQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDV  211 (248)
Q Consensus       132 ~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~  211 (248)
                      ..+=.+ |...+...-|...|++..+... -|...|.+|-++|.+.++.++|.+.|......|-. +...+..|-     
T Consensus       402 YGLGQa-Yeim~Mh~YaLyYfqkA~~~kP-nDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dt-e~~~l~~La-----  473 (559)
T KOG1155|consen  402 YGLGQA-YEIMKMHFYALYYFQKALELKP-NDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDT-EGSALVRLA-----  473 (559)
T ss_pred             hhhhHH-HHHhcchHHHHHHHHHHHhcCC-CchHHHHHHHHHHHHhccHHHHHHHHHHHHhcccc-chHHHHHHH-----
Confidence            444443 5555556667777777666432 37889999999999999999999999998765533 333344444     


Q ss_pred             hccccchHHHHHHHHHHHHHHHH
Q 039342          212 HRMWEGGAYTAISVWLNKMYEMF  234 (248)
Q Consensus       212 ~~~~~~g~~~~~~~~~~~m~~~~  234 (248)
                      +.|-+.++..+|...+.+-.+..
T Consensus       474 kLye~l~d~~eAa~~yek~v~~~  496 (559)
T KOG1155|consen  474 KLYEELKDLNEAAQYYEKYVEVS  496 (559)
T ss_pred             HHHHHHHhHHHHHHHHHHHHHHH
Confidence            67778888888888777766643

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

Probab=98.53  E-value=2.4e-05  Score=59.96  Aligned_cols=159  Identities=12%  Similarity=0.015  Sum_probs=122.1

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhH-HHHHHHHHh
Q 039342           27 NAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCY-CMLLAVYAK  105 (248)
Q Consensus        27 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~-~~li~~~~~  105 (248)
                      +-+-.+|.+.|.+.+|...|+.-.+.  .|-+.||-.|-+.|.+..++..|..++.+-.+.  .|-.+|| .-+.+.+-.
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q--~~~~dTfllLskvY~ridQP~~AL~~~~~gld~--fP~~VT~l~g~ARi~ea  302 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQ--FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS--FPFDVTYLLGQARIHEA  302 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhc--CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc--CCchhhhhhhhHHHHHH
Confidence            45677888899999999998887665  466668888999999999999999999988775  4555554 456667777


Q ss_pred             cCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHH
Q 039342          106 SNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAAR  185 (248)
Q Consensus       106 ~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~  185 (248)
                      .++.++|.+++++..+... .+...+.++-.+ +--.++++.|...++.+.+.|+. +...|+.+--+|.-.+++|.++-
T Consensus       303 m~~~~~a~~lYk~vlk~~~-~nvEaiAcia~~-yfY~~~PE~AlryYRRiLqmG~~-speLf~NigLCC~yaqQ~D~~L~  379 (478)
T KOG1129|consen  303 MEQQEDALQLYKLVLKLHP-INVEAIACIAVG-YFYDNNPEMALRYYRRILQMGAQ-SPELFCNIGLCCLYAQQIDLVLP  379 (478)
T ss_pred             HHhHHHHHHHHHHHHhcCC-ccceeeeeeeec-cccCCChHHHHHHHHHHHHhcCC-ChHHHhhHHHHHHhhcchhhhHH
Confidence            8889999999998876541 222333333333 44567789999999999999987 78888888888888899998888


Q ss_pred             HHHHHHH
Q 039342          186 VLDEATK  192 (248)
Q Consensus       186 ~~~~m~~  192 (248)
                      -|.+...
T Consensus       380 sf~RAls  386 (478)
T KOG1129|consen  380 SFQRALS  386 (478)
T ss_pred             HHHHHHh
Confidence            8887654

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

Probab=98.53  E-value=0.00011  Score=59.07  Aligned_cols=228  Identities=11%  Similarity=0.031  Sum_probs=127.0

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHH---HHHHHHhcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCChhHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNA---VIEAFRQGGRFEEAIKAYVEMEKVRCDPN-ERTLEAVLSVYCFAGLVDES   77 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~---li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~ll~~~~~~g~~~~a   77 (248)
                      |++++|.+.+++..+.. +.+...+..   ........+....+.+.+..  .....|+ ......+-..+...|++++|
T Consensus        57 g~~~~A~~~~~~~l~~~-P~~~~a~~~~~~~~~~~~~~~~~~~~~~~l~~--~~~~~~~~~~~~~~~a~~~~~~G~~~~A  133 (355)
T cd05804          57 GDLPKALALLEQLLDDY-PRDLLALKLHLGAFGLGDFSGMRDHVARVLPL--WAPENPDYWYLLGMLAFGLEEAGQYDRA  133 (355)
T ss_pred             CCHHHHHHHHHHHHHHC-CCcHHHHHHhHHHHHhcccccCchhHHHHHhc--cCcCCCCcHHHHHHHHHHHHHcCCHHHH
Confidence            78888888888876643 223444442   11111223455555555544  1222333 33444556678888999999


Q ss_pred             HHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC-chHHh-HHHHhcccccccchHHHHHHHHHHH
Q 039342           78 KEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRIS-NIHQV-TGQMIKGEFDDESNWQMVEYVFDKL  155 (248)
Q Consensus        78 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~m  155 (248)
                      .+.+++..+.. +.+...+..+-..+...|++++|...+++....... |.... ....+..++...|+++.|..+++..
T Consensus       134 ~~~~~~al~~~-p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~  212 (355)
T cd05804         134 EEAARRALELN-PDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTH  212 (355)
T ss_pred             HHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            99999988764 234567788888888999999999999887654321 22211 1112223366778889999999887


Q ss_pred             HhcCC-CCCHHHH-H--HHHHHHHhcCchHHHHHH--HHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHH
Q 039342          156 NCEGY-GLGMRFY-N--ALLEALWCLGLRERAARV--LDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNK  229 (248)
Q Consensus       156 ~~~~~-~p~~~~~-~--~li~~~~~~g~~~~a~~~--~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~  229 (248)
                      ..... .+..... +  .++.-+...|..+.+...  ...............+..+   .....+...|+.+.+.++++.
T Consensus       213 ~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~~~~w~~~~~~~~~~~~~~~~~~~~~---~~a~~~~~~~~~~~a~~~L~~  289 (355)
T cd05804         213 IAPSAESDPALDLLDAASLLWRLELAGHVDVGDRWEDLADYAAWHFPDHGLAFNDL---HAALALAGAGDKDALDKLLAA  289 (355)
T ss_pred             hccccCCChHHHHhhHHHHHHHHHhcCCCChHHHHHHHHHHHHhhcCcccchHHHH---HHHHHHhcCCCHHHHHHHHHH
Confidence            54322 2222211 1  223333334433333332  1111111111111112221   233566778888889999988


Q ss_pred             HHHHHHc
Q 039342          230 MYEMFMM  236 (248)
Q Consensus       230 m~~~~~~  236 (248)
                      ++.....
T Consensus       290 l~~~~~~  296 (355)
T cd05804         290 LKGRASS  296 (355)
T ss_pred             HHHHHhc
Confidence            8776544

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.

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

Probab=98.51  E-value=0.00011  Score=58.98  Aligned_cols=216  Identities=8%  Similarity=0.011  Sum_probs=162.8

Q ss_pred             CchHHHHHHHHHHHHcCC-C-CCHHhHHHHH-------------------------------HHHHhcCCHHHHHHHHHH
Q 039342            2 GLYKECQAILSRMSESGV-A-RNSDSFNAVI-------------------------------EAFRQGGRFEEAIKAYVE   48 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~-~-~~~~~y~~li-------------------------------~~~~~~~~~~~a~~~~~~   48 (248)
                      .|+|+|+.+|+++.+... + -|..+|..++                               +.|+-.++.++|...|++
T Consensus       276 rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~skLs~LA~~v~~idKyR~ETCCiIaNYYSlr~eHEKAv~YFkR  355 (559)
T KOG1155|consen  276 RDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSKLSYLAQNVSNIDKYRPETCCIIANYYSLRSEHEKAVMYFKR  355 (559)
T ss_pred             hhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHHHHHHHHHHHHhccCCccceeeehhHHHHHHhHHHHHHHHHH
Confidence            478999999999987642 1 1445554443                               335556678999999999


Q ss_pred             HHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchH
Q 039342           49 MEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIH  128 (248)
Q Consensus        49 m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~  128 (248)
                      ..+.+ +-....|+.+-.-|....+...|.+-++...+.. +.|-..|-.|=++|.-.+...=|+-.|++..+  ++|+.
T Consensus       356 ALkLN-p~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~-p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~--~kPnD  431 (559)
T KOG1155|consen  356 ALKLN-PKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDIN-PRDYRAWYGLGQAYEIMKMHFYALYYFQKALE--LKPND  431 (559)
T ss_pred             HHhcC-cchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcC-chhHHHHhhhhHHHHHhcchHHHHHHHHHHHh--cCCCc
Confidence            88765 3445778888999999999999999999988763 23778899999999999999999999998764  45888


Q ss_pred             HhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHH----CCCCCCcchhhh
Q 039342          129 QVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATK----RGLFPELFRHNK  204 (248)
Q Consensus       129 ~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~----~g~~p~~~t~~~  204 (248)
                      ......+-.+|.+.++.++|...|......|-. +...+..+-+.+-+.++.++|...|.+..+    .|.. +..|..+
T Consensus       432 sRlw~aLG~CY~kl~~~~eAiKCykrai~~~dt-e~~~l~~LakLye~l~d~~eAa~~yek~v~~~~~eg~~-~~~t~ka  509 (559)
T KOG1155|consen  432 SRLWVALGECYEKLNRLEEAIKCYKRAILLGDT-EGSALVRLAKLYEELKDLNEAAQYYEKYVEVSELEGEI-DDETIKA  509 (559)
T ss_pred             hHHHHHHHHHHHHhccHHHHHHHHHHHHhcccc-chHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhccc-chHHHHH
Confidence            888877878899999999999999988877644 668899999999999999999999987664    2322 3334444


Q ss_pred             HHhhhhhhccccchHHHHHHH
Q 039342          205 LVWSVDVHRMWEGGAYTAISV  225 (248)
Q Consensus       205 li~~~~~~~~~~~g~~~~~~~  225 (248)
                      .+|  +..-+.+.+++++|..
T Consensus       510 ~~f--LA~~f~k~~~~~~As~  528 (559)
T KOG1155|consen  510 RLF--LAEYFKKMKDFDEASY  528 (559)
T ss_pred             HHH--HHHHHHhhcchHHHHH
Confidence            443  2244455555555544

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

Probab=98.49  E-value=1.8e-07  Score=46.37  Aligned_cols=29  Identities=31%  Similarity=0.649  Sum_probs=17.1

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 039342           25 SFNAVIEAFRQGGRFEEAIKAYVEMEKVR   53 (248)
Q Consensus        25 ~y~~li~~~~~~~~~~~a~~~~~~m~~~~   53 (248)
                      +||++|++|++.|++++|.++|++|.+.|
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g   30 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERG   30 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCc
Confidence            45566666666666666666666665554

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.

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=98.48  E-value=4.8e-05  Score=62.98  Aligned_cols=211  Identities=14%  Similarity=0.124  Sum_probs=142.2

Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHHc-----C-CCCCHHHH-HHHHHHHHhcCChhHHHHHHHHHHHC-----C-C
Q 039342           23 SDSFNAVIEAFRQGGRFEEAIKAYVEMEKV-----R-CDPNERTL-EAVLSVYCFAGLVDESKEQFQEIKSS-----G-I   89 (248)
Q Consensus        23 ~~~y~~li~~~~~~~~~~~a~~~~~~m~~~-----~-~~p~~~t~-~~ll~~~~~~g~~~~a~~~~~~m~~~-----~-~   89 (248)
                      ..+...+-..|...|+++.|..+++...+.     | ..|...+. +.+-..|...+++++|..+|+++...     | -
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~~  278 (508)
T KOG1840|consen  199 LRTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGED  278 (508)
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCC
Confidence            456666999999999999999999887543     2 12333332 34667888999999999999998642     2 1


Q ss_pred             Cc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHH---C---CCCchHHhHHHHhcccccccchHHHHHHHHHHHHhc---C
Q 039342           90 LP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHT---N---RISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCE---G  159 (248)
Q Consensus        90 ~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~---~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~---~  159 (248)
                      .| -..+++.|-.+|.+.|++++|...+++..+   .   -..|.......-+...+...+.++.+..++....+.   -
T Consensus       279 h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~  358 (508)
T KOG1840|consen  279 HPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDA  358 (508)
T ss_pred             CHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhh
Confidence            22 346788888899999999988887776532   1   122444444444445577778888888887654332   1


Q ss_pred             CCC----CHHHHHHHHHHHHhcCchHHHHHHHHHHHHC---CCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHH
Q 039342          160 YGL----GMRFYNALLEALWCLGLRERAARVLDEATKR---GLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYE  232 (248)
Q Consensus       160 ~~p----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~---g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~  232 (248)
                      +.+    -..+++.+-..|...|++++|.+++++....   +..-...-.+..+|.+. ..|.+.++..++.++|.+=+.
T Consensus       359 ~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la-~~~~~~k~~~~a~~l~~~~~~  437 (508)
T KOG1840|consen  359 PGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLA-EAYEELKKYEEAEQLFEEAKD  437 (508)
T ss_pred             ccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHH-HHHHHhcccchHHHHHHHHHH
Confidence            222    3578999999999999999999999987642   11111111244444443 456777888878887766544


Q ss_pred             HH
Q 039342          233 MF  234 (248)
Q Consensus       233 ~~  234 (248)
                      -.
T Consensus       438 i~  439 (508)
T KOG1840|consen  438 IM  439 (508)
T ss_pred             HH
Confidence            43

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

Probab=98.48  E-value=0.00017  Score=62.13  Aligned_cols=187  Identities=11%  Similarity=0.087  Sum_probs=142.1

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|.+++.+..+... .+...|-+|-..|-+.|+.+++...+-..-.. -+-|...|..+-....+.|+++.|.-.|
T Consensus       153 g~~eeA~~i~~EvIkqdp-~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL-~p~d~e~W~~ladls~~~~~i~qA~~cy  230 (895)
T KOG2076|consen  153 GDLEEAEEILMEVIKQDP-RNPIAYYTLGEIYEQRGDIEKALNFWLLAAHL-NPKDYELWKRLADLSEQLGNINQARYCY  230 (895)
T ss_pred             CCHHHHHHHHHHHHHhCc-cchhhHHHHHHHHHHcccHHHHHHHHHHHHhc-CCCChHHHHHHHHHHHhcccHHHHHHHH
Confidence            899999999999987653 57889999999999999999998776554333 3567789999999999999999999999


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHH----HHhcccccccchHHHHHHHHHHHHh
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTG----QMIKGEFDDESNWQMVEYVFDKLNC  157 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~----~~l~~~~~~~~~~~~a~~~~~~m~~  157 (248)
                      .+..+.. +++...+--=...|-+.|+...|..-|.++....-+.+-.-+.    ..+.. +...+.-+.|.+.++....
T Consensus       231 ~rAI~~~-p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~-~~~~~~~e~a~~~le~~~s  308 (895)
T KOG2076|consen  231 SRAIQAN-PSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHY-FITHNERERAAKALEGALS  308 (895)
T ss_pred             HHHHhcC-CcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHH-HHHhhHHHHHHHHHHHHHh
Confidence            9998874 3355555566778889999999999999998765322323333    33333 3333333666666655444


Q ss_pred             -cCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          158 -EGYGLGMRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       158 -~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                       .+-..+...++++...+.+...++.+......+..
T Consensus       309 ~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~  344 (895)
T KOG2076|consen  309 KEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRN  344 (895)
T ss_pred             hccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhc
Confidence             34445677889999999999999999999888876

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

Probab=98.47  E-value=2.6e-07  Score=45.81  Aligned_cols=29  Identities=28%  Similarity=0.547  Sum_probs=16.1

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           95 CYCMLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        95 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      +|+++|++|++.|++++|.++|++|.+.|
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.

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

Probab=98.46  E-value=2.5e-06  Score=68.85  Aligned_cols=104  Identities=11%  Similarity=0.064  Sum_probs=89.8

Q ss_pred             chHHHHHHHHHHHHc--CCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            3 LYKECQAILSRMSES--GVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         3 ~~~~a~~~~~~m~~~--g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      +++.+..++.+.+..  ....-..|..++|+.|.+.|..+.++.+++.=...|+-||..|+|.||..+.+.|++..|.++
T Consensus        81 ~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~n~Lmd~fl~~~~~~~A~~V  160 (429)
T PF10037_consen   81 DLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSFNLLMDHFLKKGNYKSAAKV  160 (429)
T ss_pred             HHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhHHHHHHHHhhcccHHHHHHH
Confidence            467788888888765  222334566799999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHCCCCcCHhhHHHHHHHHHhc
Q 039342           81 FQEIKSSGILPSVMCYCMLLAVYAKS  106 (248)
Q Consensus        81 ~~~m~~~~~~p~~~~~~~li~~~~~~  106 (248)
                      ..+|...+...+..|+...+.+|.+-
T Consensus       161 ~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  161 ATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HHHHHHhhccCCchHHHHHHHHHHHh
Confidence            99998777777888888888887776

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 [].

>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=98.46  E-value=8.8e-06  Score=58.88  Aligned_cols=89  Identities=18%  Similarity=0.378  Sum_probs=71.9

Q ss_pred             CCCHHhHHHHHHHHHhc-----CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC----------------ChhHHH
Q 039342           20 ARNSDSFNAVIEAFRQG-----GRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAG----------------LVDESK   78 (248)
Q Consensus        20 ~~~~~~y~~li~~~~~~-----~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g----------------~~~~a~   78 (248)
                      ..+-.+|..++..|.+.     |.++-....++.|.+-|+.-|..+|+.||+.+=+..                +-+-|.
T Consensus        44 ~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i  123 (228)
T PF06239_consen   44 AKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAI  123 (228)
T ss_pred             cccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHH
Confidence            46889999999999865     778999999999999999999999999999876522                345667


Q ss_pred             HHHHHHHHCCCCcCHhhHHHHHHHHHhcCC
Q 039342           79 EQFQEIKSSGILPSVMCYCMLLAVYAKSNR  108 (248)
Q Consensus        79 ~~~~~m~~~~~~p~~~~~~~li~~~~~~~~  108 (248)
                      +++++|...|+.||..++..+++.+++.+.
T Consensus       124 ~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~  153 (228)
T PF06239_consen  124 DLLEQMENNGVMPDKETEQMLLNIFGRKSH  153 (228)
T ss_pred             HHHHHHHHcCCCCcHHHHHHHHHHhccccH
Confidence            777777777777777777777777776654

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

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.44  E-value=7.7e-05  Score=56.26  Aligned_cols=182  Identities=13%  Similarity=0.104  Sum_probs=108.6

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC----HHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHh---
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN----ERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVM---   94 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~----~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~---   94 (248)
                      ....+-.+...+.+.|+++.|...|++..+..  |+    ...+..+..++.+.|++++|...++++.+..  |+..   
T Consensus        32 ~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~--p~~~~~~  107 (235)
T TIGR03302        32 PAEELYEEAKEALDSGDYTEAIKYFEALESRY--PFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLH--PNHPDAD  107 (235)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHC--cCCCchH
Confidence            45677777788888899999999998886543  32    2456677788888899999999999887642  3211   


Q ss_pred             -hHHHHHHHHHhc--------CCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHH
Q 039342           95 -CYCMLLAVYAKS--------NRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMR  165 (248)
Q Consensus        95 -~~~~li~~~~~~--------~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~  165 (248)
                       ++..+-.++...        |+.++|.+.|++..+..  |+.......+.. .         ........        .
T Consensus       108 ~a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~a~~~-~---------~~~~~~~~--------~  167 (235)
T TIGR03302       108 YAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRY--PNSEYAPDAKKR-M---------DYLRNRLA--------G  167 (235)
T ss_pred             HHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHC--CCChhHHHHHHH-H---------HHHHHHHH--------H
Confidence             344444444433        56778888888776553  332211111100 0         00000000        0


Q ss_pred             HHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCC----cchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHH
Q 039342          166 FYNALLEALWCLGLRERAARVLDEATKRGLFPE----LFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMF  234 (248)
Q Consensus       166 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~----~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~  234 (248)
                      ....+-..+.+.|++++|...++...+.  .|+    ...+..+.     ..+.+.|+.+++...++.+..+.
T Consensus       168 ~~~~~a~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~a~~~l~-----~~~~~lg~~~~A~~~~~~l~~~~  233 (235)
T TIGR03302       168 KELYVARFYLKRGAYVAAINRFETVVEN--YPDTPATEEALARLV-----EAYLKLGLKDLAQDAAAVLGANY  233 (235)
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHHHH--CCCCcchHHHHHHHH-----HHHHHcCCHHHHHHHHHHHHhhC
Confidence            1123445677778888888888777654  222    22333333     66777788888888777776553

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).

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

Probab=98.44  E-value=5.2e-05  Score=58.23  Aligned_cols=219  Identities=12%  Similarity=0.001  Sum_probs=138.4

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHH-HHHHHHHhcCChhHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLE-AVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~-~ll~~~~~~g~~~~a~~~   80 (248)
                      |.+.+|++.|+.-.+.  .|-+.||-.|-.+|.+..+++.|+.++.+-.+.  .|-.+||- -+.+.+-..++.++|.++
T Consensus       237 gm~r~AekqlqssL~q--~~~~dTfllLskvY~ridQP~~AL~~~~~gld~--fP~~VT~l~g~ARi~eam~~~~~a~~l  312 (478)
T KOG1129|consen  237 GMPRRAEKQLQSSLTQ--FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS--FPFDVTYLLGQARIHEAMEQQEDALQL  312 (478)
T ss_pred             cChhhhHHHHHHHhhc--CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc--CCchhhhhhhhHHHHHHHHhHHHHHHH
Confidence            5677888888876653  477889999999999999999999999887654  46555654 455667777888888888


Q ss_pred             HHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCC
Q 039342           81 FQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGY  160 (248)
Q Consensus        81 ~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~  160 (248)
                      ++...+.. ..++....++-.+|.-.++.+-|++.++++.+-|+.... .|..+-.. |-..++++.+.--|......-.
T Consensus       313 Yk~vlk~~-~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~spe-Lf~NigLC-C~yaqQ~D~~L~sf~RAlstat  389 (478)
T KOG1129|consen  313 YKLVLKLH-PINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQSPE-LFCNIGLC-CLYAQQIDLVLPSFQRALSTAT  389 (478)
T ss_pred             HHHHHhcC-CccceeeeeeeeccccCCChHHHHHHHHHHHHhcCCChH-HHhhHHHH-HHhhcchhhhHHHHHHHHhhcc
Confidence            88876542 235666666777777788888888888888888765433 33333222 4445556666655555544433


Q ss_pred             CCC--HHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          161 GLG--MRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       161 ~p~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      .|+  ...|-.+-...+-.|++..|...|+-..... .-+...++.|-     ---.+.|+++.|..+++.-+..
T Consensus       390 ~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d-~~h~ealnNLa-----vL~~r~G~i~~Arsll~~A~s~  458 (478)
T KOG1129|consen  390 QPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSD-AQHGEALNNLA-----VLAARSGDILGARSLLNAAKSV  458 (478)
T ss_pred             CcchhhhhhhccceeEEeccchHHHHHHHHHHhccC-cchHHHHHhHH-----HHHhhcCchHHHHHHHHHhhhh
Confidence            333  2234444555555666677766666544321 11222333332     2234666666666666655443

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

Probab=98.43  E-value=6.1e-05  Score=67.63  Aligned_cols=193  Identities=11%  Similarity=0.033  Sum_probs=129.9

Q ss_pred             CchHHHHHHHHHHHHc-CCCC---CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHH
Q 039342            2 GLYKECQAILSRMSES-GVAR---NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDES   77 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~-g~~~---~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a   77 (248)
                      +++++|++++++.... +++-   -...|.++++.-..-|.-+...++|++..+.-  -....|..|...|.+.+++++|
T Consensus      1472 sEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqyc--d~~~V~~~L~~iy~k~ek~~~A 1549 (1710)
T KOG1070|consen 1472 SEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQYC--DAYTVHLKLLGIYEKSEKNDEA 1549 (1710)
T ss_pred             hhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHhc--chHHHHHHHHHHHHHhhcchhH
Confidence            4567777777776532 1111   23467777776666777777777887776531  1134567788888888888888


Q ss_pred             HHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHH-hHHHHhcccccccchHHHHHHHHHHHH
Q 039342           78 KEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQ-VTGQMIKGEFDDESNWQMVEYVFDKLN  156 (248)
Q Consensus        78 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~m~  156 (248)
                      -++++.|.+. +.-...+|...+..+.++++-+.|.+++.+..+.--+-.+. .+.....- --+.|+.+.+..+|+...
T Consensus      1550 ~ell~~m~KK-F~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv~~IskfAqL-EFk~GDaeRGRtlfEgll 1627 (1710)
T KOG1070|consen 1550 DELLRLMLKK-FGQTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVEFISKFAQL-EFKYGDAERGRTLFEGLL 1627 (1710)
T ss_pred             HHHHHHHHHH-hcchhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHHHHHHHHHH-HhhcCCchhhHHHHHHHH
Confidence            8888888754 12356788888888888888888888888766543111121 11111111 224566677788888877


Q ss_pred             hcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCc
Q 039342          157 CEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPEL  199 (248)
Q Consensus       157 ~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  199 (248)
                      ....+ -...|+..|+.-.++|+.+.+..+|++....++.|..
T Consensus      1628 ~ayPK-RtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~kk 1669 (1710)
T KOG1070|consen 1628 SAYPK-RTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSIKK 1669 (1710)
T ss_pred             hhCcc-chhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCChhH
Confidence            76444 4677899999999999999999999999888887754

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

Probab=98.41  E-value=2.2e-05  Score=60.89  Aligned_cols=154  Identities=13%  Similarity=0.192  Sum_probs=109.3

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHh----c
Q 039342           31 EAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAK----S  106 (248)
Q Consensus        31 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~----~  106 (248)
                      ..+...|++++|++++..-      .+.......+..|.+.++++.|.+.++.|.+..  .| .+...+..++..    .
T Consensus       110 ~i~~~~~~~~~AL~~l~~~------~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~--eD-~~l~qLa~awv~l~~g~  180 (290)
T PF04733_consen  110 TILFHEGDYEEALKLLHKG------GSLELLALAVQILLKMNRPDLAEKELKNMQQID--ED-SILTQLAEAWVNLATGG  180 (290)
T ss_dssp             HHHCCCCHHHHHHCCCTTT------TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCS--CC-HHHHHHHHHHHHHHHTT
T ss_pred             HHHHHcCCHHHHHHHHHcc------CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--Cc-HHHHHHHHHHHHHHhCc
Confidence            3455679999999888652      556777888999999999999999999998753  33 344445554443    3


Q ss_pred             CCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCch-HHHHH
Q 039342          107 NRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR-ERAAR  185 (248)
Q Consensus       107 ~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~-~~a~~  185 (248)
                      ..+.+|..+|+++.+. ..++..+.+..... ....|++++|+.++.+..+.+.. +..+...++-+....|+. +.+.+
T Consensus       181 e~~~~A~y~f~El~~~-~~~t~~~lng~A~~-~l~~~~~~eAe~~L~~al~~~~~-~~d~LaNliv~~~~~gk~~~~~~~  257 (290)
T PF04733_consen  181 EKYQDAFYIFEELSDK-FGSTPKLLNGLAVC-HLQLGHYEEAEELLEEALEKDPN-DPDTLANLIVCSLHLGKPTEAAER  257 (290)
T ss_dssp             TCCCHHHHHHHHHHCC-S--SHHHHHHHHHH-HHHCT-HHHHHHHHHHHCCC-CC-HHHHHHHHHHHHHHTT-TCHHHHH
T ss_pred             hhHHHHHHHHHHHHhc-cCCCHHHHHHHHHH-HHHhCCHHHHHHHHHHHHHhccC-CHHHHHHHHHHHHHhCCChhHHHH
Confidence            4699999999998665 44555666655544 67788999999999987665543 566777777777778877 67888


Q ss_pred             HHHHHHHCCCCCC
Q 039342          186 VLDEATKRGLFPE  198 (248)
Q Consensus       186 ~~~~m~~~g~~p~  198 (248)
                      ++.+++..  .|+
T Consensus       258 ~l~qL~~~--~p~  268 (290)
T PF04733_consen  258 YLSQLKQS--NPN  268 (290)
T ss_dssp             HHHHCHHH--TTT
T ss_pred             HHHHHHHh--CCC
Confidence            88887763  454

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.

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

Probab=98.39  E-value=6.3e-05  Score=56.04  Aligned_cols=172  Identities=17%  Similarity=0.111  Sum_probs=114.6

Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCc
Q 039342           47 VEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISN  126 (248)
Q Consensus        47 ~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~  126 (248)
                      +.+......-+......-...|++.|++++|.+......      +......=+..+.+..+++-|...+++|.+-.   
T Consensus        97 E~~a~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~~~------~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~id---  167 (299)
T KOG3081|consen   97 ELVADSTDGSNLIDLLLAAIIYMHDGDFDEALKALHLGE------NLEAAALNVQILLKMHRFDLAEKELKKMQQID---  167 (299)
T ss_pred             HHHHhhccchhHHHHHHhhHHhhcCCChHHHHHHHhccc------hHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc---
Confidence            333333334443444444567899999999999887622      34455555666778889999999999998764   


Q ss_pred             hHHhHHHHhccc---ccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhh
Q 039342          127 IHQVTGQMIKGE---FDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHN  203 (248)
Q Consensus       127 ~~~~~~~~l~~~---~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~  203 (248)
                      +..|.+.+..++   .........|..+|++|.+. ..|+..+.+-...++...|++++|..++++...+.-. +   +.
T Consensus       168 ed~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~~-d---pe  242 (299)
T KOG3081|consen  168 EDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDAK-D---PE  242 (299)
T ss_pred             hHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccCC-C---HH
Confidence            344444333322   34456689999999999765 6788999999999999999999999999998765211 1   12


Q ss_pred             hHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          204 KLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       204 ~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      .|+ +.++.+.-.+.+-+...+.+.+++..
T Consensus       243 tL~-Nliv~a~~~Gkd~~~~~r~l~QLk~~  271 (299)
T KOG3081|consen  243 TLA-NLIVLALHLGKDAEVTERNLSQLKLS  271 (299)
T ss_pred             HHH-HHHHHHHHhCCChHHHHHHHHHHHhc
Confidence            222 22223444445555566666666654

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

Probab=98.39  E-value=7e-05  Score=60.38  Aligned_cols=184  Identities=15%  Similarity=0.125  Sum_probs=103.3

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcC----------------------------
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVR----------------------------   53 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~----------------------------   53 (248)
                      |+.-.|..-|+...+....++ ..|--+-..|....+.++....|+...+.+                            
T Consensus       340 g~~~~a~~d~~~~I~l~~~~~-~lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp~n~dvYyHRgQm~flL~q~e~A~aDF~  418 (606)
T KOG0547|consen  340 GDSLGAQEDFDAAIKLDPAFN-SLYIKRAAAYADENQSEKMWKDFNKAEDLDPENPDVYYHRGQMRFLLQQYEEAIADFQ  418 (606)
T ss_pred             CCchhhhhhHHHHHhcCcccc-hHHHHHHHHHhhhhccHHHHHHHHHHHhcCCCCCchhHhHHHHHHHHHHHHHHHHHHH
Confidence            555566666666555433221 225555555666666555555555554332                            


Q ss_pred             ----CCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC---
Q 039342           54 ----CDP-NERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRIS---  125 (248)
Q Consensus        54 ----~~p-~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~---  125 (248)
                          +.| +...|--+--+..|.++++++...|++.++. ++..+.+|+..-..+...+++++|.+.|+...+-.-.   
T Consensus       419 Kai~L~pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkk-FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~~~~  497 (606)
T KOG0547|consen  419 KAISLDPENAYAYIQLCCALYRQHKIAESMKTFEEAKKK-FPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIELEPREHL  497 (606)
T ss_pred             HHhhcChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhhcccccc
Confidence                112 2223333333445666777777777776654 3445677777777777777777777777765432111   


Q ss_pred             ----chHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHH
Q 039342          126 ----NIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEA  190 (248)
Q Consensus       126 ----~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m  190 (248)
                          +...+-..++.  +.-.+++..|..+++...+.+.+ ....|..|-..-..+|+.++|.++|++-
T Consensus       498 ~~v~~~plV~Ka~l~--~qwk~d~~~a~~Ll~KA~e~Dpk-ce~A~~tlaq~~lQ~~~i~eAielFEks  563 (606)
T KOG0547|consen  498 IIVNAAPLVHKALLV--LQWKEDINQAENLLRKAIELDPK-CEQAYETLAQFELQRGKIDEAIELFEKS  563 (606)
T ss_pred             ccccchhhhhhhHhh--hchhhhHHHHHHHHHHHHccCch-HHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence                11111112221  22336677777777776665544 3455777777777777777777777764

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.36  E-value=8.7e-05  Score=51.45  Aligned_cols=116  Identities=9%  Similarity=-0.068  Sum_probs=90.3

Q ss_pred             HHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCC
Q 039342            9 AILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSG   88 (248)
Q Consensus         9 ~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~   88 (248)
                      .+|++..+    -++..+...-..+...|++++|...|+...... +.+...|..+-.++.+.|++++|...|+...+..
T Consensus        14 ~~~~~al~----~~p~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~   88 (144)
T PRK15359         14 DILKQLLS----VDPETVYASGYASWQEGDYSRAVIDFSWLVMAQ-PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD   88 (144)
T ss_pred             HHHHHHHH----cCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC
Confidence            44555544    233346667778889999999999999987664 4577888899999999999999999999998753


Q ss_pred             CCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHH
Q 039342           89 ILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTG  132 (248)
Q Consensus        89 ~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~  132 (248)
                       +.+...+..+-.++...|+.++|...|++..+..  |+...+.
T Consensus        89 -p~~~~a~~~lg~~l~~~g~~~eAi~~~~~Al~~~--p~~~~~~  129 (144)
T PRK15359         89 -ASHPEPVYQTGVCLKMMGEPGLAREAFQTAIKMS--YADASWS  129 (144)
T ss_pred             -CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCChHHH
Confidence             2367888888899999999999999999887654  5554444

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.34  E-value=0.00014  Score=62.93  Aligned_cols=136  Identities=15%  Similarity=0.091  Sum_probs=115.2

Q ss_pred             CCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhH
Q 039342           53 RCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVT  131 (248)
Q Consensus        53 ~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~  131 (248)
                      ....+...+-.|-....+.|..++|..+++...+.  .| +......+...+.+.+++++|+..+++..+..  |++...
T Consensus        81 ~~~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~--~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~--p~~~~~  156 (694)
T PRK15179         81 RYPHTELFQVLVARALEAAHRSDEGLAVWRGIHQR--FPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGG--SSSARE  156 (694)
T ss_pred             hccccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhh--CCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcC--CCCHHH
Confidence            35566888889999999999999999999999875  56 45677888999999999999999999988765  888888


Q ss_pred             HHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHC
Q 039342          132 GQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKR  193 (248)
Q Consensus       132 ~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  193 (248)
                      .......+...|.+++|..+|++....+. -+..++..+-.++-+.|+.++|...|+...+.
T Consensus       157 ~~~~a~~l~~~g~~~~A~~~y~~~~~~~p-~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~  217 (694)
T PRK15179        157 ILLEAKSWDEIGQSEQADACFERLSRQHP-EFENGYVGWAQSLTRRGALWRARDVLQAGLDA  217 (694)
T ss_pred             HHHHHHHHHHhcchHHHHHHHHHHHhcCC-CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            77777778899999999999999988432 24788888999999999999999999987653

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

Probab=98.29  E-value=0.00078  Score=56.56  Aligned_cols=213  Identities=13%  Similarity=0.095  Sum_probs=123.7

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |..++...+|++.... ++.....|-.....+..+||+..|..++....+.. +-+..+|-.-+..-.....++.|..+|
T Consensus       564 gt~Esl~Allqkav~~-~pkae~lwlM~ake~w~agdv~~ar~il~~af~~~-pnseeiwlaavKle~en~e~eraR~ll  641 (913)
T KOG0495|consen  564 GTRESLEALLQKAVEQ-CPKAEILWLMYAKEKWKAGDVPAARVILDQAFEAN-PNSEEIWLAAVKLEFENDELERARDLL  641 (913)
T ss_pred             CcHHHHHHHHHHHHHh-CCcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhC-CCcHHHHHHHHHHhhccccHHHHHHHH
Confidence            4556666666666543 22344556666666777788888888877776554 235677777777777888888888888


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCC
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYG  161 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~  161 (248)
                      .+.+..  .|+..+|.--+..---.++.++|.+++++..+.  -|+-.-+..++-..+...++.+.|...|..=.+. ++
T Consensus       642 akar~~--sgTeRv~mKs~~~er~ld~~eeA~rllEe~lk~--fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~-cP  716 (913)
T KOG0495|consen  642 AKARSI--SGTERVWMKSANLERYLDNVEEALRLLEEALKS--FPDFHKLWLMLGQIEEQMENIEMAREAYLQGTKK-CP  716 (913)
T ss_pred             HHHhcc--CCcchhhHHHhHHHHHhhhHHHHHHHHHHHHHh--CCchHHHHHHHhHHHHHHHHHHHHHHHHHhcccc-CC
Confidence            776653  466667766666666667777888777766543  2444444444444444445555555544432221 12


Q ss_pred             CCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHH
Q 039342          162 LGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWL  227 (248)
Q Consensus       162 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~  227 (248)
                      -.+-.|-.+.+.=-+.|.+-+|..++++-.-+  .|+    +.++|--.++.-.+.|..++|+.++
T Consensus       717 ~~ipLWllLakleEk~~~~~rAR~ildrarlk--NPk----~~~lwle~Ir~ElR~gn~~~a~~lm  776 (913)
T KOG0495|consen  717 NSIPLWLLLAKLEEKDGQLVRARSILDRARLK--NPK----NALLWLESIRMELRAGNKEQAELLM  776 (913)
T ss_pred             CCchHHHHHHHHHHHhcchhhHHHHHHHHHhc--CCC----cchhHHHHHHHHHHcCCHHHHHHHH
Confidence            22334444444445556666666666655433  233    3333433345555666666555443

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

Probab=98.29  E-value=0.0002  Score=57.91  Aligned_cols=155  Identities=10%  Similarity=0.002  Sum_probs=106.8

Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHH
Q 039342           33 FRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDA  112 (248)
Q Consensus        33 ~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a  112 (248)
                      +.-.|+.-.|.+-|+...+..-.++. .|--+-.+|....+.++....|+...+.+.. ++.+|..--..+.-.+++++|
T Consensus       336 ~fL~g~~~~a~~d~~~~I~l~~~~~~-lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp~-n~dvYyHRgQm~flL~q~e~A  413 (606)
T KOG0547|consen  336 HFLKGDSLGAQEDFDAAIKLDPAFNS-LYIKRAAAYADENQSEKMWKDFNKAEDLDPE-NPDVYYHRGQMRFLLQQYEEA  413 (606)
T ss_pred             hhhcCCchhhhhhHHHHHhcCcccch-HHHHHHHHHhhhhccHHHHHHHHHHHhcCCC-CCchhHhHHHHHHHHHHHHHH
Confidence            34468888999999998877654444 2666677888889999999999888765422 555666666666667788888


Q ss_pred             HHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          113 YGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       113 ~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                      ..=|++...-.  |....-..-+....-+.+.++.+...|++.++. ++-.+..|+..-..+.-++++++|.+.|+...+
T Consensus       414 ~aDF~Kai~L~--pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkk-FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~  490 (606)
T KOG0547|consen  414 IADFQKAISLD--PENAYAYIQLCCALYRQHKIAESMKTFEEAKKK-FPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIE  490 (606)
T ss_pred             HHHHHHHhhcC--hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHh
Confidence            88888766443  433322221221123445778888888887665 555677788888888888888888888887654

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

Probab=98.28  E-value=1.9e-05  Score=50.90  Aligned_cols=43  Identities=28%  Similarity=0.297  Sum_probs=25.4

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHCCC-CcCHhhHHHHHHHHHh
Q 039342           63 AVLSVYCFAGLVDESKEQFQEIKSSGI-LPSVMCYCMLLAVYAK  105 (248)
Q Consensus        63 ~ll~~~~~~g~~~~a~~~~~~m~~~~~-~p~~~~~~~li~~~~~  105 (248)
                      .-|..|...+++.....+|+.+++.|+ .|+..+|+.++.+.++
T Consensus        30 ~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~   73 (120)
T PF08579_consen   30 DNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAK   73 (120)
T ss_pred             HHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHH
Confidence            344455555666666666666666666 5666666666666554

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 [, , ].

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.26  E-value=0.00023  Score=53.65  Aligned_cols=103  Identities=15%  Similarity=-0.018  Sum_probs=70.8

Q ss_pred             CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcC----HhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHH-
Q 039342           55 DPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPS----VMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQ-  129 (248)
Q Consensus        55 ~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~-  129 (248)
                      ......+-.+...+.+.|+++.|...|+++.+..  |+    ...+..+-.++...|++++|...++++.+..-..... 
T Consensus        30 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~  107 (235)
T TIGR03302        30 EWPAEELYEEAKEALDSGDYTEAIKYFEALESRY--PFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDAD  107 (235)
T ss_pred             cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchH
Confidence            3456677788888999999999999999987652  32    2467778889999999999999999997654211111 


Q ss_pred             -hHHHHhcc-------cccccchHHHHHHHHHHHHhcC
Q 039342          130 -VTGQMIKG-------EFDDESNWQMVEYVFDKLNCEG  159 (248)
Q Consensus       130 -~~~~~l~~-------~~~~~~~~~~a~~~~~~m~~~~  159 (248)
                       .+..+-..       .....++++.|...++......
T Consensus       108 ~a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~  145 (235)
T TIGR03302       108 YAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRY  145 (235)
T ss_pred             HHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHC
Confidence             11111111       1123367788888888877653

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).

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

Probab=98.25  E-value=0.00017  Score=53.62  Aligned_cols=159  Identities=11%  Similarity=0.012  Sum_probs=102.5

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhc
Q 039342           27 NAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKS  106 (248)
Q Consensus        27 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~  106 (248)
                      .-+-..+...|+-+....+....... -+-|....+.......+.|++..|...|.+..... ++|...|+.+--+|.+.
T Consensus        70 ~~~a~a~~~~G~a~~~l~~~~~~~~~-~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~-p~d~~~~~~lgaaldq~  147 (257)
T COG5010          70 AKLATALYLRGDADSSLAVLQKSAIA-YPKDRELLAAQGKNQIRNGNFGEAVSVLRKAARLA-PTDWEAWNLLGAALDQL  147 (257)
T ss_pred             HHHHHHHHhcccccchHHHHhhhhcc-CcccHHHHHHHHHHHHHhcchHHHHHHHHHHhccC-CCChhhhhHHHHHHHHc
Confidence            44555566667766666665554321 23344455567777888888888888887776542 45777888888888888


Q ss_pred             CCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHH
Q 039342          107 NRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARV  186 (248)
Q Consensus       107 ~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~  186 (248)
                      |+++.|..-|.+..+-.. -.....+.+-.. +.-.|+.+.|..++......+.. |...-..+.......|+++.|.++
T Consensus       148 Gr~~~Ar~ay~qAl~L~~-~~p~~~nNlgms-~~L~gd~~~A~~lll~a~l~~~a-d~~v~~NLAl~~~~~g~~~~A~~i  224 (257)
T COG5010         148 GRFDEARRAYRQALELAP-NEPSIANNLGMS-LLLRGDLEDAETLLLPAYLSPAA-DSRVRQNLALVVGLQGDFREAEDI  224 (257)
T ss_pred             cChhHHHHHHHHHHHhcc-CCchhhhhHHHH-HHHcCCHHHHHHHHHHHHhCCCC-chHHHHHHHHHHhhcCChHHHHhh
Confidence            888888888877765432 112223333323 44566777888777776665443 555666777777888888888877


Q ss_pred             HHHH
Q 039342          187 LDEA  190 (248)
Q Consensus       187 ~~~m  190 (248)
                      ...-
T Consensus       225 ~~~e  228 (257)
T COG5010         225 AVQE  228 (257)
T ss_pred             cccc
Confidence            6543

>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=98.24  E-value=2.1e-05  Score=56.98  Aligned_cols=118  Identities=11%  Similarity=0.103  Sum_probs=88.7

Q ss_pred             CCCCHHHHHHHHHHHHh-----cCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchH
Q 039342           54 CDPNERTLEAVLSVYCF-----AGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIH  128 (248)
Q Consensus        54 ~~p~~~t~~~ll~~~~~-----~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~  128 (248)
                      -..|-.+|..++..|.+     .|.++-....+..|.+-|+.-|..+|+.||+.+=+..-.                 ..
T Consensus        43 ~~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fv-----------------p~  105 (228)
T PF06239_consen   43 QAKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFV-----------------PR  105 (228)
T ss_pred             ccccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcc-----------------cc
Confidence            36788899999998864     578888899999999999999999999999987752221                 22


Q ss_pred             HhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCch-HHHHHHHHHHH
Q 039342          129 QVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR-ERAARVLDEAT  191 (248)
Q Consensus       129 ~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~-~~a~~~~~~m~  191 (248)
                      ..+...... +  ..+-+.+.+++++|...|+.||..|+..+++.+++.+.. .+...+.-.|.
T Consensus       106 n~fQ~~F~h-y--p~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~p~~K~~rmmYWmp  166 (228)
T PF06239_consen  106 NFFQAEFMH-Y--PRQQECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSHPMKKYRRMMYWMP  166 (228)
T ss_pred             cHHHHHhcc-C--cHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccHHHHHHHHHHHHHH
Confidence            233333322 3  344579999999999999999999999999999988753 33444444443

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

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

Probab=98.23  E-value=0.00013  Score=63.33  Aligned_cols=230  Identities=11%  Similarity=0.056  Sum_probs=149.8

Q ss_pred             CchHHHHHHHHHHHHcCCCCC-HHhHHHHHHHHHhcCCHHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHhcCChhHHHH
Q 039342            2 GLYKECQAILSRMSESGVARN-SDSFNAVIEAFRQGGRFEEAIKAYVEMEKV-RCDPNERTLEAVLSVYCFAGLVDESKE   79 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~-~~~y~~li~~~~~~~~~~~a~~~~~~m~~~-~~~p~~~t~~~ll~~~~~~g~~~~a~~   79 (248)
                      ++++.|.+++..+.+.-  |+ +..|--+....-..+...+|...++..... .-.|+.  ++.+-..+.+..++..|.+
T Consensus       510 ~~~~~A~e~Yk~Ilkeh--p~YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~d~~np~a--rsl~G~~~l~k~~~~~a~k  585 (1018)
T KOG2002|consen  510 HDTEVAEEMYKSILKEH--PGYIDAYLRLGCMARDKNNLYEASLLLKDALNIDSSNPNA--RSLLGNLHLKKSEWKPAKK  585 (1018)
T ss_pred             hhhhHHHHHHHHHHHHC--chhHHHHHHhhHHHHhccCcHHHHHHHHHHHhcccCCcHH--HHHHHHHHHhhhhhccccc
Confidence            35677778888776532  43 444544543333446777788787776443 334544  4446668888888888888


Q ss_pred             HHHHHHHC-CCCcCHhhHHHHHHHHHh------------cCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHH
Q 039342           80 QFQEIKSS-GILPSVMCYCMLLAVYAK------------SNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQ  146 (248)
Q Consensus        80 ~~~~m~~~-~~~p~~~~~~~li~~~~~------------~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~  146 (248)
                      =|+...+. ...+|+.+.-+|-+.|..            .+..++|+++|.+.....  |.+.....-|...+...|++.
T Consensus       586 ~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~d--pkN~yAANGIgiVLA~kg~~~  663 (1018)
T KOG2002|consen  586 KFETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLRND--PKNMYAANGIGIVLAEKGRFS  663 (1018)
T ss_pred             HHHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHhcC--cchhhhccchhhhhhhccCch
Confidence            77666543 222565555555554432            234678888888877654  544444444445577889999


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHH
Q 039342          147 MVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVW  226 (248)
Q Consensus       147 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~  226 (248)
                      .|..+|.+..+.... ...+|-.+-.+|+.+|++..|.++|+...+.-.+-+    +.-+..++.+++-+.|.+.+|.++
T Consensus       664 ~A~dIFsqVrEa~~~-~~dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~~~~----~~~vl~~Lara~y~~~~~~eak~~  738 (1018)
T KOG2002|consen  664 EARDIFSQVREATSD-FEDVWLNLAHCYVEQGQYRLAIQMYENCLKKFYKKN----RSEVLHYLARAWYEAGKLQEAKEA  738 (1018)
T ss_pred             HHHHHHHHHHHHHhh-CCceeeeHHHHHHHHHHHHHHHHHHHHHHHHhcccC----CHHHHHHHHHHHHHhhhHHHHHHH
Confidence            999999999887542 445678899999999999999999998765433333    333444555888888888888776


Q ss_pred             HHHHHHHHHcCCCCCccc
Q 039342          227 LNKMYEMFMMGEDLPQLA  244 (248)
Q Consensus       227 ~~~m~~~~~~~~~~~~~~  244 (248)
                      +-.-  +...|..+....
T Consensus       739 ll~a--~~~~p~~~~v~F  754 (1018)
T KOG2002|consen  739 LLKA--RHLAPSNTSVKF  754 (1018)
T ss_pred             HHHH--HHhCCccchHHh
Confidence            5443  334565555443

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

Probab=98.23  E-value=0.00087  Score=56.28  Aligned_cols=185  Identities=12%  Similarity=0.085  Sum_probs=146.6

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      +||+..|+.++.+.-+... -+...|-+-+..-..+.+++.|..+|.+...  ..|+...|.--++.-.-.++.++|.++
T Consensus       597 agdv~~ar~il~~af~~~p-nseeiwlaavKle~en~e~eraR~llakar~--~sgTeRv~mKs~~~er~ld~~eeA~rl  673 (913)
T KOG0495|consen  597 AGDVPAARVILDQAFEANP-NSEEIWLAAVKLEFENDELERARDLLAKARS--ISGTERVWMKSANLERYLDNVEEALRL  673 (913)
T ss_pred             cCCcHHHHHHHHHHHHhCC-CcHHHHHHHHHHhhccccHHHHHHHHHHHhc--cCCcchhhHHHhHHHHHhhhHHHHHHH
Confidence            5899999999999887553 3678999999999999999999999999876  468888888777777778999999999


Q ss_pred             HHHHHHCCCCcC-HhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcC
Q 039342           81 FQEIKSSGILPS-VMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEG  159 (248)
Q Consensus        81 ~~~m~~~~~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~  159 (248)
                      +++-.+.  .|+ ...|-.+=+.+-+.++++.|...|..-.+  ..|...-.+.++...-...+.+-.|..+++.-.-.+
T Consensus       674 lEe~lk~--fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k--~cP~~ipLWllLakleEk~~~~~rAR~ildrarlkN  749 (913)
T KOG0495|consen  674 LEEALKS--FPDFHKLWLMLGQIEEQMENIEMAREAYLQGTK--KCPNSIPLWLLLAKLEEKDGQLVRARSILDRARLKN  749 (913)
T ss_pred             HHHHHHh--CCchHHHHHHHhHHHHHHHHHHHHHHHHHhccc--cCCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhcC
Confidence            9887765  344 34566666777778888888888875433  236666666666654556678889999999887776


Q ss_pred             CCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHC
Q 039342          160 YGLGMRFYNALLEALWCLGLRERAARVLDEATKR  193 (248)
Q Consensus       160 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  193 (248)
                      .. +...|-..|+.-.+.|+.+.|..+..+..+.
T Consensus       750 Pk-~~~lwle~Ir~ElR~gn~~~a~~lmakALQe  782 (913)
T KOG0495|consen  750 PK-NALLWLESIRMELRAGNKEQAELLMAKALQE  782 (913)
T ss_pred             CC-cchhHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            55 7888999999999999999999888776543

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

Probab=98.22  E-value=0.0016  Score=56.48  Aligned_cols=119  Identities=11%  Similarity=0.138  Sum_probs=76.2

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHH----HHHHHHHHhcCChhHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTL----EAVLSVYCFAGLVDES   77 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~----~~ll~~~~~~g~~~~a   77 (248)
                      |++++|.-.|.+..+... ++...+--=...|-+.|+...|.+.|.++....-+.|..-+    -.++..+...++.+.|
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 GNINQARYCYSRAIQANP-SNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNERERA  299 (895)
T ss_pred             ccHHHHHHHHHHHHhcCC-cchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHHHHH
Confidence            556777777777766442 34455555566777778888888888777655322222222    2334556666777777


Q ss_pred             HHHHHHHHHC-CCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 039342           78 KEQFQEIKSS-GILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHT  121 (248)
Q Consensus        78 ~~~~~~m~~~-~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  121 (248)
                      .+.++..... +-..+...+++++..|.+...++.|......+..
T Consensus       300 ~~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~  344 (895)
T KOG2076|consen  300 AKALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRN  344 (895)
T ss_pred             HHHHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhc
Confidence            7777766542 2234566778888888888888888877777765

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

Probab=98.21  E-value=0.00028  Score=51.71  Aligned_cols=119  Identities=8%  Similarity=0.046  Sum_probs=53.6

Q ss_pred             cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHH-HhcCC--HHHH
Q 039342           36 GGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVY-AKSNR--WDDA  112 (248)
Q Consensus        36 ~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~-~~~~~--~~~a  112 (248)
                      .++.+++...++...+.+ +.|...|..+-..|...|+++.|...|++..+... -+...+..+-.++ ...|+  .++|
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-PQNSEQWALLGEYYLWRNDYDNALLAYRQALQLRG-ENAELYAALATVLYYQAGQHMTPQT  129 (198)
T ss_pred             chhHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhcCCCCcHHH
Confidence            344444444444443332 34445555555555555555555555555544321 1334444444432 34344  2555


Q ss_pred             HHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhc
Q 039342          113 YGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCE  158 (248)
Q Consensus       113 ~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  158 (248)
                      ..++++..+..  |+.......+...+...|+++.|...++.+.+.
T Consensus       130 ~~~l~~al~~d--P~~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l  173 (198)
T PRK10370        130 REMIDKALALD--ANEVTALMLLASDAFMQADYAQAIELWQKVLDL  173 (198)
T ss_pred             HHHHHHHHHhC--CCChhHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            55555554443  333222222222244455555555555555444

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

Probab=98.14  E-value=0.00027  Score=48.28  Aligned_cols=105  Identities=13%  Similarity=0.070  Sum_probs=83.5

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHH
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLA  101 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~  101 (248)
                      +......+...+.+.|++++|.+.++.....+ +.+...+..+-.++.+.|+++.|..++++..+.+ +.+...+..+-.
T Consensus        16 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~   93 (135)
T TIGR02552        16 QLEQIYALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD-PDDPRPYFHAAE   93 (135)
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCChHHHHHHHH
Confidence            44566677788888999999999999987754 4577888888889999999999999999887764 335677777888


Q ss_pred             HHHhcCCHHHHHHHHHHHHHCCCCchHHh
Q 039342          102 VYAKSNRWDDAYGLLDEMHTNRISNIHQV  130 (248)
Q Consensus       102 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~~  130 (248)
                      .+...|++++|...|++..+..  |+...
T Consensus        94 ~~~~~g~~~~A~~~~~~al~~~--p~~~~  120 (135)
T TIGR02552        94 CLLALGEPESALKALDLAIEIC--GENPE  120 (135)
T ss_pred             HHHHcCCHHHHHHHHHHHHHhc--cccch
Confidence            8999999999999998887654  44443

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

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

Probab=98.13  E-value=0.0012  Score=48.32  Aligned_cols=157  Identities=10%  Similarity=0.058  Sum_probs=110.6

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCC
Q 039342           29 VIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNR  108 (248)
Q Consensus        29 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~  108 (248)
                      -+..|...|+++.+..-.+.+..    |. .       .+...++.+++...++...+.. +.+...|..+-..|...|+
T Consensus        22 ~~~~Y~~~g~~~~v~~~~~~~~~----~~-~-------~~~~~~~~~~~i~~l~~~L~~~-P~~~~~w~~Lg~~~~~~g~   88 (198)
T PRK10370         22 CVGSYLLSPKWQAVRAEYQRLAD----PL-H-------QFASQQTPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWRND   88 (198)
T ss_pred             HHHHHHHcchHHHHHHHHHHHhC----cc-c-------cccCchhHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCC
Confidence            34568889998887544432211    11 0       1122566677777777766543 3478899999999999999


Q ss_pred             HHHHHHHHHHHHHCCCCchHHhHHHH-hcccccccch--HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHH
Q 039342          109 WDDAYGLLDEMHTNRISNIHQVTGQM-IKGEFDDESN--WQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAAR  185 (248)
Q Consensus       109 ~~~a~~~~~~m~~~~~~~~~~~~~~~-l~~~~~~~~~--~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~  185 (248)
                      +++|...|++.....  |+....... -...+...|+  .+.+..++++..+.+.. +...+..+-..+.+.|++++|..
T Consensus        89 ~~~A~~a~~~Al~l~--P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP~-~~~al~~LA~~~~~~g~~~~Ai~  165 (198)
T PRK10370         89 YDNALLAYRQALQLR--GENAELYAALATVLYYQAGQHMTPQTREMIDKALALDAN-EVTALMLLASDAFMQADYAQAIE  165 (198)
T ss_pred             HHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCCC-ChhHHHHHHHHHHHcCCHHHHHH
Confidence            999999999988765  544433333 2222344444  58999999999888655 67788888899999999999999


Q ss_pred             HHHHHHHCCCCCCcchh
Q 039342          186 VLDEATKRGLFPELFRH  202 (248)
Q Consensus       186 ~~~~m~~~g~~p~~~t~  202 (248)
                      .|+++.+. .+|+...+
T Consensus       166 ~~~~aL~l-~~~~~~r~  181 (198)
T PRK10370        166 LWQKVLDL-NSPRVNRT  181 (198)
T ss_pred             HHHHHHhh-CCCCccHH
Confidence            99999875 35555443

>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=98.12  E-value=0.00015  Score=58.50  Aligned_cols=112  Identities=15%  Similarity=0.110  Sum_probs=76.8

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      ++++.|..+|+++.+..  |+  ....+...+...++-.+|.+++++..+.. +-|......-...|.+.++.+.|.++.
T Consensus       183 ~~~~~ai~lle~L~~~~--pe--v~~~LA~v~l~~~~E~~AI~ll~~aL~~~-p~d~~LL~~Qa~fLl~k~~~~lAL~iA  257 (395)
T PF09295_consen  183 QRYDEAIELLEKLRERD--PE--VAVLLARVYLLMNEEVEAIRLLNEALKEN-PQDSELLNLQAEFLLSKKKYELALEIA  257 (395)
T ss_pred             ccHHHHHHHHHHHHhcC--Cc--HHHHHHHHHHhcCcHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCHHHHHHHH
Confidence            56777888888777643  33  33446666666777777777777776432 345556666666677777888888888


Q ss_pred             HHHHHCCCCcCH-hhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 039342           82 QEIKSSGILPSV-MCYCMLLAVYAKSNRWDDAYGLLDEMH  120 (248)
Q Consensus        82 ~~m~~~~~~p~~-~~~~~li~~~~~~~~~~~a~~~~~~m~  120 (248)
                      ++..+.  .|+. .+|..|..+|.+.|+++.|+..++.+.
T Consensus       258 k~av~l--sP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  258 KKAVEL--SPSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             HHHHHh--CchhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            777764  4544 477888888888888888887777653

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

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.12  E-value=0.00029  Score=53.61  Aligned_cols=206  Identities=16%  Similarity=0.126  Sum_probs=142.0

Q ss_pred             cCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhH
Q 039342           17 SGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCY   96 (248)
Q Consensus        17 ~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~   96 (248)
                      .|+.....-+.+.+..+.+..+++.|.+++....+.. +-+....+.+-.+|.+..++..|-..++++...  .|...-|
T Consensus         4 ~g~~i~EGeftaviy~lI~d~ry~DaI~~l~s~~Er~-p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql--~P~~~qY   80 (459)
T KOG4340|consen    4 SGAQIPEGEFTAVVYRLIRDARYADAIQLLGSELERS-PRSRAGLSLLGYCYYRLQEFALAAECYEQLGQL--HPELEQY   80 (459)
T ss_pred             ccccCCCCchHHHHHHHHHHhhHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--ChHHHHH
Confidence            3444444557788888899999999999998876653 237778888999999999999999999999875  4555444


Q ss_pred             HH-HHHHHHhcCCHHHHHHHHHHHHHCC-CCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Q 039342           97 CM-LLAVYAKSNRWDDAYGLLDEMHTNR-ISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEAL  174 (248)
Q Consensus        97 ~~-li~~~~~~~~~~~a~~~~~~m~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~  174 (248)
                      .. -..++-+.+.+..|+++...|.+.. ......-..+.|   .-..+++-.+..++++....|   +..+.+..-...
T Consensus        81 rlY~AQSLY~A~i~ADALrV~~~~~D~~~L~~~~lqLqaAI---kYse~Dl~g~rsLveQlp~en---~Ad~~in~gCll  154 (459)
T KOG4340|consen   81 RLYQAQSLYKACIYADALRVAFLLLDNPALHSRVLQLQAAI---KYSEGDLPGSRSLVEQLPSEN---EADGQINLGCLL  154 (459)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHhcCCHHHHHHHHHHHHHH---hcccccCcchHHHHHhccCCC---ccchhccchhee
Confidence            42 2355667888999999999887641 111111112222   223455666666766654332   334444444556


Q ss_pred             HhcCchHHHHHHHHHHHH-CCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHHHcCC
Q 039342          175 WCLGLRERAARVLDEATK-RGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGE  238 (248)
Q Consensus       175 ~~~g~~~~a~~~~~~m~~-~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~~~~~  238 (248)
                      .+.|+++.|.+-|+...+ .|..| ...|+.-+      +..+.|+.+.|.+...+..++|+...
T Consensus       155 ykegqyEaAvqkFqaAlqvsGyqp-llAYniAL------aHy~~~qyasALk~iSEIieRG~r~H  212 (459)
T KOG4340|consen  155 YKEGQYEAAVQKFQAALQVSGYQP-LLAYNLAL------AHYSSRQYASALKHISEIIERGIRQH  212 (459)
T ss_pred             eccccHHHHHHHHHHHHhhcCCCc-hhHHHHHH------HHHhhhhHHHHHHHHHHHHHhhhhcC
Confidence            688999999999998776 45555 35566554      44567888999999999999998753

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

Probab=98.06  E-value=0.00028  Score=48.98  Aligned_cols=126  Identities=13%  Similarity=0.208  Sum_probs=77.9

Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcC--HhhHHH
Q 039342           24 DSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN---ERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPS--VMCYCM   98 (248)
Q Consensus        24 ~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~---~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~--~~~~~~   98 (248)
                      ..|..++..+ ..++...+.+.++.+.+.. +.+   ....-.+-..+...|++++|...|+...+....|+  ....-.
T Consensus        13 ~~y~~~~~~~-~~~~~~~~~~~~~~l~~~~-~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~   90 (145)
T PF09976_consen   13 ALYEQALQAL-QAGDPAKAEAAAEQLAKDY-PSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLR   90 (145)
T ss_pred             HHHHHHHHHH-HCCCHHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHH
Confidence            4555556665 3777777877777776653 222   12222344667778888888888888877652232  224444


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHH
Q 039342           99 LLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDK  154 (248)
Q Consensus        99 li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  154 (248)
                      +...+...|++++|+..++.....   +....+..+.--.+...|+++.|...|+.
T Consensus        91 LA~~~~~~~~~d~Al~~L~~~~~~---~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen   91 LARILLQQGQYDEALATLQQIPDE---AFKALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHHHcCCHHHHHHHHHhccCc---chHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            666777788888888888664333   33334444444446677778888877764

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

Probab=98.04  E-value=0.00048  Score=58.24  Aligned_cols=196  Identities=15%  Similarity=0.055  Sum_probs=118.0

Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHH
Q 039342           24 DSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVY  103 (248)
Q Consensus        24 ~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~  103 (248)
                      ..|.-+|.+|+..|+..+|..+..+-.+  -+||+..|..+.+......-+++|.++++.....       .-..+-...
T Consensus       425 emw~~vi~CY~~lg~~~kaeei~~q~le--k~~d~~lyc~LGDv~~d~s~yEkawElsn~~sar-------A~r~~~~~~  495 (777)
T KOG1128|consen  425 EMWDPVILCYLLLGQHGKAEEINRQELE--KDPDPRLYCLLGDVLHDPSLYEKAWELSNYISAR-------AQRSLALLI  495 (777)
T ss_pred             HHHHHHHHHHHHhcccchHHHHHHHHhc--CCCcchhHHHhhhhccChHHHHHHHHHhhhhhHH-------HHHhhcccc
Confidence            3455666777777777777776666555  2577777777766666666666777666654322       000011111


Q ss_pred             HhcCCHHHHHHHHHHHHHCC-CCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHH
Q 039342          104 AKSNRWDDAYGLLDEMHTNR-ISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRER  182 (248)
Q Consensus       104 ~~~~~~~~a~~~~~~m~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~  182 (248)
                      .++++++++.+.|+.-.+.. ..+  .+|... -.+.-..++++.+...|........ -+...||.+-.+|.+.+...+
T Consensus       496 ~~~~~fs~~~~hle~sl~~nplq~--~~wf~~-G~~ALqlek~q~av~aF~rcvtL~P-d~~eaWnNls~ayi~~~~k~r  571 (777)
T KOG1128|consen  496 LSNKDFSEADKHLERSLEINPLQL--GTWFGL-GCAALQLEKEQAAVKAFHRCVTLEP-DNAEAWNNLSTAYIRLKKKKR  571 (777)
T ss_pred             ccchhHHHHHHHHHHHhhcCccch--hHHHhc-cHHHHHHhhhHHHHHHHHHHhhcCC-CchhhhhhhhHHHHHHhhhHH
Confidence            22566666666666543322 111  122111 1112344567777777776655432 246779999999999999999


Q ss_pred             HHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHHHcCC
Q 039342          183 AARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGE  238 (248)
Q Consensus       183 a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~~~~~  238 (248)
                      |...+.+..+.+..+-.      +|--...--.+.|.+++|.+.+..+.+......
T Consensus       572 a~~~l~EAlKcn~~~w~------iWENymlvsvdvge~eda~~A~~rll~~~~~~~  621 (777)
T KOG1128|consen  572 AFRKLKEALKCNYQHWQ------IWENYMLVSVDVGEFEDAIKAYHRLLDLRKKYK  621 (777)
T ss_pred             HHHHHHHHhhcCCCCCe------eeechhhhhhhcccHHHHHHHHHHHHHhhhhcc
Confidence            99999998876644321      121111344688999999998888877765544

>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=98.04  E-value=0.00026  Score=57.03  Aligned_cols=125  Identities=17%  Similarity=0.156  Sum_probs=95.8

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccc
Q 039342           60 TLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEF  139 (248)
Q Consensus        60 t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~  139 (248)
                      ....+++.+...++++.|.++|+++.+..  |+  ....+.+.+...++-.+|.+++++..+..  |.....-.+-..++
T Consensus       171 Lv~~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  171 LVDTLLKYLSLTQRYDEAIELLEKLRERD--PE--VAVLLARVYLLMNEEVEAIRLLNEALKEN--PQDSELLNLQAEFL  244 (395)
T ss_pred             HHHHHHHHHhhcccHHHHHHHHHHHHhcC--Cc--HHHHHHHHHHhcCcHHHHHHHHHHHHHhC--CCCHHHHHHHHHHH
Confidence            34556777778899999999999999874  54  45568888888888899999999888553  43333333333446


Q ss_pred             cccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHH
Q 039342          140 DDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEAT  191 (248)
Q Consensus       140 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  191 (248)
                      ...++++.|..+.++..+.... +..+|..|..+|...|+++.|...++.+.
T Consensus       245 l~k~~~~lAL~iAk~av~lsP~-~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  245 LSKKKYELALEIAKKAVELSPS-EFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             HhcCCHHHHHHHHHHHHHhCch-hHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            6778889999999988876322 56689999999999999999999988764

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

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

Probab=98.01  E-value=0.002  Score=58.54  Aligned_cols=204  Identities=15%  Similarity=0.099  Sum_probs=151.1

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHc-CCCC---CHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHH
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKV-RCDP---NERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYC   97 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~-~~~p---~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~   97 (248)
                      +...|-..|......++.+.|.++.++.... ++.-   -...|.++++.-...|.-+...++|++..+.-  -.-.+|.
T Consensus      1457 SSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqyc--d~~~V~~ 1534 (1710)
T KOG1070|consen 1457 SSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQYC--DAYTVHL 1534 (1710)
T ss_pred             cchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHhc--chHHHHH
Confidence            4668999999999999999999999998543 2111   12467778887777788899999999998752  2246799


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCC---HHHHHHHHHHH
Q 039342           98 MLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLG---MRFYNALLEAL  174 (248)
Q Consensus        98 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~---~~~~~~li~~~  174 (248)
                      .|...|.+....++|-++|+.|.+.=- -....|...... .-+...-++|..++.+..+.  .|.   .....-....-
T Consensus      1535 ~L~~iy~k~ek~~~A~ell~~m~KKF~-q~~~vW~~y~~f-Ll~~ne~~aa~~lL~rAL~~--lPk~eHv~~IskfAqLE 1610 (1710)
T KOG1070|consen 1535 KLLGIYEKSEKNDEADELLRLMLKKFG-QTRKVWIMYADF-LLRQNEAEAARELLKRALKS--LPKQEHVEFISKFAQLE 1610 (1710)
T ss_pred             HHHHHHHHhhcchhHHHHHHHHHHHhc-chhhHHHHHHHH-HhcccHHHHHHHHHHHHHhh--cchhhhHHHHHHHHHHH
Confidence            999999999999999999999977532 334445444444 44455557888888765543  333   44455566667


Q ss_pred             HhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHHHcC
Q 039342          175 WCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMG  237 (248)
Q Consensus       175 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~~~~  237 (248)
                      .+.|+.+++..+|+.....  .|.    ..-+|+..+..-.++|..+.+..+|++....++.+
T Consensus      1611 Fk~GDaeRGRtlfEgll~a--yPK----RtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~ 1667 (1710)
T KOG1070|consen 1611 FKYGDAERGRTLFEGLLSA--YPK----RTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSI 1667 (1710)
T ss_pred             hhcCCchhhHHHHHHHHhh--Ccc----chhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCCh
Confidence            7899999999999987754  332    45566666688888999898999999888877665

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

Probab=98.00  E-value=0.00065  Score=50.82  Aligned_cols=174  Identities=12%  Similarity=0.093  Sum_probs=115.4

Q ss_pred             HHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 039342            8 QAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSS   87 (248)
Q Consensus         8 ~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~   87 (248)
                      .++.+.+.......+...-..-...|++.|++++|++.....      -+......=+..+.+..+++.|.+.++.|.+-
T Consensus        93 ~~l~E~~a~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~~------~~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~i  166 (299)
T KOG3081|consen   93 ASLYELVADSTDGSNLIDLLLAAIIYMHDGDFDEALKALHLG------ENLEAAALNVQILLKMHRFDLAEKELKKMQQI  166 (299)
T ss_pred             HHHHHHHHhhccchhHHHHHHhhHHhhcCCChHHHHHHHhcc------chHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            344555555444444444444456788999999999888762      22233333445566778899999999999875


Q ss_pred             CCCcCHhhHHHHHHHHHh----cCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCC
Q 039342           88 GILPSVMCYCMLLAVYAK----SNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLG  163 (248)
Q Consensus        88 ~~~p~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~  163 (248)
                         -+..|.+-|-.++.+    .+.+.+|.-+|++|-++ ..|+..+.+..... +...+++++|+.++++....... +
T Consensus       167 ---ded~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~-~l~~~~~eeAe~lL~eaL~kd~~-d  240 (299)
T KOG3081|consen  167 ---DEDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVC-HLQLGRYEEAESLLEEALDKDAK-D  240 (299)
T ss_pred             ---chHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHH-HHHhcCHHHHHHHHHHHHhccCC-C
Confidence               256677766666654    45689999999999763 45777777666554 66778899999999998887655 3


Q ss_pred             HHHHH-HHHHHHHhcCchHHHHHHHHHHHHC
Q 039342          164 MRFYN-ALLEALWCLGLRERAARVLDEATKR  193 (248)
Q Consensus       164 ~~~~~-~li~~~~~~g~~~~a~~~~~~m~~~  193 (248)
                      ..|.. .++.+.....+.+-..+.+.+++..
T Consensus       241 petL~Nliv~a~~~Gkd~~~~~r~l~QLk~~  271 (299)
T KOG3081|consen  241 PETLANLIVLALHLGKDAEVTERNLSQLKLS  271 (299)
T ss_pred             HHHHHHHHHHHHHhCCChHHHHHHHHHHHhc
Confidence            44444 4444444444545566666676654

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

Probab=98.00  E-value=0.0004  Score=51.67  Aligned_cols=151  Identities=12%  Similarity=0.055  Sum_probs=115.5

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |+-+.+..+...... ..+.+....+.......+.|++..|...+++..... ++|...|+.+--+|.+.|+++.|..-|
T Consensus        80 G~a~~~l~~~~~~~~-~~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~-p~d~~~~~~lgaaldq~Gr~~~Ar~ay  157 (257)
T COG5010          80 GDADSSLAVLQKSAI-AYPKDRELLAAQGKNQIRNGNFGEAVSVLRKAARLA-PTDWEAWNLLGAALDQLGRFDEARRAY  157 (257)
T ss_pred             ccccchHHHHhhhhc-cCcccHHHHHHHHHHHHHhcchHHHHHHHHHHhccC-CCChhhhhHHHHHHHHccChhHHHHHH
Confidence            444555555555432 223466677779999999999999999999987654 789999999999999999999999999


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHh
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNC  157 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  157 (248)
                      .+..+... -+...+|.+--.+.-.|+.+.|..++......+.. +..+-..+... ....|+++.|+.+...-..
T Consensus       158 ~qAl~L~~-~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~~a-d~~v~~NLAl~-~~~~g~~~~A~~i~~~e~~  230 (257)
T COG5010         158 RQALELAP-NEPSIANNLGMSLLLRGDLEDAETLLLPAYLSPAA-DSRVRQNLALV-VGLQGDFREAEDIAVQELL  230 (257)
T ss_pred             HHHHHhcc-CCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCCCC-chHHHHHHHHH-HhhcCChHHHHhhcccccc
Confidence            99887522 25678899999999999999999999998877632 33334444433 6778888999988665443

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=97.99  E-value=0.00031  Score=48.67  Aligned_cols=89  Identities=12%  Similarity=0.030  Sum_probs=77.1

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|...|+....... .+...|..+-.++.+.|++++|...|+...+.+ +.+...+..+-.++.+.|++++|...|
T Consensus        38 g~~~~A~~~~~~al~~~P-~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~-p~~~~a~~~lg~~l~~~g~~~eAi~~~  115 (144)
T PRK15359         38 GDYSRAVIDFSWLVMAQP-WSWRAHIALAGTWMMLKEYTTAINFYGHALMLD-ASHPEPVYQTGVCLKMMGEPGLAREAF  115 (144)
T ss_pred             CCHHHHHHHHHHHHHcCC-CcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHH
Confidence            889999999999987543 478899999999999999999999999998764 467788999999999999999999999


Q ss_pred             HHHHHCCCCcCHh
Q 039342           82 QEIKSSGILPSVM   94 (248)
Q Consensus        82 ~~m~~~~~~p~~~   94 (248)
                      +...+.  .|+..
T Consensus       116 ~~Al~~--~p~~~  126 (144)
T PRK15359        116 QTAIKM--SYADA  126 (144)
T ss_pred             HHHHHh--CCCCh
Confidence            998875  45443

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

Probab=97.99  E-value=0.0027  Score=52.42  Aligned_cols=197  Identities=14%  Similarity=0.146  Sum_probs=136.7

Q ss_pred             CchHHHHHHHHHHHHcCCCCC-HHhHHHHHHHHHhcCCHHHHHHHHHHHHHc--CC-CCCHHHHHHHHHHHHhcCChhHH
Q 039342            2 GLYKECQAILSRMSESGVARN-SDSFNAVIEAFRQGGRFEEAIKAYVEMEKV--RC-DPNERTLEAVLSVYCFAGLVDES   77 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~-~~~y~~li~~~~~~~~~~~a~~~~~~m~~~--~~-~p~~~t~~~ll~~~~~~g~~~~a   77 (248)
                      |..++|++.|.....  +.|+ ...|-.+-+.|+-.|..++|+..+...-+.  |. .|.  .|  +---|.+.+..+.|
T Consensus       326 ~k~seARry~SKat~--lD~~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl~~G~hlP~--LY--lgmey~~t~n~kLA  399 (611)
T KOG1173|consen  326 GKYSEARRYFSKATT--LDPTFGPAWLAFGHSFAGEGEHDQAMAAYFTAARLMPGCHLPS--LY--LGMEYMRTNNLKLA  399 (611)
T ss_pred             cCcHHHHHHHHHHhh--cCccccHHHHHHhHHhhhcchHHHHHHHHHHHHHhccCCcchH--HH--HHHHHHHhccHHHH
Confidence            566777777776543  2233 457777778888888888887777665332  22 222  12  33457778899999


Q ss_pred             HHHHHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHC----C--CCchHHhHHHHhcccccccchHHHHHH
Q 039342           78 KEQFQEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTN----R--ISNIHQVTGQMIKGEFDDESNWQMVEY  150 (248)
Q Consensus        78 ~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~--~~~~~~~~~~~l~~~~~~~~~~~~a~~  150 (248)
                      .+.|.+...  +.| |+...+-+--..-..+.+.+|..+|+.-...    +  ..-+..+++.+=.. +++.+.+++|..
T Consensus       400 e~Ff~~A~a--i~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~-~Rkl~~~~eAI~  476 (611)
T KOG1173|consen  400 EKFFKQALA--IAPSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHA-YRKLNKYEEAID  476 (611)
T ss_pred             HHHHHHHHh--cCCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHH-HHHHhhHHHHHH
Confidence            999987665  345 5666776666666678899999998876521    1  11244455555444 788888999999


Q ss_pred             HHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhh
Q 039342          151 VFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVD  210 (248)
Q Consensus       151 ~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~  210 (248)
                      .++.-.....+ +..++.++--.|...|+++.|.+.|.+..  .+.|+-.+.+.++...+
T Consensus       477 ~~q~aL~l~~k-~~~~~asig~iy~llgnld~Aid~fhKaL--~l~p~n~~~~~lL~~ai  533 (611)
T KOG1173|consen  477 YYQKALLLSPK-DASTHASIGYIYHLLGNLDKAIDHFHKAL--ALKPDNIFISELLKLAI  533 (611)
T ss_pred             HHHHHHHcCCC-chhHHHHHHHHHHHhcChHHHHHHHHHHH--hcCCccHHHHHHHHHHH
Confidence            99887776444 78899999999999999999999999865  46888766666665443

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

Probab=97.97  E-value=0.0025  Score=51.68  Aligned_cols=114  Identities=16%  Similarity=0.130  Sum_probs=62.1

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCChhHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN-ERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      |..++|+..++.+...- +-|+.-+......+.+.++..+|.+.++.+...  .|+ ....-.+-.+|.+.|++.+|..+
T Consensus       320 ~~~d~A~~~l~~L~~~~-P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l--~P~~~~l~~~~a~all~~g~~~eai~~  396 (484)
T COG4783         320 GQYDEALKLLQPLIAAQ-PDNPYYLELAGDILLEANKAKEAIERLKKALAL--DPNSPLLQLNLAQALLKGGKPQEAIRI  396 (484)
T ss_pred             cccchHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCCccHHHHHHHHHHHhcCChHHHHHH
Confidence            45556666666654422 124444445555566666666666666665543  344 23333445566666666666666


Q ss_pred             HHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHH
Q 039342           81 FQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEM  119 (248)
Q Consensus        81 ~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m  119 (248)
                      ++...... +-|+..|..|-.+|...|+..++..-..+.
T Consensus       397 L~~~~~~~-p~dp~~w~~LAqay~~~g~~~~a~~A~AE~  434 (484)
T COG4783         397 LNRYLFND-PEDPNGWDLLAQAYAELGNRAEALLARAEG  434 (484)
T ss_pred             HHHHhhcC-CCCchHHHHHHHHHHHhCchHHHHHHHHHH
Confidence            66555432 235556666666666666666655555543

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

Probab=97.95  E-value=0.0065  Score=49.39  Aligned_cols=163  Identities=14%  Similarity=0.038  Sum_probs=111.7

Q ss_pred             CCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCc-CHhhHHHH
Q 039342           21 RNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILP-SVMCYCML   99 (248)
Q Consensus        21 ~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~l   99 (248)
                      |+...+...+.+......-..+..++.+-.+.  .-...-|..-+. +...|+.++|+..++.+...  .| |..-+...
T Consensus       272 ~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~--~~~aa~YG~A~~-~~~~~~~d~A~~~l~~L~~~--~P~N~~~~~~~  346 (484)
T COG4783         272 PDFQLARARIRAKYEALPNQQAADLLAKRSKR--GGLAAQYGRALQ-TYLAGQYDEALKLLQPLIAA--QPDNPYYLELA  346 (484)
T ss_pred             ccHHHHHHHHHHHhccccccchHHHHHHHhCc--cchHHHHHHHHH-HHHhcccchHHHHHHHHHHh--CCCCHHHHHHH
Confidence            45555555555554444333333333332221  222334554444 44678999999999998865  35 56667778


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCc
Q 039342          100 LAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGL  179 (248)
Q Consensus       100 i~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~  179 (248)
                      ...+.+.++.++|.+.++.+....  |+...........+-..|+++++..+++...... +-|+..|..|-++|...|+
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--PNSPLLQLNLAQALLKGGKPQEAIRILNRYLFND-PEDPNGWDLLAQAYAELGN  423 (484)
T ss_pred             HHHHHHcCChHHHHHHHHHHHhcC--CCccHHHHHHHHHHHhcCChHHHHHHHHHHhhcC-CCCchHHHHHHHHHHHhCc
Confidence            888999999999999999988654  6655554444444667788889998888877664 3478899999999999999


Q ss_pred             hHHHHHHHHHHH
Q 039342          180 RERAARVLDEAT  191 (248)
Q Consensus       180 ~~~a~~~~~~m~  191 (248)
                      ..++..-..+..
T Consensus       424 ~~~a~~A~AE~~  435 (484)
T COG4783         424 RAEALLARAEGY  435 (484)
T ss_pred             hHHHHHHHHHHH
Confidence            888888777654

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.95  E-value=0.0025  Score=57.89  Aligned_cols=231  Identities=13%  Similarity=0.091  Sum_probs=137.3

Q ss_pred             CchHHHHHHHHHHHHc----CC-CCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHH----cCCC--C-CHHHHHHHHHHHH
Q 039342            2 GLYKECQAILSRMSES----GV-ARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEK----VRCD--P-NERTLEAVLSVYC   69 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~----g~-~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~----~~~~--p-~~~t~~~ll~~~~   69 (248)
                      |++++|...+++....    |- .+...+++.+-..+...|+++.|...+++...    .+..  | ....+..+-..+.
T Consensus       505 G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~  584 (903)
T PRK04841        505 GELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLW  584 (903)
T ss_pred             CCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHH
Confidence            7888888888876532    11 11123555566677889999999998887643    2321  1 2334445556677


Q ss_pred             hcCChhHHHHHHHHHHHC--CCCc--CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCC--C-chH--HhHHHHhccccc
Q 039342           70 FAGLVDESKEQFQEIKSS--GILP--SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRI--S-NIH--QVTGQMIKGEFD  140 (248)
Q Consensus        70 ~~g~~~~a~~~~~~m~~~--~~~p--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~--~-~~~--~~~~~~l~~~~~  140 (248)
                      ..|++++|...+.+....  ...+  ....+..+...+...|+.++|.+.+.+......  . +..  .....+....+.
T Consensus       585 ~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  664 (903)
T PRK04841        585 EWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISLARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQ  664 (903)
T ss_pred             HhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHH
Confidence            789999999988876542  1112  234455566677789999999998888744211  1 100  111111111133


Q ss_pred             ccchHHHHHHHHHHHHhcCCCCC---HHHHHHHHHHHHhcCchHHHHHHHHHHHHC----CCCCCcchhhhHHhhhhhhc
Q 039342          141 DESNWQMVEYVFDKLNCEGYGLG---MRFYNALLEALWCLGLRERAARVLDEATKR----GLFPELFRHNKLVWSVDVHR  213 (248)
Q Consensus       141 ~~~~~~~a~~~~~~m~~~~~~p~---~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~~~t~~~li~~~~~~~  213 (248)
                      ..|+.+.+...+...........   ...+..+..++...|+.++|...+++....    |..++    ..-.....-..
T Consensus       665 ~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~l~~al~~~~~~g~~~~----~a~~~~~la~a  740 (903)
T PRK04841        665 MTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIARAQILLGQFDEAEIILEELNENARSLRLMSD----LNRNLILLNQL  740 (903)
T ss_pred             HCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCchHH----HHHHHHHHHHH
Confidence            45677888877766443211111   111345667788899999999999887642    32221    11112222356


Q ss_pred             cccchHHHHHHHHHHHHHHHHHc
Q 039342          214 MWEGGAYTAISVWLNKMYEMFMM  236 (248)
Q Consensus       214 ~~~~g~~~~~~~~~~~m~~~~~~  236 (248)
                      +...|+.++|...+.+-.+..-.
T Consensus       741 ~~~~G~~~~A~~~L~~Al~la~~  763 (903)
T PRK04841        741 YWQQGRKSEAQRVLLEALKLANR  763 (903)
T ss_pred             HHHcCCHHHHHHHHHHHHHHhCc
Confidence            67888888888888777766543

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

Probab=97.95  E-value=0.0024  Score=51.80  Aligned_cols=184  Identities=10%  Similarity=0.025  Sum_probs=133.0

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      +++..|.++|++...... .+...|--.+..=.++..+..|..+++.....=-..| ..|--.+.+=-..|++..|.++|
T Consensus        87 ~e~~RARSv~ERALdvd~-r~itLWlkYae~Emknk~vNhARNv~dRAvt~lPRVd-qlWyKY~ymEE~LgNi~gaRqif  164 (677)
T KOG1915|consen   87 KEIQRARSVFERALDVDY-RNITLWLKYAEFEMKNKQVNHARNVWDRAVTILPRVD-QLWYKYIYMEEMLGNIAGARQIF  164 (677)
T ss_pred             HHHHHHHHHHHHHHhccc-ccchHHHHHHHHHHhhhhHhHHHHHHHHHHHhcchHH-HHHHHHHHHHHHhcccHHHHHHH
Confidence            467889999999887553 5778888888888899999999999999865422223 33444555556679999999999


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhc-CC
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCE-GY  160 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~-~~  160 (248)
                      ++..+  ..|+...|++.|+.=.+-+.++.|..++++..-..  |....|-....- -.++|....+..+|+...+. |-
T Consensus       165 erW~~--w~P~eqaW~sfI~fElRykeieraR~IYerfV~~H--P~v~~wikyarF-E~k~g~~~~aR~VyerAie~~~~  239 (677)
T KOG1915|consen  165 ERWME--WEPDEQAWLSFIKFELRYKEIERARSIYERFVLVH--PKVSNWIKYARF-EEKHGNVALARSVYERAIEFLGD  239 (677)
T ss_pred             HHHHc--CCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHheec--ccHHHHHHHHHH-HHhcCcHHHHHHHHHHHHHHhhh
Confidence            98876  47999999999999999999999999999987544  777666555443 45667778888888766553 21


Q ss_pred             -CCCHHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          161 -GLGMRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       161 -~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                       .-+...|.++..-=.++..++.|.-+|+-..+
T Consensus       240 d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld  272 (677)
T KOG1915|consen  240 DEEAEILFVAFAEFEERQKEYERARFIYKYALD  272 (677)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             11223344444434456677777777766554

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

Probab=97.95  E-value=0.0036  Score=51.73  Aligned_cols=219  Identities=14%  Similarity=0.039  Sum_probs=140.7

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      ++++.+..++++...+.. ++....+..=|..+...|+-.+-+.+=.+|.+. .+-...+|-++---|.-.|+..+|++.
T Consensus       257 ~c~f~~c~kit~~lle~d-pfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~-yP~~a~sW~aVg~YYl~i~k~seARry  334 (611)
T KOG1173|consen  257 GCRFKECLKITEELLEKD-PFHLPCLPLHIACLYELGKSNKLFLLSHKLVDL-YPSKALSWFAVGCYYLMIGKYSEARRY  334 (611)
T ss_pred             cChHHHHHHHhHHHHhhC-CCCcchHHHHHHHHHHhcccchHHHHHHHHHHh-CCCCCcchhhHHHHHHHhcCcHHHHHH
Confidence            467888888888887643 356677777788888888888777776777654 345567888888888888999999999


Q ss_pred             HHHHHHCCCCcC-HhhHHHHHHHHHhcCCHHHHHHHHHHHHH--------------------------------CCCCch
Q 039342           81 FQEIKSSGILPS-VMCYCMLLAVYAKSNRWDDAYGLLDEMHT--------------------------------NRISNI  127 (248)
Q Consensus        81 ~~~m~~~~~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~--------------------------------~~~~~~  127 (248)
                      |.+-...  .|+ ...|-..-.+|+-.+..|+|+..+...-+                                .++-|.
T Consensus       335 ~SKat~l--D~~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl~~G~hlP~LYlgmey~~t~n~kLAe~Ff~~A~ai~P~  412 (611)
T KOG1173|consen  335 FSKATTL--DPTFGPAWLAFGHSFAGEGEHDQAMAAYFTAARLMPGCHLPSLYLGMEYMRTNNLKLAEKFFKQALAIAPS  412 (611)
T ss_pred             HHHHhhc--CccccHHHHHHhHHhhhcchHHHHHHHHHHHHHhccCCcchHHHHHHHHHHhccHHHHHHHHHHHHhcCCC
Confidence            9876543  221 23555555666666666665555443211                                123343


Q ss_pred             HHhHHHHhcccccccchHHHHHHHHHHHHhc--CCC----CCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcch
Q 039342          128 HQVTGQMIKGEFDDESNWQMVEYVFDKLNCE--GYG----LGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFR  201 (248)
Q Consensus       128 ~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~--~~~----p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t  201 (248)
                      ......=+....-..+.+.+|..+|+.-...  .+.    --..+++.|-.+|.+.+.+++|...+++.... .+-+..|
T Consensus       413 Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~q~aL~l-~~k~~~~  491 (611)
T KOG1173|consen  413 DPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYYQKALLL-SPKDAST  491 (611)
T ss_pred             cchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHHHHHHHc-CCCchhH
Confidence            3333222222122346678888877765521  111    12346788889999999999999999987654 2446667


Q ss_pred             hhhHHhhhhhhccccchHHHHHHHHHHH
Q 039342          202 HNKLVWSVDVHRMWEGGAYTAISVWLNK  229 (248)
Q Consensus       202 ~~~li~~~~~~~~~~~g~~~~~~~~~~~  229 (248)
                      |.++-     -.|...|+++.|.+.|.+
T Consensus       492 ~asig-----~iy~llgnld~Aid~fhK  514 (611)
T KOG1173|consen  492 HASIG-----YIYHLLGNLDKAIDHFHK  514 (611)
T ss_pred             HHHHH-----HHHHHhcChHHHHHHHHH
Confidence            77666     345566777776665543

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

Probab=97.93  E-value=0.00063  Score=47.20  Aligned_cols=128  Identities=10%  Similarity=0.061  Sum_probs=88.9

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCc--CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHh-HHHHh
Q 039342           59 RTLEAVLSVYCFAGLVDESKEQFQEIKSSGILP--SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQV-TGQMI  135 (248)
Q Consensus        59 ~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~-~~~~l  135 (248)
                      ..|..++..+. .++...+...++.+.+..-..  .....-.+-..+...|++++|...|+...+....|.... ...-+
T Consensus        13 ~~y~~~~~~~~-~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~L   91 (145)
T PF09976_consen   13 ALYEQALQALQ-AGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRL   91 (145)
T ss_pred             HHHHHHHHHHH-CCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHH
Confidence            45666666664 888999999999998753111  123344455778889999999999999988763332221 22223


Q ss_pred             cccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHH
Q 039342          136 KGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDE  189 (248)
Q Consensus       136 ~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  189 (248)
                      ...+...++++.|...++......+  ....+...-+.+.+.|++++|...|+.
T Consensus        92 A~~~~~~~~~d~Al~~L~~~~~~~~--~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen   92 ARILLQQGQYDEALATLQQIPDEAF--KALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHHcCCHHHHHHHHHhccCcch--HHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            3446678889999999876443333  345666778889999999999999875

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

Probab=97.91  E-value=0.008  Score=48.93  Aligned_cols=224  Identities=10%  Similarity=0.036  Sum_probs=130.1

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++..|.++|++-.+  ..|+...|++.|..=.+-+.++.|..+++...-  +.|+..+|--....=-+.|.+..+.++|
T Consensus       155 gNi~gaRqiferW~~--w~P~eqaW~sfI~fElRykeieraR~IYerfV~--~HP~v~~wikyarFE~k~g~~~~aR~Vy  230 (677)
T KOG1915|consen  155 GNIAGARQIFERWME--WEPDEQAWLSFIKFELRYKEIERARSIYERFVL--VHPKVSNWIKYARFEEKHGNVALARSVY  230 (677)
T ss_pred             cccHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhe--ecccHHHHHHHHHHHHhcCcHHHHHHHH
Confidence            567777777776544  357777777777777777777777777777754  3477777777777777777777777777


Q ss_pred             HHHHHC-CC-CcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCch-HHhHHHHhcccccccchHHHHHHH-------
Q 039342           82 QEIKSS-GI-LPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNI-HQVTGQMIKGEFDDESNWQMVEYV-------  151 (248)
Q Consensus        82 ~~m~~~-~~-~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~-------  151 (248)
                      +...+. |- .-+...|.+....=.++..++.|.-+|+-..+.-.+.. ...|..+.. +-..-|+-...+..       
T Consensus       231 erAie~~~~d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~~pk~raeeL~k~~~~-fEKqfGd~~gIEd~Iv~KRk~  309 (677)
T KOG1915|consen  231 ERAIEFLGDDEEAEILFVAFAEFEERQKEYERARFIYKYALDHIPKGRAEELYKKYTA-FEKQFGDKEGIEDAIVGKRKF  309 (677)
T ss_pred             HHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHHHH-HHHHhcchhhhHHHHhhhhhh
Confidence            776643 21 01122333333333345667777777766554422211 122222221 11122222222221       


Q ss_pred             -HHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcc-----hhhhHHhhhhhhccccchHHHHHHH
Q 039342          152 -FDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELF-----RHNKLVWSVDVHRMWEGGAYTAISV  225 (248)
Q Consensus       152 -~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~-----t~~~li~~~~~~~~~~~g~~~~~~~  225 (248)
                       ++.+.+.+ .-|-.+|-..++.--..|+.+...++|++...+ ++|-..     -|--|.-++++-.-....+.+....
T Consensus       310 qYE~~v~~n-p~nYDsWfdylrL~e~~g~~~~Ire~yErAIan-vpp~~ekr~W~RYIYLWinYalyeEle~ed~ertr~  387 (677)
T KOG1915|consen  310 QYEKEVSKN-PYNYDSWFDYLRLEESVGDKDRIRETYERAIAN-VPPASEKRYWRRYIYLWINYALYEELEAEDVERTRQ  387 (677)
T ss_pred             HHHHHHHhC-CCCchHHHHHHHHHHhcCCHHHHHHHHHHHHcc-CCchhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Confidence             23333332 236677778888888889999999999998754 566321     1222332333333345567777777


Q ss_pred             HHHHHHH
Q 039342          226 WLNKMYE  232 (248)
Q Consensus       226 ~~~~m~~  232 (248)
                      +++...+
T Consensus       388 vyq~~l~  394 (677)
T KOG1915|consen  388 VYQACLD  394 (677)
T ss_pred             HHHHHHh
Confidence            7777666

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.89  E-value=0.00057  Score=52.08  Aligned_cols=180  Identities=14%  Similarity=0.073  Sum_probs=112.3

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEK-VRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~-~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      ||+..++.++++....   -+..+.+..-....+.|+++.|.+-|+...+ .|..| ...||..+..| +.|+.+.|.+.
T Consensus       126 ~Dl~g~rsLveQlp~e---n~Ad~~in~gCllykegqyEaAvqkFqaAlqvsGyqp-llAYniALaHy-~~~qyasALk~  200 (459)
T KOG4340|consen  126 GDLPGSRSLVEQLPSE---NEADGQINLGCLLYKEGQYEAAVQKFQAALQVSGYQP-LLAYNLALAHY-SSRQYASALKH  200 (459)
T ss_pred             ccCcchHHHHHhccCC---CccchhccchheeeccccHHHHHHHHHHHHhhcCCCc-hhHHHHHHHHH-hhhhHHHHHHH
Confidence            3444455555555432   2344455555556688999999999988755 45554 45788766544 56889999999


Q ss_pred             HHHHHHCCCC-------------cC--------HhhHHHHHHH-------HHhcCCHHHHHHHHHHHHHC-CCCchHHhH
Q 039342           81 FQEIKSSGIL-------------PS--------VMCYCMLLAV-------YAKSNRWDDAYGLLDEMHTN-RISNIHQVT  131 (248)
Q Consensus        81 ~~~m~~~~~~-------------p~--------~~~~~~li~~-------~~~~~~~~~a~~~~~~m~~~-~~~~~~~~~  131 (248)
                      .+++.++|++             ||        ...-+.++.+       +-+.++.+.|.+-+-.|.-. ....|..|.
T Consensus       201 iSEIieRG~r~HPElgIGm~tegiDvrsvgNt~~lh~Sal~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTL  280 (459)
T KOG4340|consen  201 ISEIIERGIRQHPELGIGMTTEGIDVRSVGNTLVLHQSALVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTL  280 (459)
T ss_pred             HHHHHHhhhhcCCccCccceeccCchhcccchHHHHHHHHHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhh
Confidence            9999887654             22        1223344444       34668888888888877422 233456666


Q ss_pred             HHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHH
Q 039342          132 GQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDE  189 (248)
Q Consensus       132 ~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  189 (248)
                      ..+...  ...+++-...+-+.-+.+...- ...||..++-.||+..-++.|.+++.+
T Consensus       281 HN~Al~--n~~~~p~~g~~KLqFLL~~nPf-P~ETFANlLllyCKNeyf~lAADvLAE  335 (459)
T KOG4340|consen  281 HNQALM--NMDARPTEGFEKLQFLLQQNPF-PPETFANLLLLYCKNEYFDLAADVLAE  335 (459)
T ss_pred             hHHHHh--cccCCccccHHHHHHHHhcCCC-ChHHHHHHHHHHhhhHHHhHHHHHHhh
Confidence            655332  2223333333333333334332 468899999999999999999888875

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

Probab=97.87  E-value=0.00061  Score=42.51  Aligned_cols=95  Identities=15%  Similarity=0.225  Sum_probs=71.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHh
Q 039342           26 FNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAK  105 (248)
Q Consensus        26 y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~  105 (248)
                      |..+...+...|++++|...++...+.. +.+...+..+...+...+++++|.+.++...+.. +.+..++..+...+..
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~   80 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALELD-PDNAKAYYNLGLAYYK   80 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CcchhHHHHHHHHHHH
Confidence            4556667778888999999888886653 2344667778888888889999999888877653 2244677788888888


Q ss_pred             cCCHHHHHHHHHHHHHC
Q 039342          106 SNRWDDAYGLLDEMHTN  122 (248)
Q Consensus       106 ~~~~~~a~~~~~~m~~~  122 (248)
                      .|+.+.|...+.+..+.
T Consensus        81 ~~~~~~a~~~~~~~~~~   97 (100)
T cd00189          81 LGKYEEALEAYEKALEL   97 (100)
T ss_pred             HHhHHHHHHHHHHHHcc
Confidence            88888888888876543

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.86  E-value=0.0014  Score=43.38  Aligned_cols=100  Identities=11%  Similarity=0.058  Sum_probs=74.5

Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC--CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCC--CcCHhhHHHH
Q 039342           24 DSFNAVIEAFRQGGRFEEAIKAYVEMEKVRC--DPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGI--LPSVMCYCML   99 (248)
Q Consensus        24 ~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~--~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~--~p~~~~~~~l   99 (248)
                      .++......+.+.|++++|.+.|..+.+..-  +.....+..+..++.+.|+++.|.+.|+.+.....  ......+..+
T Consensus         3 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~   82 (119)
T TIGR02795         3 EAYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKL   82 (119)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHH
Confidence            4566677778888999999999998876431  11234566688888999999999999998876421  1124567777


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHCC
Q 039342          100 LAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus       100 i~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      ..++.+.|+.++|...+++..+..
T Consensus        83 ~~~~~~~~~~~~A~~~~~~~~~~~  106 (119)
T TIGR02795        83 GMSLQELGDKEKAKATLQQVIKRY  106 (119)
T ss_pred             HHHHHHhCChHHHHHHHHHHHHHC
Confidence            788888899999999999887764

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.

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=97.86  E-value=0.0047  Score=53.86  Aligned_cols=133  Identities=8%  Similarity=0.011  Sum_probs=101.8

Q ss_pred             CCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCc-CHhhH
Q 039342           19 VARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNE-RTLEAVLSVYCFAGLVDESKEQFQEIKSSGILP-SVMCY   96 (248)
Q Consensus        19 ~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~   96 (248)
                      ...++..+-.|-....+.|+.++|..+++...+.  .||. .....+...+.+.+++++|....++..+..  | +....
T Consensus        82 ~~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~--~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~--p~~~~~~  157 (694)
T PRK15179         82 YPHTELFQVLVARALEAAHRSDEGLAVWRGIHQR--FPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGG--SSSAREI  157 (694)
T ss_pred             ccccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhh--CCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcC--CCCHHHH
Confidence            3446778888888888899999999999998764  5655 455677888999999999999999988763  4 55677


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHCCCCch-HHhHHHHhcccccccchHHHHHHHHHHHHhc
Q 039342           97 CMLLAVYAKSNRWDDAYGLLDEMHTNRISNI-HQVTGQMIKGEFDDESNWQMVEYVFDKLNCE  158 (248)
Q Consensus        97 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  158 (248)
                      ..+-.++.+.|+.++|..+|++....+  |+ ...+...-.. +...|+.++|...|+...+.
T Consensus       158 ~~~a~~l~~~g~~~~A~~~y~~~~~~~--p~~~~~~~~~a~~-l~~~G~~~~A~~~~~~a~~~  217 (694)
T PRK15179        158 LLEAKSWDEIGQSEQADACFERLSRQH--PEFENGYVGWAQS-LTRRGALWRARDVLQAGLDA  217 (694)
T ss_pred             HHHHHHHHHhcchHHHHHHHHHHHhcC--CCcHHHHHHHHHH-HHHcCCHHHHHHHHHHHHHh
Confidence            788888889999999999999998744  33 3333333333 66778888888888887665

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

Probab=97.85  E-value=0.0079  Score=50.06  Aligned_cols=216  Identities=13%  Similarity=0.047  Sum_probs=126.2

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|.+.-..+...+ +-+...+.+=+-+..+.+.+++|+.+.+.-..  ...+.+-+--=..+..+.++.|+|...+
T Consensus        26 ~e~e~a~k~~~Kil~~~-pdd~~a~~cKvValIq~~ky~~ALk~ikk~~~--~~~~~~~~fEKAYc~Yrlnk~Dealk~~  102 (652)
T KOG2376|consen   26 GEYEEAVKTANKILSIV-PDDEDAIRCKVVALIQLDKYEDALKLIKKNGA--LLVINSFFFEKAYCEYRLNKLDEALKTL  102 (652)
T ss_pred             hHHHHHHHHHHHHHhcC-CCcHhhHhhhHhhhhhhhHHHHHHHHHHhcch--hhhcchhhHHHHHHHHHcccHHHHHHHH
Confidence            67888888888888765 34567777778888888999988855444211  0111111111234445788899998888


Q ss_pred             HHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCC
Q 039342           82 QEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGY  160 (248)
Q Consensus        82 ~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~  160 (248)
                      +     |..+ +..+-..--..+-+.+++++|+.+|+.+.+++..--..-...-+.+..       .+.. ...+.....
T Consensus       103 ~-----~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~-------a~l~-~~~~q~v~~  169 (652)
T KOG2376|consen  103 K-----GLDRLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVA-------AALQ-VQLLQSVPE  169 (652)
T ss_pred             h-----cccccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHH-------Hhhh-HHHHHhccC
Confidence            7     3333 333555666677889999999999999987765443332222222100       1111 113334444


Q ss_pred             CCCHHHHHHHHH---HHHhcCchHHHHHHHHHHHHCC---CCC-C--cchhhhHHhh---hhhhccccchHHHHHHHHHH
Q 039342          161 GLGMRFYNALLE---ALWCLGLRERAARVLDEATKRG---LFP-E--LFRHNKLVWS---VDVHRMWEGGAYTAISVWLN  228 (248)
Q Consensus       161 ~p~~~~~~~li~---~~~~~g~~~~a~~~~~~m~~~g---~~p-~--~~t~~~li~~---~~~~~~~~~g~~~~~~~~~~  228 (248)
                      .| ..+|..+.+   .+...|++.+|++++....+-+   +.- |  ..-+..-+..   =+.-.+-..|+-+++..++.
T Consensus       170 v~-e~syel~yN~Ac~~i~~gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~Gqt~ea~~iy~  248 (652)
T KOG2376|consen  170 VP-EDSYELLYNTACILIENGKYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQGQTAEASSIYV  248 (652)
T ss_pred             CC-cchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHHHH
Confidence            44 445555554   4556899999999998873211   000 0  0111111111   11133456788889999888


Q ss_pred             HHHHHH
Q 039342          229 KMYEMF  234 (248)
Q Consensus       229 ~m~~~~  234 (248)
                      ......
T Consensus       249 ~~i~~~  254 (652)
T KOG2376|consen  249 DIIKRN  254 (652)
T ss_pred             HHHHhc
Confidence            887774

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

Probab=97.85  E-value=5.8e-05  Score=47.07  Aligned_cols=47  Identities=30%  Similarity=0.458  Sum_probs=20.0

Q ss_pred             CCHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHhcCChhHHHHHHHH
Q 039342           37 GRFEEAIKAYVEMEKVRC-DPNERTLEAVLSVYCFAGLVDESKEQFQE   83 (248)
Q Consensus        37 ~~~~~a~~~~~~m~~~~~-~p~~~t~~~ll~~~~~~g~~~~a~~~~~~   83 (248)
                      |+++.|+.+++++.+..- .|+...+-.+-.+|.+.|++++|..+++.
T Consensus         3 ~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~   50 (84)
T PF12895_consen    3 GNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK   50 (84)
T ss_dssp             T-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC
T ss_pred             ccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            444455555555443321 11222233344455555555555555544

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=97.82  E-value=0.0057  Score=53.18  Aligned_cols=222  Identities=14%  Similarity=0.100  Sum_probs=134.6

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHH--hcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFR--QGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKE   79 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~--~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~   79 (248)
                      +++..|.+....+.+.-  |+ ..|..++.++.  +.|+.++|..+++.....+.. |..|...+-.+|...++.++|..
T Consensus        23 ~qfkkal~~~~kllkk~--Pn-~~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~-D~~tLq~l~~~y~d~~~~d~~~~   98 (932)
T KOG2053|consen   23 SQFKKALAKLGKLLKKH--PN-ALYAKVLKALSLFRLGKGDEALKLLEALYGLKGT-DDLTLQFLQNVYRDLGKLDEAVH   98 (932)
T ss_pred             HHHHHHHHHHHHHHHHC--CC-cHHHHHHHHHHHHHhcCchhHHHHHhhhccCCCC-chHHHHHHHHHHHHHhhhhHHHH
Confidence            56778888888765432  43 34555666554  679999999999988766654 88999999999999999999999


Q ss_pred             HHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccc----ccc-----chHHHHHH
Q 039342           80 QFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEF----DDE-----SNWQMVEY  150 (248)
Q Consensus        80 ~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~----~~~-----~~~~~a~~  150 (248)
                      +|++..+.  .|+......+..+|+|.+++.+-.++--+|.+ ..+-....|++++.-..    ...     --...|.+
T Consensus        99 ~Ye~~~~~--~P~eell~~lFmayvR~~~yk~qQkaa~~LyK-~~pk~~yyfWsV~Slilqs~~~~~~~~~~i~l~LA~~  175 (932)
T KOG2053|consen   99 LYERANQK--YPSEELLYHLFMAYVREKSYKKQQKAALQLYK-NFPKRAYYFWSVISLILQSIFSENELLDPILLALAEK  175 (932)
T ss_pred             HHHHHHhh--CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hCCcccchHHHHHHHHHHhccCCcccccchhHHHHHH
Confidence            99998875  57777788888899998887654444333332 22222334444433211    111     12345556


Q ss_pred             HHHHHHhcC-CCCCHHHHHHHHHHHHhcCchHHHHHHHHH-HHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHH
Q 039342          151 VFDKLNCEG-YGLGMRFYNALLEALWCLGLRERAARVLDE-ATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLN  228 (248)
Q Consensus       151 ~~~~m~~~~-~~p~~~~~~~li~~~~~~g~~~~a~~~~~~-m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~  228 (248)
                      .++.+.+.+ ..-+..-...-...+-..|.+++|.+++.. ..+.-..-     +.-+......-+...+++.+..++..
T Consensus       176 m~~~~l~~~gk~~s~aE~~Lyl~iL~~~~k~~eal~~l~~~la~~l~~~-----~~~l~~~~~dllk~l~~w~~l~~l~~  250 (932)
T KOG2053|consen  176 MVQKLLEKKGKIESEAEIILYLLILELQGKYQEALEFLAITLAEKLTSA-----NLYLENKKLDLLKLLNRWQELFELSS  250 (932)
T ss_pred             HHHHHhccCCccchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcccc-----chHHHHHHHHHHHHhcChHHHHHHHH
Confidence            666666554 222222223333445567889999999843 33321111     11111122233445556666666665


Q ss_pred             HHHHHHH
Q 039342          229 KMYEMFM  235 (248)
Q Consensus       229 ~m~~~~~  235 (248)
                      ++.+.|-
T Consensus       251 ~Ll~k~~  257 (932)
T KOG2053|consen  251 RLLEKGN  257 (932)
T ss_pred             HHHHhCC
Confidence            5555543

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

Probab=97.81  E-value=0.001  Score=45.40  Aligned_cols=93  Identities=15%  Similarity=0.134  Sum_probs=76.9

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|.+.|+...+.+ +.+...|..+-..+.+.|++++|...++...+.+ +.+...+..+-..|...|++++|...|
T Consensus        31 ~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~  108 (135)
T TIGR02552        31 GRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD-PDDPRPYFHAAECLLALGEPESALKAL  108 (135)
T ss_pred             ccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHHcCCHHHHHHHH
Confidence            78999999999987755 3478889999999999999999999999987664 456777888888999999999999999


Q ss_pred             HHHHHCCCCcCHhhHHH
Q 039342           82 QEIKSSGILPSVMCYCM   98 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~   98 (248)
                      +...+.  .|+...+..
T Consensus       109 ~~al~~--~p~~~~~~~  123 (135)
T TIGR02552       109 DLAIEI--CGENPEYSE  123 (135)
T ss_pred             HHHHHh--ccccchHHH
Confidence            998875  455544443

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

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

Probab=97.79  E-value=0.0044  Score=51.07  Aligned_cols=150  Identities=9%  Similarity=0.050  Sum_probs=108.3

Q ss_pred             HHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHH
Q 039342           39 FEEAIKAYVEMEKV-RCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLL  116 (248)
Q Consensus        39 ~~~a~~~~~~m~~~-~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~  116 (248)
                      .+.....++++... .+.|+ .+|...|+.-.|..-++.|+.+|.+.++.+..+ .+.+++++|.-||. ++..-|.++|
T Consensus       347 ~~~~~~~~~~ll~~~~~~~t-Lv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~cs-kD~~~AfrIF  424 (656)
T KOG1914|consen  347 EKKVHEIYNKLLKIEDIDLT-LVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCS-KDKETAFRIF  424 (656)
T ss_pred             hhhhHHHHHHHHhhhccCCc-eehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhc-CChhHHHHHH
Confidence            55566666666443 45555 478888999999999999999999999887777 78899999998875 6778899999


Q ss_pred             HHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCC--HHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          117 DEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLG--MRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       117 ~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                      +--...-  ++...|..--..++..-++-..+..+|+.....++.||  ...|..+|+.=..-|++..+.++-+++..
T Consensus       425 eLGLkkf--~d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~  500 (656)
T KOG1914|consen  425 ELGLKKF--GDSPEYVLKYLDFLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRFT  500 (656)
T ss_pred             HHHHHhc--CCChHHHHHHHHHHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            8643321  23323322211223334444678889999888866665  46799999999999999999998887653

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

Probab=97.77  E-value=0.01  Score=48.96  Aligned_cols=153  Identities=12%  Similarity=0.158  Sum_probs=115.1

Q ss_pred             ChhHHHHHHHHHHHC-CCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchH-HhHHHHhcccccccchHHHHHH
Q 039342           73 LVDESKEQFQEIKSS-GILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIH-QVTGQMIKGEFDDESNWQMVEY  150 (248)
Q Consensus        73 ~~~~a~~~~~~m~~~-~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~  150 (248)
                      ..+...++++++... .+.| +.+|-..|+.--|..-++.|..+|.+.++.+..+.. .+..+++.  +-..++.+.|.+
T Consensus       346 ~~~~~~~~~~~ll~~~~~~~-tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mE--y~cskD~~~Afr  422 (656)
T KOG1914|consen  346 KEKKVHEIYNKLLKIEDIDL-TLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALME--YYCSKDKETAFR  422 (656)
T ss_pred             hhhhhHHHHHHHHhhhccCC-ceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHH--HHhcCChhHHHH
Confidence            366777777777654 3344 567888999999999999999999999999998844 44455555  445567799999


Q ss_pred             HHHHHHh-cCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHH
Q 039342          151 VFDKLNC-EGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNK  229 (248)
Q Consensus       151 ~~~~m~~-~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~  229 (248)
                      +|+.=.. .|-  ++.--...++-+...++-..+..+|++....++.|+.   ..-||.-++.--+.-|++..+.++-++
T Consensus       423 IFeLGLkkf~d--~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~k---s~~Iw~r~l~yES~vGdL~si~~lekR  497 (656)
T KOG1914|consen  423 IFELGLKKFGD--SPEYVLKYLDFLSHLNDDNNARALFERVLTSVLSADK---SKEIWDRMLEYESNVGDLNSILKLEKR  497 (656)
T ss_pred             HHHHHHHhcCC--ChHHHHHHHHHHHHhCcchhHHHHHHHHHhccCChhh---hHHHHHHHHHHHHhcccHHHHHHHHHH
Confidence            9986433 332  3344467888888999999999999999988777765   344555555888889999988888877


Q ss_pred             HHHH
Q 039342          230 MYEM  233 (248)
Q Consensus       230 m~~~  233 (248)
                      +..+
T Consensus       498 ~~~a  501 (656)
T KOG1914|consen  498 RFTA  501 (656)
T ss_pred             HHHh
Confidence            7665

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

Probab=97.72  E-value=8.2e-05  Score=46.37  Aligned_cols=80  Identities=19%  Similarity=0.238  Sum_probs=57.0

Q ss_pred             CchHHHHHHHHHHHHcCC-CCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            2 GLYKECQAILSRMSESGV-ARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~-~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      |+++.|+.+|+++.+... .++...+-.+-.++.+.|++++|..+++. .+.+. .+....-.+-.+|.+.|++++|.++
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            788999999999887543 22455566688889999999999999988 22221 2224444557888899999999998


Q ss_pred             HHH
Q 039342           81 FQE   83 (248)
Q Consensus        81 ~~~   83 (248)
                      +++
T Consensus        81 l~~   83 (84)
T PF12895_consen   81 LEK   83 (84)
T ss_dssp             HHH
T ss_pred             Hhc
Confidence            875

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.69  E-value=0.011  Score=44.09  Aligned_cols=150  Identities=13%  Similarity=0.069  Sum_probs=70.2

Q ss_pred             CCHHHHHHHHHHHHH---cC-CCCCHHH-HHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCH-hhHHHHHHHHHhcCCHH
Q 039342           37 GRFEEAIKAYVEMEK---VR-CDPNERT-LEAVLSVYCFAGLVDESKEQFQEIKSSGILPSV-MCYCMLLAVYAKSNRWD  110 (248)
Q Consensus        37 ~~~~~a~~~~~~m~~---~~-~~p~~~t-~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~-~~~~~li~~~~~~~~~~  110 (248)
                      .+.++..+++.++..   +| ..++..+ |..++-+..-.|+.+.|...++++.+.-  |.+ .+-..=---+-..|+++
T Consensus        26 rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~f--p~S~RV~~lkam~lEa~~~~~  103 (289)
T KOG3060|consen   26 RNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRF--PGSKRVGKLKAMLLEATGNYK  103 (289)
T ss_pred             cCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhC--CCChhHHHHHHHHHHHhhchh
Confidence            345566666655532   23 4455432 3344555555666666666666665442  222 11111111122345666


Q ss_pred             HHHHHHHHHHHCCCCchHHhHH-HHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHH
Q 039342          111 DAYGLLDEMHTNRISNIHQVTG-QMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDE  189 (248)
Q Consensus       111 ~a~~~~~~m~~~~~~~~~~~~~-~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  189 (248)
                      +|+++++.+.+.+  |++..+. .-+.. ....|..-.|.+-+....+. +..|...|.-+-..|...|++++|.-.+++
T Consensus       104 ~A~e~y~~lL~dd--pt~~v~~KRKlAi-lka~GK~l~aIk~ln~YL~~-F~~D~EAW~eLaeiY~~~~~f~kA~fClEE  179 (289)
T KOG3060|consen  104 EAIEYYESLLEDD--PTDTVIRKRKLAI-LKAQGKNLEAIKELNEYLDK-FMNDQEAWHELAEIYLSEGDFEKAAFCLEE  179 (289)
T ss_pred             hHHHHHHHHhccC--cchhHHHHHHHHH-HHHcCCcHHHHHHHHHHHHH-hcCcHHHHHHHHHHHHhHhHHHHHHHHHHH
Confidence            6666666666555  3333322 11111 12222222333222222222 445666666666666666666666666666


Q ss_pred             HHH
Q 039342          190 ATK  192 (248)
Q Consensus       190 m~~  192 (248)
                      +.-
T Consensus       180 ~ll  182 (289)
T KOG3060|consen  180 LLL  182 (289)
T ss_pred             HHH
Confidence            543

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.67  E-value=0.032  Score=50.86  Aligned_cols=232  Identities=12%  Similarity=0.011  Sum_probs=136.8

Q ss_pred             CCchHHHHHHHHHHHHcCCCCC----HHhHHHHHHHHHhcCCHHHHHHHHHHHHHc----CC-CCCHHHHHHHHHHHHhc
Q 039342            1 GGLYKECQAILSRMSESGVARN----SDSFNAVIEAFRQGGRFEEAIKAYVEMEKV----RC-DPNERTLEAVLSVYCFA   71 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~----~~~y~~li~~~~~~~~~~~a~~~~~~m~~~----~~-~p~~~t~~~ll~~~~~~   71 (248)
                      .|++++|...+++..+.-...+    ....+.+-..+...|++++|...+.+....    |- .+-..++..+-..+...
T Consensus       465 ~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~  544 (903)
T PRK04841        465 DGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQ  544 (903)
T ss_pred             CCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHC
Confidence            3788999999988765211112    134455666677899999999998887532    11 11123445566678889


Q ss_pred             CChhHHHHHHHHHHH----CCCC--c-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCC--CCchH-HhHHHHhcccccc
Q 039342           72 GLVDESKEQFQEIKS----SGIL--P-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNR--ISNIH-QVTGQMIKGEFDD  141 (248)
Q Consensus        72 g~~~~a~~~~~~m~~----~~~~--p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~--~~~~~-~~~~~~l~~~~~~  141 (248)
                      |+++.|...+++..+    .+..  | ....+..+-..+...|++++|...+.+.....  ..+.. ......+......
T Consensus       545 G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~  624 (903)
T PRK04841        545 GFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISLA  624 (903)
T ss_pred             CCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHHH
Confidence            999999999887654    2221  1 22334455556777899999999988765421  11211 1112222223456


Q ss_pred             cchHHHHHHHHHHHHhc----CCCCCHHH--HHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccc
Q 039342          142 ESNWQMVEYVFDKLNCE----GYGLGMRF--YNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMW  215 (248)
Q Consensus       142 ~~~~~~a~~~~~~m~~~----~~~p~~~~--~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~  215 (248)
                      .|+++.|...+......    +..+....  -...+..+...|+.+.|...+........... .. ...........+.
T Consensus       625 ~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~-~~-~~~~~~~~a~~~~  702 (903)
T PRK04841        625 RGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANN-HF-LQGQWRNIARAQI  702 (903)
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccc-hh-HHHHHHHHHHHHH
Confidence            78888888888776542    11111101  01123445668899999999877543211111 11 1111222335667


Q ss_pred             cchHHHHHHHHHHHHHHHH
Q 039342          216 EGGAYTAISVWLNKMYEMF  234 (248)
Q Consensus       216 ~~g~~~~~~~~~~~m~~~~  234 (248)
                      ..|+.+++...+++..+..
T Consensus       703 ~~g~~~~A~~~l~~al~~~  721 (903)
T PRK04841        703 LLGQFDEAEIILEELNENA  721 (903)
T ss_pred             HcCCHHHHHHHHHHHHHHH
Confidence            7888899988888877654

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

Probab=97.67  E-value=0.035  Score=49.01  Aligned_cols=162  Identities=22%  Similarity=0.276  Sum_probs=83.0

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHH--HHHHHHHhcCChhHHHHHHHHHHHCCCCc-CHhhHHHHHH
Q 039342           25 SFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLE--AVLSVYCFAGLVDESKEQFQEIKSSGILP-SVMCYCMLLA  101 (248)
Q Consensus        25 ~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~--~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~  101 (248)
                      .|--+-++|-..|++++|...|.+-.+.  .||.+++.  -+-..|.+.|+++.+...|+.+.+.  .| +..+..++-.
T Consensus       309 s~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~--~~d~~~l~~~GlgQm~i~~~dle~s~~~fEkv~k~--~p~~~etm~iLG~  384 (1018)
T KOG2002|consen  309 SFYQLGRSYHAQGDFEKAFKYYMESLKA--DNDNFVLPLVGLGQMYIKRGDLEESKFCFEKVLKQ--LPNNYETMKILGC  384 (1018)
T ss_pred             HHHHHHHHHHhhccHHHHHHHHHHHHcc--CCCCccccccchhHHHHHhchHHHHHHHHHHHHHh--CcchHHHHHHHHh
Confidence            3444555555556666665555444322  33332222  2445555566666666666555543  23 2334444444


Q ss_pred             HHHhcC----CHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHH----HHHHHhcCCCCCHHHHHHHHHH
Q 039342          102 VYAKSN----RWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYV----FDKLNCEGYGLGMRFYNALLEA  173 (248)
Q Consensus       102 ~~~~~~----~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~----~~~m~~~~~~p~~~~~~~li~~  173 (248)
                      .|+..+    ..+.|..++.+-.+.-  |...--+..+...+.. ++.......    .+.+...+-.+.+...|.+-..
T Consensus       385 Lya~~~~~~~~~d~a~~~l~K~~~~~--~~d~~a~l~laql~e~-~d~~~sL~~~~~A~d~L~~~~~~ip~E~LNNvasl  461 (1018)
T KOG2002|consen  385 LYAHSAKKQEKRDKASNVLGKVLEQT--PVDSEAWLELAQLLEQ-TDPWASLDAYGNALDILESKGKQIPPEVLNNVASL  461 (1018)
T ss_pred             HHHhhhhhhHHHHHHHHHHHHHHhcc--cccHHHHHHHHHHHHh-cChHHHHHHHHHHHHHHHHcCCCCCHHHHHhHHHH
Confidence            444332    2344444444433322  1111111111111222 222222333    3345556666778889999999


Q ss_pred             HHhcCchHHHHHHHHHHHHC
Q 039342          174 LWCLGLRERAARVLDEATKR  193 (248)
Q Consensus       174 ~~~~g~~~~a~~~~~~m~~~  193 (248)
                      ....|++.+|...|......
T Consensus       462 hf~~g~~~~A~~~f~~A~~~  481 (1018)
T KOG2002|consen  462 HFRLGNIEKALEHFKSALGK  481 (1018)
T ss_pred             HHHhcChHHHHHHHHHHhhh
Confidence            99999999999999987654

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

Probab=97.66  E-value=0.0013  Score=51.07  Aligned_cols=142  Identities=9%  Similarity=0.029  Sum_probs=90.9

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHCC-CCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcc
Q 039342           59 RTLEAVLSVYCFAGLVDESKEQFQEIKSSG-ILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKG  137 (248)
Q Consensus        59 ~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~-~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~  137 (248)
                      .+|..++....+.+..+.|..+|.+.++.+ +........+++.. ...++.+.|..+|+...+. ...+...+...+.-
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 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALMEY-YCNKDPKRARKIFERGLKK-FPSDPDFWLEYLDF   79 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHHH-HTCS-HHHHHHHHHHHHHH-HTT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHHH-HhCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHH
Confidence            468888888888888999999998887543 23333444444433 3346677799999887764 22333334444433


Q ss_pred             cccccchHHHHHHHHHHHHhcCCCCC---HHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHH
Q 039342          138 EFDDESNWQMVEYVFDKLNCEGYGLG---MRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLV  206 (248)
Q Consensus       138 ~~~~~~~~~~a~~~~~~m~~~~~~p~---~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li  206 (248)
                       ....++.+.+..+|+..... +.++   ...|...++.=.+.|+++.+.++.+++.+.  .|+......++
T Consensus        80 -l~~~~d~~~aR~lfer~i~~-l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~--~~~~~~~~~f~  147 (280)
T PF05843_consen   80 -LIKLNDINNARALFERAISS-LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL--FPEDNSLELFS  147 (280)
T ss_dssp             -HHHTT-HHHHHHHHHHHCCT-SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH--TTTS-HHHHHH
T ss_pred             -HHHhCcHHHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--hhhhhHHHHHH
Confidence             44566788888888887765 3222   247888888888888888888888888764  55544444444

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.

>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=97.66  E-value=0.0013  Score=44.27  Aligned_cols=28  Identities=11%  Similarity=0.240  Sum_probs=18.2

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHH
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEM   49 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m   49 (248)
                      |..++.++|.++++.|+.+....+++..
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~   28 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSV   28 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHh
Confidence            3456667777777777777666666544

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

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

Probab=97.62  E-value=0.021  Score=50.89  Aligned_cols=191  Identities=10%  Similarity=0.031  Sum_probs=115.8

Q ss_pred             CCCC-CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHH-HHHHHHHHhcCChhHHHHH---------------
Q 039342           18 GVAR-NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTL-EAVLSVYCFAGLVDESKEQ---------------   80 (248)
Q Consensus        18 g~~~-~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~-~~ll~~~~~~g~~~~a~~~---------------   80 (248)
                      .+.| +...+..|+..+...+++++|.++.+.-.+.  .|+...+ -.+-..+.+.++.+.+..+               
T Consensus        25 ~~~p~n~~a~~~Li~~~~~~~~~deai~i~~~~l~~--~P~~i~~yy~~G~l~~q~~~~~~~~lv~~l~~~~~~~~~~~v  102 (906)
T PRK14720         25 NYSLSKFKELDDLIDAYKSENLTDEAKDICEEHLKE--HKKSISALYISGILSLSRRPLNDSNLLNLIDSFSQNLKWAIV  102 (906)
T ss_pred             cCCcchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh--CCcceehHHHHHHHHHhhcchhhhhhhhhhhhcccccchhHH
Confidence            3443 5778999999999999999999999966544  3443222 2222245555555555444               


Q ss_pred             ---HHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHH-hHHHHhcccccccchHHHHHHHHHHHH
Q 039342           81 ---FQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQ-VTGQMIKGEFDDESNWQMVEYVFDKLN  156 (248)
Q Consensus        81 ---~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~m~  156 (248)
                         ...|.+.  .-+...+-.+..+|-+.|+.++|..++++..+..  |++. ..+.+-.. +... +.++|..++....
T Consensus       103 e~~~~~i~~~--~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D--~~n~~aLNn~AY~-~ae~-dL~KA~~m~~KAV  176 (906)
T PRK14720        103 EHICDKILLY--GENKLALRTLAEAYAKLNENKKLKGVWERLVKAD--RDNPEIVKKLATS-YEEE-DKEKAITYLKKAI  176 (906)
T ss_pred             HHHHHHHHhh--hhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC--cccHHHHHHHHHH-HHHh-hHHHHHHHHHHHH
Confidence               2222221  1133566777778888899999999999998877  5444 44444433 5555 8888888776654


Q ss_pred             hcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhh----------------hhhccccchHH
Q 039342          157 CEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSV----------------DVHRMWEGGAY  220 (248)
Q Consensus       157 ~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~----------------~~~~~~~~g~~  220 (248)
                      ..               +...+++..+.++|.++...  .|+...+-..+...                +-..|-+..++
T Consensus       177 ~~---------------~i~~kq~~~~~e~W~k~~~~--~~~d~d~f~~i~~ki~~~~~~~~~~~~~~~l~~~y~~~~~~  239 (906)
T PRK14720        177 YR---------------FIKKKQYVGIEEIWSKLVHY--NSDDFDFFLRIERKVLGHREFTRLVGLLEDLYEPYKALEDW  239 (906)
T ss_pred             HH---------------HHhhhcchHHHHHHHHHHhc--CcccchHHHHHHHHHHhhhccchhHHHHHHHHHHHhhhhhh
Confidence            43               55555666666666666553  23322221111111                11456666777


Q ss_pred             HHHHHHHHHHHHH
Q 039342          221 TAISVWLNKMYEM  233 (248)
Q Consensus       221 ~~~~~~~~~m~~~  233 (248)
                      +++..+|+...+.
T Consensus       240 ~~~i~iLK~iL~~  252 (906)
T PRK14720        240 DEVIYILKKILEH  252 (906)
T ss_pred             hHHHHHHHHHHhc
Confidence            7777777776654

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

Probab=97.61  E-value=0.0053  Score=47.64  Aligned_cols=131  Identities=12%  Similarity=0.072  Sum_probs=92.9

Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH-HHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHH
Q 039342           24 DSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSV-YCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAV  102 (248)
Q Consensus        24 ~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~-~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~  102 (248)
                      .+|..+|...-+.+..+.|..+|.+.++.+ ..+...|-..... |...++.+.|.++|+...+. +..+...|..-++.
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~-~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~-f~~~~~~~~~Y~~~   79 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDK-RCTYHVYVAYALMEYYCNKDPKRARKIFERGLKK-FPSDPDFWLEYLDF   79 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHH-HTT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHH
Confidence            578899999999999999999999998543 2333444433333 33356777799999998765 44577889999999


Q ss_pred             HHhcCCHHHHHHHHHHHHHCCCCchH---HhHHHHhcccccccchHHHHHHHHHHHHhc
Q 039342          103 YAKSNRWDDAYGLLDEMHTNRISNIH---QVTGQMIKGEFDDESNWQMVEYVFDKLNCE  158 (248)
Q Consensus       103 ~~~~~~~~~a~~~~~~m~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  158 (248)
                      +.+.++.+.|..+|++.... +.+..   ..|...+.- -...|+++.+..+.+.+.+.
T Consensus        80 l~~~~d~~~aR~lfer~i~~-l~~~~~~~~iw~~~i~f-E~~~Gdl~~v~~v~~R~~~~  136 (280)
T PF05843_consen   80 LIKLNDINNARALFERAISS-LPKEKQSKKIWKKFIEF-ESKYGDLESVRKVEKRAEEL  136 (280)
T ss_dssp             HHHTT-HHHHHHHHHHHCCT-SSCHHHCHHHHHHHHHH-HHHHS-HHHHHHHHHHHHHH
T ss_pred             HHHhCcHHHHHHHHHHHHHh-cCchhHHHHHHHHHHHH-HHHcCCHHHHHHHHHHHHHH
Confidence            99999999999999998765 33332   355555553 45667888888888887774

The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.59  E-value=0.0036  Score=41.39  Aligned_cols=87  Identities=15%  Similarity=0.151  Sum_probs=69.7

Q ss_pred             CchHHHHHHHHHHHHcCC--CCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCCCHHHHHHHHHHHHhcCChhHH
Q 039342            2 GLYKECQAILSRMSESGV--ARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVR--CDPNERTLEAVLSVYCFAGLVDES   77 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~--~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~--~~p~~~t~~~ll~~~~~~g~~~~a   77 (248)
                      |++++|.+.|..+.+...  ......+..+...+.+.|+++.|...|+......  -+.....+..+..++.+.|+.++|
T Consensus        16 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~A   95 (119)
T TIGR02795        16 GDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLGMSLQELGDKEKA   95 (119)
T ss_pred             CCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHHHHHHHhCChHHH
Confidence            789999999999976432  1124567778999999999999999999987643  112356677888899999999999


Q ss_pred             HHHHHHHHHCC
Q 039342           78 KEQFQEIKSSG   88 (248)
Q Consensus        78 ~~~~~~m~~~~   88 (248)
                      .+.++++.+..
T Consensus        96 ~~~~~~~~~~~  106 (119)
T TIGR02795        96 KATLQQVIKRY  106 (119)
T ss_pred             HHHHHHHHHHC
Confidence            99999998763

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.

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

Probab=97.57  E-value=0.013  Score=49.94  Aligned_cols=185  Identities=14%  Similarity=0.127  Sum_probs=137.5

Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHH
Q 039342           24 DSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVY  103 (248)
Q Consensus        24 ~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~  103 (248)
                      ..=..+-..+...|-..+|..++++..         .|.-+|.+|...|+..+|..+..+..++  +||+..|..+.+..
T Consensus       399 q~q~~laell~slGitksAl~I~Erle---------mw~~vi~CY~~lg~~~kaeei~~q~lek--~~d~~lyc~LGDv~  467 (777)
T KOG1128|consen  399 QLQRLLAELLLSLGITKSALVIFERLE---------MWDPVILCYLLLGQHGKAEEINRQELEK--DPDPRLYCLLGDVL  467 (777)
T ss_pred             hHHHHHHHHHHHcchHHHHHHHHHhHH---------HHHHHHHHHHHhcccchHHHHHHHHhcC--CCcchhHHHhhhhc
Confidence            333445667777888888998888864         5788999999999999999999888774  68999999999998


Q ss_pred             HhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHH
Q 039342          104 AKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERA  183 (248)
Q Consensus       104 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a  183 (248)
                      ....-+++|.++.+.....     ...+...  . ..+.++++.+.+.++.-.+... .-..+|-..-.+..+.++++.|
T Consensus       468 ~d~s~yEkawElsn~~sar-----A~r~~~~--~-~~~~~~fs~~~~hle~sl~~np-lq~~~wf~~G~~ALqlek~q~a  538 (777)
T KOG1128|consen  468 HDPSLYEKAWELSNYISAR-----AQRSLAL--L-ILSNKDFSEADKHLERSLEINP-LQLGTWFGLGCAALQLEKEQAA  538 (777)
T ss_pred             cChHHHHHHHHHhhhhhHH-----HHHhhcc--c-cccchhHHHHHHHHHHHhhcCc-cchhHHHhccHHHHHHhhhHHH
Confidence            8888899999999875432     1111000  1 2336788888888876554432 2457777788888889999999


Q ss_pred             HHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHH
Q 039342          184 ARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMF  234 (248)
Q Consensus       184 ~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~  234 (248)
                      .+.|.....  ..||    +..-|+-+-.+|.+.|+-.++.+.+.+-.+-.
T Consensus       539 v~aF~rcvt--L~Pd----~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn  583 (777)
T KOG1128|consen  539 VKAFHRCVT--LEPD----NAEAWNNLSTAYIRLKKKKRAFRKLKEALKCN  583 (777)
T ss_pred             HHHHHHHhh--cCCC----chhhhhhhhHHHHHHhhhHHHHHHHHHHhhcC
Confidence            999998765  4676    44445555588999999999888887765544

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=97.56  E-value=0.00063  Score=57.99  Aligned_cols=104  Identities=13%  Similarity=0.225  Sum_probs=69.8

Q ss_pred             HhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHH
Q 039342          104 AKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERA  183 (248)
Q Consensus       104 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a  183 (248)
                      .....|.+|+.+++.+++..   +..-|...+...|...|+++.|+++|.+         ...++-.|..|.+.|+|.+|
T Consensus       743 i~akew~kai~ildniqdqk---~~s~yy~~iadhyan~~dfe~ae~lf~e---------~~~~~dai~my~k~~kw~da  810 (1636)
T KOG3616|consen  743 IGAKEWKKAISILDNIQDQK---TASGYYGEIADHYANKGDFEIAEELFTE---------ADLFKDAIDMYGKAGKWEDA  810 (1636)
T ss_pred             hhhhhhhhhHhHHHHhhhhc---cccccchHHHHHhccchhHHHHHHHHHh---------cchhHHHHHHHhccccHHHH
Confidence            45567888888888887664   3344566666668899999999998875         23478889999999999999


Q ss_pred             HHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHH
Q 039342          184 ARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVW  226 (248)
Q Consensus       184 ~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~  226 (248)
                      .++-.+....  +.....|-.-.     .-+-++|++.+++++
T Consensus       811 ~kla~e~~~~--e~t~~~yiaka-----edldehgkf~eaeql  846 (1636)
T KOG3616|consen  811 FKLAEECHGP--EATISLYIAKA-----EDLDEHGKFAEAEQL  846 (1636)
T ss_pred             HHHHHHhcCc--hhHHHHHHHhH-----HhHHhhcchhhhhhe
Confidence            9987765422  22333332222     334455555555543

>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=97.54  E-value=0.0014  Score=44.03  Aligned_cols=82  Identities=13%  Similarity=0.148  Sum_probs=62.9

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHH---------------CCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 039342           57 NERTLEAVLSVYCFAGLVDESKEQFQEIKS---------------SGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHT  121 (248)
Q Consensus        57 ~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~---------------~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  121 (248)
                      |..++..+|.++++.|+++....+.+..=.               ....|+..+..+++.+|+.++++..|+++++...+
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~~~~~spl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~   80 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGDYPPSSPLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSR   80 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCccCCCCCCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            567899999999999999999998876521               23457888888888888888888888888888754


Q ss_pred             -CCCCchHHhHHHHhccc
Q 039342          122 -NRISNIHQVTGQMIKGE  138 (248)
Q Consensus       122 -~~~~~~~~~~~~~l~~~  138 (248)
                       .+++.+..++..++.-.
T Consensus        81 ~Y~I~i~~~~W~~Ll~W~   98 (126)
T PF12921_consen   81 KYPIPIPKEFWRRLLEWA   98 (126)
T ss_pred             HcCCCCCHHHHHHHHHHH
Confidence             35555666666666543

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

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

Probab=97.52  E-value=0.0042  Score=49.95  Aligned_cols=96  Identities=10%  Similarity=0.062  Sum_probs=75.8

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|++.|++..+... -+...|..+-.+|.+.|++++|+..+++..+.. +.+...|..+-.+|...|+++.|...
T Consensus        15 ~~~~~~Ai~~~~~Al~~~P-~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~-P~~~~a~~~lg~~~~~lg~~~eA~~~   92 (356)
T PLN03088         15 DDDFALAVDLYTQAIDLDP-NNAELYADRAQANIKLGNFTEAVADANKAIELD-PSLAKAYLRKGTACMKLEEYQTAKAA   92 (356)
T ss_pred             cCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhCCHHHHHHH
Confidence            4789999999999887543 357788888889999999999999999987754 34667788888899999999999999


Q ss_pred             HHHHHHCCCCcCHhhHHHHH
Q 039342           81 FQEIKSSGILPSVMCYCMLL  100 (248)
Q Consensus        81 ~~~m~~~~~~p~~~~~~~li  100 (248)
                      |++..+.  .|+.......+
T Consensus        93 ~~~al~l--~P~~~~~~~~l  110 (356)
T PLN03088         93 LEKGASL--APGDSRFTKLI  110 (356)
T ss_pred             HHHHHHh--CCCCHHHHHHH
Confidence            9998875  45544444443

>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=97.52  E-value=0.0011  Score=45.98  Aligned_cols=71  Identities=17%  Similarity=0.149  Sum_probs=43.6

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHH-----HCCCCchHHhH
Q 039342           60 TLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMH-----TNRISNIHQVT  131 (248)
Q Consensus        60 t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~-----~~~~~~~~~~~  131 (248)
                      ....++..+...|+++.|..+.+.+.... +.+...|..+|.+|...|+...|.+.|+++.     +-|+.|+..+-
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~d-P~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~  139 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALD-PYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETR  139 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHH
Confidence            45566667777777777777777776542 2256677777777777777777777777663     34666665543

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

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

Probab=97.51  E-value=0.041  Score=45.82  Aligned_cols=213  Identities=15%  Similarity=0.084  Sum_probs=142.4

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++.+|.-.|+...+... -+...|--|=..-+.+++-..|+..+++..+.. +-|....-.|--.|...|.-..|...+
T Consensus       299 G~L~~A~LafEAAVkqdP-~haeAW~~LG~~qaENE~E~~ai~AL~rcl~Ld-P~NleaLmaLAVSytNeg~q~~Al~~L  376 (579)
T KOG1125|consen  299 GDLSEAALAFEAAVKQDP-QHAEAWQKLGITQAENENEQNAISALRRCLELD-PTNLEALMALAVSYTNEGLQNQALKML  376 (579)
T ss_pred             CCchHHHHHHHHHHhhCh-HHHHHHHHhhhHhhhccchHHHHHHHHHHHhcC-CccHHHHHHHHHHHhhhhhHHHHHHHH
Confidence            678888888888776542 367788888888888888888988888887653 234455666777788888888888888


Q ss_pred             HHHHHCCCC-----c---CHhhHHHHHHHHHhcCCHHHHHHHHHHH-HHCC--CCchHHhHHHHhcccccccchHHHHHH
Q 039342           82 QEIKSSGIL-----P---SVMCYCMLLAVYAKSNRWDDAYGLLDEM-HTNR--ISNIHQVTGQMIKGEFDDESNWQMVEY  150 (248)
Q Consensus        82 ~~m~~~~~~-----p---~~~~~~~li~~~~~~~~~~~a~~~~~~m-~~~~--~~~~~~~~~~~l~~~~~~~~~~~~a~~  150 (248)
                      +.......+     +   +...-+.  ..+.....+....++|-++ ++.+  +.|+....-.+|   |...+.++.+..
T Consensus       377 ~~Wi~~~p~y~~l~~a~~~~~~~~~--~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVL---y~ls~efdraiD  451 (579)
T KOG1125|consen  377 DKWIRNKPKYVHLVSAGENEDFENT--KSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVL---YNLSGEFDRAVD  451 (579)
T ss_pred             HHHHHhCccchhccccCccccccCC--cCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHH---HhcchHHHHHHH
Confidence            776543210     0   0000000  2222233344455555554 3444  445555444444   556788999999


Q ss_pred             HHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcc--hhhhHHhhhhhhccccchHHHHHHHHHH
Q 039342          151 VFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELF--RHNKLVWSVDVHRMWEGGAYTAISVWLN  228 (248)
Q Consensus       151 ~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~--t~~~li~~~~~~~~~~~g~~~~~~~~~~  228 (248)
                      .|+........ |..+||-|-..++...+..+|...|++..+  ++|+-+  -||.-|      .|...|.+.+|...|=
T Consensus       452 cf~~AL~v~Pn-d~~lWNRLGAtLAN~~~s~EAIsAY~rALq--LqP~yVR~RyNlgI------S~mNlG~ykEA~~hlL  522 (579)
T KOG1125|consen  452 CFEAALQVKPN-DYLLWNRLGATLANGNRSEEAISAYNRALQ--LQPGYVRVRYNLGI------SCMNLGAYKEAVKHLL  522 (579)
T ss_pred             HHHHHHhcCCc-hHHHHHHhhHHhcCCcccHHHHHHHHHHHh--cCCCeeeeehhhhh------hhhhhhhHHHHHHHHH
Confidence            99988776543 678899999999999999999999999876  466532  355544      5667788888777554


Q ss_pred             HH
Q 039342          229 KM  230 (248)
Q Consensus       229 ~m  230 (248)
                      +-
T Consensus       523 ~A  524 (579)
T KOG1125|consen  523 EA  524 (579)
T ss_pred             HH
Confidence            43

>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=97.47  E-value=0.00084  Score=39.76  Aligned_cols=50  Identities=20%  Similarity=0.271  Sum_probs=21.7

Q ss_pred             cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 039342           36 GGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKS   86 (248)
Q Consensus        36 ~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~   86 (248)
                      .|++++|.++|+...+.. +-+...+-.+..+|.+.|++++|.++++.+..
T Consensus         4 ~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~   53 (68)
T PF14559_consen    4 QGDYDEAIELLEKALQRN-PDNPEARLLLAQCYLKQGQYDEAEELLERLLK   53 (68)
T ss_dssp             TTHHHHHHHHHHHHHHHT-TTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHG
T ss_pred             ccCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            444444444444443332 12333444444444444444444444444443

...

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

Probab=97.46  E-value=0.0058  Score=49.20  Aligned_cols=101  Identities=11%  Similarity=0.017  Sum_probs=82.0

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHH
Q 039342           31 EAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWD  110 (248)
Q Consensus        31 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~  110 (248)
                      ..+...|+++.|++.|++..+.. +-+...|..+-.+|.+.|++++|...+++..+.. +.+...|..+-.+|...|+++
T Consensus        10 ~~a~~~~~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~-P~~~~a~~~lg~~~~~lg~~~   87 (356)
T PLN03088         10 KEAFVDDDFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANKAIELD-PSLAKAYLRKGTACMKLEEYQ   87 (356)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhCCHH
Confidence            45567899999999999998764 3466788888899999999999999999998763 226678888999999999999


Q ss_pred             HHHHHHHHHHHCCCCchHHhHHHHh
Q 039342          111 DAYGLLDEMHTNRISNIHQVTGQMI  135 (248)
Q Consensus       111 ~a~~~~~~m~~~~~~~~~~~~~~~l  135 (248)
                      +|+..|++..+..  |+...+...+
T Consensus        88 eA~~~~~~al~l~--P~~~~~~~~l  110 (356)
T PLN03088         88 TAKAALEKGASLA--PGDSRFTKLI  110 (356)
T ss_pred             HHHHHHHHHHHhC--CCCHHHHHHH
Confidence            9999999988654  5555554444

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

Probab=97.43  E-value=0.0021  Score=48.76  Aligned_cols=100  Identities=17%  Similarity=0.228  Sum_probs=79.9

Q ss_pred             CCCHHhHHHHHHHHHhc-----CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC----------------ChhHHH
Q 039342           20 ARNSDSFNAVIEAFRQG-----GRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAG----------------LVDESK   78 (248)
Q Consensus        20 ~~~~~~y~~li~~~~~~-----~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g----------------~~~~a~   78 (248)
                      +.|-.+|-+.+..|...     +.++-....++.|++-|+.-|..+|+.||+.+-+-.                +-+=+.
T Consensus        64 ~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C~I  143 (406)
T KOG3941|consen   64 KRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNCAI  143 (406)
T ss_pred             cccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhHHH
Confidence            46778888888888754     678888889999999999999999999999875533                234467


Q ss_pred             HHHHHHHHCCCCcCHhhHHHHHHHHHhcCC-HHHHHHHHHHH
Q 039342           79 EQFQEIKSSGILPSVMCYCMLLAVYAKSNR-WDDAYGLLDEM  119 (248)
Q Consensus        79 ~~~~~m~~~~~~p~~~~~~~li~~~~~~~~-~~~a~~~~~~m  119 (248)
                      .++++|...|+.||..+-..+++++.+.+- ..+..+++--|
T Consensus       144 ~vLeqME~hGVmPdkE~e~~lvn~FGr~~~p~~K~~Rm~yWm  185 (406)
T KOG3941|consen  144 KVLEQMEWHGVMPDKEIEDILVNAFGRWNFPTKKVKRMLYWM  185 (406)
T ss_pred             HHHHHHHHcCCCCchHHHHHHHHHhccccccHHHHHHHHHhh
Confidence            899999999999999999999999998875 33344444333

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

Probab=97.43  E-value=0.0036  Score=38.87  Aligned_cols=58  Identities=19%  Similarity=0.220  Sum_probs=27.3

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 039342           62 EAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMH  120 (248)
Q Consensus        62 ~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~  120 (248)
                      ..+...+...|++++|...+++..+.. +.+...+..+...+...+++++|.+.+++..
T Consensus         4 ~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~   61 (100)
T cd00189           4 LNLGNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKAL   61 (100)
T ss_pred             HHHHHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334444555555555555555554431 1122344444444444455555555544443

>PLN02789 farnesyltranstransferase

Probab=97.41  E-value=0.041  Score=43.54  Aligned_cols=187  Identities=8%  Similarity=-0.083  Sum_probs=116.6

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcC-CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCh--hHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGG-RFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLV--DESK   78 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~-~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~--~~a~   78 (248)
                      ++.++|+.+..++.+... -+..+|+.--..+.+.| ++++++..++++.+.+ +-+..+|+.--..+.+.|+.  +++.
T Consensus        51 e~serAL~lt~~aI~lnP-~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~n-pknyqaW~~R~~~l~~l~~~~~~~el  128 (320)
T PLN02789         51 ERSPRALDLTADVIRLNP-GNYTVWHFRRLCLEALDADLEEELDFAEDVAEDN-PKNYQIWHHRRWLAEKLGPDAANKEL  128 (320)
T ss_pred             CCCHHHHHHHHHHHHHCc-hhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHC-CcchHHhHHHHHHHHHcCchhhHHHH
Confidence            567889999998876332 23456665555556666 6789999999987765 34445676555555556653  6778


Q ss_pred             HHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHH-Hhcccccccc----hHHHHHHHHH
Q 039342           79 EQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQ-MIKGEFDDES----NWQMVEYVFD  153 (248)
Q Consensus        79 ~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~-~l~~~~~~~~----~~~~a~~~~~  153 (248)
                      ++++.+.+... -+-.+|+..-..+.+.|+++++++.++++.+.+......-.+. .+.......+    ..+.......
T Consensus       129 ~~~~kal~~dp-kNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~N~sAW~~R~~vl~~~~~l~~~~~~~e~el~y~~  207 (320)
T PLN02789        129 EFTRKILSLDA-KNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVRNNSAWNQRYFVITRSPLLGGLEAMRDSELKYTI  207 (320)
T ss_pred             HHHHHHHHhCc-ccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCchhHHHHHHHHHHhccccccccccHHHHHHHHH
Confidence            88888876542 2678888888888888999999999999988764433322221 1211111111    1244555555


Q ss_pred             HHHhcCCCCCHHHHHHHHHHHHhc----CchHHHHHHHHHHHH
Q 039342          154 KLNCEGYGLGMRFYNALLEALWCL----GLRERAARVLDEATK  192 (248)
Q Consensus       154 ~m~~~~~~p~~~~~~~li~~~~~~----g~~~~a~~~~~~m~~  192 (248)
                      ........ |...|+.+-..+...    ++..+|.+.+.+..+
T Consensus       208 ~aI~~~P~-N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~  249 (320)
T PLN02789        208 DAILANPR-NESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLS  249 (320)
T ss_pred             HHHHhCCC-CcCHHHHHHHHHhcCCcccccchhHHHHHHHhhc
Confidence            55544332 566677666666652    344567777777555

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

Probab=97.36  E-value=0.1  Score=46.80  Aligned_cols=210  Identities=10%  Similarity=0.056  Sum_probs=131.0

Q ss_pred             CchHHHHHHHHHHHHcCCCCCH-HhHHHHHHHHHhcCCHHHHHHH------------------HHHHHHcCCCCCHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNS-DSFNAVIEAFRQGGRFEEAIKA------------------YVEMEKVRCDPNERTLE   62 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~-~~y~~li~~~~~~~~~~~a~~~------------------~~~m~~~~~~p~~~t~~   62 (248)
                      |++++|.++.+...+.  .|+. ..|-.+-..+.+.++.+.+..+                  ...|.+  ..-+...+-
T Consensus        45 ~~~deai~i~~~~l~~--~P~~i~~yy~~G~l~~q~~~~~~~~lv~~l~~~~~~~~~~~ve~~~~~i~~--~~~~k~Al~  120 (906)
T PRK14720         45 NLTDEAKDICEEHLKE--HKKSISALYISGILSLSRRPLNDSNLLNLIDSFSQNLKWAIVEHICDKILL--YGENKLALR  120 (906)
T ss_pred             CCHHHHHHHHHHHHHh--CCcceehHHHHHHHHHhhcchhhhhhhhhhhhcccccchhHHHHHHHHHHh--hhhhhHHHH
Confidence            6788999998866553  2432 2233222255566666555444                  111111  111224666


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCC-----CchHHhHHHHhcc
Q 039342           63 AVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRI-----SNIHQVTGQMIKG  137 (248)
Q Consensus        63 ~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-----~~~~~~~~~~l~~  137 (248)
                      .+..+|-+.|+.+++..+++++.+.. +-|+.+.|.+-..|+.. ++++|+.++.+....-+     ..-...|..++..
T Consensus       121 ~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-dL~KA~~m~~KAV~~~i~~kq~~~~~e~W~k~~~~  198 (906)
T PRK14720        121 TLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-DKEKAITYLKKAIYRFIKKKQYVGIEEIWSKLVHY  198 (906)
T ss_pred             HHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-hHHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHhc
Confidence            77788889999999999999999876 33788999999999999 99999999988754311     1112223333322


Q ss_pred             cccccchHHHHHHHHHHHHhc-CCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhcccc
Q 039342          138 EFDDESNWQMVEYVFDKLNCE-GYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWE  216 (248)
Q Consensus       138 ~~~~~~~~~~a~~~~~~m~~~-~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~  216 (248)
                         ...+.+.-.++.+.+... |..--..++-.+-..|-..++|+++..+++...+.. +-|.....-++.++. ..|..
T Consensus       199 ---~~~d~d~f~~i~~ki~~~~~~~~~~~~~~~l~~~y~~~~~~~~~i~iLK~iL~~~-~~n~~a~~~l~~~y~-~kY~~  273 (906)
T PRK14720        199 ---NSDDFDFFLRIERKVLGHREFTRLVGLLEDLYEPYKALEDWDEVIYILKKILEHD-NKNNKAREELIRFYK-EKYKD  273 (906)
T ss_pred             ---CcccchHHHHHHHHHHhhhccchhHHHHHHHHHHHhhhhhhhHHHHHHHHHHhcC-CcchhhHHHHHHHHH-HHccC
Confidence               233444555555555544 544456667777788889999999999999988642 113334444553333 44555


Q ss_pred             chHHHH
Q 039342          217 GGAYTA  222 (248)
Q Consensus       217 ~g~~~~  222 (248)
                      +..+++
T Consensus       274 ~~~~ee  279 (906)
T PRK14720        274 HSLLED  279 (906)
T ss_pred             cchHHH
Confidence            445544

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.36  E-value=0.012  Score=41.80  Aligned_cols=110  Identities=14%  Similarity=0.133  Sum_probs=69.4

Q ss_pred             HHHHHHHH-HHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHhcCChhHHHHHHHH
Q 039342            7 CQAILSRM-SESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDP--NERTLEAVLSVYCFAGLVDESKEQFQE   83 (248)
Q Consensus         7 a~~~~~~m-~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p--~~~t~~~ll~~~~~~g~~~~a~~~~~~   83 (248)
                      +...+..+ ...+-.-....|..+...+...|++++|+..|+........|  ...+|..+-..+...|++++|...++.
T Consensus        18 ~~~~l~~~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~   97 (168)
T CHL00033         18 VADILLRILPTTSGEKEAFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQ   97 (168)
T ss_pred             chhhhhHhccCCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            34444444 233333345667777777778888888888888876543222  234777788888888888888888888


Q ss_pred             HHHCCCCcCHhhHHHHHHHHH-------hcCCHHHHHHHHH
Q 039342           84 IKSSGILPSVMCYCMLLAVYA-------KSNRWDDAYGLLD  117 (248)
Q Consensus        84 m~~~~~~p~~~~~~~li~~~~-------~~~~~~~a~~~~~  117 (248)
                      ..+.. +....++..+...+.       +.|+++.|+..++
T Consensus        98 Al~~~-~~~~~~~~~la~i~~~~~~~~~~~g~~~~A~~~~~  137 (168)
T CHL00033         98 ALERN-PFLPQALNNMAVICHYRGEQAIEQGDSEIAEAWFD  137 (168)
T ss_pred             HHHhC-cCcHHHHHHHHHHHHHhhHHHHHcccHHHHHHHHH
Confidence            77542 123445555555665       5556555544444

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

Probab=97.35  E-value=0.025  Score=49.34  Aligned_cols=171  Identities=12%  Similarity=0.156  Sum_probs=91.4

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHc-C--------CCCCHHHHHHHHHHHHhcC
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKV-R--------CDPNERTLEAVLSVYCFAG   72 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~-~--------~~p~~~t~~~ll~~~~~~g   72 (248)
                      |+.|.|.+-.+.++      +...|..|-+.|.+..+.+-|.-.+-.|... |        -.|+ .+-.-+.-.....|
T Consensus       742 G~MD~AfksI~~Ik------S~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~-e~eakvAvLAieLg  814 (1416)
T KOG3617|consen  742 GSMDAAFKSIQFIK------SDSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQNGE-EDEAKVAVLAIELG  814 (1416)
T ss_pred             ccHHHHHHHHHHHh------hhHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhCCc-chhhHHHHHHHHHh
Confidence            56666665555553      4567888888888888877776666666322 1        1222 22222233344567


Q ss_pred             ChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHH
Q 039342           73 LVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVF  152 (248)
Q Consensus        73 ~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  152 (248)
                      .+++|+.+|.+-++         |..|=+.|-..|.|++|.++-+.=   ...--..||...... +...++.+.|.+.|
T Consensus       815 MlEeA~~lYr~ckR---------~DLlNKlyQs~g~w~eA~eiAE~~---DRiHLr~Tyy~yA~~-Lear~Di~~Aleyy  881 (1416)
T KOG3617|consen  815 MLEEALILYRQCKR---------YDLLNKLYQSQGMWSEAFEIAETK---DRIHLRNTYYNYAKY-LEARRDIEAALEYY  881 (1416)
T ss_pred             hHHHHHHHHHHHHH---------HHHHHHHHHhcccHHHHHHHHhhc---cceehhhhHHHHHHH-HHhhccHHHHHHHH
Confidence            77777777766554         334445566667777777665532   111122233332222 33344444444443


Q ss_pred             HH-----------HHhc--------CCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          153 DK-----------LNCE--------GYGLGMRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       153 ~~-----------m~~~--------~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                      +.           +.+.        .-.-|...|...-..+-..|+.|.|+.+|...++
T Consensus       882 EK~~~hafev~rmL~e~p~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D  940 (1416)
T KOG3617|consen  882 EKAGVHAFEVFRMLKEYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAKD  940 (1416)
T ss_pred             HhcCChHHHHHHHHHhChHHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhhh
Confidence            32           2111        0123445566666666667777777777776554

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.31  E-value=0.023  Score=40.57  Aligned_cols=91  Identities=20%  Similarity=0.251  Sum_probs=68.0

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCc-CHhhHHH
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN--ERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILP-SVMCYCM   98 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~--~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~   98 (248)
                      ....|..+-..+...|++++|...|++..+..-.+.  ...+..+...+.+.|++++|...+++..+.  .| +...+..
T Consensus        34 ~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~  111 (172)
T PRK02603         34 EAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALEL--NPKQPSALNN  111 (172)
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CcccHHHHHH
Confidence            345677788888899999999999999876543332  467888888999999999999999988775  23 4556666


Q ss_pred             HHHHHHhcCCHHHHHH
Q 039342           99 LLAVYAKSNRWDDAYG  114 (248)
Q Consensus        99 li~~~~~~~~~~~a~~  114 (248)
                      +...+...|+...+..
T Consensus       112 lg~~~~~~g~~~~a~~  127 (172)
T PRK02603        112 IAVIYHKRGEKAEEAG  127 (172)
T ss_pred             HHHHHHHcCChHhHhh
Confidence            7777777776544443

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

Probab=97.31  E-value=0.067  Score=47.87  Aligned_cols=136  Identities=18%  Similarity=0.221  Sum_probs=79.0

Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHH
Q 039342           24 DSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVY  103 (248)
Q Consensus        24 ~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~  103 (248)
                      ..|..+-.+-.+.|.+.+|.+-|-+      .-|+..|.-++..+.+.|.+++-.+.+...++..-.|.  .=+.||-+|
T Consensus      1105 ~vWsqlakAQL~~~~v~dAieSyik------adDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~--id~eLi~Ay 1176 (1666)
T KOG0985|consen 1105 AVWSQLAKAQLQGGLVKDAIESYIK------ADDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPY--IDSELIFAY 1176 (1666)
T ss_pred             HHHHHHHHHHHhcCchHHHHHHHHh------cCCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCcc--chHHHHHHH
Confidence            4555555555555555555544433      24566788888888888888888888766666544443  445788888


Q ss_pred             HhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHH
Q 039342          104 AKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERA  183 (248)
Q Consensus       104 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a  183 (248)
                      ++.+++.+.++++.     |  |+......+=.. |-..+.++.|.-+|..         ..-|.-+-..+...|++..|
T Consensus      1177 Akt~rl~elE~fi~-----g--pN~A~i~~vGdr-cf~~~~y~aAkl~y~~---------vSN~a~La~TLV~LgeyQ~A 1239 (1666)
T KOG0985|consen 1177 AKTNRLTELEEFIA-----G--PNVANIQQVGDR-CFEEKMYEAAKLLYSN---------VSNFAKLASTLVYLGEYQGA 1239 (1666)
T ss_pred             HHhchHHHHHHHhc-----C--CCchhHHHHhHH-HhhhhhhHHHHHHHHH---------hhhHHHHHHHHHHHHHHHHH
Confidence            88888777666553     2  444444444333 3334455555555543         22344444444444444444


Q ss_pred             H
Q 039342          184 A  184 (248)
Q Consensus       184 ~  184 (248)
                      .
T Consensus      1240 V 1240 (1666)
T KOG0985|consen 1240 V 1240 (1666)
T ss_pred             H
Confidence            3

>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=97.28  E-value=0.0018  Score=38.25  Aligned_cols=62  Identities=19%  Similarity=0.362  Sum_probs=50.1

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVL   65 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll   65 (248)
                      .|++++|.++|+.+.+... -+...+..+..+|.+.|++++|.++++.+...  .|+...|..++
T Consensus         4 ~~~~~~A~~~~~~~l~~~p-~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~--~~~~~~~~~l~   65 (68)
T PF14559_consen    4 QGDYDEAIELLEKALQRNP-DNPEARLLLAQCYLKQGQYDEAEELLERLLKQ--DPDNPEYQQLL   65 (68)
T ss_dssp             TTHHHHHHHHHHHHHHHTT-TSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG--GTTHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CcCHHHHHHHH
Confidence            4899999999999987543 37888889999999999999999999999776  47755555544

...

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.21  E-value=0.011  Score=41.14  Aligned_cols=99  Identities=7%  Similarity=-0.095  Sum_probs=76.3

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHH
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLA  101 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~  101 (248)
                      +....-.+-..+...|++++|..+|+.+..-. +-+..-|-.|-.+|-..|++++|...|........ -++..+-.+-.
T Consensus        34 ~l~~lY~~A~~ly~~G~l~~A~~~f~~L~~~D-p~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~-ddp~~~~~ag~  111 (157)
T PRK15363         34 PLNTLYRYAMQLMEVKEFAGAARLFQLLTIYD-AWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKI-DAPQAPWAAAE  111 (157)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCchHHHHHHH
Confidence            34455556666778899999999999987654 24445556677778888999999999998887653 36778888888


Q ss_pred             HHHhcCCHHHHHHHHHHHHHC
Q 039342          102 VYAKSNRWDDAYGLLDEMHTN  122 (248)
Q Consensus       102 ~~~~~~~~~~a~~~~~~m~~~  122 (248)
                      ++...|+.+.|.+-|+.....
T Consensus       112 c~L~lG~~~~A~~aF~~Ai~~  132 (157)
T PRK15363        112 CYLACDNVCYAIKALKAVVRI  132 (157)
T ss_pred             HHHHcCCHHHHHHHHHHHHHH
Confidence            899999999999999877654

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.21  E-value=0.024  Score=40.50  Aligned_cols=75  Identities=16%  Similarity=0.191  Sum_probs=56.8

Q ss_pred             CCchHHHHHHHHHHHHcCCCCC--HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhH
Q 039342            1 GGLYKECQAILSRMSESGVARN--SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDE   76 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~--~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~   76 (248)
                      .|++++|...|++..+....+.  ...|..+-..+.+.|++++|...+++..+.. +-+...+..+..++...|+...
T Consensus        48 ~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~  124 (172)
T PRK02603         48 DGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELN-PKQPSALNNIAVIYHKRGEKAE  124 (172)
T ss_pred             cCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChHh
Confidence            3899999999999876543332  4688889999999999999999999987653 2345666667777777776433

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

Probab=97.20  E-value=0.046  Score=45.76  Aligned_cols=186  Identities=12%  Similarity=0.100  Sum_probs=116.8

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHH--HHHHHH-
Q 039342           28 AVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCM--LLAVYA-  104 (248)
Q Consensus        28 ~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~--li~~~~-  104 (248)
                      +=++-+.+.|++++|.....++...+ +-|...+.+-+-+..+.+++++|..+.+.=.   .   ..+++.  +=.+|| 
T Consensus        17 t~ln~~~~~~e~e~a~k~~~Kil~~~-pdd~~a~~cKvValIq~~ky~~ALk~ikk~~---~---~~~~~~~~fEKAYc~   89 (652)
T KOG2376|consen   17 TDLNRHGKNGEYEEAVKTANKILSIV-PDDEDAIRCKVVALIQLDKYEDALKLIKKNG---A---LLVINSFFFEKAYCE   89 (652)
T ss_pred             HHHHHhccchHHHHHHHHHHHHHhcC-CCcHhhHhhhHhhhhhhhHHHHHHHHHHhcc---h---hhhcchhhHHHHHHH
Confidence            34566778899999999999998766 5566778888889999999999985544322   1   112222  356666 


Q ss_pred             -hcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHH
Q 039342          105 -KSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERA  183 (248)
Q Consensus       105 -~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a  183 (248)
                       +.+..|+|+..++     |..+.+.-...+=...+-+.++++++..+|+.+.+.+..    .+..-+++-+..  ...+
T Consensus        90 Yrlnk~Dealk~~~-----~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~d----d~d~~~r~nl~a--~~a~  158 (652)
T KOG2376|consen   90 YRLNKLDEALKTLK-----GLDRLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNSD----DQDEERRANLLA--VAAA  158 (652)
T ss_pred             HHcccHHHHHHHHh-----cccccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCc----hHHHHHHHHHHH--HHHh
Confidence             6789999999998     333333322222223355788999999999999877543    222222221110  0011


Q ss_pred             HHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHHH
Q 039342          184 ARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFM  235 (248)
Q Consensus       184 ~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~~  235 (248)
                      ... +.+......| ..||..+....+  .+...|++.+|+++++.-.+.+.
T Consensus       159 l~~-~~~q~v~~v~-e~syel~yN~Ac--~~i~~gky~qA~elL~kA~~~~~  206 (652)
T KOG2376|consen  159 LQV-QLLQSVPEVP-EDSYELLYNTAC--ILIENGKYNQAIELLEKALRICR  206 (652)
T ss_pred             hhH-HHHHhccCCC-cchHHHHHHHHH--HHHhcccHHHHHHHHHHHHHHHH
Confidence            111 1233333344 346766665553  46789999999999988744443

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=97.20  E-value=0.06  Score=40.88  Aligned_cols=81  Identities=10%  Similarity=0.104  Sum_probs=53.5

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH-HHH---HHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHH
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNE-RTL---EAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYC   97 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~t~---~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~   97 (248)
                      +...+-..-..+.+.|++++|.+.|+.+...-  |+. ..-   -.+..++.+.++++.|...+++..+.-..-...-|.
T Consensus        31 ~~~~~Y~~A~~~~~~g~y~~Ai~~f~~l~~~y--P~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a  108 (243)
T PRK10866         31 PPSEIYATAQQKLQDGNWKQAITQLEALDNRY--PFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYV  108 (243)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHH
Confidence            34444344555567899999999999997753  333 222   345678899999999999999998753222233444


Q ss_pred             HHHHHHH
Q 039342           98 MLLAVYA  104 (248)
Q Consensus        98 ~li~~~~  104 (248)
                      ..+.+.+
T Consensus       109 ~Y~~g~~  115 (243)
T PRK10866        109 LYMRGLT  115 (243)
T ss_pred             HHHHHHh
Confidence            4555543

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

Probab=97.18  E-value=0.0096  Score=45.27  Aligned_cols=117  Identities=14%  Similarity=0.160  Sum_probs=82.1

Q ss_pred             CCCHHHHHHHHHHHH-----hcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHH
Q 039342           55 DPNERTLEAVLSVYC-----FAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQ  129 (248)
Q Consensus        55 ~p~~~t~~~ll~~~~-----~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~  129 (248)
                      +-|-.+|-..+..+.     +.++++-.-..++.|++.|+.-|..+|+.||..+=+..                ..|.+ 
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            456667777766664     34677777888899999999999999999988765532                22332 


Q ss_pred             hHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchH-HHHHHHHHHH
Q 039342          130 VTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRE-RAARVLDEAT  191 (248)
Q Consensus       130 ~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~-~a~~~~~~m~  191 (248)
                      +|..+... |.+..  +-+..++++|...|+.||-.+-..+++++.+.+..- +...+.-.|.
T Consensus       127 vfQ~~F~H-YP~QQ--~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~p~~K~~Rm~yWmP  186 (406)
T KOG3941|consen  127 VFQKVFLH-YPQQQ--NCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNFPTKKVKRMLYWMP  186 (406)
T ss_pred             HHHHHHhh-Cchhh--hHHHHHHHHHHHcCCCCchHHHHHHHHHhccccccHHHHHHHHHhhh
Confidence            33333333 44433  578899999999999999999999999999887532 3333333343

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.13  E-value=0.033  Score=43.83  Aligned_cols=173  Identities=11%  Similarity=0.080  Sum_probs=94.2

Q ss_pred             HHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH--Hhc-------CChh
Q 039342            5 KECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVY--CFA-------GLVD   75 (248)
Q Consensus         5 ~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~--~~~-------g~~~   75 (248)
                      +.|++++-.+.+  +-|  ..--.|+-.|.+.+++.+|..+.+++.    +.++.-|  ++++.  ++.       .+..
T Consensus       271 EgALqVLP~L~~--~IP--EARlNL~iYyL~q~dVqeA~~L~Kdl~----PttP~Ey--ilKgvv~aalGQe~gSreHlK  340 (557)
T KOG3785|consen  271 EGALQVLPSLMK--HIP--EARLNLIIYYLNQNDVQEAISLCKDLD----PTTPYEY--ILKGVVFAALGQETGSREHLK  340 (557)
T ss_pred             ccHHHhchHHHh--hCh--HhhhhheeeecccccHHHHHHHHhhcC----CCChHHH--HHHHHHHHHhhhhcCcHHHHH
Confidence            345555554443  112  223345556788888888888877653    2222222  23222  222       2355


Q ss_pred             HHHHHHHHHHHCCCCcCH-hhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHH
Q 039342           76 ESKEQFQEIKSSGILPSV-MCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDK  154 (248)
Q Consensus        76 ~a~~~~~~m~~~~~~p~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  154 (248)
                      -|.+.|+-.-+++..-|+ .--.++...+.-..++|+++..++.++..=..-|...++ +..+ ....|++.+++++|-.
T Consensus       341 iAqqffqlVG~Sa~ecDTIpGRQsmAs~fFL~~qFddVl~YlnSi~sYF~NdD~Fn~N-~AQA-k~atgny~eaEelf~~  418 (557)
T KOG3785|consen  341 IAQQFFQLVGESALECDTIPGRQSMASYFFLSFQFDDVLTYLNSIESYFTNDDDFNLN-LAQA-KLATGNYVEAEELFIR  418 (557)
T ss_pred             HHHHHHHHhcccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhhhH-HHHH-HHHhcChHHHHHHHhh
Confidence            566666555555554433 334455555566667777777777665443222222222 2222 4556677777777776


Q ss_pred             HHhcCCCCCHHHHH-HHHHHHHhcCchHHHHHHHHHH
Q 039342          155 LNCEGYGLGMRFYN-ALLEALWCLGLRERAARVLDEA  190 (248)
Q Consensus       155 m~~~~~~p~~~~~~-~li~~~~~~g~~~~a~~~~~~m  190 (248)
                      +....++ |..+|. .+.++|.+.+..+.|++++-++
T Consensus       419 is~~~ik-n~~~Y~s~LArCyi~nkkP~lAW~~~lk~  454 (557)
T KOG3785|consen  419 ISGPEIK-NKILYKSMLARCYIRNKKPQLAWDMMLKT  454 (557)
T ss_pred             hcChhhh-hhHHHHHHHHHHHHhcCCchHHHHHHHhc
Confidence            6655555 455554 4445777777777777776554

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=97.09  E-value=0.033  Score=42.77  Aligned_cols=98  Identities=13%  Similarity=0.120  Sum_probs=68.6

Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH----HHHHHHHHHHHhcCChhHHHHHHHHHHHCCC--CcCHhhHH
Q 039342           24 DSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNE----RTLEAVLSVYCFAGLVDESKEQFQEIKSSGI--LPSVMCYC   97 (248)
Q Consensus        24 ~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~----~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~--~p~~~~~~   97 (248)
                      ..|...+..+.+.|++++|...|+.+.+.-  |+.    ..+-.+-.+|...|++++|...|+.+.+.-.  ......+-
T Consensus       144 ~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~y--P~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~  221 (263)
T PRK10803        144 TDYNAAIALVQDKSRQDDAIVAFQNFVKKY--PDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMF  221 (263)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHC--cCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHH
Confidence            456666666677788999988888887652  332    4556678888888999999999888875411  11233444


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           98 MLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        98 ~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      .+...+...|+.++|..+|++..+..
T Consensus       222 klg~~~~~~g~~~~A~~~~~~vi~~y  247 (263)
T PRK10803        222 KVGVIMQDKGDTAKAKAVYQQVIKKY  247 (263)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence            45556777888888888888877653

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.08  E-value=0.018  Score=40.98  Aligned_cols=82  Identities=12%  Similarity=0.096  Sum_probs=60.8

Q ss_pred             CchHHHHHHHHHHHHcCCCC--CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH-------hcC
Q 039342            2 GLYKECQAILSRMSESGVAR--NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYC-------FAG   72 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~--~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~-------~~g   72 (248)
                      |++++|+..|++.......+  ...+|..+-..+.+.|++++|.+.++...+.. +....++..+...+.       +.|
T Consensus        49 g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~-~~~~~~~~~la~i~~~~~~~~~~~g  127 (168)
T CHL00033         49 GEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERN-PFLPQALNNMAVICHYRGEQAIEQG  127 (168)
T ss_pred             CCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHhhHHHHHcc
Confidence            78999999999987643322  24588889999999999999999999987652 333455666666666       777


Q ss_pred             ChhHHHHHHHHH
Q 039342           73 LVDESKEQFQEI   84 (248)
Q Consensus        73 ~~~~a~~~~~~m   84 (248)
                      +++.|...+++-
T Consensus       128 ~~~~A~~~~~~a  139 (168)
T CHL00033        128 DSEIAEAWFDQA  139 (168)
T ss_pred             cHHHHHHHHHHH
Confidence            877666655543

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=97.07  E-value=0.078  Score=41.47  Aligned_cols=132  Identities=17%  Similarity=0.183  Sum_probs=69.6

Q ss_pred             hhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHh--cC----CHHHHHHHHHHHHHCCC---CchHHhHHHHhccccccc-c
Q 039342           74 VDESKEQFQEIKSSGILPSVMCYCMLLAVYAK--SN----RWDDAYGLLDEMHTNRI---SNIHQVTGQMIKGEFDDE-S  143 (248)
Q Consensus        74 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~--~~----~~~~a~~~~~~m~~~~~---~~~~~~~~~~l~~~~~~~-~  143 (248)
                      ++...++++.|.+.|+.-+..+|-+-......  ..    ...+|..+|+.|++...   .++...+..++...-... .
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~~~~~~e~  157 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAMTSEDVEE  157 (297)
T ss_pred             HHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhcccccHHH
Confidence            45556677777777777666655542222222  22    24567777777766542   234444444444311111 1


Q ss_pred             hHHHHHHHHHHHHhcCCCCCHH--HHHHHHHHHHhcCc--hHHHHHHHHHHHHCCCCCCcchhhhH
Q 039342          144 NWQMVEYVFDKLNCEGYGLGMR--FYNALLEALWCLGL--RERAARVLDEATKRGLFPELFRHNKL  205 (248)
Q Consensus       144 ~~~~a~~~~~~m~~~~~~p~~~--~~~~li~~~~~~g~--~~~a~~~~~~m~~~g~~p~~~t~~~l  205 (248)
                      -.+.++.+|+.+.+.|+..+-.  ....++..+-....  ..++.++++.+.+.|+++....|..+
T Consensus       158 l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~l  223 (297)
T PF13170_consen  158 LAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYPTL  223 (297)
T ss_pred             HHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccccHH
Confidence            2356666777777766654322  22222222222111  34677777777777777776666544

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

Probab=97.06  E-value=0.13  Score=43.72  Aligned_cols=174  Identities=14%  Similarity=0.100  Sum_probs=111.7

Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHH
Q 039342           24 DSFNAVIEAFRQGGRFEEAIKAYVEMEK-VRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAV  102 (248)
Q Consensus        24 ~~y~~li~~~~~~~~~~~a~~~~~~m~~-~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~  102 (248)
                      ..|-..+....+.|++......|+.... .-+.--..+|...|......+-++-+..++++..+.    ++..-+--|..
T Consensus       103 RIwl~Ylq~l~~Q~~iT~tR~tfdrALraLpvtqH~rIW~lyl~Fv~~~~lPets~rvyrRYLk~----~P~~~eeyie~  178 (835)
T KOG2047|consen  103 RIWLDYLQFLIKQGLITRTRRTFDRALRALPVTQHDRIWDLYLKFVESHGLPETSIRVYRRYLKV----APEAREEYIEY  178 (835)
T ss_pred             HHHHHHHHHHHhcchHHHHHHHHHHHHHhCchHhhccchHHHHHHHHhCCChHHHHHHHHHHHhc----CHHHHHHHHHH
Confidence            4566666677777888888888877643 233334467888888888889999999999998874    34457888899


Q ss_pred             HHhcCCHHHHHHHHHHHHHCC------CCchHHhHHHHhcccccccc---hHHHHHHHHHHHHhcCCCCC--HHHHHHHH
Q 039342          103 YAKSNRWDDAYGLLDEMHTNR------ISNIHQVTGQMIKGEFDDES---NWQMVEYVFDKLNCEGYGLG--MRFYNALL  171 (248)
Q Consensus       103 ~~~~~~~~~a~~~~~~m~~~~------~~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~m~~~~~~p~--~~~~~~li  171 (248)
                      +++.+++++|-+.+.......      .+.+...|..+..- ...+.   .--....+++.+...  -||  ...|++|.
T Consensus       179 L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdl-is~~p~~~~slnvdaiiR~gi~r--ftDq~g~Lw~SLA  255 (835)
T KOG2047|consen  179 LAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDL-ISQNPDKVQSLNVDAIIRGGIRR--FTDQLGFLWCSLA  255 (835)
T ss_pred             HHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHH-HHhCcchhcccCHHHHHHhhccc--CcHHHHHHHHHHH
Confidence            999999999998887764321      12223333322211 11111   111222333333221  233  45689999


Q ss_pred             HHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHH
Q 039342          172 EALWCLGLRERAARVLDEATKRGLFPELFRHNKLV  206 (248)
Q Consensus       172 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li  206 (248)
                      +.|.+.|.+++|.++|++-.+.  ..++.-|+.+.
T Consensus       256 dYYIr~g~~ekarDvyeeai~~--v~tvrDFt~if  288 (835)
T KOG2047|consen  256 DYYIRSGLFEKARDVYEEAIQT--VMTVRDFTQIF  288 (835)
T ss_pred             HHHHHhhhhHHHHHHHHHHHHh--heehhhHHHHH
Confidence            9999999999999999987664  33334444444

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

Probab=97.04  E-value=0.16  Score=43.11  Aligned_cols=126  Identities=11%  Similarity=0.006  Sum_probs=72.6

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Q 039342           95 CYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEAL  174 (248)
Q Consensus        95 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~  174 (248)
                      ++--++..|-+.|+++.|+..++...+.  .|+..-...+=...+...|.++.|..++++..+.+. ||...=.--....
T Consensus       373 t~y~laqh~D~~g~~~~A~~yId~AIdH--TPTliEly~~KaRI~kH~G~l~eAa~~l~ea~elD~-aDR~INsKcAKYm  449 (700)
T KOG1156|consen  373 TLYFLAQHYDKLGDYEVALEYIDLAIDH--TPTLIELYLVKARIFKHAGLLDEAAAWLDEAQELDT-ADRAINSKCAKYM  449 (700)
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHhcc--CchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhccc-hhHHHHHHHHHHH
Confidence            3445667777778888888777766543  355544443333335667777777777777666543 2333222344455


Q ss_pred             HhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhh-----hhhccccchHHHHHHH
Q 039342          175 WCLGLRERAARVLDEATKRGLFPELFRHNKLVWSV-----DVHRMWEGGAYTAISV  225 (248)
Q Consensus       175 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~-----~~~~~~~~g~~~~~~~  225 (248)
                      .+.++.++|.++.....+.|.  +...+-..+++.     .-.+|.+.|++..|.+
T Consensus       450 LrAn~i~eA~~~~skFTr~~~--~~~~~L~~mqcmWf~~E~g~ay~r~~k~g~ALK  503 (700)
T KOG1156|consen  450 LRANEIEEAEEVLSKFTREGF--GAVNNLAEMQCMWFQLEDGEAYLRQNKLGLALK  503 (700)
T ss_pred             HHccccHHHHHHHHHhhhccc--chhhhHHHhhhHHHhHhhhHHHHHHHHHHHHHH
Confidence            667778888888777777665  333333333222     2345555555544444

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.03  E-value=0.085  Score=39.64  Aligned_cols=186  Identities=16%  Similarity=0.105  Sum_probs=114.0

Q ss_pred             CchHHHHHHHHHHHH---cC-CCCCHH-hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhH
Q 039342            2 GLYKECQAILSRMSE---SG-VARNSD-SFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDE   76 (248)
Q Consensus         2 g~~~~a~~~~~~m~~---~g-~~~~~~-~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~   76 (248)
                      .+.++..+++.++..   .| ..++.. .|.-++-+....|+.+.|...++.+.+.= +-+...-..----+-..|++++
T Consensus        26 rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~f-p~S~RV~~lkam~lEa~~~~~~  104 (289)
T KOG3060|consen   26 RNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRF-PGSKRVGKLKAMLLEATGNYKE  104 (289)
T ss_pred             cCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhC-CCChhHHHHHHHHHHHhhchhh
Confidence            456777888877753   34 445543 45566666777788888888888886652 2222222222223345678888


Q ss_pred             HHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHH
Q 039342           77 SKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLN  156 (248)
Q Consensus        77 a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~  156 (248)
                      |.++++.+.+.. +.|.++|--=+...-..|+--+|++-+.+..+. +..|...|..+-.- |...+++++|...++++.
T Consensus       105 A~e~y~~lL~dd-pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~-F~~D~EAW~eLaei-Y~~~~~f~kA~fClEE~l  181 (289)
T KOG3060|consen  105 AIEYYESLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDK-FMNDQEAWHELAEI-YLSEGDFEKAAFCLEELL  181 (289)
T ss_pred             HHHHHHHHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHH-hcCcHHHHHHHHHH-HHhHhHHHHHHHHHHHHH
Confidence            888888888765 335666665555555666666777666666543 34556666666554 667788888888888877


Q ss_pred             hcCCCCCHHH-HHHHHHHHHh---cCchHHHHHHHHHHHHC
Q 039342          157 CEGYGLGMRF-YNALLEALWC---LGLRERAARVLDEATKR  193 (248)
Q Consensus       157 ~~~~~p~~~~-~~~li~~~~~---~g~~~~a~~~~~~m~~~  193 (248)
                      -.  .|.... |..+-..+--   ..+...+.++|.+..+.
T Consensus       182 l~--~P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alkl  220 (289)
T KOG3060|consen  182 LI--QPFNPLYFQRLAEVLYTQGGAENLELARKYYERALKL  220 (289)
T ss_pred             Hc--CCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHh
Confidence            64  343333 3333333322   33566777777776653

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

Probab=97.02  E-value=0.0056  Score=35.80  Aligned_cols=53  Identities=23%  Similarity=0.264  Sum_probs=24.6

Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHH
Q 039342           32 AFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIK   85 (248)
Q Consensus        32 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~   85 (248)
                      .+.+.|++++|.+.|++..+.. +-+...+..+-.++.+.|++++|...|++..
T Consensus         6 ~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~   58 (65)
T PF13432_consen    6 ALYQQGDYDEAIAAFEQALKQD-PDNPEAWYLLGRILYQQGRYDEALAYYERAL   58 (65)
T ss_dssp             HHHHCTHHHHHHHHHHHHHCCS-TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            3444455555555555554443 2233444444445555555555555555444

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.00  E-value=0.095  Score=39.69  Aligned_cols=147  Identities=10%  Similarity=-0.009  Sum_probs=105.0

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhc---
Q 039342           60 TLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIK---  136 (248)
Q Consensus        60 t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~---  136 (248)
                      .-++++..+.-.|.+.-...++.+.++..-+-++...+.+.+.--..|+.+.|...|++..+..-..+..+++.++.   
T Consensus       179 Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~  258 (366)
T KOG2796|consen  179 VMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNS  258 (366)
T ss_pred             HHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhh
Confidence            34566777777888888899999998876566788888888888899999999999998776554444444444332   


Q ss_pred             -ccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhh
Q 039342          137 -GEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSV  209 (248)
Q Consensus       137 -~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~  209 (248)
                       ..+.-..++..+...+.++...+.+ |+...|.=.-+..-.|+..+|.+.++.|.+.  .|...+.++++.++
T Consensus       259 a~i~lg~nn~a~a~r~~~~i~~~D~~-~~~a~NnKALcllYlg~l~DAiK~~e~~~~~--~P~~~l~es~~~nL  329 (366)
T KOG2796|consen  259 AFLHLGQNNFAEAHRFFTEILRMDPR-NAVANNNKALCLLYLGKLKDALKQLEAMVQQ--DPRHYLHESVLFNL  329 (366)
T ss_pred             hhheecccchHHHHHHHhhccccCCC-chhhhchHHHHHHHHHHHHHHHHHHHHHhcc--CCccchhhhHHHHH
Confidence             2244456677777778777766433 4444454444444568899999999999875  78777778777665

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=96.99  E-value=0.015  Score=40.49  Aligned_cols=91  Identities=9%  Similarity=-0.020  Sum_probs=68.1

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcC
Q 039342           99 LLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLG  178 (248)
Q Consensus        99 li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g  178 (248)
                      +-.-+...|++++|.++|+.+....  |....+..-+-.++...|++++|...|......++ -|...+-.+-.++...|
T Consensus        41 ~A~~ly~~G~l~~A~~~f~~L~~~D--p~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~-ddp~~~~~ag~c~L~lG  117 (157)
T PRK15363         41 YAMQLMEVKEFAGAARLFQLLTIYD--AWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKI-DAPQAPWAAAECYLACD  117 (157)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC--cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCchHHHHHHHHHHHcC
Confidence            3334456788888888888776554  66666666666667778888888888888777764 36777888888899999


Q ss_pred             chHHHHHHHHHHHH
Q 039342          179 LRERAARVLDEATK  192 (248)
Q Consensus       179 ~~~~a~~~~~~m~~  192 (248)
                      +.+.|.+-|+....
T Consensus       118 ~~~~A~~aF~~Ai~  131 (157)
T PRK15363        118 NVCYAIKALKAVVR  131 (157)
T ss_pred             CHHHHHHHHHHHHH
Confidence            99999999987654

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=96.97  E-value=0.026  Score=48.63  Aligned_cols=101  Identities=17%  Similarity=0.293  Sum_probs=53.0

Q ss_pred             chHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHH
Q 039342            3 LYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQ   82 (248)
Q Consensus         3 ~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~   82 (248)
                      .|.+|+.+++.+.....  -..-|.-+-..|+..|+++.|.++|-+-         ..++-.|.+|.+.|+|+.|.++-+
T Consensus       747 ew~kai~ildniqdqk~--~s~yy~~iadhyan~~dfe~ae~lf~e~---------~~~~dai~my~k~~kw~da~kla~  815 (1636)
T KOG3616|consen  747 EWKKAISILDNIQDQKT--ASGYYGEIADHYANKGDFEIAEELFTEA---------DLFKDAIDMYGKAGKWEDAFKLAE  815 (1636)
T ss_pred             hhhhhHhHHHHhhhhcc--ccccchHHHHHhccchhHHHHHHHHHhc---------chhHHHHHHHhccccHHHHHHHHH
Confidence            45556666665554321  2233555556666667777666666542         124556667777777776666654


Q ss_pred             HHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHH
Q 039342           83 EIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLL  116 (248)
Q Consensus        83 ~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~  116 (248)
                      +..  |...+...|-+-..-+-++|++.+|.++|
T Consensus       816 e~~--~~e~t~~~yiakaedldehgkf~eaeqly  847 (1636)
T KOG3616|consen  816 ECH--GPEATISLYIAKAEDLDEHGKFAEAEQLY  847 (1636)
T ss_pred             Hhc--CchhHHHHHHHhHHhHHhhcchhhhhhee
Confidence            433  22223444444444444445444444443

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

Probab=96.97  E-value=0.0065  Score=35.50  Aligned_cols=59  Identities=14%  Similarity=0.188  Sum_probs=47.3

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           64 VLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        64 ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      +-..+.+.|++++|.+.|++..+.. +-+...+..+-..+...|++++|...|++..+..
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~   61 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQALKQD-PDNPEAWYLLGRILYQQGRYDEALAYYERALELD   61 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHHHCCS-TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence            3456788999999999999998775 2267788888899999999999999999887543

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=96.96  E-value=0.12  Score=40.35  Aligned_cols=155  Identities=16%  Similarity=0.192  Sum_probs=100.7

Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh--c----CChhHHHHHHHHHHHCCC---CcCHhhHHHHHHHHHhcCC-
Q 039342           39 FEEAIKAYVEMEKVRCDPNERTLEAVLSVYCF--A----GLVDESKEQFQEIKSSGI---LPSVMCYCMLLAVYAKSNR-  108 (248)
Q Consensus        39 ~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~--~----g~~~~a~~~~~~m~~~~~---~p~~~~~~~li~~~~~~~~-  108 (248)
                      +++...+++.|.+.|++-+..+|-+.......  .    ....+|.++|+.|++.-.   .++..++..++..  ...+ 
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--~~~~~  155 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--TSEDV  155 (297)
T ss_pred             HHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc--ccccH
Confidence            56678889999999999998888664443333  2    247789999999997632   2456677777665  3333 


Q ss_pred             ---HHHHHHHHHHHHHCCCCchHH--hHHHHhcccccccc--hHHHHHHHHHHHHhcCCCCCHHHHHHHHHHH-HhcCc-
Q 039342          109 ---WDDAYGLLDEMHTNRISNIHQ--VTGQMIKGEFDDES--NWQMVEYVFDKLNCEGYGLGMRFYNALLEAL-WCLGL-  179 (248)
Q Consensus       109 ---~~~a~~~~~~m~~~~~~~~~~--~~~~~l~~~~~~~~--~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~-~~~g~-  179 (248)
                         .+.++.+|+.+.+.|......  ....++.- .....  ....+..+++.+++.|+++....|..+--.. ...+. 
T Consensus       156 e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL-~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~lGlLall~~~~~  234 (297)
T PF13170_consen  156 EELAERMEQCYQKLADAGFKKGNDLQFLSHILAL-SEGDDQEKVARVIELYNALKKNGVKIKYMHYPTLGLLALLEDPEE  234 (297)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHh-ccccchHHHHHHHHHHHHHHHcCCccccccccHHHHHHhcCCchH
Confidence               467888899999888776554  23333322 22222  2568888999999999998888877554333 33333 


Q ss_pred             --hHHHHHHHHHHHH-CCCC
Q 039342          180 --RERAARVLDEATK-RGLF  196 (248)
Q Consensus       180 --~~~a~~~~~~m~~-~g~~  196 (248)
                        .+...++.+.+.+ .|+.
T Consensus       235 ~~~~~i~ev~~~L~~~k~~~  254 (297)
T PF13170_consen  235 KIVEEIKEVIDELKEQKGFG  254 (297)
T ss_pred             HHHHHHHHHHHHHhhCcccC
Confidence              4455555555554 3433

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=96.94  E-value=0.059  Score=45.64  Aligned_cols=59  Identities=19%  Similarity=0.116  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHH
Q 039342           59 RTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEM  119 (248)
Q Consensus        59 ~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m  119 (248)
                      ..|..+--.+...|++++|...+++..+.+  |+...|..+-..+...|+.++|.+.+++.
T Consensus       421 ~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A  479 (517)
T PRK10153        421 RIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTA  479 (517)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            334333333333444444444444444432  34444444444444444444444444443

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

Probab=96.93  E-value=0.19  Score=42.09  Aligned_cols=199  Identities=15%  Similarity=0.129  Sum_probs=142.6

Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHH
Q 039342           33 FRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILP-SVMCYCMLLAVYAKSNRWDD  111 (248)
Q Consensus        33 ~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~  111 (248)
                      +.+.|+..+|.-.|+...+.+ +-+...|.-|-......++-..|...+.+-.+.  .| +....-.|--.|...|.-..
T Consensus       295 lm~nG~L~~A~LafEAAVkqd-P~haeAW~~LG~~qaENE~E~~ai~AL~rcl~L--dP~NleaLmaLAVSytNeg~q~~  371 (579)
T KOG1125|consen  295 LMKNGDLSEAALAFEAAVKQD-PQHAEAWQKLGITQAENENEQNAISALRRCLEL--DPTNLEALMALAVSYTNEGLQNQ  371 (579)
T ss_pred             HHhcCCchHHHHHHHHHHhhC-hHHHHHHHHhhhHhhhccchHHHHHHHHHHHhc--CCccHHHHHHHHHHHhhhhhHHH
Confidence            457888999988888887664 446688888888888999989999998888775  45 66788888899999999999


Q ss_pred             HHHHHHHHHHCCCCchHHhHH---HHh---cccccccchHHHHHHHHHHHH-hcCCCCCHHHHHHHHHHHHhcCchHHHH
Q 039342          112 AYGLLDEMHTNRISNIHQVTG---QMI---KGEFDDESNWQMVEYVFDKLN-CEGYGLGMRFYNALLEALWCLGLRERAA  184 (248)
Q Consensus       112 a~~~~~~m~~~~~~~~~~~~~---~~l---~~~~~~~~~~~~a~~~~~~m~-~~~~~p~~~~~~~li~~~~~~g~~~~a~  184 (248)
                      |++.|+.-.....+--.....   ...   .+ +........+.++|-++. +.+..+|..+...|--.|--.|++++|.
T Consensus       372 Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~~~s-~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdrai  450 (579)
T KOG1125|consen  372 ALKMLDKWIRNKPKYVHLVSAGENEDFENTKS-FLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAV  450 (579)
T ss_pred             HHHHHHHHHHhCccchhccccCccccccCCcC-CCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHH
Confidence            999998875443110000000   000   11 233334455555555554 4465678888888888888899999999


Q ss_pred             HHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHHHcCCCCCcc
Q 039342          185 RVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMGEDLPQL  243 (248)
Q Consensus       185 ~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~~~~~~~~~~  243 (248)
                      +.|+....  ++|+    +.++|+-+-..++...+-++|...+++-.+.  +|+.+-..
T Consensus       451 Dcf~~AL~--v~Pn----d~~lWNRLGAtLAN~~~s~EAIsAY~rALqL--qP~yVR~R  501 (579)
T KOG1125|consen  451 DCFEAALQ--VKPN----DYLLWNRLGATLANGNRSEEAISAYNRALQL--QPGYVRVR  501 (579)
T ss_pred             HHHHHHHh--cCCc----hHHHHHHhhHHhcCCcccHHHHHHHHHHHhc--CCCeeeee
Confidence            99999876  4787    6777777778888988999988888776554  66554433

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

Probab=96.93  E-value=0.21  Score=42.50  Aligned_cols=200  Identities=14%  Similarity=0.068  Sum_probs=125.4

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |+-++|.+..+.-....+ .+.++|..+--.+....++++|.+.|......+ +-|...|.-+--.=++.|+++......
T Consensus        55 g~~~ea~~~vr~glr~d~-~S~vCwHv~gl~~R~dK~Y~eaiKcy~nAl~~~-~dN~qilrDlslLQ~QmRd~~~~~~tr  132 (700)
T KOG1156|consen   55 GKKEEAYELVRLGLRNDL-KSHVCWHVLGLLQRSDKKYDEAIKCYRNALKIE-KDNLQILRDLSLLQIQMRDYEGYLETR  132 (700)
T ss_pred             cchHHHHHHHHHHhccCc-ccchhHHHHHHHHhhhhhHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHHHhhhhHHHHH
Confidence            556677776666555443 356777777777777788888988888876654 345566766655566777777777777


Q ss_pred             HHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCC-CchHHhHHHHhccc-----ccccchHHHHHHHHHH
Q 039342           82 QEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRI-SNIHQVTGQMIKGE-----FDDESNWQMVEYVFDK  154 (248)
Q Consensus        82 ~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~~~~~~~~~~l~~~-----~~~~~~~~~a~~~~~~  154 (248)
                      .++.+.  .| ....|....-++.-.|+...|..++++..+... .|+...+.....-.     ....|..+.+.+.+..
T Consensus       133 ~~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  133 NQLLQL--RPSQRASWIGFAVAQHLLGEYKMALEILEEFEKTQNTSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLD  210 (700)
T ss_pred             HHHHHh--hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHh
Confidence            777664  33 446688888888888999999999988876552 34444443221111     2234445555554443


Q ss_pred             HHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhh
Q 039342          155 LNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWS  208 (248)
Q Consensus       155 m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~  208 (248)
                      -... +.-....-.+-...+.+.+++++|..++..+...  .||-.-|...+..
T Consensus       211 ~e~~-i~Dkla~~e~ka~l~~kl~~lEeA~~~y~~Ll~r--nPdn~~Yy~~l~~  261 (700)
T KOG1156|consen  211 NEKQ-IVDKLAFEETKADLLMKLGQLEEAVKVYRRLLER--NPDNLDYYEGLEK  261 (700)
T ss_pred             hhhH-HHHHHHHhhhHHHHHHHHhhHHhHHHHHHHHHhh--CchhHHHHHHHHH
Confidence            2221 1111222234455677788888888888887765  5766666655543

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

Probab=96.92  E-value=0.22  Score=42.56  Aligned_cols=221  Identities=11%  Similarity=0.083  Sum_probs=132.2

Q ss_pred             CchHHHHHHHHHHHHcCCCC------CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHHHhcC
Q 039342            2 GLYKECQAILSRMSESGVAR------NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN---ERTLEAVLSVYCFAG   72 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~------~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~---~~t~~~ll~~~~~~g   72 (248)
                      |+..+-...+.+..+. +.|      -...|..+-..|-..|+.+.|..+|++..+...+-=   ..+|..--..=.+..
T Consensus       361 ~~~~~~i~tyteAv~~-vdP~ka~Gs~~~Lw~~faklYe~~~~l~~aRvifeka~~V~y~~v~dLa~vw~~waemElrh~  439 (835)
T KOG2047|consen  361 GNAAEQINTYTEAVKT-VDPKKAVGSPGTLWVEFAKLYENNGDLDDARVIFEKATKVPYKTVEDLAEVWCAWAEMELRHE  439 (835)
T ss_pred             CChHHHHHHHHHHHHc-cCcccCCCChhhHHHHHHHHHHhcCcHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHhhh
Confidence            3444555556655432 222      124677888888889999999999998876554322   344444445555666


Q ss_pred             ChhHHHHHHHHHHHCC-----------CC------cCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHh
Q 039342           73 LVDESKEQFQEIKSSG-----------IL------PSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMI  135 (248)
Q Consensus        73 ~~~~a~~~~~~m~~~~-----------~~------p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l  135 (248)
                      +++.|.++.+......           .+      -+...|+..++---..|-++....+++++.+-.+.......|..+
T Consensus       440 ~~~~Al~lm~~A~~vP~~~~~~~yd~~~pvQ~rlhrSlkiWs~y~DleEs~gtfestk~vYdriidLriaTPqii~NyAm  519 (835)
T KOG2047|consen  440 NFEAALKLMRRATHVPTNPELEYYDNSEPVQARLHRSLKIWSMYADLEESLGTFESTKAVYDRIIDLRIATPQIIINYAM  519 (835)
T ss_pred             hHHHHHHHHHhhhcCCCchhhhhhcCCCcHHHHHHHhHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence            7888877766554211           11      123345555555556678888888888888877665555554433


Q ss_pred             cccccccchHHHHHHHHHHHHhcCCCCC-HHHHHHHHHHHHh---cCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhh
Q 039342          136 KGEFDDESNWQMVEYVFDKLNCEGYGLG-MRFYNALLEALWC---LGLRERAARVLDEATKRGLFPELFRHNKLVWSVDV  211 (248)
Q Consensus       136 ~~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~---~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~  211 (248)
                      -  +..+..++.+.++++.=...=--|+ ...|+.-+.-+.+   ...++.|..+|++..+ |++|...-+--|+++-+-
T Consensus       520 f--LEeh~yfeesFk~YErgI~LFk~p~v~diW~tYLtkfi~rygg~klEraRdLFEqaL~-~Cpp~~aKtiyLlYA~lE  596 (835)
T KOG2047|consen  520 F--LEEHKYFEESFKAYERGISLFKWPNVYDIWNTYLTKFIKRYGGTKLERARDLFEQALD-GCPPEHAKTIYLLYAKLE  596 (835)
T ss_pred             H--HHhhHHHHHHHHHHHcCCccCCCccHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHh-cCCHHHHHHHHHHHHHHH
Confidence            2  4456667788877765333211133 3345555555444   2368899999999887 788876555555555432


Q ss_pred             hccccchHHHHHHHHHHH
Q 039342          212 HRMWEGGAYTAISVWLNK  229 (248)
Q Consensus       212 ~~~~~~g~~~~~~~~~~~  229 (248)
                      .   +.|....+..++++
T Consensus       597 E---e~GLar~amsiyer  611 (835)
T KOG2047|consen  597 E---EHGLARHAMSIYER  611 (835)
T ss_pred             H---HhhHHHHHHHHHHH
Confidence            2   23555555555544

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

Probab=96.90  E-value=0.011  Score=40.90  Aligned_cols=58  Identities=9%  Similarity=0.168  Sum_probs=25.2

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHH-hHHHHhcccccccchHHHHHHHHHHH
Q 039342           95 CYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQ-VTGQMIKGEFDDESNWQMVEYVFDKL  155 (248)
Q Consensus        95 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~m  155 (248)
                      +...++..+...|++++|....+.+....  |... .+..++.. +...|+...|.+.|+.+
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~d--P~~E~~~~~lm~~-~~~~g~~~~A~~~Y~~~  122 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALD--PYDEEAYRLLMRA-LAAQGRRAEALRVYERY  122 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHS--TT-HHHHHHHHHH-HHHTT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcC--CCCHHHHHHHHHH-HHHCcCHHHHHHHHHHH
Confidence            34444444555555555555555554433  3322 33333333 44444455555555443

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

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=96.89  E-value=0.13  Score=43.61  Aligned_cols=143  Identities=12%  Similarity=-0.019  Sum_probs=89.7

Q ss_pred             CCCCCHHHHHHHHHHHHhcC-----ChhHHHHHHHHHHHCCCCcC-HhhHHHHHHHHHhc--------CCHHHHHHHHHH
Q 039342           53 RCDPNERTLEAVLSVYCFAG-----LVDESKEQFQEIKSSGILPS-VMCYCMLLAVYAKS--------NRWDDAYGLLDE  118 (248)
Q Consensus        53 ~~~p~~~t~~~ll~~~~~~g-----~~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~--------~~~~~a~~~~~~  118 (248)
                      +.+.|...|...+.+.....     ..+.|.++|++..+.  .|+ ...|..+..++...        .++..+.+...+
T Consensus       332 ~~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~l--dP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~  409 (517)
T PRK10153        332 GLPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKS--EPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDN  409 (517)
T ss_pred             cCCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHH
Confidence            45677788888888765433     366888888888765  453 34444443333222        123344444444


Q ss_pred             HHHCCCCc-hHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCC
Q 039342          119 MHTNRISN-IHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFP  197 (248)
Q Consensus       119 m~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  197 (248)
                      .......| +...+..+-.. ....|+++.|...+++..+.+  |+...|..+-..+...|+.++|.+.+.+..+  +.|
T Consensus       410 a~al~~~~~~~~~~~ala~~-~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~--L~P  484 (517)
T PRK10153        410 IVALPELNVLPRIYEILAVQ-ALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTAFN--LRP  484 (517)
T ss_pred             hhhcccCcCChHHHHHHHHH-HHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh--cCC
Confidence            33321122 22333322111 334688999999999988876  6788999999999999999999999998765  356


Q ss_pred             Ccchh
Q 039342          198 ELFRH  202 (248)
Q Consensus       198 ~~~t~  202 (248)
                      ...||
T Consensus       485 ~~pt~  489 (517)
T PRK10153        485 GENTL  489 (517)
T ss_pred             CCchH
Confidence            55553

>PLN02789 farnesyltranstransferase

Probab=96.83  E-value=0.17  Score=40.08  Aligned_cols=140  Identities=6%  Similarity=-0.019  Sum_probs=58.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHhcC-ChhHHHHHHHHHHHCCCCcCHhhHHHHHHHH
Q 039342           26 FNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNE-RTLEAVLSVYCFAG-LVDESKEQFQEIKSSGILPSVMCYCMLLAVY  103 (248)
Q Consensus        26 y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~t~~~ll~~~~~~g-~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~  103 (248)
                      ++.+-..+...++.++|+.+.++..+..  |+. ..|+.--.++.+.| +++++...++++.+.... +..+|+.--..+
T Consensus        40 ~~~~ra~l~~~e~serAL~lt~~aI~ln--P~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~npk-nyqaW~~R~~~l  116 (320)
T PLN02789         40 MDYFRAVYASDERSPRALDLTADVIRLN--PGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDNPK-NYQIWHHRRWLA  116 (320)
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHHHHHHC--chhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCCc-chHHhHHHHHHH
Confidence            3333344444455556666655554432  222 23333323333334 345556655555543211 223344333333


Q ss_pred             HhcCC--HHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHH
Q 039342          104 AKSNR--WDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALL  171 (248)
Q Consensus       104 ~~~~~--~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li  171 (248)
                      .+.|+  .++++.+++++.+..  |.......-....+...+.++.+.+.++.+.+.+.. +...|+...
T Consensus       117 ~~l~~~~~~~el~~~~kal~~d--pkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~-N~sAW~~R~  183 (320)
T PLN02789        117 EKLGPDAANKELEFTRKILSLD--AKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVR-NNSAWNQRY  183 (320)
T ss_pred             HHcCchhhHHHHHHHHHHHHhC--cccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCC-chhHHHHHH
Confidence            33333  244555555555443  222111111111123334455666666665555444 334444333

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=96.82  E-value=0.064  Score=35.77  Aligned_cols=88  Identities=24%  Similarity=0.132  Sum_probs=53.0

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCCCH--HHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcC----HhhHHHHHHHHH
Q 039342           31 EAFRQGGRFEEAIKAYVEMEKVRCDPNE--RTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPS----VMCYCMLLAVYA  104 (248)
Q Consensus        31 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~--~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~----~~~~~~li~~~~  104 (248)
                      .++-..|+.++|..+|++....|.....  ..+-.+-+.+...|++++|..++++.....  |+    ......+-.++.
T Consensus         9 ~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~--p~~~~~~~l~~f~Al~L~   86 (120)
T PF12688_consen    9 WAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEF--PDDELNAALRVFLALALY   86 (120)
T ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCccccHHHHHHHHHHHH
Confidence            3455567777777777777777765442  344445566777777777777777766531  22    112222233556


Q ss_pred             hcCCHHHHHHHHHHHH
Q 039342          105 KSNRWDDAYGLLDEMH  120 (248)
Q Consensus       105 ~~~~~~~a~~~~~~m~  120 (248)
                      ..|+.++|++.+-...
T Consensus        87 ~~gr~~eAl~~~l~~l  102 (120)
T PF12688_consen   87 NLGRPKEALEWLLEAL  102 (120)
T ss_pred             HCCCHHHHHHHHHHHH
Confidence            6677777777665543

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

Probab=96.82  E-value=0.12  Score=40.25  Aligned_cols=169  Identities=11%  Similarity=0.189  Sum_probs=101.8

Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHH----CCCCc-CH
Q 039342           24 DSFNAVIEAFRQGGRFEEAIKAYVEMEKV----RCDP-NERTLEAVLSVYCFAGLVDESKEQFQEIKS----SGILP-SV   93 (248)
Q Consensus        24 ~~y~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p-~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~----~~~~p-~~   93 (248)
                      ..|.-.-..|...+++++|.+.|.+..+.    +-+. -...|.....+|.+. ++++|.+.+++..+    .|-.. -.
T Consensus        36 ~~y~~Aa~~fk~~~~~~~A~~ay~kAa~~~~~~~~~~~Aa~~~~~Aa~~~k~~-~~~~Ai~~~~~A~~~y~~~G~~~~aA  114 (282)
T PF14938_consen   36 DLYEKAANCFKLAKDWEKAAEAYEKAADCYEKLGDKFEAAKAYEEAANCYKKG-DPDEAIECYEKAIEIYREAGRFSQAA  114 (282)
T ss_dssp             HHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHCT-HHHHH
T ss_pred             HHHHHHHHHHHHHhccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhh-CHHHHHHHHHHHHHHHHhcCcHHHHH
Confidence            46777777888889999998888876322    2111 123444445555444 88888888877653    34221 23


Q ss_pred             hhHHHHHHHHHhc-CCHHHHHHHHHHHHH----CCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCC-----CCC
Q 039342           94 MCYCMLLAVYAKS-NRWDDAYGLLDEMHT----NRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGY-----GLG  163 (248)
Q Consensus        94 ~~~~~li~~~~~~-~~~~~a~~~~~~m~~----~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~-----~p~  163 (248)
                      .++..+-..|-.. |+++.|++.|++-.+    .+.+....-+..-+...+...++++.|..+|++......     +++
T Consensus       115 ~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~  194 (282)
T PF14938_consen  115 KCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYS  194 (282)
T ss_dssp             HHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchh
Confidence            5677777788888 899999999887643    342222222222222336677899999999998876532     222


Q ss_pred             HH-HHHHHHHHHHhcCchHHHHHHHHHHHHC
Q 039342          164 MR-FYNALLEALWCLGLRERAARVLDEATKR  193 (248)
Q Consensus       164 ~~-~~~~li~~~~~~g~~~~a~~~~~~m~~~  193 (248)
                      .. .|-..+-++...|+...|.+.+++....
T Consensus       195 ~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~  225 (282)
T PF14938_consen  195 AKEYFLKAILCHLAMGDYVAARKALERYCSQ  225 (282)
T ss_dssp             HHHHHHHHHHHHHHTT-HHHHHHHHHHHGTT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            22 2333444666678999999999987653

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.77  E-value=0.19  Score=39.79  Aligned_cols=125  Identities=16%  Similarity=0.193  Sum_probs=57.5

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHH-HHHHHHHhcCC
Q 039342           30 IEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYC-MLLAVYAKSNR  108 (248)
Q Consensus        30 i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~-~li~~~~~~~~  108 (248)
                      -+.+.-.-++++++-.++..+.-=..-|...| .+..+++..|.+.+|+++|-+.....++ |..+|- .|.++|.+++.
T Consensus       366 As~fFL~~qFddVl~YlnSi~sYF~NdD~Fn~-N~AQAk~atgny~eaEelf~~is~~~ik-n~~~Y~s~LArCyi~nkk  443 (557)
T KOG3785|consen  366 ASYFFLSFQFDDVLTYLNSIESYFTNDDDFNL-NLAQAKLATGNYVEAEELFIRISGPEIK-NKILYKSMLARCYIRNKK  443 (557)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCcchhhh-HHHHHHHHhcChHHHHHHHhhhcChhhh-hhHHHHHHHHHHHHhcCC
Confidence            33333344455555555554433222222222 3455556666666666666554433333 333443 33445556666


Q ss_pred             HHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcC
Q 039342          109 WDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEG  159 (248)
Q Consensus       109 ~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~  159 (248)
                      ++.|+.++-.+   ..+....+.-.+|..-|-..+.+--+.+.|+.+...+
T Consensus       444 P~lAW~~~lk~---~t~~e~fsLLqlIAn~CYk~~eFyyaaKAFd~lE~lD  491 (557)
T KOG3785|consen  444 PQLAWDMMLKT---NTPSERFSLLQLIANDCYKANEFYYAAKAFDELEILD  491 (557)
T ss_pred             chHHHHHHHhc---CCchhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHccC
Confidence            66665555433   2222333333444433444444444555555554443

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=96.74  E-value=0.084  Score=35.22  Aligned_cols=98  Identities=18%  Similarity=0.213  Sum_probs=71.8

Q ss_pred             CchHHHHHHHHHHHHcCCCCC--HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC----HHHHHHHHHHHHhcCChh
Q 039342            2 GLYKECQAILSRMSESGVARN--SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN----ERTLEAVLSVYCFAGLVD   75 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~--~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~----~~t~~~ll~~~~~~g~~~   75 (248)
                      |+.++|..+|++..+.|....  ...+-.+-+.+...|++++|..++++.....  |+    ......+-.++...|+.+
T Consensus        15 G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~--p~~~~~~~l~~f~Al~L~~~gr~~   92 (120)
T PF12688_consen   15 GREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEF--PDDELNAALRVFLALALYNLGRPK   92 (120)
T ss_pred             CCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCccccHHHHHHHHHHHHHCCCHH
Confidence            889999999999999887544  3466667788899999999999999987652  43    222223345678889999


Q ss_pred             HHHHHHHHHHHCCCCcCHhhHHHHHHHHHh
Q 039342           76 ESKEQFQEIKSSGILPSVMCYCMLLAVYAK  105 (248)
Q Consensus        76 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~  105 (248)
                      +|.+.+-....    ++..-|.--|..|+.
T Consensus        93 eAl~~~l~~la----~~~~~y~ra~~~ya~  118 (120)
T PF12688_consen   93 EALEWLLEALA----ETLPRYRRAIRFYAD  118 (120)
T ss_pred             HHHHHHHHHHH----HHHHHHHHHHHHHHh
Confidence            99998866553    344466666666653

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=96.73  E-value=0.38  Score=42.55  Aligned_cols=187  Identities=11%  Similarity=0.127  Sum_probs=128.8

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |+.++|..+++.....+.. |..|...+-..|...++.++|..+|++....  .|+..-...+..+|.|.+.+.+-.++-
T Consensus        57 gk~~ea~~~Le~~~~~~~~-D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~~--~P~eell~~lFmayvR~~~yk~qQkaa  133 (932)
T KOG2053|consen   57 GKGDEALKLLEALYGLKGT-DDLTLQFLQNVYRDLGKLDEAVHLYERANQK--YPSEELLYHLFMAYVREKSYKKQQKAA  133 (932)
T ss_pred             cCchhHHHHHhhhccCCCC-chHHHHHHHHHHHHHhhhhHHHHHHHHHHhh--CCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            7788999888888766554 8899999999999999999999999998654  688888888999999999888777666


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcC----------CHHHHHHHHHHHHHCCCC--chHHhHHHHhcccccccchHHHHH
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSN----------RWDDAYGLLDEMHTNRIS--NIHQVTGQMIKGEFDDESNWQMVE  149 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~----------~~~~a~~~~~~m~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~  149 (248)
                      =+|-+. ++-+...|=++++.....-          -+.-|.+.++.+.+.+-+  ......-.+..  ....+.+++|.
T Consensus       134 ~~LyK~-~pk~~yyfWsV~Slilqs~~~~~~~~~~i~l~LA~~m~~~~l~~~gk~~s~aE~~Lyl~i--L~~~~k~~eal  210 (932)
T KOG2053|consen  134 LQLYKN-FPKRAYYFWSVISLILQSIFSENELLDPILLALAEKMVQKLLEKKGKIESEAEIILYLLI--LELQGKYQEAL  210 (932)
T ss_pred             HHHHHh-CCcccchHHHHHHHHHHhccCCcccccchhHHHHHHHHHHHhccCCccchHHHHHHHHHH--HHhcccHHHHH
Confidence            555543 2224444445555444321          133466777777665511  11111111111  34566789999


Q ss_pred             HHH-HHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCC
Q 039342          150 YVF-DKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRG  194 (248)
Q Consensus       150 ~~~-~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  194 (248)
                      .++ ....+.-...+...-+--+..+...++|++..++-.++..+|
T Consensus       211 ~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l~~~Ll~k~  256 (932)
T KOG2053|consen  211 EFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFELSSRLLEKG  256 (932)
T ss_pred             HHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHHHHHHHHhC
Confidence            888 444444444455666677788888999999998888888765

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

Probab=96.71  E-value=0.018  Score=34.05  Aligned_cols=60  Identities=17%  Similarity=0.201  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcC-CHHHHHHHHHHH
Q 039342           59 RTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSN-RWDDAYGLLDEM  119 (248)
Q Consensus        59 ~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~-~~~~a~~~~~~m  119 (248)
                      .+|..+-..+.+.|++++|...|++..+.. +-+...|..+-.+|.+.| ++++|++.+++.
T Consensus         4 ~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~a   64 (69)
T PF13414_consen    4 EAWYNLGQIYFQQGDYEEAIEYFEKAIELD-PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKA   64 (69)
T ss_dssp             HHHHHHHHHHHHTTHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhCccHHHHHHHHHHH
Confidence            344444445555555555555555544432 113344444444555554 355555555443

...

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=96.64  E-value=0.19  Score=38.13  Aligned_cols=165  Identities=11%  Similarity=-0.005  Sum_probs=96.4

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCH-hhH---HHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHh
Q 039342           60 TLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSV-MCY---CMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMI  135 (248)
Q Consensus        60 t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~-~~~---~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l  135 (248)
                      .|. ....+.+.|++++|.+.|+.+...-  |+. ...   -.+..++.+.++.++|...+++..+..-.-...-+...+
T Consensus        35 ~Y~-~A~~~~~~g~y~~Ai~~f~~l~~~y--P~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~  111 (243)
T PRK10866         35 IYA-TAQQKLQDGNWKQAITQLEALDNRY--PFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLYM  111 (243)
T ss_pred             HHH-HHHHHHHCCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHHH
Confidence            444 4455567899999999999998752  332 222   345677889999999999999997654221111221222


Q ss_pred             cccc-------------------cccchHHHHHHHHHHHHhcC----CCCCHHHHH------------HHHHHHHhcCch
Q 039342          136 KGEF-------------------DDESNWQMVEYVFDKLNCEG----YGLGMRFYN------------ALLEALWCLGLR  180 (248)
Q Consensus       136 ~~~~-------------------~~~~~~~~a~~~~~~m~~~~----~~p~~~~~~------------~li~~~~~~g~~  180 (248)
                      .+.+                   ........|...|+.+.+.=    ..|+....-            .+.+-|.+.|.+
T Consensus       112 ~g~~~~~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~~yP~S~ya~~A~~rl~~l~~~la~~e~~ia~~Y~~~~~y  191 (243)
T PRK10866        112 RGLTNMALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYELSVAEYYTKRGAY  191 (243)
T ss_pred             HHHhhhhcchhhhhhccCCCccccCHHHHHHHHHHHHHHHHHCcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCch
Confidence            2211                   01112344555666655541    122222211            233457888999


Q ss_pred             HHHHHHHHHHHHCCCCCCcc-hhhhHHhhhhhhccccchHHHHHHHHHHHHH
Q 039342          181 ERAARVLDEATKRGLFPELF-RHNKLVWSVDVHRMWEGGAYTAISVWLNKMY  231 (248)
Q Consensus       181 ~~a~~~~~~m~~~g~~p~~~-t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~  231 (248)
                      ..|..-++.+.+.  -|+.. +...|.  .+..+|...|..+++..+...+.
T Consensus       192 ~AA~~r~~~v~~~--Yp~t~~~~eal~--~l~~ay~~lg~~~~a~~~~~~l~  239 (243)
T PRK10866        192 VAVVNRVEQMLRD--YPDTQATRDALP--LMENAYRQLQLNAQADKVAKIIA  239 (243)
T ss_pred             HHHHHHHHHHHHH--CCCCchHHHHHH--HHHHHHHHcCChHHHHHHHHHHh
Confidence            9899888888864  33322 222222  23377888888888777666553

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

Probab=96.63  E-value=0.018  Score=34.04  Aligned_cols=64  Identities=20%  Similarity=0.296  Sum_probs=52.6

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC-ChhHHHHHHHHHHH
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAG-LVDESKEQFQEIKS   86 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g-~~~~a~~~~~~m~~   86 (248)
                      ++..|..+-..+.+.|++++|+..|++..+.+ +-+...|..+-.+|.+.| ++++|.+.+++..+
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~   66 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELD-PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALK   66 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence            46778888888999999999999999987764 346677888888888888 69999999888765

...

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

Probab=96.61  E-value=0.29  Score=39.63  Aligned_cols=135  Identities=16%  Similarity=0.081  Sum_probs=92.1

Q ss_pred             HHHHhcCChhHHHHHHHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHH-hcccccccc
Q 039342           66 SVYCFAGLVDESKEQFQEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQM-IKGEFDDES  143 (248)
Q Consensus        66 ~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~-l~~~~~~~~  143 (248)
                      ..+...++++.|.-.|+..+..  .| +..+|.-|+.+|...|++.+|..+-+.-... ...+..+...+ -..++....
T Consensus       342 ~lL~~~~R~~~A~IaFR~Aq~L--ap~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~-~~~sA~~LtL~g~~V~~~dp~  418 (564)
T KOG1174|consen  342 RLLIALERHTQAVIAFRTAQML--APYRLEIYRGLFHSYLAQKRFKEANALANWTIRL-FQNSARSLTLFGTLVLFPDPR  418 (564)
T ss_pred             HHHHhccchHHHHHHHHHHHhc--chhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHH-hhcchhhhhhhcceeeccCch
Confidence            3566788999999999887654  44 6789999999999999999987766543321 11122222222 112233444


Q ss_pred             hHHHHHHHHHHHHhcCCCCC-HHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHh
Q 039342          144 NWQMVEYVFDKLNCEGYGLG-MRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVW  207 (248)
Q Consensus       144 ~~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~  207 (248)
                      .-++|..+++.-..  +.|+ ....+.+...+...|..+++..+++.-...  .||...++.|-.
T Consensus       419 ~rEKAKkf~ek~L~--~~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~--~~D~~LH~~Lgd  479 (564)
T KOG1174|consen  419 MREKAKKFAEKSLK--INPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLII--FPDVNLHNHLGD  479 (564)
T ss_pred             hHHHHHHHHHhhhc--cCCccHHHHHHHHHHHHhhCccchHHHHHHHHHhh--ccccHHHHHHHH
Confidence            45888888876544  3343 455667777888899999999999986653  788888777763

>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=96.58  E-value=0.24  Score=38.46  Aligned_cols=224  Identities=13%  Similarity=0.140  Sum_probs=127.3

Q ss_pred             CchHHHHHHHHHHHHcC--CCCCH------HhHHHHHHHHHhcCCHHHHHHHHHHHHHc--------CCCCCH-----HH
Q 039342            2 GLYKECQAILSRMSESG--VARNS------DSFNAVIEAFRQGGRFEEAIKAYVEMEKV--------RCDPNE-----RT   60 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g--~~~~~------~~y~~li~~~~~~~~~~~a~~~~~~m~~~--------~~~p~~-----~t   60 (248)
                      ||.+.|..++.+.+..-  ..|+.      ..||.-...+.+..+++.|...+++..+-        ...|+.     .+
T Consensus         7 ~~~~~A~~~~~K~~~~~~~~~~~~~~~La~~~yn~G~~l~~~~~~~~~a~~wL~~a~~~l~~~~~~~~~~~~~~elr~~i   86 (278)
T PF08631_consen    7 GDLDLAEHMYSKAKDLLNSLDPDMAEELARVCYNIGKSLLSKKDKYEEAVKWLQRAYDILEKPGKMDKLSPDGSELRLSI   86 (278)
T ss_pred             CCHHHHHHHHHHhhhHHhcCCcHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhhhccccCCcHHHHHHHH
Confidence            89999999999987543  23332      35666666666664777776666554221        233333     56


Q ss_pred             HHHHHHHHHhcCChh---HHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCc--hHHhHHHHh
Q 039342           61 LEAVLSVYCFAGLVD---ESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISN--IHQVTGQMI  135 (248)
Q Consensus        61 ~~~ll~~~~~~g~~~---~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~--~~~~~~~~l  135 (248)
                      +..++.+|...+..+   +|.++++.+.... .-.+.++-.=+..+.+.++.+.+.+++.+|...-..+  +-..+-..+
T Consensus        87 L~~La~~~l~~~~~~~~~ka~~~l~~l~~e~-~~~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~~~~~e~~~~~~l~~i  165 (278)
T PF08631_consen   87 LRLLANAYLEWDTYESVEKALNALRLLESEY-GNKPEVFLLKLEILLKSFDEEEYEEILMRMIRSVDHSESNFDSILHHI  165 (278)
T ss_pred             HHHHHHHHHcCCChHHHHHHHHHHHHHHHhC-CCCcHHHHHHHHHHhccCChhHHHHHHHHHHHhcccccchHHHHHHHH
Confidence            677888888877655   4555666664332 1125566667777777899999999999998764312  222222222


Q ss_pred             cccccccchHHHHHHHHHHHHhcCCCCCHH-HHH-HHHHH-HHhcC--------chHHHHHHHHHHHH-CCCCCC---cc
Q 039342          136 KGEFDDESNWQMVEYVFDKLNCEGYGLGMR-FYN-ALLEA-LWCLG--------LRERAARVLDEATK-RGLFPE---LF  200 (248)
Q Consensus       136 ~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~-~~~-~li~~-~~~~g--------~~~~a~~~~~~m~~-~g~~p~---~~  200 (248)
                      .......  ...+...+..+....+.|... ... .++.- +...+        ..+...++++...+ .+.+.+   ..
T Consensus       166 ~~l~~~~--~~~a~~~ld~~l~~r~~~~~~~~~e~~vl~~~~~~~~~~~~~~~~~i~~l~~~~~~v~~~~~~~ls~~~~~  243 (278)
T PF08631_consen  166 KQLAEKS--PELAAFCLDYLLLNRFKSSEDQWLEKLVLTRVLLTTQSKDLSSSEKIESLEELLSIVEHSLGKQLSAEAAS  243 (278)
T ss_pred             HHHHhhC--cHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHcCCccccchhHHHHHHHHHHHHHHHhcCCCCHHHHH
Confidence            2212222  245555565555554555543 111 12221 11111        14455555654333 222222   23


Q ss_pred             hhhhHHhhhhhhccccchHHHHHHHHHHH
Q 039342          201 RHNKLVWSVDVHRMWEGGAYTAISVWLNK  229 (248)
Q Consensus       201 t~~~li~~~~~~~~~~~g~~~~~~~~~~~  229 (248)
                      +..+++|+... ...+.++++.|..+++-
T Consensus       244 a~~~LLW~~~~-~~~~~k~y~~A~~w~~~  271 (278)
T PF08631_consen  244 AIHTLLWNKGK-KHYKAKNYDEAIEWYEL  271 (278)
T ss_pred             HHHHHHHHHHH-HHHhhcCHHHHHHHHHH
Confidence            45677888764 45677899999998874

It is also involved in sporulation [].

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=96.52  E-value=0.58  Score=42.14  Aligned_cols=163  Identities=14%  Similarity=0.126  Sum_probs=108.1

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcc-
Q 039342           59 RTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKG-  137 (248)
Q Consensus        59 ~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~-  137 (248)
                      ..|..|-..|+...+...|.+.|+...+-. ..+........+.|++..+++.|..+.-.--+.. +.....++..-++ 
T Consensus       493 paf~~LG~iYrd~~Dm~RA~kCf~KAFeLD-atdaeaaaa~adtyae~~~we~a~~I~l~~~qka-~a~~~k~nW~~rG~  570 (1238)
T KOG1127|consen  493 PAFAFLGQIYRDSDDMKRAKKCFDKAFELD-ATDAEAAAASADTYAEESTWEEAFEICLRAAQKA-PAFACKENWVQRGP  570 (1238)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-chhhhhHHHHHHHhhccccHHHHHHHHHHHhhhc-hHHHHHhhhhhccc
Confidence            466777777777778888888888877643 2266788999999999999999999933322221 1122223322232 


Q ss_pred             cccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccc
Q 039342          138 EFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEG  217 (248)
Q Consensus       138 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~  217 (248)
                      ++-..++...+..-|+.-....+. |...|..+.++|.+.|++..|.++|.+...  +.|+ .+|.....+.+   .+..
T Consensus       571 yyLea~n~h~aV~~fQsALR~dPk-D~n~W~gLGeAY~~sGry~~AlKvF~kAs~--LrP~-s~y~~fk~A~~---ecd~  643 (1238)
T KOG1127|consen  571 YYLEAHNLHGAVCEFQSALRTDPK-DYNLWLGLGEAYPESGRYSHALKVFTKASL--LRPL-SKYGRFKEAVM---ECDN  643 (1238)
T ss_pred             cccCccchhhHHHHHHHHhcCCch-hHHHHHHHHHHHHhcCceehHHHhhhhhHh--cCcH-hHHHHHHHHHH---HHHh
Confidence            355667778888777776665544 778899999999999999999999987654  3554 33333333322   2345


Q ss_pred             hHHHHHHHHHHHH
Q 039342          218 GAYTAISVWLNKM  230 (248)
Q Consensus       218 g~~~~~~~~~~~m  230 (248)
                      |.+.++...+...
T Consensus       644 GkYkeald~l~~i  656 (1238)
T KOG1127|consen  644 GKYKEALDALGLI  656 (1238)
T ss_pred             hhHHHHHHHHHHH
Confidence            5665555555444

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

Probab=96.49  E-value=0.28  Score=38.19  Aligned_cols=90  Identities=16%  Similarity=0.182  Sum_probs=52.8

Q ss_pred             cccc-chHHHHHHHHHHHHhc----CCCCC--HHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchh---hhHHhh
Q 039342          139 FDDE-SNWQMVEYVFDKLNCE----GYGLG--MRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRH---NKLVWS  208 (248)
Q Consensus       139 ~~~~-~~~~~a~~~~~~m~~~----~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~---~~li~~  208 (248)
                      +... ++++.|.+.|+...+.    + .+.  ..++..+...+.+.|++++|.++|++........+..-|   ..++.+
T Consensus       124 ye~~~~d~e~Ai~~Y~~A~~~y~~e~-~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a  202 (282)
T PF14938_consen  124 YEEQLGDYEKAIEYYQKAAELYEQEG-SPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKA  202 (282)
T ss_dssp             HCCTT--HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHHHCC-ChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHH
Confidence            5566 7888998888775543    3 222  445677788899999999999999998875443322111   122222


Q ss_pred             hhhhccccchHHHHHHHHHHHHH
Q 039342          209 VDVHRMWEGGAYTAISVWLNKMY  231 (248)
Q Consensus       209 ~~~~~~~~~g~~~~~~~~~~~m~  231 (248)
                      .+  .+...|+...|.+.+++..
T Consensus       203 ~l--~~L~~~D~v~A~~~~~~~~  223 (282)
T PF14938_consen  203 IL--CHLAMGDYVAARKALERYC  223 (282)
T ss_dssp             HH--HHHHTT-HHHHHHHHHHHG
T ss_pred             HH--HHHHcCCHHHHHHHHHHHH
Confidence            22  2233466666766666654

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=96.49  E-value=0.33  Score=38.89  Aligned_cols=203  Identities=12%  Similarity=0.025  Sum_probs=108.8

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHC---CCC-cCHhhHHHHHHHHH
Q 039342           29 VIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSS---GIL-PSVMCYCMLLAVYA  104 (248)
Q Consensus        29 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~---~~~-p~~~~~~~li~~~~  104 (248)
                      ...+..+.|+|+...+........  .++...|.++...  +.++.+++....+...+.   .+. .....|........
T Consensus         4 ~~eaaWrl~~Wd~l~~~~~~~~~~--~~~~~~~~al~~l--~~~~~~~~~~~i~~~r~~~~~~l~~~~~~s~~~~y~~l~   79 (352)
T PF02259_consen    4 AAEAAWRLGDWDLLEEYLSQSNED--SPEYSFYRALLAL--RQGDYDEAKKYIEKARQLLLDELSALSSESYQRAYPSLV   79 (352)
T ss_pred             HHHHHHhcCChhhHHHHHhhccCC--ChhHHHHHHHHHH--hCccHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHH
Confidence            356777888888855555554422  2355555555554  778888888887777643   111 12334444444444


Q ss_pred             hcCCHHHHHHHHHHHHHCCC-CchH----HhHHHHhcccccccchHHHHHHHHHHHHh--cCCCCCHHHHHHHHHHHHhc
Q 039342          105 KSNRWDDAYGLLDEMHTNRI-SNIH----QVTGQMIKGEFDDESNWQMVEYVFDKLNC--EGYGLGMRFYNALLEALWCL  177 (248)
Q Consensus       105 ~~~~~~~a~~~~~~m~~~~~-~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~m~~--~~~~p~~~~~~~li~~~~~~  177 (248)
                      +...+.+..++.+-...... ....    ..|..-+......-..|+....+-..+..  ........++..+.+.+.+.
T Consensus        80 ~lq~L~Elee~~~~~~~~~~~~~~~~~l~~~W~~Rl~~~~~~~~~~~~il~~R~~~l~~~~~~~~~~~~~l~~a~~aRk~  159 (352)
T PF02259_consen   80 KLQQLVELEEIIELKSNLSQNPQDLKSLLKRWRSRLPNMQDDFSVWEPILSLRRLVLSLILLPEELAETWLKFAKLARKA  159 (352)
T ss_pred             HHhHHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHC
Confidence            44444444444433311110 1111    12222222212222334444443333333  12334567788899999999


Q ss_pred             CchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHHHcC
Q 039342          178 GLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMG  237 (248)
Q Consensus       178 g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~~~~  237 (248)
                      |+++.|...+..+.+.+..+........+...  +-.+..|+..+|...+++..+.....
T Consensus       160 g~~~~A~~~l~~~~~~~~~~~~~~~~v~~e~a--kllw~~g~~~~Ai~~L~~~~~~~~~~  217 (352)
T PF02259_consen  160 GNFQLALSALNRLFQLNPSSESLLPRVFLEYA--KLLWAQGEQEEAIQKLRELLKCRLSK  217 (352)
T ss_pred             CCcHHHHHHHHHHhccCCcccCCCcchHHHHH--HHHHHcCCHHHHHHHHHHHHHHHhhh
Confidence            99999999999988754222211111111111  44567788888888888888744443

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.45  E-value=0.035  Score=33.12  Aligned_cols=54  Identities=13%  Similarity=0.134  Sum_probs=25.8

Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 039342           32 AFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKS   86 (248)
Q Consensus        32 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~   86 (248)
                      .|.+.++++.|.++++.+.+.+ +.+...+...-.++.+.|++++|.+.|+...+
T Consensus         4 ~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~   57 (73)
T PF13371_consen    4 IYLQQEDYEEALEVLERALELD-PDDPELWLQRARCLFQLGRYEEALEDLERALE   57 (73)
T ss_pred             HHHhCCCHHHHHHHHHHHHHhC-cccchhhHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            3444555555555555554432 22334444444455555555555555555443

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.42  E-value=0.035  Score=33.14  Aligned_cols=57  Identities=11%  Similarity=0.049  Sum_probs=47.6

Q ss_pred             HHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           66 SVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        66 ~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      ..|.+.+++++|.++++.+.+.+ +.+...+...-..+.+.|++++|...|++..+.+
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~   59 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELD-PDDPELWLQRARCLFQLGRYEEALEDLERALELS   59 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC-cccchhhHHHHHHHHHhccHHHHHHHHHHHHHHC
Confidence            56788999999999999998763 2266778888888999999999999999988665

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=96.33  E-value=0.64  Score=40.51  Aligned_cols=102  Identities=12%  Similarity=0.105  Sum_probs=62.3

Q ss_pred             cCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCH-hh
Q 039342           17 SGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSV-MC   95 (248)
Q Consensus        17 ~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~-~~   95 (248)
                      ..+.-+...|..+--+....|+++.+-+.|++....- .-....|+.+-..|...|.-..|..+++.-....-.|+. ..
T Consensus       317 ~~~qnd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~-~~~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~ps~~s~  395 (799)
T KOG4162|consen  317 KKFQNDAAIFDHLTFALSRCGQFEVLAEQFEQALPFS-FGEHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQPSDISV  395 (799)
T ss_pred             hhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhh-hhhHHHHHHHHHHHHHhccchHHHHHHHhhcccccCCCcchH
Confidence            3445577888888888888888888888888765332 234566777777777888888888887765543223433 33


Q ss_pred             HHHHHHHHHh-cCCHHHHHHHHHHH
Q 039342           96 YCMLLAVYAK-SNRWDDAYGLLDEM  119 (248)
Q Consensus        96 ~~~li~~~~~-~~~~~~a~~~~~~m  119 (248)
                      +-..-..|.+ -+..++++.+-.+.
T Consensus       396 ~Lmasklc~e~l~~~eegldYA~ka  420 (799)
T KOG4162|consen  396 LLMASKLCIERLKLVEEGLDYAQKA  420 (799)
T ss_pred             HHHHHHHHHhchhhhhhHHHHHHHH
Confidence            3333333332 23445544444443

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=96.32  E-value=0.27  Score=36.19  Aligned_cols=59  Identities=17%  Similarity=0.148  Sum_probs=38.3

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcC--CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 039342           29 VIEAFRQGGRFEEAIKAYVEMEKVR--CDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSS   87 (248)
Q Consensus        29 li~~~~~~~~~~~a~~~~~~m~~~~--~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~   87 (248)
                      .-..+...|++.+|.+.|+.+...-  -+--....-.+..++.+.|+++.|...++++.+.
T Consensus        11 ~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~   71 (203)
T PF13525_consen   11 KALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKL   71 (203)
T ss_dssp             HHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            3445567788888888888886541  1222344455677888888888888888887654

>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=96.31  E-value=0.019  Score=34.93  Aligned_cols=61  Identities=25%  Similarity=0.485  Sum_probs=28.4

Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHHc--CCC---CC-HHHHHHHHHHHHhcCChhHHHHHHHHH
Q 039342           24 DSFNAVIEAFRQGGRFEEAIKAYVEMEKV--RCD---PN-ERTLEAVLSVYCFAGLVDESKEQFQEI   84 (248)
Q Consensus        24 ~~y~~li~~~~~~~~~~~a~~~~~~m~~~--~~~---p~-~~t~~~ll~~~~~~g~~~~a~~~~~~m   84 (248)
                      .+|+.+-..|...|++++|+..|++..+.  ...   |+ ..+++.+-.+|...|++++|.+.+++.
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            34555555555555555555555554321  011   11 234444445555555555555555443

...

>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=96.30  E-value=0.022  Score=34.63  Aligned_cols=62  Identities=16%  Similarity=0.217  Sum_probs=48.5

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHC----CC-CcC-HhhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 039342           59 RTLEAVLSVYCFAGLVDESKEQFQEIKSS----GI-LPS-VMCYCMLLAVYAKSNRWDDAYGLLDEMH  120 (248)
Q Consensus        59 ~t~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~-~p~-~~~~~~li~~~~~~~~~~~a~~~~~~m~  120 (248)
                      .+|+.+-..|.+.|++++|.+.|++..+.    |- .|. ..+++.+-..|...|++++|++.+++-.
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al   73 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKAL   73 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            57888889999999999999999887643    21 132 5678888889999999999999988754

...

>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=96.28  E-value=0.24  Score=35.09  Aligned_cols=138  Identities=12%  Similarity=0.118  Sum_probs=80.0

Q ss_pred             HHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccc-cccchHHHHHHHHHHHH
Q 039342           78 KEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEF-DDESNWQMVEYVFDKLN  156 (248)
Q Consensus        78 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~-~~~~~~~~a~~~~~~m~  156 (248)
                      .+..+.+.+.++.|+...|..+|+.+.+.|++..    +.++...++-+|+......+...- ....-.+.+.+++.++.
T Consensus        14 lEYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~----L~qllq~~Vi~DSk~lA~~LLs~~~~~~~~~Ql~lDMLkRL~   89 (167)
T PF07035_consen   14 LEYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQ----LHQLLQYHVIPDSKPLACQLLSLGNQYPPAYQLGLDMLKRLG   89 (167)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHH----HHHHHhhcccCCcHHHHHHHHHhHccChHHHHHHHHHHHHhh
Confidence            3455566667778888888888888888877544    444555566666666655544311 11222344444444443


Q ss_pred             hcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHHHc
Q 039342          157 CEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMM  236 (248)
Q Consensus       157 ~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~~~  236 (248)
                      .        .+..+++.+...|++-+|..+.+......-.|    ...++     .+-.+.++...-..+++-+.+++..
T Consensus        90 ~--------~~~~iievLL~~g~vl~ALr~ar~~~~~~~~~----~~~fL-----eAA~~~~D~~lf~~V~~ff~~~n~~  152 (167)
T PF07035_consen   90 T--------AYEEIIEVLLSKGQVLEALRYARQYHKVDSVP----ARKFL-----EAAANSNDDQLFYAVFRFFEERNLR  152 (167)
T ss_pred             h--------hHHHHHHHHHhCCCHHHHHHHHHHcCCcccCC----HHHHH-----HHHHHcCCHHHHHHHHHHHHHhhHh
Confidence            2        26777888888888888888887643221111    13444     3334455555555566666665543

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

Probab=96.26  E-value=0.055  Score=42.80  Aligned_cols=86  Identities=17%  Similarity=0.105  Sum_probs=72.4

Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHH
Q 039342           23 SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAV  102 (248)
Q Consensus        23 ~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~  102 (248)
                      -.+.+..|.-+...|+...|.++-.+.+    .||..-|-..|.+++..++|++-.++...   .   -++.-|..++.+
T Consensus       177 ~~Sl~~Ti~~li~~~~~k~A~kl~k~Fk----v~dkrfw~lki~aLa~~~~w~eL~~fa~s---k---KsPIGyepFv~~  246 (319)
T PF04840_consen  177 GLSLNDTIRKLIEMGQEKQAEKLKKEFK----VPDKRFWWLKIKALAENKDWDELEKFAKS---K---KSPIGYEPFVEA  246 (319)
T ss_pred             cCCHHHHHHHHHHCCCHHHHHHHHHHcC----CcHHHHHHHHHHHHHhcCCHHHHHHHHhC---C---CCCCChHHHHHH
Confidence            3467777888899999999988877774    49999999999999999999987765432   1   256899999999


Q ss_pred             HHhcCCHHHHHHHHHH
Q 039342          103 YAKSNRWDDAYGLLDE  118 (248)
Q Consensus       103 ~~~~~~~~~a~~~~~~  118 (248)
                      |.+.|+..+|..++..
T Consensus       247 ~~~~~~~~eA~~yI~k  262 (319)
T PF04840_consen  247 CLKYGNKKEASKYIPK  262 (319)
T ss_pred             HHHCCCHHHHHHHHHh
Confidence            9999999999999987

Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm

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

Probab=96.21  E-value=0.12  Score=39.82  Aligned_cols=100  Identities=14%  Similarity=0.162  Sum_probs=78.3

Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHH
Q 039342           33 FRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILP-SVMCYCMLLAVYAKSNRWDD  111 (248)
Q Consensus        33 ~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~  111 (248)
                      +.+.+++++|+..|.+..+.. +-|.+-|..=-.+|.+.|.++.|.+=.+.-...  .| ...+|..|=.+|...|++++
T Consensus        91 ~m~~~~Y~eAv~kY~~AI~l~-P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~i--Dp~yskay~RLG~A~~~~gk~~~  167 (304)
T KOG0553|consen   91 LMKNKDYQEAVDKYTEAIELD-PTNAVYYCNRAAAYSKLGEYEDAVKDCESALSI--DPHYSKAYGRLGLAYLALGKYEE  167 (304)
T ss_pred             HHHhhhHHHHHHHHHHHHhcC-CCcchHHHHHHHHHHHhcchHHHHHHHHHHHhc--ChHHHHHHHHHHHHHHccCcHHH
Confidence            456778888888888887653 345666777788999999999998877766654  34 46789999999999999999


Q ss_pred             HHHHHHHHHHCCCCchHHhHHHHhcc
Q 039342          112 AYGLLDEMHTNRISNIHQVTGQMIKG  137 (248)
Q Consensus       112 a~~~~~~m~~~~~~~~~~~~~~~l~~  137 (248)
                      |++.|++-.+  +.|+..+|..-+..
T Consensus       168 A~~aykKaLe--ldP~Ne~~K~nL~~  191 (304)
T KOG0553|consen  168 AIEAYKKALE--LDPDNESYKSNLKI  191 (304)
T ss_pred             HHHHHHhhhc--cCCCcHHHHHHHHH
Confidence            9999998764  45888888776654

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

Probab=96.14  E-value=0.37  Score=42.54  Aligned_cols=136  Identities=13%  Similarity=0.109  Sum_probs=81.4

Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHH
Q 039342           33 FRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDA  112 (248)
Q Consensus        33 ~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a  112 (248)
                      ....|..++|+.+|++.++         |..|=+.|-..|+|++|.++-+.=-+..   -..||-.-...+-..++++.|
T Consensus       810 AieLgMlEeA~~lYr~ckR---------~DLlNKlyQs~g~w~eA~eiAE~~DRiH---Lr~Tyy~yA~~Lear~Di~~A  877 (1416)
T KOG3617|consen  810 AIELGMLEEALILYRQCKR---------YDLLNKLYQSQGMWSEAFEIAETKDRIH---LRNTYYNYAKYLEARRDIEAA  877 (1416)
T ss_pred             HHHHhhHHHHHHHHHHHHH---------HHHHHHHHHhcccHHHHHHHHhhcccee---hhhhHHHHHHHHHhhccHHHH
Confidence            3466888888888888775         3445566777888998888765422221   234566666666667788888


Q ss_pred             HHHHHHH----------HHCCCC--------chHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Q 039342          113 YGLLDEM----------HTNRIS--------NIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEAL  174 (248)
Q Consensus       113 ~~~~~~m----------~~~~~~--------~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~  174 (248)
                      ++.|++-          .....+        ....+...-...+....|..+.|..+|...++         |-++++..
T Consensus       878 leyyEK~~~hafev~rmL~e~p~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D---------~fs~VrI~  948 (1416)
T KOG3617|consen  878 LEYYEKAGVHAFEVFRMLKEYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAKD---------YFSMVRIK  948 (1416)
T ss_pred             HHHHHhcCChHHHHHHHHHhChHHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhhh---------hhhheeeE
Confidence            8887642          111100        00011111112234456777777777765443         55666666


Q ss_pred             HhcCchHHHHHHHHH
Q 039342          175 WCLGLRERAARVLDE  189 (248)
Q Consensus       175 ~~~g~~~~a~~~~~~  189 (248)
                      |-+|+.++|..+-++
T Consensus       949 C~qGk~~kAa~iA~e  963 (1416)
T KOG3617|consen  949 CIQGKTDKAARIAEE  963 (1416)
T ss_pred             eeccCchHHHHHHHh
Confidence            777777777776655

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=96.05  E-value=0.67  Score=38.99  Aligned_cols=154  Identities=18%  Similarity=0.110  Sum_probs=102.8

Q ss_pred             CCchHHHHHHHHHHHHc-CCCCC-----HHhHHHHHHHHHhc----CCHHHHHHHHHHHHHcCCCCCHHHHHHH-HHHHH
Q 039342            1 GGLYKECQAILSRMSES-GVARN-----SDSFNAVIEAFRQG----GRFEEAIKAYVEMEKVRCDPNERTLEAV-LSVYC   69 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~-g~~~~-----~~~y~~li~~~~~~----~~~~~a~~~~~~m~~~~~~p~~~t~~~l-l~~~~   69 (248)
                      .||-+.+++.+.+-.+. ++.-.     .-.|+.++..++..    .+.+.|.++++.+.+.  -|+...|... -+.+.
T Consensus       201 ~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~--yP~s~lfl~~~gR~~~  278 (468)
T PF10300_consen  201 SGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKR--YPNSALFLFFEGRLER  278 (468)
T ss_pred             CCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHH
Confidence            36778888888776543 33221     23577777666654    5678899999999865  6887777544 35667


Q ss_pred             hcCChhHHHHHHHHHHHC--CC-CcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchH-
Q 039342           70 FAGLVDESKEQFQEIKSS--GI-LPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNW-  145 (248)
Q Consensus        70 ~~g~~~~a~~~~~~m~~~--~~-~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~-  145 (248)
                      ..|++++|.+.|+.....  .. +.....+--+...+.-..+|++|...|.++.+..- -...+|..+..+++...++. 
T Consensus       279 ~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s~-WSka~Y~Y~~a~c~~~l~~~~  357 (468)
T PF10300_consen  279 LKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKESK-WSKAFYAYLAAACLLMLGREE  357 (468)
T ss_pred             HhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhccc-cHHHHHHHHHHHHHHhhccch
Confidence            789999999999975431  11 12344555666677888999999999999987542 23455555555555555555 


Q ss_pred             ------HHHHHHHHHHHh
Q 039342          146 ------QMVEYVFDKLNC  157 (248)
Q Consensus       146 ------~~a~~~~~~m~~  157 (248)
                            ++|..++.+...
T Consensus       358 ~~~~~~~~a~~l~~~vp~  375 (468)
T PF10300_consen  358 EAKEHKKEAEELFRKVPK  375 (468)
T ss_pred             hhhhhHHHHHHHHHHHHH
Confidence                  677777766543

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.

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=96.00  E-value=0.96  Score=39.50  Aligned_cols=80  Identities=13%  Similarity=0.094  Sum_probs=63.0

Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCc
Q 039342           47 VEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISN  126 (248)
Q Consensus        47 ~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~  126 (248)
                      .++....+..|...|..+--+..+.|+++.+.+.|++.... ..-....|..+-..|...|.-..|..++++-....-.|
T Consensus       312 ~k~r~~~~qnd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~-~~~~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~p  390 (799)
T KOG4162|consen  312 RKLRLKKFQNDAAIFDHLTFALSRCGQFEVLAEQFEQALPF-SFGEHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQP  390 (799)
T ss_pred             HHHHHhhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHh-hhhhHHHHHHHHHHHHHhccchHHHHHHHhhcccccCC
Confidence            33344456788999999999999999999999999997754 23357789999999999999999999998876554334


Q ss_pred             h
Q 039342          127 I  127 (248)
Q Consensus       127 ~  127 (248)
                      +
T Consensus       391 s  391 (799)
T KOG4162|consen  391 S  391 (799)
T ss_pred             C
Confidence            3

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=95.98  E-value=0.22  Score=38.29  Aligned_cols=86  Identities=8%  Similarity=0.023  Sum_probs=65.6

Q ss_pred             CchHHHHHHHHHHHHcCCCC--CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCCCHHHHHHHHHHHHhcCChhHH
Q 039342            2 GLYKECQAILSRMSESGVAR--NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVR--CDPNERTLEAVLSVYCFAGLVDES   77 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~--~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~--~~p~~~t~~~ll~~~~~~g~~~~a   77 (248)
                      |++++|...|+.+.+.-...  ....+--+-..|...|++++|...|+.+.+.-  -+.....+-.+...+...|+.++|
T Consensus       157 ~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg~~~~~~g~~~~A  236 (263)
T PRK10803        157 SRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVGVIMQDKGDTAKA  236 (263)
T ss_pred             CCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHHHHHHHcCCHHHH
Confidence            78999999999988643211  13567778888999999999999999997542  112234455566678899999999


Q ss_pred             HHHHHHHHHC
Q 039342           78 KEQFQEIKSS   87 (248)
Q Consensus        78 ~~~~~~m~~~   87 (248)
                      ..+|+.+.+.
T Consensus       237 ~~~~~~vi~~  246 (263)
T PRK10803        237 KAVYQQVIKK  246 (263)
T ss_pred             HHHHHHHHHH
Confidence            9999999875

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=95.96  E-value=0.42  Score=43.00  Aligned_cols=86  Identities=14%  Similarity=0.075  Sum_probs=53.2

Q ss_pred             HHhcCChhHHHHHHHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHH
Q 039342           68 YCFAGLVDESKEQFQEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQ  146 (248)
Q Consensus        68 ~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~  146 (248)
                      |.+.++...+..-|+...+.  .| |...|..+..+|.++|+...|.++|.+...-+  |...--.......-...|.+.
T Consensus       572 yLea~n~h~aV~~fQsALR~--dPkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~Lr--P~s~y~~fk~A~~ecd~GkYk  647 (1238)
T KOG1127|consen  572 YLEAHNLHGAVCEFQSALRT--DPKDYNLWLGLGEAYPESGRYSHALKVFTKASLLR--PLSKYGRFKEAVMECDNGKYK  647 (1238)
T ss_pred             ccCccchhhHHHHHHHHhcC--CchhHHHHHHHHHHHHhcCceehHHHhhhhhHhcC--cHhHHHHHHHHHHHHHhhhHH
Confidence            33444455554444444332  34 67789999999999999999999998776543  443322222222234566677


Q ss_pred             HHHHHHHHHHh
Q 039342          147 MVEYVFDKLNC  157 (248)
Q Consensus       147 ~a~~~~~~m~~  157 (248)
                      .+...+.....
T Consensus       648 eald~l~~ii~  658 (1238)
T KOG1127|consen  648 EALDALGLIIY  658 (1238)
T ss_pred             HHHHHHHHHHH
Confidence            77777666543

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

Probab=95.88  E-value=0.13  Score=39.51  Aligned_cols=95  Identities=19%  Similarity=0.252  Sum_probs=75.0

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCChhHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN-ERTLEAVLSVYCFAGLVDESKE   79 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~ll~~~~~~g~~~~a~~   79 (248)
                      .+++++|+..|.+..+... .|+.-|..=-.+|++.|.++.|.+-.+...+-  .|. ..+|..|-.+|...|++++|.+
T Consensus        94 ~~~Y~eAv~kY~~AI~l~P-~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~i--Dp~yskay~RLG~A~~~~gk~~~A~~  170 (304)
T KOG0553|consen   94 NKDYQEAVDKYTEAIELDP-TNAVYYCNRAAAYSKLGEYEDAVKDCESALSI--DPHYSKAYGRLGLAYLALGKYEEAIE  170 (304)
T ss_pred             hhhHHHHHHHHHHHHhcCC-CcchHHHHHHHHHHHhcchHHHHHHHHHHHhc--ChHHHHHHHHHHHHHHccCcHHHHHH
Confidence            3689999999999987432 36777777788999999999998877766543  343 4788999999999999999999


Q ss_pred             HHHHHHHCCCCcCHhhHHHHH
Q 039342           80 QFQEIKSSGILPSVMCYCMLL  100 (248)
Q Consensus        80 ~~~~m~~~~~~p~~~~~~~li  100 (248)
                      .|+...+  +.|+-.+|-.=+
T Consensus       171 aykKaLe--ldP~Ne~~K~nL  189 (304)
T KOG0553|consen  171 AYKKALE--LDPDNESYKSNL  189 (304)
T ss_pred             HHHhhhc--cCCCcHHHHHHH
Confidence            9988776  578777665433

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=95.85  E-value=0.35  Score=39.71  Aligned_cols=65  Identities=8%  Similarity=0.132  Sum_probs=56.7

Q ss_pred             CCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH----HHHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 039342           21 RNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNE----RTLEAVLSVYCFAGLVDESKEQFQEIKSS   87 (248)
Q Consensus        21 ~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~----~t~~~ll~~~~~~g~~~~a~~~~~~m~~~   87 (248)
                      .+...|+.+-.+|.+.|++++|+..|++..+.  .|+.    .+|..+-.+|.+.|+.++|.+.+++..+.
T Consensus        73 ~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL--~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         73 KTAEDAVNLGLSLFSKGRVKDALAQFETALEL--NPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            35778999999999999999999999997765  4664    46899999999999999999999998874

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=95.79  E-value=0.34  Score=39.72  Aligned_cols=131  Identities=11%  Similarity=0.103  Sum_probs=90.4

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHCC-CCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhc
Q 039342           58 ERTLEAVLSVYCFAGLVDESKEQFQEIKSSG-ILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIK  136 (248)
Q Consensus        58 ~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~-~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~  136 (248)
                      +..|...|++-.+..-++.|..+|-+.++.| +.+++..++++|..++. |+...|.++|+--...  -|+...|..-..
T Consensus       397 t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~~-~d~~ta~~ifelGl~~--f~d~~~y~~kyl  473 (660)
T COG5107         397 TFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYAT-GDRATAYNIFELGLLK--FPDSTLYKEKYL  473 (660)
T ss_pred             hhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhc-CCcchHHHHHHHHHHh--CCCchHHHHHHH
Confidence            4567778888888888999999999999888 66789999999998875 6778888888754332  144444432222


Q ss_pred             ccccccchHHHHHHHHHHHHhcCCCC--CHHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          137 GEFDDESNWQMVEYVFDKLNCEGYGL--GMRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       137 ~~~~~~~~~~~a~~~~~~m~~~~~~p--~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                      .+...-++-+.|..+|+.-.+. +.-  -...|..+|+.-..-|++..+..+-+.|..
T Consensus       474 ~fLi~inde~naraLFetsv~r-~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e  530 (660)
T COG5107         474 LFLIRINDEENARALFETSVER-LEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFRE  530 (660)
T ss_pred             HHHHHhCcHHHHHHHHHHhHHH-HHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHH
Confidence            2233445557778888743322 111  145788888888888988777776666643

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

Probab=95.77  E-value=0.75  Score=36.49  Aligned_cols=112  Identities=13%  Similarity=0.103  Sum_probs=80.2

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcc
Q 039342           58 ERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKG  137 (248)
Q Consensus        58 ~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~  137 (248)
                      ..+.+..|.-+...|+...|.++-++++    .|+..-|-..|.+++..++|++-..+-..    .-+|  .-|..++..
T Consensus       177 ~~Sl~~Ti~~li~~~~~k~A~kl~k~Fk----v~dkrfw~lki~aLa~~~~w~eL~~fa~s----kKsP--IGyepFv~~  246 (319)
T PF04840_consen  177 GLSLNDTIRKLIEMGQEKQAEKLKKEFK----VPDKRFWWLKIKALAENKDWDELEKFAKS----KKSP--IGYEPFVEA  246 (319)
T ss_pred             cCCHHHHHHHHHHCCCHHHHHHHHHHcC----CcHHHHHHHHHHHHHhcCCHHHHHHHHhC----CCCC--CChHHHHHH
Confidence            4466777888889999998888876664    47899999999999999999998876543    1122  334444444


Q ss_pred             cccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHH
Q 039342          138 EFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEA  190 (248)
Q Consensus       138 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m  190 (248)
                       |...|+...|..+...     +     .+..-+..|.+.|++.+|.+.-.+.
T Consensus       247 -~~~~~~~~eA~~yI~k-----~-----~~~~rv~~y~~~~~~~~A~~~A~~~  288 (319)
T PF04840_consen  247 -CLKYGNKKEASKYIPK-----I-----PDEERVEMYLKCGDYKEAAQEAFKE  288 (319)
T ss_pred             -HHHCCCHHHHHHHHHh-----C-----ChHHHHHHHHHCCCHHHHHHHHHHc
Confidence             3345566777777665     2     2466788899999999988775443

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

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=95.60  E-value=0.62  Score=34.30  Aligned_cols=50  Identities=24%  Similarity=0.355  Sum_probs=24.1

Q ss_pred             CchHHHHHHHHHHHHcCC--CCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 039342            2 GLYKECQAILSRMSESGV--ARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEK   51 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~--~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~   51 (248)
                      |++++|.+.|+.+...-.  +-.....-.+..++-+.|+++.|...++++.+
T Consensus        19 g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~   70 (203)
T PF13525_consen   19 GDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIK   70 (203)
T ss_dssp             T-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            555666666666554321  11123344445555566666666666665544

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.53  E-value=0.78  Score=35.00  Aligned_cols=135  Identities=8%  Similarity=0.034  Sum_probs=94.6

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHH----
Q 039342           25 SFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLL----  100 (248)
Q Consensus        25 ~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li----  100 (248)
                      .-++++....-.+.+.-...++++..+..-+.++...+.+.+.-.+.|+.+.|...|++..+..-..|..+++.++    
T Consensus       179 Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~  258 (366)
T KOG2796|consen  179 VMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNS  258 (366)
T ss_pred             HHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhh
Confidence            4566777777788888899999999888777888888999999999999999999999887654344544554444    


Q ss_pred             -HHHHhcCCHHHHHHHHHHHHHCCCCchHHhH-HHHhcccccccchHHHHHHHHHHHHhcCCCC
Q 039342          101 -AVYAKSNRWDDAYGLLDEMHTNRISNIHQVT-GQMIKGEFDDESNWQMVEYVFDKLNCEGYGL  162 (248)
Q Consensus       101 -~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~-~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p  162 (248)
                       ..|.-++++-.|...+.+....+-......- .+++   .--.|+...|.+..+.|.+.-..|
T Consensus       259 a~i~lg~nn~a~a~r~~~~i~~~D~~~~~a~NnKALc---llYlg~l~DAiK~~e~~~~~~P~~  319 (366)
T KOG2796|consen  259 AFLHLGQNNFAEAHRFFTEILRMDPRNAVANNNKALC---LLYLGKLKDALKQLEAMVQQDPRH  319 (366)
T ss_pred             hhheecccchHHHHHHHhhccccCCCchhhhchHHHH---HHHHHHHHHHHHHHHHHhccCCcc
Confidence             3455677888899999887655422111111 1222   223456778888888888764443

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

Probab=95.51  E-value=0.32  Score=37.52  Aligned_cols=77  Identities=13%  Similarity=0.143  Sum_probs=56.2

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHH-----CCCCchHHhHHH
Q 039342           59 RTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHT-----NRISNIHQVTGQ  133 (248)
Q Consensus        59 ~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~~~~~~~~~~~  133 (248)
                      .++..++..+...|+.+.+.+.++++.... +-+...|..+|.+|.+.|+...|+..|+++.+     .|+.|...+...
T Consensus       154 ~~l~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~  232 (280)
T COG3629         154 KALTKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRAL  232 (280)
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHH
Confidence            467778888888888888888888887653 23677888888888888888888888887744     567776665544


Q ss_pred             Hhc
Q 039342          134 MIK  136 (248)
Q Consensus       134 ~l~  136 (248)
                      ...
T Consensus       233 y~~  235 (280)
T COG3629         233 YEE  235 (280)
T ss_pred             HHH
Confidence            433

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=95.47  E-value=0.24  Score=42.80  Aligned_cols=72  Identities=10%  Similarity=0.119  Sum_probs=33.7

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKV-RCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~-~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      |++++|++++-+|.++..         .|..+.+.|||-.+.++++.=-.. .=..-...|+.+-..++....|++|.+.
T Consensus       748 g~feeaek~yld~drrDL---------Aielr~klgDwfrV~qL~r~g~~d~dD~~~e~A~r~ig~~fa~~~~We~A~~y  818 (1189)
T KOG2041|consen  748 GEFEEAEKLYLDADRRDL---------AIELRKKLGDWFRVYQLIRNGGSDDDDEGKEDAFRNIGETFAEMMEWEEAAKY  818 (1189)
T ss_pred             cchhHhhhhhhccchhhh---------hHHHHHhhhhHHHHHHHHHccCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            566777777766655332         244455556665555554331000 0001123444444445544455555544


Q ss_pred             HH
Q 039342           81 FQ   82 (248)
Q Consensus        81 ~~   82 (248)
                      +.
T Consensus       819 Y~  820 (1189)
T KOG2041|consen  819 YS  820 (1189)
T ss_pred             HH
Confidence            43

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.40  E-value=0.15  Score=39.65  Aligned_cols=103  Identities=13%  Similarity=0.206  Sum_probs=74.3

Q ss_pred             CCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHh
Q 039342           18 GVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKV---RCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVM   94 (248)
Q Consensus        18 g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~---~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~   94 (248)
                      |...+..+-..++..-....+++.+...+-+++..   ...|+...| ++++.|.+ =+.+++..++..-.+.|+-||.+
T Consensus        59 g~~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~-~~irlllk-y~pq~~i~~l~npIqYGiF~dqf  136 (418)
T KOG4570|consen   59 GLPVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTIH-TWIRLLLK-YDPQKAIYTLVNPIQYGIFPDQF  136 (418)
T ss_pred             CCCcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccHH-HHHHHHHc-cChHHHHHHHhCcchhccccchh
Confidence            44455666667777777778888888888887654   233443322 23333333 35678888888888899999999


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 039342           95 CYCMLLAVYAKSNRWDDAYGLLDEMHTN  122 (248)
Q Consensus        95 ~~~~li~~~~~~~~~~~a~~~~~~m~~~  122 (248)
                      +++.+|+.+.+.++..+|.++.-.|...
T Consensus       137 ~~c~l~D~flk~~n~~~aa~vvt~~~~q  164 (418)
T KOG4570|consen  137 TFCLLMDSFLKKENYKDAASVVTEVMMQ  164 (418)
T ss_pred             hHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            9999999999999999988887776543

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.36  E-value=0.95  Score=39.46  Aligned_cols=111  Identities=11%  Similarity=0.034  Sum_probs=72.0

Q ss_pred             CcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHH
Q 039342           90 LPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNA  169 (248)
Q Consensus        90 ~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~  169 (248)
                      .-..-+.+--+.-++.-|+-.+|.++-.+.+    .|+-..|+.-+.+ +...++|++.+++-+.++.      +.=|.-
T Consensus       681 ~f~dlSl~dTv~~li~~g~~k~a~ql~~~Fk----ipdKr~~wLk~~a-La~~~kweeLekfAkskks------PIGy~P  749 (829)
T KOG2280|consen  681 SFVDLSLHDTVTTLILIGQNKRAEQLKSDFK----IPDKRLWWLKLTA-LADIKKWEELEKFAKSKKS------PIGYLP  749 (829)
T ss_pred             ccccCcHHHHHHHHHHccchHHHHHHHHhcC----CcchhhHHHHHHH-HHhhhhHHHHHHHHhccCC------CCCchh
Confidence            3344455555666667777777777766543    3666666666666 7777888888877666553      223555


Q ss_pred             HHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHH
Q 039342          170 LLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISV  225 (248)
Q Consensus       170 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~  225 (248)
                      ++.+|.+.|+.++|.+++-+....         .-..     ..|.+.|++.+|.+
T Consensus       750 FVe~c~~~~n~~EA~KYiprv~~l---------~ekv-----~ay~~~~~~~eAad  791 (829)
T KOG2280|consen  750 FVEACLKQGNKDEAKKYIPRVGGL---------QEKV-----KAYLRVGDVKEAAD  791 (829)
T ss_pred             HHHHHHhcccHHHHhhhhhccCCh---------HHHH-----HHHHHhccHHHHHH
Confidence            889999999999999998764321         1233     45556666655544

>PRK15331 chaperone protein SicA; Provisional

Probab=95.29  E-value=0.25  Score=34.76  Aligned_cols=91  Identities=9%  Similarity=-0.046  Sum_probs=62.7

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCH
Q 039342           30 IEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRW  109 (248)
Q Consensus        30 i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~  109 (248)
                      -..+-..|++++|..+|.-+...+. -|..-|..|-.+|-..+++++|...|...-..+. -|+..+--.-.+|...|+.
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 AYEFYNQGRLDEAETFFRFLCIYDF-YNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLK-NDYRPVFFTGQCQLLMRKA  121 (165)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCc-CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc-CCCCccchHHHHHHHhCCH
Confidence            3445578888888888888866543 3444455666666677888888888877654432 2344444556677788888


Q ss_pred             HHHHHHHHHHHHC
Q 039342          110 DDAYGLLDEMHTN  122 (248)
Q Consensus       110 ~~a~~~~~~m~~~  122 (248)
                      +.|...|....+.
T Consensus       122 ~~A~~~f~~a~~~  134 (165)
T PRK15331        122 AKARQCFELVNER  134 (165)
T ss_pred             HHHHHHHHHHHhC
Confidence            8888888887764

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=95.22  E-value=1.2  Score=35.35  Aligned_cols=188  Identities=11%  Similarity=0.074  Sum_probs=121.6

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHH---HHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHH-HHHHHHhcCChhHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVI---EAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEA-VLSVYCFAGLVDES   77 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li---~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~-ll~~~~~~g~~~~a   77 (248)
                      |++..|+.-|....+    -|+..|-++.   ..|...|+...|+.=+....+  ++||-..-.+ --..+.+.|.++.|
T Consensus        52 ~Q~sDALt~yHaAve----~dp~~Y~aifrRaT~yLAmGksk~al~Dl~rVle--lKpDF~~ARiQRg~vllK~Gele~A  125 (504)
T KOG0624|consen   52 GQLSDALTHYHAAVE----GDPNNYQAIFRRATVYLAMGKSKAALQDLSRVLE--LKPDFMAARIQRGVVLLKQGELEQA  125 (504)
T ss_pred             hhHHHHHHHHHHHHc----CCchhHHHHHHHHHHHhhhcCCccchhhHHHHHh--cCccHHHHHHHhchhhhhcccHHHH
Confidence            455566666665554    4445555443   345566666666665655544  3566322111 12356789999999


Q ss_pred             HHHHHHHHHCCCC------------cCHhh--HHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccc
Q 039342           78 KEQFQEIKSSGIL------------PSVMC--YCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDES  143 (248)
Q Consensus        78 ~~~~~~m~~~~~~------------p~~~~--~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~  143 (248)
                      ..=|+.+.+....            +....  ....+..+.-.|+...|+.....+.+.  .|+...+..+-..++...|
T Consensus       126 ~~DF~~vl~~~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi--~~Wda~l~~~Rakc~i~~~  203 (504)
T KOG0624|consen  126 EADFDQVLQHEPSNGLVLEAQSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEI--QPWDASLRQARAKCYIAEG  203 (504)
T ss_pred             HHHHHHHHhcCCCcchhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhc--CcchhHHHHHHHHHHHhcC
Confidence            9999998875321            11222  223455667788999999999988864  5888888887777788888


Q ss_pred             hHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcc
Q 039342          144 NWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELF  200 (248)
Q Consensus       144 ~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  200 (248)
                      .+..|..=++...+..-. ++.++--+-..+-..|+.+.++...++..+.  .||-.
T Consensus       204 e~k~AI~Dlk~askLs~D-nTe~~ykis~L~Y~vgd~~~sL~~iRECLKl--dpdHK  257 (504)
T KOG0624|consen  204 EPKKAIHDLKQASKLSQD-NTEGHYKISQLLYTVGDAENSLKEIRECLKL--DPDHK  257 (504)
T ss_pred             cHHHHHHHHHHHHhcccc-chHHHHHHHHHHHhhhhHHHHHHHHHHHHcc--Ccchh
Confidence            888888766665554333 4455555666777888888888888887753  56543

>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=95.10  E-value=0.64  Score=31.46  Aligned_cols=65  Identities=17%  Similarity=0.197  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC
Q 039342           60 TLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRIS  125 (248)
Q Consensus        60 t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~  125 (248)
                      .....+......|+-|.-.+++..+.+. -.|++...-.+-.+|.+-|+..++.+++.+.-+.|++
T Consensus        88 ~vD~ALd~lv~~~kkDqLdki~~~l~kn-~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~k  152 (161)
T PF09205_consen   88 YVDLALDILVKQGKKDQLDKIYNELKKN-EEINPEFLVKIANAYKKLGNTREANELLKEACEKGLK  152 (161)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-H
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHhhc-cCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhchH
Confidence            3455566666666666666666666542 2455556666666666666666666666666666543

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.02  E-value=0.79  Score=34.94  Aligned_cols=96  Identities=17%  Similarity=0.198  Sum_probs=74.5

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcC----CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHC-CCCc-CHhhHHH
Q 039342           25 SFNAVIEAFRQGGRFEEAIKAYVEMEKVR----CDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSS-GILP-SVMCYCM   98 (248)
Q Consensus        25 ~y~~li~~~~~~~~~~~a~~~~~~m~~~~----~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~-~~~p-~~~~~~~   98 (248)
                      .|+.-+..+ +.|++..|...|....+..    +.||..-  .|-.++...|++++|..+|..+.+. +-.| -+..+--
T Consensus       144 ~Y~~A~~~~-ksgdy~~A~~~F~~fi~~YP~s~~~~nA~y--WLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallK  220 (262)
T COG1729         144 LYNAALDLY-KSGDYAEAEQAFQAFIKKYPNSTYTPNAYY--WLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLK  220 (262)
T ss_pred             HHHHHHHHH-HcCCHHHHHHHHHHHHHcCCCCcccchhHH--HHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHH
Confidence            588777765 5667999999999997752    4455544  4999999999999999999998754 2223 2356777


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           99 LLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        99 li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      |-....+.|+.++|..+|++..+.-
T Consensus       221 lg~~~~~l~~~d~A~atl~qv~k~Y  245 (262)
T COG1729         221 LGVSLGRLGNTDEACATLQQVIKRY  245 (262)
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHC
Confidence            7778889999999999999987663

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=94.98  E-value=0.73  Score=31.51  Aligned_cols=129  Identities=16%  Similarity=0.172  Sum_probs=78.1

Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHH
Q 039342           24 DSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVY  103 (248)
Q Consensus        24 ~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~  103 (248)
                      .....++..+.+.+.+.....+++.+...+ ..+...++.++..|++.+. .+..+.++.      .++......+++.|
T Consensus         8 ~~~~~vv~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~ly~~~~~-~~ll~~l~~------~~~~yd~~~~~~~c   79 (140)
T smart00299        8 IDVSEVVELFEKRNLLEELIPYLESALKLN-SENPALQTKLIELYAKYDP-QKEIERLDN------KSNHYDIEKVGKLC   79 (140)
T ss_pred             CCHHHHHHHHHhCCcHHHHHHHHHHHHccC-ccchhHHHHHHHHHHHHCH-HHHHHHHHh------ccccCCHHHHHHHH
Confidence            344567788888888888888888887776 3677788888888887643 333333331      13445555677888


Q ss_pred             HhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHH
Q 039342          104 AKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALW  175 (248)
Q Consensus       104 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  175 (248)
                      .+.+.++++.-++.++..     .......++.    ..++.+.|.+.+.+      ..+...|..++..+.
T Consensus        80 ~~~~l~~~~~~l~~k~~~-----~~~Al~~~l~----~~~d~~~a~~~~~~------~~~~~lw~~~~~~~l  136 (140)
T smart00299       80 EKAKLYEEAVELYKKDGN-----FKDAIVTLIE----HLGNYEKAIEYFVK------QNNPELWAEVLKALL  136 (140)
T ss_pred             HHcCcHHHHHHHHHhhcC-----HHHHHHHHHH----cccCHHHHHHHHHh------CCCHHHHHHHHHHHH
Confidence            888888888888776521     1222222222    22445666655553      114455665555544

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=94.95  E-value=0.75  Score=31.47  Aligned_cols=110  Identities=15%  Similarity=0.122  Sum_probs=68.1

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccc
Q 039342           62 EAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDD  141 (248)
Q Consensus        62 ~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~  141 (248)
                      ..++..+...+.......+++.+...+. .+...++.++..|++.+ ..+.+..++.   .   ++......++.- |.+
T Consensus        11 ~~vv~~~~~~~~~~~l~~yLe~~~~~~~-~~~~~~~~li~ly~~~~-~~~ll~~l~~---~---~~~yd~~~~~~~-c~~   81 (140)
T smart00299       11 SEVVELFEKRNLLEELIPYLESALKLNS-ENPALQTKLIELYAKYD-PQKEIERLDN---K---SNHYDIEKVGKL-CEK   81 (140)
T ss_pred             HHHHHHHHhCCcHHHHHHHHHHHHccCc-cchhHHHHHHHHHHHHC-HHHHHHHHHh---c---cccCCHHHHHHH-HHH
Confidence            4567777777788888888888876653 56778888888888764 3444444442   1   111222223333 566


Q ss_pred             cchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhc-CchHHHHHHHHH
Q 039342          142 ESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCL-GLRERAARVLDE  189 (248)
Q Consensus       142 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~-g~~~~a~~~~~~  189 (248)
                      .+.++.+..++..+..         |...++.+... ++.+.|.++..+
T Consensus        82 ~~l~~~~~~l~~k~~~---------~~~Al~~~l~~~~d~~~a~~~~~~  121 (140)
T smart00299       82 AKLYEEAVELYKKDGN---------FKDAIVTLIEHLGNYEKAIEYFVK  121 (140)
T ss_pred             cCcHHHHHHHHHhhcC---------HHHHHHHHHHcccCHHHHHHHHHh
Confidence            6677777777776533         33344444444 777777777765

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=94.91  E-value=0.28  Score=31.35  Aligned_cols=62  Identities=15%  Similarity=0.021  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHH
Q 039342           39 FEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLA  101 (248)
Q Consensus        39 ~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~  101 (248)
                      .-+..+-++.+....+.|++.+..+.+++|.|.+++..|.++|+-.+.+ +.+....|..+++
T Consensus        26 ~we~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K-~~~~~~~Y~~~lq   87 (108)
T PF02284_consen   26 GWELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDK-CGNKKEIYPYILQ   87 (108)
T ss_dssp             HHHHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TTT-TTHHHHHHH
T ss_pred             HHHHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-ccChHHHHHHHHH
Confidence            3355566666777788888888888888888888888888888888743 1122236666654

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 ....

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=94.91  E-value=0.34  Score=30.65  Aligned_cols=63  Identities=14%  Similarity=0.032  Sum_probs=43.0

Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHH
Q 039342           38 RFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLA  101 (248)
Q Consensus        38 ~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~  101 (248)
                      |.-++.+-++.+....+.|++....+.+++|.|.+++..|.++|+-.+.+ +..+...|..+++
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            44456666677777777888888888888888888888888888877633 1123445655544

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.

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=94.88  E-value=1.9  Score=36.38  Aligned_cols=160  Identities=14%  Similarity=0.138  Sum_probs=93.8

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHc-CCCC-----CHHHHHHHHHHHHh----cCChhHHHHHHHHHHHCCCCcCHhhHH
Q 039342           28 AVIEAFRQGGRFEEAIKAYVEMEKV-RCDP-----NERTLEAVLSVYCF----AGLVDESKEQFQEIKSSGILPSVMCYC   97 (248)
Q Consensus        28 ~li~~~~~~~~~~~a~~~~~~m~~~-~~~p-----~~~t~~~ll~~~~~----~g~~~~a~~~~~~m~~~~~~p~~~~~~   97 (248)
                      .++....=.||-+.+++.+.+-.+. ++.-     -.-+|+.++..++.    ....+.|.++++.+.+.  -|+...|.
T Consensus       193 kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~--yP~s~lfl  270 (468)
T PF10300_consen  193 KLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKR--YPNSALFL  270 (468)
T ss_pred             HHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHh--CCCcHHHH
Confidence            3444455568888888888776443 2322     12334444444433    45678888889888875  57766665


Q ss_pred             HHH-HHHHhcCCHHHHHHHHHHHHHCC--CC-chHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHH-
Q 039342           98 MLL-AVYAKSNRWDDAYGLLDEMHTNR--IS-NIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLE-  172 (248)
Q Consensus        98 ~li-~~~~~~~~~~~a~~~~~~m~~~~--~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~-  172 (248)
                      ..- +.+...|++++|++.|++.....  .+ .....+..+... +....+|+.|...|..+.+.. ..+..+|.-+.- 
T Consensus       271 ~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~-~~~~~~w~~A~~~f~~L~~~s-~WSka~Y~Y~~a~  348 (468)
T PF10300_consen  271 FFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWC-HMFQHDWEEAAEYFLRLLKES-KWSKAFYAYLAAA  348 (468)
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHH-HHHHchHHHHHHHHHHHHhcc-ccHHHHHHHHHHH
Confidence            433 33456788999999998754311  11 112222222222 555678899999998888752 223444443333 


Q ss_pred             HHHhcCch-------HHHHHHHHHHH
Q 039342          173 ALWCLGLR-------ERAARVLDEAT  191 (248)
Q Consensus       173 ~~~~~g~~-------~~a~~~~~~m~  191 (248)
                      ++...|+.       ++|.++|.+..
T Consensus       349 c~~~l~~~~~~~~~~~~a~~l~~~vp  374 (468)
T PF10300_consen  349 CLLMLGREEEAKEHKKEAEELFRKVP  374 (468)
T ss_pred             HHHhhccchhhhhhHHHHHHHHHHHH
Confidence            23445666       77888887654

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.

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.84  E-value=0.24  Score=38.54  Aligned_cols=102  Identities=16%  Similarity=0.044  Sum_probs=71.7

Q ss_pred             CCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCC---Cc--hHHhHHHHhcccccccchHHHHHHHHHHHHhcCCC
Q 039342           87 SGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRI---SN--IHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYG  161 (248)
Q Consensus        87 ~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~---~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~  161 (248)
                      .|...+..+....+..-....+++.++..+-+++...-   .|  +..++-.++..     -+++.+..++..=.+.|+-
T Consensus        58 ~g~~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~~~irlllk-----y~pq~~i~~l~npIqYGiF  132 (418)
T KOG4570|consen   58 RGLPVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTIHTWIRLLLK-----YDPQKAIYTLVNPIQYGIF  132 (418)
T ss_pred             cCCCcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccHHHHHHHHHc-----cChHHHHHHHhCcchhccc
Confidence            35555677777777777777788888888888765421   11  12222222222     2346777777777788999


Q ss_pred             CCHHHHHHHHHHHHhcCchHHHHHHHHHHHHC
Q 039342          162 LGMRFYNALLEALWCLGLRERAARVLDEATKR  193 (248)
Q Consensus       162 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  193 (248)
                      ||..+++.+|+.+.+.+++.+|..+...|..+
T Consensus       133 ~dqf~~c~l~D~flk~~n~~~aa~vvt~~~~q  164 (418)
T KOG4570|consen  133 PDQFTFCLLMDSFLKKENYKDAASVVTEVMMQ  164 (418)
T ss_pred             cchhhHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            99999999999999999999998888776644

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=94.70  E-value=0.37  Score=39.59  Aligned_cols=66  Identities=14%  Similarity=0.026  Sum_probs=57.7

Q ss_pred             CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCH----hhHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 039342           55 DPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSV----MCYCMLLAVYAKSNRWDDAYGLLDEMHTN  122 (248)
Q Consensus        55 ~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~  122 (248)
                      +.+...++.+-.+|.+.|++++|...|++..+.  .|+.    .+|..+-.+|...|+.++|+..+++..+.
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            346688999999999999999999999998875  4653    46999999999999999999999998875

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=94.66  E-value=1.6  Score=33.84  Aligned_cols=101  Identities=10%  Similarity=0.168  Sum_probs=65.9

Q ss_pred             CCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc---CChhHHHHHHHHHHHCCCCcCHhhHH
Q 039342           21 RNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFA---GLVDESKEQFQEIKSSGILPSVMCYC   97 (248)
Q Consensus        21 ~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~---g~~~~a~~~~~~m~~~~~~p~~~~~~   97 (248)
                      -|...|-.|-..|...|+...|..-|....+.. .+|...+..+-.++...   .+..++..+|++..... .-++.+-.
T Consensus       154 ~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~-g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D-~~~iral~  231 (287)
T COG4235         154 GDAEGWDLLGRAYMALGRASDALLAYRNALRLA-GDNPEILLGLAEALYYQAGQQMTAKARALLRQALALD-PANIRALS  231 (287)
T ss_pred             CCchhHHHHHHHHHHhcchhHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcC-CccHHHHH
Confidence            367778888888888888888887777765432 34444555444444332   24667777777776643 12556666


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           98 MLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        98 ~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      .|-..+...|++.+|...|+.|.+..
T Consensus       232 lLA~~afe~g~~~~A~~~Wq~lL~~l  257 (287)
T COG4235         232 LLAFAAFEQGDYAEAAAAWQMLLDLL  257 (287)
T ss_pred             HHHHHHHHcccHHHHHHHHHHHHhcC
Confidence            66677777788888888888777654

>PRK15331 chaperone protein SicA; Provisional

Probab=94.32  E-value=0.42  Score=33.60  Aligned_cols=86  Identities=7%  Similarity=-0.087  Sum_probs=55.1

Q ss_pred             HhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHH
Q 039342          104 AKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERA  183 (248)
Q Consensus       104 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a  183 (248)
                      -..|++++|..+|.-+...+  |...-|..-+.+++...+.++.|...|...-..+. -|...+-..-.++...|+.+.|
T Consensus        48 y~~Gk~~eA~~~F~~L~~~d--~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~-~dp~p~f~agqC~l~l~~~~~A  124 (165)
T PRK15331         48 YNQGRLDEAETFFRFLCIYD--FYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLK-NDYRPVFFTGQCQLLMRKAAKA  124 (165)
T ss_pred             HHCCCHHHHHHHHHHHHHhC--cCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc-CCCCccchHHHHHHHhCCHHHH
Confidence            35677777777777765543  44444555555556667777777777766544432 1333355566778888888888


Q ss_pred             HHHHHHHHH
Q 039342          184 ARVLDEATK  192 (248)
Q Consensus       184 ~~~~~~m~~  192 (248)
                      ...|....+
T Consensus       125 ~~~f~~a~~  133 (165)
T PRK15331        125 RQCFELVNE  133 (165)
T ss_pred             HHHHHHHHh
Confidence            888877665

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=94.31  E-value=1.1  Score=30.81  Aligned_cols=82  Identities=10%  Similarity=0.092  Sum_probs=39.0

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcC---C--CCCHHHHHHHHHHHHhcCC-hhHHHHHHHHHHHCCCCcCHhhHHH
Q 039342           25 SFNAVIEAFRQGGRFEEAIKAYVEMEKVR---C--DPNERTLEAVLSVYCFAGL-VDESKEQFQEIKSSGILPSVMCYCM   98 (248)
Q Consensus        25 ~y~~li~~~~~~~~~~~a~~~~~~m~~~~---~--~p~~~t~~~ll~~~~~~g~-~~~a~~~~~~m~~~~~~p~~~~~~~   98 (248)
                      ..|+++...+..+.......+++.+..-.   +  ..+..+|++++.+.++..- ---+..+|+.|++.+.+++..-|..
T Consensus        41 fiN~iL~hl~~~~nf~~~v~~L~~l~~l~~~~~~~~~~~ssf~~if~SlsnSsSaK~~~~~Lf~~Lk~~~~~~t~~dy~~  120 (145)
T PF13762_consen   41 FINCILNHLASYQNFSGVVSILEHLHFLNTDNIIGWLDNSSFHIIFKSLSNSSSAKLTSLTLFNFLKKNDIEFTPSDYSC  120 (145)
T ss_pred             HHHHHHHHHHHccchHHHHHHHHHHHHhhHHHHhhhcccchHHHHHHHHccChHHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            34555555555555555555555542110   0  1233445555555544333 2333445555555555555555555


Q ss_pred             HHHHHHhc
Q 039342           99 LLAVYAKS  106 (248)
Q Consensus        99 li~~~~~~  106 (248)
                      +|.++.+.
T Consensus       121 li~~~l~g  128 (145)
T PF13762_consen  121 LIKAALRG  128 (145)
T ss_pred             HHHHHHcC
Confidence            55555443

>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=94.24  E-value=1.1  Score=32.13  Aligned_cols=62  Identities=19%  Similarity=0.284  Sum_probs=34.3

Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH--HHHHHHHHHHHhcCChhHHHHHHHHHH
Q 039342           24 DSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNE--RTLEAVLSVYCFAGLVDESKEQFQEIK   85 (248)
Q Consensus        24 ~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~--~t~~~ll~~~~~~g~~~~a~~~~~~m~   85 (248)
                      ..+..+...|++.|+.+.|++.|.++.+....|..  ..+-.+|..+.-.+++..+....++..
T Consensus        37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~  100 (177)
T PF10602_consen   37 MALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAE  100 (177)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            35555666666666666666666666554333322  333445555556666666665555554

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.

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

Probab=94.24  E-value=0.88  Score=35.17  Aligned_cols=79  Identities=9%  Similarity=0.025  Sum_probs=59.0

Q ss_pred             HhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHh-----cCCCCCHHHH
Q 039342           93 VMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNC-----EGYGLGMRFY  167 (248)
Q Consensus        93 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~-----~~~~p~~~~~  167 (248)
                      ..++..++..+...|+.+.+.+.++++.... +-+...+..++.+ +...|+...+...|+.+.+     .|+.|...+.
T Consensus       153 ~~~l~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~-y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~  230 (280)
T COG3629         153 IKALTKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEA-YLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELR  230 (280)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHH-HHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHH
Confidence            4477888888888889999999888887664 2345566666666 6667777888888777654     4888888887


Q ss_pred             HHHHHH
Q 039342          168 NALLEA  173 (248)
Q Consensus       168 ~~li~~  173 (248)
                      ......
T Consensus       231 ~~y~~~  236 (280)
T COG3629         231 ALYEEI  236 (280)
T ss_pred             HHHHHH
Confidence            777766

>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=94.17  E-value=2.4  Score=35.42  Aligned_cols=133  Identities=14%  Similarity=0.078  Sum_probs=87.9

Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHH
Q 039342           23 SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAV  102 (248)
Q Consensus        23 ~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~  102 (248)
                      ..-.+.+++.+-+.|..+.|+++...         .   ..-.....+.|+++.|.++-++.      ++...|..|-+.
T Consensus       295 ~~~~~~i~~fL~~~G~~e~AL~~~~D---------~---~~rFeLAl~lg~L~~A~~~a~~~------~~~~~W~~Lg~~  356 (443)
T PF04053_consen  295 KDQGQSIARFLEKKGYPELALQFVTD---------P---DHRFELALQLGNLDIALEIAKEL------DDPEKWKQLGDE  356 (443)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHSS----------H---HHHHHHHHHCT-HHHHHHHCCCC------STHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHCCCHHHHHhhcCC---------h---HHHhHHHHhcCCHHHHHHHHHhc------CcHHHHHHHHHH
Confidence            45578888888888888888877433         2   22345566778888887765443      367799999999


Q ss_pred             HHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHH
Q 039342          103 YAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRER  182 (248)
Q Consensus       103 ~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~  182 (248)
                      ..+.|+++-|++.|.+..+         +..++.- +...|+.+...++.+.....|-      +|....++.-.|+.++
T Consensus       357 AL~~g~~~lAe~c~~k~~d---------~~~L~lL-y~~~g~~~~L~kl~~~a~~~~~------~n~af~~~~~lgd~~~  420 (443)
T PF04053_consen  357 ALRQGNIELAEECYQKAKD---------FSGLLLL-YSSTGDREKLSKLAKIAEERGD------INIAFQAALLLGDVEE  420 (443)
T ss_dssp             HHHTTBHHHHHHHHHHCT----------HHHHHHH-HHHCT-HHHHHHHHHHHHHTT-------HHHHHHHHHHHT-HHH
T ss_pred             HHHcCCHHHHHHHHHhhcC---------ccccHHH-HHHhCCHHHHHHHHHHHHHccC------HHHHHHHHHHcCCHHH
Confidence            9999999999999986532         1222111 3344555677777666655542      6777777788888888


Q ss_pred             HHHHHHH
Q 039342          183 AARVLDE  189 (248)
Q Consensus       183 a~~~~~~  189 (248)
                      ..+++.+
T Consensus       421 cv~lL~~  427 (443)
T PF04053_consen  421 CVDLLIE  427 (443)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8888765

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=94.13  E-value=1.1  Score=30.83  Aligned_cols=92  Identities=14%  Similarity=0.152  Sum_probs=58.5

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcC--CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCC
Q 039342           31 EAFRQGGRFEEAIKAYVEMEKVR--CDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNR  108 (248)
Q Consensus        31 ~~~~~~~~~~~a~~~~~~m~~~~--~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~  108 (248)
                      ....+.|++++|.+.|+.+...=  -+-....--.++.+|.+.+++++|...++++.+....--..-|-..+.+++.-..
T Consensus        18 ~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~vdYa~Y~~gL~~~~~   97 (142)
T PF13512_consen   18 QEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNVDYAYYMRGLSYYEQ   97 (142)
T ss_pred             HHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCccHHHHHHHHHHHHH
Confidence            34456788888888888886651  1223345556788888888888888888888775322223445555555443221


Q ss_pred             -----------------HHHHHHHHHHHHHC
Q 039342          109 -----------------WDDAYGLLDEMHTN  122 (248)
Q Consensus       109 -----------------~~~a~~~~~~m~~~  122 (248)
                                       ...|..-|+++.+.
T Consensus        98 ~~~~~~~~~~~drD~~~~~~A~~~f~~lv~~  128 (142)
T PF13512_consen   98 DEGSLQSFFRSDRDPTPARQAFRDFEQLVRR  128 (142)
T ss_pred             hhhHHhhhcccccCcHHHHHHHHHHHHHHHH
Confidence                             55677777777654

>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=94.10  E-value=0.75  Score=38.29  Aligned_cols=79  Identities=16%  Similarity=0.146  Sum_probs=45.8

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCH
Q 039342           30 IEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRW  109 (248)
Q Consensus        30 i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~  109 (248)
                      .....+.|+.+.|.++.++      ..+...|..|-....+.|+++-|++.|.+..         -|..|+-.|.-.|+.
T Consensus       325 FeLAl~lg~L~~A~~~a~~------~~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~---------d~~~L~lLy~~~g~~  389 (443)
T PF04053_consen  325 FELALQLGNLDIALEIAKE------LDDPEKWKQLGDEALRQGNIELAEECYQKAK---------DFSGLLLLYSSTGDR  389 (443)
T ss_dssp             HHHHHHCT-HHHHHHHCCC------CSTHHHHHHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHCT-H
T ss_pred             hHHHHhcCCHHHHHHHHHh------cCcHHHHHHHHHHHHHcCCHHHHHHHHHhhc---------CccccHHHHHHhCCH
Confidence            3445566666666655443      2355667777777777777777776665533         345555566666666


Q ss_pred             HHHHHHHHHHHHCC
Q 039342          110 DDAYGLLDEMHTNR  123 (248)
Q Consensus       110 ~~a~~~~~~m~~~~  123 (248)
                      +...++.+.....|
T Consensus       390 ~~L~kl~~~a~~~~  403 (443)
T PF04053_consen  390 EKLSKLAKIAEERG  403 (443)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHcc
Confidence            66666665555554

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.

>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=94.06  E-value=1.3  Score=31.89  Aligned_cols=62  Identities=15%  Similarity=0.281  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcC--HhhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 039342           59 RTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPS--VMCYCMLLAVYAKSNRWDDAYGLLDEMH  120 (248)
Q Consensus        59 ~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~--~~~~~~li~~~~~~~~~~~a~~~~~~m~  120 (248)
                      ..+..+...|++.|+.+.|.+.|.++.+....|.  ...+-.+|....-.+++..+...+.+..
T Consensus        37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~  100 (177)
T PF10602_consen   37 MALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAE  100 (177)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            3455566666666666666666666665533332  2345555666666666666665555543

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.

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=93.94  E-value=2.6  Score=33.57  Aligned_cols=187  Identities=11%  Similarity=0.050  Sum_probs=119.6

Q ss_pred             CchHHHHHHHHHHHHcCCCC--CH----------Hh--HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVAR--NS----------DS--FNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSV   67 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~--~~----------~~--y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   67 (248)
                      |.+++|..=|+...+....-  +.          ..  ....+..+...||...|.+....+.+-. +.|...|..--.+
T Consensus       120 Gele~A~~DF~~vl~~~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi~-~Wda~l~~~Rakc  198 (504)
T KOG0624|consen  120 GELEQAEADFDQVLQHEPSNGLVLEAQSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEIQ-PWDASLRQARAKC  198 (504)
T ss_pred             ccHHHHHHHHHHHHhcCCCcchhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhcC-cchhHHHHHHHHH
Confidence            78899999999887654211  11          11  2234556777899999999999988764 5788888888999


Q ss_pred             HHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcc----------
Q 039342           68 YCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKG----------  137 (248)
Q Consensus        68 ~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~----------  137 (248)
                      |...|++..|..=++...+.. .-++.++--+-..+-..|+.+.++...++..+-+  |++......-..          
T Consensus       199 ~i~~~e~k~AI~Dlk~askLs-~DnTe~~ykis~L~Y~vgd~~~sL~~iRECLKld--pdHK~Cf~~YKklkKv~K~les  275 (504)
T KOG0624|consen  199 YIAEGEPKKAIHDLKQASKLS-QDNTEGHYKISQLLYTVGDAENSLKEIRECLKLD--PDHKLCFPFYKKLKKVVKSLES  275 (504)
T ss_pred             HHhcCcHHHHHHHHHHHHhcc-ccchHHHHHHHHHHHhhhhHHHHHHHHHHHHccC--cchhhHHHHHHHHHHHHHHHHH
Confidence            999999998877666655432 1245556666677777888888888888877543  555443222111          


Q ss_pred             --cccccchHHHHHHHHHHHHhcCCCCCHHHHH---HHHHHHHhcCchHHHHHHHHHHHH
Q 039342          138 --EFDDESNWQMVEYVFDKLNCEGYGLGMRFYN---ALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       138 --~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~---~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                        .....++|-.+..-.+...+.........||   .+-.++...|++.+|.+...+..+
T Consensus       276 ~e~~ie~~~~t~cle~ge~vlk~ep~~~~ir~~~~r~~c~C~~~d~~~~eAiqqC~evL~  335 (504)
T KOG0624|consen  276 AEQAIEEKHWTECLEAGEKVLKNEPEETMIRYNGFRVLCTCYREDEQFGEAIQQCKEVLD  335 (504)
T ss_pred             HHHHHhhhhHHHHHHHHHHHHhcCCcccceeeeeeheeeecccccCCHHHHHHHHHHHHh
Confidence              0223445555555555554443332233333   344455567777788777777664

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=93.74  E-value=2.3  Score=32.26  Aligned_cols=171  Identities=16%  Similarity=0.158  Sum_probs=98.6

Q ss_pred             CCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHC-CCCcCHhhHH
Q 039342           21 RNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVR--CDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSS-GILPSVMCYC   97 (248)
Q Consensus        21 ~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~--~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~-~~~p~~~~~~   97 (248)
                      |-...|+--+. -.+.|++++|.+.|+.+.+.-  -+-...+--.++.++.+.++.+.|....++..+. +-.|| .-|-
T Consensus        33 p~~~LY~~g~~-~L~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~~n-~dY~  110 (254)
T COG4105          33 PASELYNEGLT-ELQKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTHPN-ADYA  110 (254)
T ss_pred             CHHHHHHHHHH-HHhcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCCCC-hhHH
Confidence            33444554444 457899999999999997542  2334566667788889999999999999998764 33333 3455


Q ss_pred             HHHHHHHhc-------CCHHH---HHHHHHHHHHC----CCCchHHhH-----------HHHhcccccccchHHHHHHHH
Q 039342           98 MLLAVYAKS-------NRWDD---AYGLLDEMHTN----RISNIHQVT-----------GQMIKGEFDDESNWQMVEYVF  152 (248)
Q Consensus        98 ~li~~~~~~-------~~~~~---a~~~~~~m~~~----~~~~~~~~~-----------~~~l~~~~~~~~~~~~a~~~~  152 (248)
                      .-|.+++.-       .+...   |..-|+++.+.    .-.|+...-           ...|..++.+.+.+..|..-+
T Consensus       111 ~YlkgLs~~~~i~~~~rDq~~~~~A~~~f~~~i~ryPnS~Ya~dA~~~i~~~~d~LA~~Em~IaryY~kr~~~~AA~nR~  190 (254)
T COG4105         111 YYLKGLSYFFQIDDVTRDQSAARAAFAAFKELVQRYPNSRYAPDAKARIVKLNDALAGHEMAIARYYLKRGAYVAAINRF  190 (254)
T ss_pred             HHHHHHHHhccCCccccCHHHHHHHHHHHHHHHHHCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHH
Confidence            455554432       23333   34444444332    222322221           112223455666777777777


Q ss_pred             HHHHhc--CCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHC
Q 039342          153 DKLNCE--GYGLGMRFYNALLEALWCLGLRERAARVLDEATKR  193 (248)
Q Consensus       153 ~~m~~~--~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  193 (248)
                      +.|.+.  ...-.....-.+..+|-..|..++|.+.-.-+..+
T Consensus       191 ~~v~e~y~~t~~~~eaL~~l~eaY~~lgl~~~a~~~~~vl~~N  233 (254)
T COG4105         191 EEVLENYPDTSAVREALARLEEAYYALGLTDEAKKTAKVLGAN  233 (254)
T ss_pred             HHHHhccccccchHHHHHHHHHHHHHhCChHHHHHHHHHHHhc
Confidence            777765  11112233445666777777777777666555443

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

Probab=93.73  E-value=5.6  Score=36.60  Aligned_cols=117  Identities=11%  Similarity=0.131  Sum_probs=75.7

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcc
Q 039342           58 ERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKG  137 (248)
Q Consensus        58 ~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~  137 (248)
                      +..|+.+-.+-.+.|.+.+|.+-|=   +.   -|+..|.-+|+...+.|.+++-.+.+...++....|...+  .++.+
T Consensus      1104 p~vWsqlakAQL~~~~v~dAieSyi---ka---dDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id~--eLi~A 1175 (1666)
T KOG0985|consen 1104 PAVWSQLAKAQLQGGLVKDAIESYI---KA---DDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYIDS--ELIFA 1175 (1666)
T ss_pred             hHHHHHHHHHHHhcCchHHHHHHHH---hc---CCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccchH--HHHHH
Confidence            3457777777777777766665442   21   2667888888888888888888888887777766665443  23333


Q ss_pred             cccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHH
Q 039342          138 EFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEA  190 (248)
Q Consensus       138 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m  190 (248)
                       +.+.++..+.+++.       .-|+......+-+-|...|.++.|.-+|...
T Consensus      1176 -yAkt~rl~elE~fi-------~gpN~A~i~~vGdrcf~~~~y~aAkl~y~~v 1220 (1666)
T KOG0985|consen 1176 -YAKTNRLTELEEFI-------AGPNVANIQQVGDRCFEEKMYEAAKLLYSNV 1220 (1666)
T ss_pred             -HHHhchHHHHHHHh-------cCCCchhHHHHhHHHhhhhhhHHHHHHHHHh
Confidence             44444444433332       3466666777777777778877777776643

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=93.64  E-value=2.3  Score=35.15  Aligned_cols=138  Identities=10%  Similarity=0.154  Sum_probs=74.2

Q ss_pred             hcCCHHHHHHHHHHHHHcCCCCCH------HHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHH--Hhc
Q 039342           35 QGGRFEEAIKAYVEMEKVRCDPNE------RTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVY--AKS  106 (248)
Q Consensus        35 ~~~~~~~a~~~~~~m~~~~~~p~~------~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~--~~~  106 (248)
                      +.+++.++.++|.+.-++. .-++      ..-+.+|++|.. ++.+.+...+..+.+.  .| ...|-.+..+.  -+.
T Consensus        18 kq~~~~esEkifskI~~e~-~~~~f~lkeEvl~grilnAffl-~nld~Me~~l~~l~~~--~~-~s~~l~LF~~L~~Y~~   92 (549)
T PF07079_consen   18 KQKKFQESEKIFSKIYDEK-ESSPFLLKEEVLGGRILNAFFL-NNLDLMEKQLMELRQQ--FG-KSAYLPLFKALVAYKQ   92 (549)
T ss_pred             HHhhhhHHHHHHHHHHHHh-hcchHHHHHHHHhhHHHHHHHH-hhHHHHHHHHHHHHHh--cC-CchHHHHHHHHHHHHh
Confidence            5677788888887774432 1221      223456666664 4566666666666643  22 23344444433  255


Q ss_pred             CCHHHHHHHHHHHHHC--CCCc-----------hHHhHHHHhcccccccchHHHHHHHHHHHHhc----CCCCCHHHHHH
Q 039342          107 NRWDDAYGLLDEMHTN--RISN-----------IHQVTGQMIKGEFDDESNWQMVEYVFDKLNCE----GYGLGMRFYNA  169 (248)
Q Consensus       107 ~~~~~a~~~~~~m~~~--~~~~-----------~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~----~~~p~~~~~~~  169 (248)
                      +..++|.+.+..-.+.  +..|           ++..+..+...+....|.+.++..+++++...    ....+..+|+.
T Consensus        93 k~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~yd~  172 (549)
T PF07079_consen   93 KEYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMYDR  172 (549)
T ss_pred             hhHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHHHH
Confidence            6677777776655433  2211           12222223333345566667777666666544    23367777777


Q ss_pred             HHHHHHhc
Q 039342          170 LLEALWCL  177 (248)
Q Consensus       170 li~~~~~~  177 (248)
                      ++-.+++.
T Consensus       173 ~vlmlsrS  180 (549)
T PF07079_consen  173 AVLMLSRS  180 (549)
T ss_pred             HHHHHhHH
Confidence            77666654

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

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

Probab=93.44  E-value=3.7  Score=33.63  Aligned_cols=154  Identities=10%  Similarity=0.099  Sum_probs=85.8

Q ss_pred             HHhcCCHHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCH-hhHHHHHHHHHhcCCHH
Q 039342           33 FRQGGRFEEAIKAYVEMEKV-RCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSV-MCYCMLLAVYAKSNRWD  110 (248)
Q Consensus        33 ~~~~~~~~~a~~~~~~m~~~-~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~-~~~~~li~~~~~~~~~~  110 (248)
                      .+..++...+.+++-.+... -++-|......+-+.+...|+.+.|...|++.+..  .|+. .....---.+.+.|+.+
T Consensus       206 q~~~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~--dpy~i~~MD~Ya~LL~~eg~~e  283 (564)
T KOG1174|consen  206 QMFNFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCA--NPDNVEAMDLYAVLLGQEGGCE  283 (564)
T ss_pred             HHHhcccchhhhHHHHHHhhccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhhC--ChhhhhhHHHHHHHHHhccCHh
Confidence            33456666666666555433 45667777888889999999999999999887754  2332 22222223344566666


Q ss_pred             HHHHHHHHHHHCCC---Cch---------------------------HHhHHH-Hhcc-cccccchHHHHHHHHHHHHhc
Q 039342          111 DAYGLLDEMHTNRI---SNI---------------------------HQVTGQ-MIKG-EFDDESNWQMVEYVFDKLNCE  158 (248)
Q Consensus       111 ~a~~~~~~m~~~~~---~~~---------------------------~~~~~~-~l~~-~~~~~~~~~~a~~~~~~m~~~  158 (248)
                      ....+...+....-   .|.                           ...... ++.+ .....++.+.|.-.|+..+..
T Consensus       284 ~~~~L~~~Lf~~~~~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I~~~~r~~~alilKG~lL~~~~R~~~A~IaFR~Aq~L  363 (564)
T KOG1174|consen  284 QDSALMDYLFAKVKYTASHWFVHAQLLYDEKKFERALNFVEKCIDSEPRNHEALILKGRLLIALERHTQAVIAFRTAQML  363 (564)
T ss_pred             hHHHHHHHHHhhhhcchhhhhhhhhhhhhhhhHHHHHHHHHHHhccCcccchHHHhccHHHHhccchHHHHHHHHHHHhc
Confidence            66666555533220   010                           000011 1111 122334555555556554443


Q ss_pred             CCCCCHHHHHHHHHHHHhcCchHHHHHHHHH
Q 039342          159 GYGLGMRFYNALLEALWCLGLRERAARVLDE  189 (248)
Q Consensus       159 ~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  189 (248)
                      .. -+...|.-|+.+|...|++.+|.-+-+.
T Consensus       364 ap-~rL~~Y~GL~hsYLA~~~~kEA~~~An~  393 (564)
T KOG1174|consen  364 AP-YRLEIYRGLFHSYLAQKRFKEANALANW  393 (564)
T ss_pred             ch-hhHHHHHHHHHHHHhhchHHHHHHHHHH
Confidence            21 2566777777777777777776665544

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=93.42  E-value=2.9  Score=32.42  Aligned_cols=113  Identities=12%  Similarity=-0.088  Sum_probs=79.6

Q ss_pred             CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHC-CCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHH
Q 039342           92 SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTN-RISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNAL  170 (248)
Q Consensus        92 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l  170 (248)
                      |...|-.|-..|...|+.+.|..-|.+-.+- |-.|+...-..=+..+-.....-.++..++++....+.. |+.+-..+
T Consensus       155 d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D~~-~iral~lL  233 (287)
T COG4235         155 DAEGWDLLGRAYMALGRASDALLAYRNALRLAGDNPEILLGLAEALYYQAGQQMTAKARALLRQALALDPA-NIRALSLL  233 (287)
T ss_pred             CchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcCCc-cHHHHHHH
Confidence            7889999999999999999999999987643 322322221111111123344557888999998887544 66777777


Q ss_pred             HHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHh
Q 039342          171 LEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVW  207 (248)
Q Consensus       171 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~  207 (248)
                      -..+...|++.+|...|+.|.+.  -|.......+|.
T Consensus       234 A~~afe~g~~~~A~~~Wq~lL~~--lp~~~~rr~~ie  268 (287)
T COG4235         234 AFAAFEQGDYAEAAAAWQMLLDL--LPADDPRRSLIE  268 (287)
T ss_pred             HHHHHHcccHHHHHHHHHHHHhc--CCCCCchHHHHH
Confidence            78899999999999999999875  333334455553

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=93.40  E-value=4.9  Score=34.95  Aligned_cols=86  Identities=7%  Similarity=0.054  Sum_probs=53.6

Q ss_pred             ccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchh-hhHHhh-----hhhh
Q 039342          139 FDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRH-NKLVWS-----VDVH  212 (248)
Q Consensus       139 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~-~~li~~-----~~~~  212 (248)
                      +.+...+..|.++|..|-+         ...+++.....++|++|+.+-+...+  +.||+... ...+-.     =..+
T Consensus       757 lk~l~~~gLAaeIF~k~gD---------~ksiVqlHve~~~W~eAFalAe~hPe--~~~dVy~pyaqwLAE~DrFeEAqk  825 (1081)
T KOG1538|consen  757 LKKLDSPGLAAEIFLKMGD---------LKSLVQLHVETQRWDEAFALAEKHPE--FKDDVYMPYAQWLAENDRFEEAQK  825 (1081)
T ss_pred             HhhccccchHHHHHHHhcc---------HHHHhhheeecccchHhHhhhhhCcc--ccccccchHHHHhhhhhhHHHHHH
Confidence            4445556667777776644         24577777888899999888776543  34554321 111100     0246


Q ss_pred             ccccchHHHHHHHHHHHHHHHHH
Q 039342          213 RMWEGGAYTAISVWLNKMYEMFM  235 (248)
Q Consensus       213 ~~~~~g~~~~~~~~~~~m~~~~~  235 (248)
                      +|-+.|+-.+|..+++++....+
T Consensus       826 AfhkAGr~~EA~~vLeQLtnnav  848 (1081)
T KOG1538|consen  826 AFHKAGRQREAVQVLEQLTNNAV  848 (1081)
T ss_pred             HHHHhcchHHHHHHHHHhhhhhh
Confidence            77788888888888888765543

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=93.40  E-value=0.039  Score=38.04  Aligned_cols=85  Identities=19%  Similarity=0.181  Sum_probs=64.8

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcC
Q 039342           28 AVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSN  107 (248)
Q Consensus        28 ~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~  107 (248)
                      .+|..+.+.+.+.....+++.+...+-..+....+.++..|++.++.++..++++   .    .+..-...++..|-+.|
T Consensus        12 ~vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~---~----~~~yd~~~~~~~c~~~~   84 (143)
T PF00637_consen   12 EVISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLK---T----SNNYDLDKALRLCEKHG   84 (143)
T ss_dssp             CCHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTT---S----SSSS-CTHHHHHHHTTT
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcc---c----ccccCHHHHHHHHHhcc
Confidence            3577777888889999999999887767778889999999999988888887776   1    22244456778888888


Q ss_pred             CHHHHHHHHHHH
Q 039342          108 RWDDAYGLLDEM  119 (248)
Q Consensus       108 ~~~~a~~~~~~m  119 (248)
                      .+++|.-++.++
T Consensus        85 l~~~a~~Ly~~~   96 (143)
T PF00637_consen   85 LYEEAVYLYSKL   96 (143)
T ss_dssp             SHHHHHHHHHCC
T ss_pred             hHHHHHHHHHHc
Confidence            888888888765

These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents the 7-fold alpha-alpha-superhelical ARM-type repeat found at the C-terminal of clathrin heavy chains and in VPS (vacuolar protein sorting-associated) proteins. In clathrin heavy chains, the C-terminal 7-fold ARM-type repeats interact to form the central hub of the triskelion. VPS proteins are required for vacuolar assembly and vacuolar traffick, and contain one clathrin-type repeat []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport; PDB: 3LVH_A 3LVG_C 1B89_A 3QIL_L.

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=93.38  E-value=1.7  Score=29.53  Aligned_cols=134  Identities=13%  Similarity=0.137  Sum_probs=74.4

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHH---HHHHHHHHhcCChhHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTL---EAVLSVYCFAGLVDESK   78 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~---~~ll~~~~~~g~~~~a~   78 (248)
                      |.+++..++..+...+   .+..-||=+|......-+-+...++++..-+   -.|...+   ..++.+|++.|.     
T Consensus        16 G~V~qGveii~k~v~S---sni~E~NWvICNiiDaa~C~yvv~~LdsIGk---iFDis~C~NlKrVi~C~~~~n~-----   84 (161)
T PF09205_consen   16 GDVKQGVEIIEKTVNS---SNIKEYNWVICNIIDAADCDYVVETLDSIGK---IFDISKCGNLKRVIECYAKRNK-----   84 (161)
T ss_dssp             T-HHHHHHHHHHHHHH---S-HHHHTHHHHHHHHH--HHHHHHHHHHHGG---GS-GGG-S-THHHHHHHHHTT------
T ss_pred             chHHHHHHHHHHHcCc---CCccccceeeeecchhhchhHHHHHHHHHhh---hcCchhhcchHHHHHHHHHhcc-----
Confidence            5566666666655542   3445555555555555555555555544421   2222221   223333333332     


Q ss_pred             HHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhc
Q 039342           79 EQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCE  158 (248)
Q Consensus        79 ~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  158 (248)
                                   +..-.+.-++.....|+-|.-.+++.++.+.+ .++......+-.+ |.+-|+..++.+++.+.-+.
T Consensus        85 -------------~se~vD~ALd~lv~~~kkDqLdki~~~l~kn~-~~~p~~L~kia~A-y~klg~~r~~~ell~~ACek  149 (161)
T PF09205_consen   85 -------------LSEYVDLALDILVKQGKKDQLDKIYNELKKNE-EINPEFLVKIANA-YKKLGNTREANELLKEACEK  149 (161)
T ss_dssp             ---------------HHHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHH-HHHTT-HHHHHHHHHHHHHT
T ss_pred             -------------hHHHHHHHHHHHHHhccHHHHHHHHHHHhhcc-CCCHHHHHHHHHH-HHHhcchhhHHHHHHHHHHh
Confidence                         34556677888899999999999999987633 4555555555555 89999999999999999998


Q ss_pred             CCC
Q 039342          159 GYG  161 (248)
Q Consensus       159 ~~~  161 (248)
                      |++
T Consensus       150 G~k  152 (161)
T PF09205_consen  150 GLK  152 (161)
T ss_dssp             T-H
T ss_pred             chH
Confidence            875

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=93.28  E-value=3.1  Score=32.29  Aligned_cols=117  Identities=15%  Similarity=0.157  Sum_probs=67.4

Q ss_pred             cCCHHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHh-cC-ChhHHHHHHHHHHH-CCCCcCHhhHHHHHHHHHhcCCHHH
Q 039342           36 GGRFEEAIKAYVEMEK-VRCDPNERTLEAVLSVYCF-AG-LVDESKEQFQEIKS-SGILPSVMCYCMLLAVYAKSNRWDD  111 (248)
Q Consensus        36 ~~~~~~a~~~~~~m~~-~~~~p~~~t~~~ll~~~~~-~g-~~~~a~~~~~~m~~-~~~~p~~~~~~~li~~~~~~~~~~~  111 (248)
                      +..+.+|+.+|+...- ..+--|..+...+++.... .+ ....--++.+-+.. .+-.++..+.-.+|..+++.++|.+
T Consensus       141 N~~Vv~aL~L~~~~~~~~~Ii~d~evislLL~sMv~~~~~~l~alYEvV~~l~~t~~~~l~~~vi~~Il~~L~~~~dW~k  220 (292)
T PF13929_consen  141 NKIVVEALKLYDGLNPDESIIFDEEVISLLLKSMVIDENTKLNALYEVVDFLVSTFSKSLTRNVIISILEILAESRDWNK  220 (292)
T ss_pred             hHHHHHHHHHhhccCcccceeeChHHHHHHHHHHHhccccchhhHHHHHHHHHhccccCCChhHHHHHHHHHHhcccHHH
Confidence            3445667777764322 3455667777777776665 22 33333344444442 2445667777777777777777777


Q ss_pred             HHHHHHHHHHC-CCCchHHhHHHHhcccccccchHHHHHHHHH
Q 039342          112 AYGLLDEMHTN-RISNIHQVTGQMIKGEFDDESNWQMVEYVFD  153 (248)
Q Consensus       112 a~~~~~~m~~~-~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  153 (248)
                      -+++++..... +...|...+..+|.. ....|+......+.+
T Consensus       221 l~~fW~~~~~~~~~~~D~rpW~~FI~l-i~~sgD~~~~~kiI~  262 (292)
T PF13929_consen  221 LFQFWEQCIPNSVPGNDPRPWAEFIKL-IVESGDQEVMRKIID  262 (292)
T ss_pred             HHHHHHHhcccCCCCCCCchHHHHHHH-HHHcCCHHHHHHHhh
Confidence            77777766544 333455555555555 445555555555443

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=93.01  E-value=2.3  Score=30.16  Aligned_cols=99  Identities=9%  Similarity=0.156  Sum_probs=45.3

Q ss_pred             HHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCC
Q 039342           11 LSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGIL   90 (248)
Q Consensus        11 ~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~   90 (248)
                      .+.+.+.+++|+...|..+|..+.+.|++..    +..+...++-+|+......+-.+..  ....+.++=-.|..+   
T Consensus        17 irSl~~~~i~~~~~L~~lli~lLi~~~~~~~----L~qllq~~Vi~DSk~lA~~LLs~~~--~~~~~~Ql~lDMLkR---   87 (167)
T PF07035_consen   17 IRSLNQHNIPVQHELYELLIDLLIRNGQFSQ----LHQLLQYHVIPDSKPLACQLLSLGN--QYPPAYQLGLDMLKR---   87 (167)
T ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHHcCCHHH----HHHHHhhcccCCcHHHHHHHHHhHc--cChHHHHHHHHHHHH---
Confidence            3344455555666666666666666665432    3333444555555444443333322  122233332222221   


Q ss_pred             cCHhhHHHHHHHHHhcCCHHHHHHHHHHH
Q 039342           91 PSVMCYCMLLAVYAKSNRWDDAYGLLDEM  119 (248)
Q Consensus        91 p~~~~~~~li~~~~~~~~~~~a~~~~~~m  119 (248)
                       =...+..++..+...|++-+|+++.+..
T Consensus        88 -L~~~~~~iievLL~~g~vl~ALr~ar~~  115 (167)
T PF07035_consen   88 -LGTAYEEIIEVLLSKGQVLEALRYARQY  115 (167)
T ss_pred             -hhhhHHHHHHHHHhCCCHHHHHHHHHHc
Confidence             0113444555555556666666555543

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=93.00  E-value=4.2  Score=33.03  Aligned_cols=170  Identities=14%  Similarity=0.043  Sum_probs=105.0

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcC---CCCCHHHHHHHHHHHHh---cCChhHHHHHHHHHHHCCCCcCHhh
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVR---CDPNERTLEAVLSVYCF---AGLVDESKEQFQEIKSSGILPSVMC   95 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~---~~p~~~t~~~ll~~~~~---~g~~~~a~~~~~~m~~~~~~p~~~~   95 (248)
                      +..+-..++-+|....+++...++.+.+...-   +.-+...--...-++.|   .|+.++|.+++..+....-.+++.+
T Consensus       140 s~div~~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~  219 (374)
T PF13281_consen  140 SPDIVINLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDT  219 (374)
T ss_pred             ChhHHHHHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHH
Confidence            33444566667999999999999999997651   11122222234445566   8999999999999665555678888


Q ss_pred             HHHHHHHHHh---------cCCHHHHHHHHHHHHHCCCCchHH---hHHHHhcccccccchHHHHHHHH---H-HHHhcC
Q 039342           96 YCMLLAVYAK---------SNRWDDAYGLLDEMHTNRISNIHQ---VTGQMIKGEFDDESNWQMVEYVF---D-KLNCEG  159 (248)
Q Consensus        96 ~~~li~~~~~---------~~~~~~a~~~~~~m~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~---~-~m~~~~  159 (248)
                      |..+-..|-.         ...+++|+..|.+--+..  |+..   -+..++...-.....-.+..++.   . .+.+.|
T Consensus       220 ~gL~GRIyKD~~~~s~~~d~~~ldkAi~~Y~kgFe~~--~~~Y~GIN~AtLL~~~g~~~~~~~el~~i~~~l~~llg~kg  297 (374)
T PF13281_consen  220 LGLLGRIYKDLFLESNFTDRESLDKAIEWYRKGFEIE--PDYYSGINAATLLMLAGHDFETSEELRKIGVKLSSLLGRKG  297 (374)
T ss_pred             HHHHHHHHHHHHHHcCccchHHHHHHHHHHHHHHcCC--ccccchHHHHHHHHHcCCcccchHHHHHHHHHHHHHHHhhc
Confidence            8888777642         224788888888764433  2211   01111111000111112222332   2 222333


Q ss_pred             C---CCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHC
Q 039342          160 Y---GLGMRFYNALLEALWCLGLRERAARVLDEATKR  193 (248)
Q Consensus       160 ~---~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  193 (248)
                      .   ..+--.+.+++.++.-.|+.++|.+..++|.+.
T Consensus       298 ~~~~~~dYWd~ATl~Ea~vL~~d~~ka~~a~e~~~~l  334 (374)
T PF13281_consen  298 SLEKMQDYWDVATLLEASVLAGDYEKAIQAAEKAFKL  334 (374)
T ss_pred             cccccccHHHHHHHHHHHHHcCCHHHHHHHHHHHhhc
Confidence            2   345556678999999999999999999999865

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=92.87  E-value=4.8  Score=33.40  Aligned_cols=131  Identities=14%  Similarity=0.109  Sum_probs=88.1

Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhH-HHHH
Q 039342           23 SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVR-CDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCY-CMLL  100 (248)
Q Consensus        23 ~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~-~~li  100 (248)
                      ...|...|.+..+..-++.|..+|-+..+.| +.++..+++++|..++. |+..-|..+|+.=...  -||...| +-.+
T Consensus       397 t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~~-~d~~ta~~ifelGl~~--f~d~~~y~~kyl  473 (660)
T COG5107         397 TFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYAT-GDRATAYNIFELGLLK--FPDSTLYKEKYL  473 (660)
T ss_pred             hhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhc-CCcchHHHHHHHHHHh--CCCchHHHHHHH
Confidence            4567788888888888999999999999888 77888999999988775 6778888888764433  2455444 4667


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHCCCC-chHHhHHHHhcccccccchHHHHHHHHHHHHh
Q 039342          101 AVYAKSNRWDDAYGLLDEMHTNRIS-NIHQVTGQMIKGEFDDESNWQMVEYVFDKLNC  157 (248)
Q Consensus       101 ~~~~~~~~~~~a~~~~~~m~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  157 (248)
                      ..+.+-++-+.|..+|+.-...--. --..+|..+|.. -..-|+...+..+-+.|.+
T Consensus       474 ~fLi~inde~naraLFetsv~r~~~~q~k~iy~kmi~Y-Es~~G~lN~v~sLe~rf~e  530 (660)
T COG5107         474 LFLIRINDEENARALFETSVERLEKTQLKRIYDKMIEY-ESMVGSLNNVYSLEERFRE  530 (660)
T ss_pred             HHHHHhCcHHHHHHHHHHhHHHHHHhhhhHHHHHHHHH-HHhhcchHHHHhHHHHHHH
Confidence            7778888888888888843321100 113345555543 3344555555555444444

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=92.82  E-value=2.1  Score=29.06  Aligned_cols=104  Identities=11%  Similarity=0.092  Sum_probs=57.0

Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHC-CCCcCHhhHHH---HHHHHHhcC
Q 039342           32 AFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSS-GILPSVMCYCM---LLAVYAKSN  107 (248)
Q Consensus        32 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~-~~~p~~~~~~~---li~~~~~~~  107 (248)
                      +.+..|+.+.|++.|.+.... .+-....||.--.++.-.|+.++|.+=+++..+. |-+ +.....+   --..|-..|
T Consensus        52 alaE~g~Ld~AlE~F~qal~l-~P~raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~-trtacqa~vQRg~lyRl~g  129 (175)
T KOG4555|consen   52 ALAEAGDLDGALELFGQALCL-APERASAYNNRAQALRLQGDDEEALDDLNKALELAGDQ-TRTACQAFVQRGLLYRLLG  129 (175)
T ss_pred             HHHhccchHHHHHHHHHHHHh-cccchHhhccHHHHHHHcCChHHHHHHHHHHHHhcCcc-chHHHHHHHHHHHHHHHhC
Confidence            345667777777777665432 2345566777777777777777776666665543 222 2222222   222344566


Q ss_pred             CHHHHHHHHHHHHHCC----------CCchHHhHHHHhcc
Q 039342          108 RWDDAYGLLDEMHTNR----------ISNIHQVTGQMIKG  137 (248)
Q Consensus       108 ~~~~a~~~~~~m~~~~----------~~~~~~~~~~~l~~  137 (248)
                      +.+.|..-|+..-+-|          +.|-...++.++..
T Consensus       130 ~dd~AR~DFe~AA~LGS~FAr~QLV~lNPYAAlCN~MLa~  169 (175)
T KOG4555|consen  130 NDDAARADFEAAAQLGSKFAREQLVELNPYAALCNQMLAD  169 (175)
T ss_pred             chHHHHHhHHHHHHhCCHHHHHHHHhcChHHHHHHHHHHH
Confidence            6666666665443333          33666666666554

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

Probab=92.78  E-value=0.34  Score=24.38  Aligned_cols=23  Identities=17%  Similarity=0.327  Sum_probs=10.7

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHH
Q 039342           61 LEAVLSVYCFAGLVDESKEQFQE   83 (248)
Q Consensus        61 ~~~ll~~~~~~g~~~~a~~~~~~   83 (248)
                      |+.|-..|.+.|++++|.++|++
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            34444445555555555555544

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=92.75  E-value=1  Score=34.84  Aligned_cols=111  Identities=14%  Similarity=0.069  Sum_probs=73.2

Q ss_pred             HHHHHHHHHHHHH-CCCCchHHhHHHHhccccc-ccchHHHHHHHHHHHHhc-CCCCCHHHHHHHHHHHHhcCchHHHHH
Q 039342          109 WDDAYGLLDEMHT-NRISNIHQVTGQMIKGEFD-DESNWQMVEYVFDKLNCE-GYGLGMRFYNALLEALWCLGLRERAAR  185 (248)
Q Consensus       109 ~~~a~~~~~~m~~-~~~~~~~~~~~~~l~~~~~-~~~~~~~a~~~~~~m~~~-~~~p~~~~~~~li~~~~~~g~~~~a~~  185 (248)
                      +.+|+.+|+.... ..+.-+..+...++..... .+......-++.+.+... +-.++..+...+|+.+++.++|++-.+
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            4566666663221 2355566677666666544 333444455555555543 567888889999999999999999999


Q ss_pred             HHHHHHHC-CCCCCcchhhhHHhhhhhhccccchHHHHHH
Q 039342          186 VLDEATKR-GLFPELFRHNKLVWSVDVHRMWEGGAYTAIS  224 (248)
Q Consensus       186 ~~~~m~~~-g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~  224 (248)
                      +++..... +-.-|..-+..+|     +...+.|+..-+.
T Consensus       224 fW~~~~~~~~~~~D~rpW~~FI-----~li~~sgD~~~~~  258 (292)
T PF13929_consen  224 FWEQCIPNSVPGNDPRPWAEFI-----KLIVESGDQEVMR  258 (292)
T ss_pred             HHHHhcccCCCCCCCchHHHHH-----HHHHHcCCHHHHH
Confidence            99986654 4455666667777     6666777766433

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=92.71  E-value=2.8  Score=30.36  Aligned_cols=126  Identities=13%  Similarity=0.028  Sum_probs=71.8

Q ss_pred             CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCC---CCchHHh
Q 039342           54 CDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNR---ISNIHQV  130 (248)
Q Consensus        54 ~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~---~~~~~~~  130 (248)
                      +.|+...--.|-.+..+.|+..+|...|++-..--+.-|....-.+-++....+++..|...++.+.+..   .+|+...
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            3566666666777777777777777777776544344466666666667777777777777777765543   2344433


Q ss_pred             HHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHH
Q 039342          131 TGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAA  184 (248)
Q Consensus       131 ~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~  184 (248)
                      ...-.   +...|.+..++.-|+.....-.-|....  .--..+.++|+.+++.
T Consensus       165 l~aR~---laa~g~~a~Aesafe~a~~~ypg~~ar~--~Y~e~La~qgr~~ea~  213 (251)
T COG4700         165 LFART---LAAQGKYADAESAFEVAISYYPGPQARI--YYAEMLAKQGRLREAN  213 (251)
T ss_pred             HHHHH---HHhcCCchhHHHHHHHHHHhCCCHHHHH--HHHHHHHHhcchhHHH
Confidence            22211   3345566666666666665433332222  2233445555544443

>PF07163 Pex26: Pex26 protein; InterPro: IPR010797 This family consists of Pex26 and related mammalian proteins

Probab=92.69  E-value=2.6  Score=32.47  Aligned_cols=91  Identities=15%  Similarity=0.107  Sum_probs=66.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHh
Q 039342           26 FNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAK  105 (248)
Q Consensus        26 y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~  105 (248)
                      +..=|.+++..++|.+++...-+.-+.--+.-..+....|-.|.+.+.+..+.++-+...+..-.-+...|.++...|..
T Consensus        86 cvvGIQALAEmnrWreVLsWvlqyYq~pEklPpkIleLCILLysKv~Ep~amlev~~~WL~~p~Nq~lp~y~~vaELyLl  165 (309)
T PF07163_consen   86 CVVGIQALAEMNRWREVLSWVLQYYQVPEKLPPKILELCILLYSKVQEPAAMLEVASAWLQDPSNQSLPEYGTVAELYLL  165 (309)
T ss_pred             hhhhHHHHHHHhhHHHHHHHHHHHhcCcccCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhCcccCCchhhHHHHHHHHH
Confidence            34458899999999999877666533322333456777888899999999999999887654222244558888887776


Q ss_pred             -----cCCHHHHHHHH
Q 039342          106 -----SNRWDDAYGLL  116 (248)
Q Consensus       106 -----~~~~~~a~~~~  116 (248)
                           .|.+++|+++.
T Consensus       166 ~VLlPLG~~~eAeelv  181 (309)
T PF07163_consen  166 HVLLPLGHFSEAEELV  181 (309)
T ss_pred             HHHhccccHHHHHHHH
Confidence                 58999999887

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

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=92.68  E-value=0.49  Score=24.99  Aligned_cols=27  Identities=19%  Similarity=0.165  Sum_probs=14.3

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHC
Q 039342           61 LEAVLSVYCFAGLVDESKEQFQEIKSS   87 (248)
Q Consensus        61 ~~~ll~~~~~~g~~~~a~~~~~~m~~~   87 (248)
                      +..+-..|.+.|++++|.++|++..+.
T Consensus         4 ~~~la~~~~~~G~~~~A~~~~~~~l~~   30 (44)
T PF13428_consen    4 WLALARAYRRLGQPDEAERLLRRALAL   30 (44)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            444455555555555555555555543

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=92.68  E-value=5.5  Score=33.56  Aligned_cols=183  Identities=10%  Similarity=0.026  Sum_probs=85.3

Q ss_pred             hHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHH-------HHHHHHhcCChhH
Q 039342            4 YKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEA-------VLSVYCFAGLVDE   76 (248)
Q Consensus         4 ~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~-------ll~~~~~~g~~~~   76 (248)
                      ++.|++-+....+..  .++.-++..-.+|...|....+...-..-.+.|-. ...-|+.       +-.+|.+.++.+.
T Consensus       240 f~~a~q~y~~a~el~--~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gre-~rad~klIak~~~r~g~a~~k~~~~~~  316 (539)
T KOG0548|consen  240 FETAIQHYAKALELA--TDITYLNNIAAVYLERGKYAECIELCEKAVEVGRE-LRADYKLIAKALARLGNAYTKREDYEG  316 (539)
T ss_pred             HHHHHHHHHHHHhHh--hhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhHH-HHHHHHHHHHHHHHhhhhhhhHHhHHH
Confidence            445555555544432  34445555566666767666655555544443311 1111222       2235555666777


Q ss_pred             HHHHHHHHHHCCCCcCHhhHH-------------------------HHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhH
Q 039342           77 SKEQFQEIKSSGILPSVMCYC-------------------------MLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVT  131 (248)
Q Consensus        77 a~~~~~~m~~~~~~p~~~~~~-------------------------~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~  131 (248)
                      +...|.+....--.|+..+-.                         .--..+.+.|++..|+..|.++....  |+..+.
T Consensus       317 ai~~~~kaLte~Rt~~~ls~lk~~Ek~~k~~e~~a~~~pe~A~e~r~kGne~Fk~gdy~~Av~~YteAIkr~--P~Da~l  394 (539)
T KOG0548|consen  317 AIKYYQKALTEHRTPDLLSKLKEAEKALKEAERKAYINPEKAEEEREKGNEAFKKGDYPEAVKHYTEAIKRD--PEDARL  394 (539)
T ss_pred             HHHHHHHHhhhhcCHHHHHHHHHHHHHHHHHHHHHhhChhHHHHHHHHHHHHHhccCHHHHHHHHHHHHhcC--CchhHH
Confidence            777766654322222211110                         01123345566777777777766554  555554


Q ss_pred             HHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          132 GQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       132 ~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                      .+--..++.+.+.+..+..=.+...+.... ....|.-=..++....++++|.+.|.+-.+
T Consensus       395 YsNRAac~~kL~~~~~aL~Da~~~ieL~p~-~~kgy~RKg~al~~mk~ydkAleay~eale  454 (539)
T KOG0548|consen  395 YSNRAACYLKLGEYPEALKDAKKCIELDPN-FIKAYLRKGAALRAMKEYDKALEAYQEALE  454 (539)
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHhcCch-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            444444455555555555444333333111 122222222223333455566666655443

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=92.66  E-value=3.6  Score=31.48  Aligned_cols=87  Identities=16%  Similarity=0.188  Sum_probs=67.4

Q ss_pred             CCchHHHHHHHHHHHHcCCC--CCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHc-CCCC-CHHHHHHHHHHHHhcCChhH
Q 039342            1 GGLYKECQAILSRMSESGVA--RNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKV-RCDP-NERTLEAVLSVYCFAGLVDE   76 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~--~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~-~~~p-~~~t~~~ll~~~~~~g~~~~   76 (248)
                      +|++..|..-|....+....  -....+-=|-.++...|++++|..+|..+.+. +-.| -+..+--|-.+..+.|+.++
T Consensus       154 sgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKlg~~~~~l~~~d~  233 (262)
T COG1729         154 SGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLGVSLGRLGNTDE  233 (262)
T ss_pred             cCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHhcCHHH
Confidence            48899999999998875431  23344555889999999999999999999664 2222 23566677788899999999


Q ss_pred             HHHHHHHHHHC
Q 039342           77 SKEQFQEIKSS   87 (248)
Q Consensus        77 a~~~~~~m~~~   87 (248)
                      |...|+++.+.
T Consensus       234 A~atl~qv~k~  244 (262)
T COG1729         234 ACATLQQVIKR  244 (262)
T ss_pred             HHHHHHHHHHH
Confidence            99999999875

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=92.63  E-value=4.7  Score=32.72  Aligned_cols=168  Identities=10%  Similarity=0.022  Sum_probs=95.0

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHCC---CCcCHhhHHHHHHHHHh---cCCHHHHHHHHHHHHHCCCCchHHhHH
Q 039342           59 RTLEAVLSVYCFAGLVDESKEQFQEIKSSG---ILPSVMCYCMLLAVYAK---SNRWDDAYGLLDEMHTNRISNIHQVTG  132 (248)
Q Consensus        59 ~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~---~~p~~~~~~~li~~~~~---~~~~~~a~~~~~~m~~~~~~~~~~~~~  132 (248)
                      .+...++-+|....+++.+.++.+.+....   +.-+..+--...-++.+   .|+-++|++++.........++..++.
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            334456667999999999999999998751   11123333344556667   899999999999966655556555554


Q ss_pred             HH--------hcccccccchHHHHHHHHHHHHhcCCCCCHHH---HHHHHHHHHhcC-chHHHHHHH---H-HHHHCCCC
Q 039342          133 QM--------IKGEFDDESNWQMVEYVFDKLNCEGYGLGMRF---YNALLEALWCLG-LRERAARVL---D-EATKRGLF  196 (248)
Q Consensus       133 ~~--------l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~---~~~li~~~~~~g-~~~~a~~~~---~-~m~~~g~~  196 (248)
                      .+        +.+........+.|...|.+--+.  .||...   +.+|+......- .-.+..++-   . ...++|..
T Consensus       222 L~GRIyKD~~~~s~~~d~~~ldkAi~~Y~kgFe~--~~~~Y~GIN~AtLL~~~g~~~~~~~el~~i~~~l~~llg~kg~~  299 (374)
T PF13281_consen  222 LLGRIYKDLFLESNFTDRESLDKAIEWYRKGFEI--EPDYYSGINAATLLMLAGHDFETSEELRKIGVKLSSLLGRKGSL  299 (374)
T ss_pred             HHHHHHHHHHHHcCccchHHHHHHHHHHHHHHcC--CccccchHHHHHHHHHcCCcccchHHHHHHHHHHHHHHHhhccc
Confidence            32        222233444577777777654333  244332   222332222211 111223332   2 22244543


Q ss_pred             CCc---chhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          197 PEL---FRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       197 p~~---~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      -..   ..+.+++     ....-.|+.+.+.+..+.|.+.
T Consensus       300 ~~~~dYWd~ATl~-----Ea~vL~~d~~ka~~a~e~~~~l  334 (374)
T PF13281_consen  300 EKMQDYWDVATLL-----EASVLAGDYEKAIQAAEKAFKL  334 (374)
T ss_pred             cccccHHHHHHHH-----HHHHHcCCHHHHHHHHHHHhhc
Confidence            333   3334444     5555577888888888888765

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=92.56  E-value=2.8  Score=29.96  Aligned_cols=141  Identities=13%  Similarity=0.106  Sum_probs=93.1

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCH-hhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHh
Q 039342           57 NERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSV-MCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMI  135 (248)
Q Consensus        57 ~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l  135 (248)
                      ....|..-++ ..+.+..++|+.-|..+.+.|...-+ ..---.-......|+-..|...|++.-.....|-..--..-+
T Consensus        58 sgd~flaAL~-lA~~~k~d~Alaaf~~lektg~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt~~P~~~rd~ARl  136 (221)
T COG4649          58 SGDAFLAALK-LAQENKTDDALAAFTDLEKTGYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRDLARL  136 (221)
T ss_pred             chHHHHHHHH-HHHcCCchHHHHHHHHHHhcCCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhccCCCcchhhHHHHH
Confidence            3445555554 45678899999999999987644211 122223334567889999999999987665555333111112


Q ss_pred             cc--cccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCC
Q 039342          136 KG--EFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPE  198 (248)
Q Consensus       136 ~~--~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  198 (248)
                      ++  .+...|.++.+....+-+...+-..-...-..|--+-.+.|++.+|.+.|..+...-..|-
T Consensus       137 raa~lLvD~gsy~dV~srvepLa~d~n~mR~sArEALglAa~kagd~a~A~~~F~qia~Da~apr  201 (221)
T COG4649         137 RAAYLLVDNGSYDDVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIANDAQAPR  201 (221)
T ss_pred             HHHHHHhccccHHHHHHHhhhccCCCChhHHHHHHHHhHHHHhccchHHHHHHHHHHHccccCcH
Confidence            21  1456788888888777776665554555556777778889999999999999877555553

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

Probab=92.52  E-value=0.45  Score=23.92  Aligned_cols=26  Identities=23%  Similarity=0.109  Sum_probs=20.7

Q ss_pred             HHHHHHHHHHhcCchHHHHHHHHHHH
Q 039342          166 FYNALLEALWCLGLRERAARVLDEAT  191 (248)
Q Consensus       166 ~~~~li~~~~~~g~~~~a~~~~~~m~  191 (248)
                      +|+.|-+.|.+.|++++|.++|++..
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL   26 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQAL   26 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            46778889999999999999998743

>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=92.46  E-value=2.4  Score=30.98  Aligned_cols=79  Identities=14%  Similarity=0.164  Sum_probs=54.6

Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHC---CCCcCHhhHHHHHHHHHhcCCH
Q 039342           33 FRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSS---GILPSVMCYCMLLAVYAKSNRW  109 (248)
Q Consensus        33 ~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~---~~~p~~~~~~~li~~~~~~~~~  109 (248)
                      +.+.|+ +.|.+.|-.+...+.--|+..--.|...|. ..+.+++..++-...+.   +-.+|+..+.+|...|-+.++.
T Consensus       117 Wsr~~d-~~A~~~fL~~E~~~~l~t~elq~aLAtyY~-krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~  194 (203)
T PF11207_consen  117 WSRFGD-QEALRRFLQLEGTPELETAELQYALATYYT-KRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNY  194 (203)
T ss_pred             hhccCc-HHHHHHHHHHcCCCCCCCHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcch
Confidence            344444 557777777777776555555555554444 67788888888776542   3367888889999999988888


Q ss_pred             HHHH
Q 039342          110 DDAY  113 (248)
Q Consensus       110 ~~a~  113 (248)
                      +.|.
T Consensus       195 e~AY  198 (203)
T PF11207_consen  195 EQAY  198 (203)
T ss_pred             hhhh
Confidence            8774

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=92.38  E-value=2.5  Score=29.04  Aligned_cols=64  Identities=13%  Similarity=0.101  Sum_probs=46.9

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHC-CC-CcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           59 RTLEAVLSVYCFAGLVDESKEQFQEIKSS-GI-LPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        59 ~t~~~ll~~~~~~g~~~~a~~~~~~m~~~-~~-~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      ..|+.-. ...+.|++++|.+.|+.+... -. .-.....-.++.+|.+.+++++|...++++.+..
T Consensus        12 ~ly~~a~-~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLh   77 (142)
T PF13512_consen   12 ELYQEAQ-EALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLH   77 (142)
T ss_pred             HHHHHHH-HHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC
Confidence            3444333 345678999999999998865 11 1245677788899999999999999999887654

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=92.19  E-value=4.1  Score=33.04  Aligned_cols=99  Identities=11%  Similarity=0.014  Sum_probs=53.9

Q ss_pred             HHHhcCCHHHHHHHHHHHHHc-----CC---------CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHH
Q 039342           32 AFRQGGRFEEAIKAYVEMEKV-----RC---------DPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYC   97 (248)
Q Consensus        32 ~~~~~~~~~~a~~~~~~m~~~-----~~---------~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~   97 (248)
                      .|.+.|++..|...|++..+.     +.         ..-...+..+.-+|.+.+++..|.+.-+.....+ ++|.-..-
T Consensus       217 ~~fK~gk~~~A~~~Yerav~~l~~~~~~~~ee~~~~~~~k~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~-~~N~KALy  295 (397)
T KOG0543|consen  217 VLFKEGKFKLAKKRYERAVSFLEYRRSFDEEEQKKAEALKLACHLNLAACYLKLKEYKEAIESCNKVLELD-PNNVKALY  295 (397)
T ss_pred             HHHhhchHHHHHHHHHHHHHHhhccccCCHHHHHHHHHHHHHHhhHHHHHHHhhhhHHHHHHHHHHHHhcC-CCchhHHH
Confidence            567788888887777764321     11         1122334455556666666666666666655543 22444433


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHH
Q 039342           98 MLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQ  133 (248)
Q Consensus        98 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~  133 (248)
                      ---.+|...|+++.|+..|+++.+..  |++.....
T Consensus       296 RrG~A~l~~~e~~~A~~df~ka~k~~--P~Nka~~~  329 (397)
T KOG0543|consen  296 RRGQALLALGEYDLARDDFQKALKLE--PSNKAARA  329 (397)
T ss_pred             HHHHHHHhhccHHHHHHHHHHHHHhC--CCcHHHHH
Confidence            44455555666666666666665432  44444433

>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=91.90  E-value=4.9  Score=31.26  Aligned_cols=165  Identities=13%  Similarity=0.051  Sum_probs=97.4

Q ss_pred             HhHHHHHHHHHhcCCHH---HHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHH
Q 039342           24 DSFNAVIEAFRQGGRFE---EAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLL  100 (248)
Q Consensus        24 ~~y~~li~~~~~~~~~~---~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li  100 (248)
                      .++..++.+|...+..+   +|..+++.+.+.. +-....+-.-++.+.+.++.+.+.+++.+|...- .-+...+..++
T Consensus        85 ~iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~-~~~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~~-~~~e~~~~~~l  162 (278)
T PF08631_consen   85 SILRLLANAYLEWDTYESVEKALNALRLLESEY-GNKPEVFLLKLEILLKSFDEEEYEEILMRMIRSV-DHSESNFDSIL  162 (278)
T ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhC-CCCcHHHHHHHHHHhccCChhHHHHHHHHHHHhc-ccccchHHHHH
Confidence            46777888888887654   4566666664442 2224566667888888999999999999998762 22445666666


Q ss_pred             HHHHh--cCCHHHHHHHHHHHHHCCCCchHH-hHHH-----Hhcccc----cccchHHHHHHHHHHHHhc-CCCCCHHHH
Q 039342          101 AVYAK--SNRWDDAYGLLDEMHTNRISNIHQ-VTGQ-----MIKGEF----DDESNWQMVEYVFDKLNCE-GYGLGMRFY  167 (248)
Q Consensus       101 ~~~~~--~~~~~~a~~~~~~m~~~~~~~~~~-~~~~-----~l~~~~----~~~~~~~~a~~~~~~m~~~-~~~p~~~~~  167 (248)
                      ..+-.  ......|...+..+....+.|... ....     ++....    ......+.+..+++..... +.+.+..+-
T Consensus       163 ~~i~~l~~~~~~~a~~~ld~~l~~r~~~~~~~~~e~~vl~~~~~~~~~~~~~~~~~i~~l~~~~~~v~~~~~~~ls~~~~  242 (278)
T PF08631_consen  163 HHIKQLAEKSPELAAFCLDYLLLNRFKSSEDQWLEKLVLTRVLLTTQSKDLSSSEKIESLEELLSIVEHSLGKQLSAEAA  242 (278)
T ss_pred             HHHHHHHhhCcHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHcCCccccchhHHHHHHHHHHHHHHHhcCCCCHHHH
Confidence            66522  233456667777666555555443 1111     111101    1112255566666644433 444455554


Q ss_pred             HHHHH-------HHHhcCchHHHHHHHHHH
Q 039342          168 NALLE-------ALWCLGLRERAARVLDEA  190 (248)
Q Consensus       168 ~~li~-------~~~~~g~~~~a~~~~~~m  190 (248)
                      .++..       .+.+.++++.|.+.|+--
T Consensus       243 ~a~~~LLW~~~~~~~~~k~y~~A~~w~~~a  272 (278)
T PF08631_consen  243 SAIHTLLWNKGKKHYKAKNYDEAIEWYELA  272 (278)
T ss_pred             HHHHHHHHHHHHHHHhhcCHHHHHHHHHHH
Confidence            44443       355678899999988743

It is also involved in sporulation [].

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=91.77  E-value=7.1  Score=32.83  Aligned_cols=61  Identities=13%  Similarity=0.113  Sum_probs=46.4

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHC-CCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           63 AVLSVYCFAGLVDESKEQFQEIKSS-GILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        63 ~ll~~~~~~g~~~~a~~~~~~m~~~-~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      .+-.++.+.|+.++|.+.|.+|.+. ...-.......||.++...+...++..++.+-.+..
T Consensus       264 RLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~  325 (539)
T PF04184_consen  264 RLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDIS  325 (539)
T ss_pred             HHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhcccc
Confidence            4555667889999999999998754 222234577889999999999999999999865443

The molecular function of this protein is uncertain.

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=91.76  E-value=2.3  Score=27.28  Aligned_cols=59  Identities=12%  Similarity=-0.052  Sum_probs=40.4

Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHH
Q 039342          147 MVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLV  206 (248)
Q Consensus       147 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li  206 (248)
                      ...+-++.+....+.|++....+.+++|-+.+++..|..+|+-.+.+ +.+....|..++
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K-~~~~~~~Y~~~l   86 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDK-CGNKKEIYPYIL   86 (108)
T ss_dssp             HHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TTT-TTHHHHHH
T ss_pred             HHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-ccChHHHHHHHH
Confidence            44555566666788999999999999999999999999999987754 223333566665

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 ....

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=91.16  E-value=4.5  Score=29.39  Aligned_cols=102  Identities=12%  Similarity=0.036  Sum_probs=63.0

Q ss_pred             CCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcC---CCCCHH
Q 039342           89 ILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEG---YGLGMR  165 (248)
Q Consensus        89 ~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~---~~p~~~  165 (248)
                      ..|+...--.|-.+....|+..+|...|++-...-..-+....-.+..+ .-..+++..+...++.+-+..   -+||. 
T Consensus        85 ~ApTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~A-qfa~~~~A~a~~tLe~l~e~~pa~r~pd~-  162 (251)
T COG4700          85 IAPTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQA-QFAIQEFAAAQQTLEDLMEYNPAFRSPDG-  162 (251)
T ss_pred             hchhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHH-HHhhccHHHHHHHHHHHhhcCCccCCCCc-
Confidence            3566666666777777777777777777776554444455555555544 333455666666776665542   23333 


Q ss_pred             HHHHHHHHHHhcCchHHHHHHHHHHHHC
Q 039342          166 FYNALLEALWCLGLRERAARVLDEATKR  193 (248)
Q Consensus       166 ~~~~li~~~~~~g~~~~a~~~~~~m~~~  193 (248)
                       .-.+-+.+...|...+|+.-|+.....
T Consensus       163 -~Ll~aR~laa~g~~a~Aesafe~a~~~  189 (251)
T COG4700         163 -HLLFARTLAAQGKYADAESAFEVAISY  189 (251)
T ss_pred             -hHHHHHHHHhcCCchhHHHHHHHHHHh
Confidence             345566777777777777777776653

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=91.15  E-value=8.4  Score=32.51  Aligned_cols=165  Identities=15%  Similarity=0.105  Sum_probs=109.2

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHH---
Q 039342           25 SFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLA---  101 (248)
Q Consensus        25 ~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~---  101 (248)
                      -+-.+.++.-+..+++.+.+-+....+..  -+..-++..-.+|...|+.......-+.-.+.|-. ...-|+.+-.   
T Consensus       226 ~ek~lgnaaykkk~f~~a~q~y~~a~el~--~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gre-~rad~klIak~~~  302 (539)
T KOG0548|consen  226 KEKELGNAAYKKKDFETAIQHYAKALELA--TDITYLNNIAAVYLERGKYAECIELCEKAVEVGRE-LRADYKLIAKALA  302 (539)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHhHh--hhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhHH-HHHHHHHHHHHHH
Confidence            35556777778888888888888877654  44444566667788888877777666665555432 2333444444   


Q ss_pred             ----HHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcc------------------------cccccchHHHHHHHHH
Q 039342          102 ----VYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKG------------------------EFDDESNWQMVEYVFD  153 (248)
Q Consensus       102 ----~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~------------------------~~~~~~~~~~a~~~~~  153 (248)
                          +|.+.++.+.++..|.+-......|+...=......                        .+-..+++..|...|.
T Consensus       303 r~g~a~~k~~~~~~ai~~~~kaLte~Rt~~~ls~lk~~Ek~~k~~e~~a~~~pe~A~e~r~kGne~Fk~gdy~~Av~~Yt  382 (539)
T KOG0548|consen  303 RLGNAYTKREDYEGAIKYYQKALTEHRTPDLLSKLKEAEKALKEAERKAYINPEKAEEEREKGNEAFKKGDYPEAVKHYT  382 (539)
T ss_pred             HhhhhhhhHHhHHHHHHHHHHHhhhhcCHHHHHHHHHHHHHHHHHHHHHhhChhHHHHHHHHHHHHHhccCHHHHHHHHH
Confidence                455567788899998887665555544332221110                        1224567888888888


Q ss_pred             HHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHC
Q 039342          154 KLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKR  193 (248)
Q Consensus       154 ~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  193 (248)
                      ++.... +-|...|...--+|.+.|.+..|.+=.+...+.
T Consensus       383 eAIkr~-P~Da~lYsNRAac~~kL~~~~~aL~Da~~~ieL  421 (539)
T KOG0548|consen  383 EAIKRD-PEDARLYSNRAACYLKLGEYPEALKDAKKCIEL  421 (539)
T ss_pred             HHHhcC-CchhHHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            888776 337788888888888999888888766655543

>KOG1550 consensus Extracellular protein SEL-1 and related proteins [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=91.10  E-value=9.5  Score=33.03  Aligned_cols=184  Identities=9%  Similarity=0.010  Sum_probs=109.8

Q ss_pred             hHHHHHHHHHHHHcCCCCCHHhHHHHHH--H-HHhcCCHHHHHHHHHHHHH-------cCCCCCHHHHHHHHHHHHhcC-
Q 039342            4 YKECQAILSRMSESGVARNSDSFNAVIE--A-FRQGGRFEEAIKAYVEMEK-------VRCDPNERTLEAVLSVYCFAG-   72 (248)
Q Consensus         4 ~~~a~~~~~~m~~~g~~~~~~~y~~li~--~-~~~~~~~~~a~~~~~~m~~-------~~~~p~~~t~~~ll~~~~~~g-   72 (248)
                      ...|.+.++...+.|.. .....-..+.  + +....|++.|+..|+...+       .|.   .....-+-.+|.+.. 
T Consensus       228 ~~~a~~~~~~~a~~g~~-~a~~~~g~~y~~G~~g~~~d~e~a~~~l~~aa~~~~~~a~~~~---~~a~~~lg~~Y~~g~~  303 (552)
T KOG1550|consen  228 LSEAFKYYREAAKLGHS-EAQYALGICYLAGTYGVTQDLESAIEYLKLAAESFKKAATKGL---PPAQYGLGRLYLQGLG  303 (552)
T ss_pred             hhHHHHHHHHHHhhcch-HHHHHHHHHHhhccccccccHHHHHHHHHHHHHHHHHHHhhcC---CccccHHHHHHhcCCC
Confidence            46788888888776652 2222222222  2 4567789999999999866       452   224455666666543 


Q ss_pred             ----ChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHh-cCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHH
Q 039342           73 ----LVDESKEQFQEIKSSGILPSVMCYCMLLAVYAK-SNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQM  147 (248)
Q Consensus        73 ----~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~-~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~  147 (248)
                          +.+.|..++...-+.|. |+....-..+.-... ..+...|.+.|..--+.|..+-.--+..+.........+...
T Consensus       304 ~~~~d~~~A~~~~~~aA~~g~-~~a~~~lg~~~~~g~~~~d~~~A~~yy~~Aa~~G~~~A~~~la~~y~~G~gv~r~~~~  382 (552)
T KOG1550|consen  304 VEKIDYEKALKLYTKAAELGN-PDAQYLLGVLYETGTKERDYRRAFEYYSLAAKAGHILAIYRLALCYELGLGVERNLEL  382 (552)
T ss_pred             CccccHHHHHHHHHHHHhcCC-chHHHHHHHHHHcCCccccHHHHHHHHHHHHHcCChHHHHHHHHHHHhCCCcCCCHHH
Confidence                56778888888877764 344433333333333 356789999999988888544332222222222445567788


Q ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCC
Q 039342          148 VEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRG  194 (248)
Q Consensus       148 a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  194 (248)
                      |..++...-+.| .|...---..+..+.. +.++.+.-.+..+.+.|
T Consensus       383 A~~~~k~aA~~g-~~~A~~~~~~~~~~g~-~~~~~~~~~~~~~a~~g  427 (552)
T KOG1550|consen  383 AFAYYKKAAEKG-NPSAAYLLGAFYEYGV-GRYDTALALYLYLAELG  427 (552)
T ss_pred             HHHHHHHHHHcc-ChhhHHHHHHHHHHcc-ccccHHHHHHHHHHHhh
Confidence            888888888887 3332222333444444 66666666655555444

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.09  E-value=6.7  Score=31.29  Aligned_cols=85  Identities=13%  Similarity=0.062  Sum_probs=42.4

Q ss_pred             cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHC---CCCcCHhhHHHHHHHHHhcCCHHHH
Q 039342           36 GGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSS---GILPSVMCYCMLLAVYAKSNRWDDA  112 (248)
Q Consensus        36 ~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~---~~~p~~~~~~~li~~~~~~~~~~~a  112 (248)
                      .|...+|-..++++.+. .+-|...++-.=.+|.-.|+.+.....+++....   +++..+.+-...--++...|-+++|
T Consensus       116 ~g~~h~a~~~wdklL~d-~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~wn~dlp~~sYv~GmyaFgL~E~g~y~dA  194 (491)
T KOG2610|consen  116 RGKHHEAAIEWDKLLDD-YPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPKWNADLPCYSYVHGMYAFGLEECGIYDDA  194 (491)
T ss_pred             cccccHHHHHHHHHHHh-CchhhhhhhhhhhHHHhccchhhhhhHHHHhccccCCCCcHHHHHHHHHHhhHHHhccchhH
Confidence            34444455555555432 3455555555556666666666666666665532   2211222222233333455666666


Q ss_pred             HHHHHHHHH
Q 039342          113 YGLLDEMHT  121 (248)
Q Consensus       113 ~~~~~~m~~  121 (248)
                      ++.-++-.+
T Consensus       195 Ek~A~ralq  203 (491)
T KOG2610|consen  195 EKQADRALQ  203 (491)
T ss_pred             HHHHHhhcc
Confidence            666655443

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

Probab=90.61  E-value=0.87  Score=23.29  Aligned_cols=25  Identities=24%  Similarity=0.361  Sum_probs=12.3

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHH
Q 039342           60 TLEAVLSVYCFAGLVDESKEQFQEI   84 (248)
Q Consensus        60 t~~~ll~~~~~~g~~~~a~~~~~~m   84 (248)
                      +++.+-..|...|++++|..++++.
T Consensus         4 ~~~~la~~~~~~g~~~~A~~~~~~a   28 (42)
T PF13374_consen    4 ALNNLANAYRAQGRYEEALELLEEA   28 (42)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhcchhhHHHHHH
Confidence            4445555555555555555555444

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

Probab=90.48  E-value=1  Score=22.99  Aligned_cols=29  Identities=31%  Similarity=0.304  Sum_probs=23.3

Q ss_pred             HHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          164 MRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       164 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                      ..+++.+-..|...|++++|..++++...
T Consensus         2 a~~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    2 ASALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            45788889999999999999999988653

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=90.00  E-value=7.5  Score=33.53  Aligned_cols=133  Identities=13%  Similarity=0.038  Sum_probs=89.6

Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHH
Q 039342           24 DSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVY  103 (248)
Q Consensus        24 ~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~  103 (248)
                      ..-+.+.+.+-+.|-.++|+++         .+|..-   -.....+.|+++.|.++..+..      +..-|..|-++.
T Consensus       615 ~~rt~va~Fle~~g~~e~AL~~---------s~D~d~---rFelal~lgrl~iA~~la~e~~------s~~Kw~~Lg~~a  676 (794)
T KOG0276|consen  615 EIRTKVAHFLESQGMKEQALEL---------STDPDQ---RFELALKLGRLDIAFDLAVEAN------SEVKWRQLGDAA  676 (794)
T ss_pred             hhhhhHHhHhhhccchHhhhhc---------CCChhh---hhhhhhhcCcHHHHHHHHHhhc------chHHHHHHHHHH
Confidence            3555666667777777777654         333321   1234456788888887765533      677899999999


Q ss_pred             HhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHH
Q 039342          104 AKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERA  183 (248)
Q Consensus       104 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a  183 (248)
                      ...+++..|.+.|..-++-+         .++.. +...|+-+....+-...++.|.      .|...-+|...|+++++
T Consensus       677 l~~~~l~lA~EC~~~a~d~~---------~LlLl-~t~~g~~~~l~~la~~~~~~g~------~N~AF~~~~l~g~~~~C  740 (794)
T KOG0276|consen  677 LSAGELPLASECFLRARDLG---------SLLLL-YTSSGNAEGLAVLASLAKKQGK------NNLAFLAYFLSGDYEEC  740 (794)
T ss_pred             hhcccchhHHHHHHhhcchh---------hhhhh-hhhcCChhHHHHHHHHHHhhcc------cchHHHHHHHcCCHHHH
Confidence            99999999999998765433         33333 4445554555555555555554      46677788899999999


Q ss_pred             HHHHHHH
Q 039342          184 ARVLDEA  190 (248)
Q Consensus       184 ~~~~~~m  190 (248)
                      .+++.+-
T Consensus       741 ~~lLi~t  747 (794)
T KOG0276|consen  741 LELLIST  747 (794)
T ss_pred             HHHHHhc
Confidence            9998753

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=89.95  E-value=1.8  Score=22.78  Aligned_cols=29  Identities=21%  Similarity=0.261  Sum_probs=25.7

Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 039342           24 DSFNAVIEAFRQGGRFEEAIKAYVEMEKV   52 (248)
Q Consensus        24 ~~y~~li~~~~~~~~~~~a~~~~~~m~~~   52 (248)
                      .+|..+-..|...|++++|.++|++..+.
T Consensus         2 ~~~~~la~~~~~~G~~~~A~~~~~~~l~~   30 (44)
T PF13428_consen    2 AAWLALARAYRRLGQPDEAERLLRRALAL   30 (44)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            46778889999999999999999999876

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.92  E-value=8.7  Score=30.69  Aligned_cols=149  Identities=8%  Similarity=0.001  Sum_probs=101.0

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHhcCChhHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKV---RCDPNERTLEAVLSVYCFAGLVDESK   78 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~---~~~p~~~t~~~ll~~~~~~g~~~~a~   78 (248)
                      |...+|-..++++.+. .+.|...++..=.+|.-.|+...-...+++..-.   +++..+......--++...|-+++|+
T Consensus       117 g~~h~a~~~wdklL~d-~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~wn~dlp~~sYv~GmyaFgL~E~g~y~dAE  195 (491)
T KOG2610|consen  117 GKHHEAAIEWDKLLDD-YPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPKWNADLPCYSYVHGMYAFGLEECGIYDDAE  195 (491)
T ss_pred             ccccHHHHHHHHHHHh-CchhhhhhhhhhhHHHhccchhhhhhHHHHhccccCCCCcHHHHHHHHHHhhHHHhccchhHH
Confidence            6677777888887653 5578888888889999999998888888887433   33333333344444556889999999


Q ss_pred             HHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCC----CCchHHhHHHHhcccccccchHHHHHHHHHH
Q 039342           79 EQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNR----ISNIHQVTGQMIKGEFDDESNWQMVEYVFDK  154 (248)
Q Consensus        79 ~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~----~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  154 (248)
                      +.-++-.+.+ +.|...-.+.-..+--++++.++.++..+-.+.-    ....+.-+...+-  +...+.++.|..+|+.
T Consensus       196 k~A~ralqiN-~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~s~mlasHNyWH~Al~--~iE~aeye~aleIyD~  272 (491)
T KOG2610|consen  196 KQADRALQIN-RFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWMLASHNYWHTALF--HIEGAEYEKALEIYDR  272 (491)
T ss_pred             HHHHhhccCC-CcchHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHHHhhhhHHHHHh--hhcccchhHHHHHHHH
Confidence            9888877654 3366777788888888899999988876543221    1112222222222  4455778888888865

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=89.72  E-value=4.8  Score=27.39  Aligned_cols=105  Identities=12%  Similarity=0.022  Sum_probs=69.7

Q ss_pred             HHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhc--ccccccch
Q 039342           67 VYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIK--GEFDDESN  144 (248)
Q Consensus        67 ~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~--~~~~~~~~  144 (248)
                      +.+..|+++.|.+.|.+....- +-....||.-..++--.|+.++|++-+++..+-.-.-+.......+.  ..|+..|+
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            5678899999999998877641 22678899999999999999999998888765432223333332222  11455566


Q ss_pred             HHHHHHHHHHHHhcC----------CCCCHHHHHHHHH
Q 039342          145 WQMVEYVFDKLNCEG----------YGLGMRFYNALLE  172 (248)
Q Consensus       145 ~~~a~~~~~~m~~~~----------~~p~~~~~~~li~  172 (248)
                      -+.|..=|+..-+.|          +.|-...+|-++.
T Consensus       131 dd~AR~DFe~AA~LGS~FAr~QLV~lNPYAAlCN~MLa  168 (175)
T KOG4555|consen  131 DDAARADFEAAAQLGSKFAREQLVELNPYAALCNQMLA  168 (175)
T ss_pred             hHHHHHhHHHHHHhCCHHHHHHHHhcChHHHHHHHHHH
Confidence            666666655544443          4576667776664

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=89.71  E-value=3.7  Score=26.12  Aligned_cols=67  Identities=12%  Similarity=-0.022  Sum_probs=47.6

Q ss_pred             ccccc-hHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHH
Q 039342          139 FDDES-NWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLV  206 (248)
Q Consensus       139 ~~~~~-~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li  206 (248)
                      +.+.. +.-.+.+-++.+...+..|++....+.+++|-+.+++..|..+|+-.+.+ +..+...|..++
T Consensus        16 F~~~~iD~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K-~~~~~~~y~~~l   83 (103)
T cd00923          16 FNRPDIDGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDK-CGAHKEIYPYIL   83 (103)
T ss_pred             hCCcCccHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-ccCchhhHHHHH
Confidence            44442 34455566667777788999999999999999999999999999877743 122334555555

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.

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=89.36  E-value=5.8  Score=27.90  Aligned_cols=52  Identities=19%  Similarity=0.205  Sum_probs=23.1

Q ss_pred             HhcCChhHHHHHHHHHHHCCCCcCHhhHH-HHHHHHHhcCCHHHHHHHHHHHHHC
Q 039342           69 CFAGLVDESKEQFQEIKSSGILPSVMCYC-MLLAVYAKSNRWDDAYGLLDEMHTN  122 (248)
Q Consensus        69 ~~~g~~~~a~~~~~~m~~~~~~p~~~~~~-~li~~~~~~~~~~~a~~~~~~m~~~  122 (248)
                      .+.++.+.+..++..++-.  .|...... .--..+.+.|+|++|+++|+++.+.
T Consensus        21 l~~~~~~D~e~lL~ALrvL--RP~~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~   73 (160)
T PF09613_consen   21 LRLGDPDDAEALLDALRVL--RPEFPELDLFDGWLHIVRGDWDDALRLLRELEER   73 (160)
T ss_pred             HccCChHHHHHHHHHHHHh--CCCchHHHHHHHHHHHHhCCHHHHHHHHHHHhcc
Confidence            3444555555555555432  23221111 1112234555566666666555433

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=89.05  E-value=8.9  Score=31.22  Aligned_cols=96  Identities=15%  Similarity=0.160  Sum_probs=70.9

Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhH-HHHHH
Q 039342           23 SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCY-CMLLA  101 (248)
Q Consensus        23 ~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~-~~li~  101 (248)
                      ..+++.+..++.+.+++..|++.-+.....+ ++|.-..----.+|...|+++.|+..|+.+.+.  .|+...- +-|+.
T Consensus       257 ~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~-~~N~KALyRrG~A~l~~~e~~~A~~df~ka~k~--~P~Nka~~~el~~  333 (397)
T KOG0543|consen  257 LACHLNLAACYLKLKEYKEAIESCNKVLELD-PNNVKALYRRGQALLALGEYDLARDDFQKALKL--EPSNKAARAELIK  333 (397)
T ss_pred             HHHhhHHHHHHHhhhhHHHHHHHHHHHHhcC-CCchhHHHHHHHHHHhhccHHHHHHHHHHHHHh--CCCcHHHHHHHHH
Confidence            4578888889999999999999988887765 466666666677899999999999999999885  5755444 44444


Q ss_pred             HHHhcCCH-HHHHHHHHHHHH
Q 039342          102 VYAKSNRW-DDAYGLLDEMHT  121 (248)
Q Consensus       102 ~~~~~~~~-~~a~~~~~~m~~  121 (248)
                      .-.+.... +...++|..|-.
T Consensus       334 l~~k~~~~~~kekk~y~~mF~  354 (397)
T KOG0543|consen  334 LKQKIREYEEKEKKMYANMFA  354 (397)
T ss_pred             HHHHHHHHHHHHHHHHHHHhh
Confidence            44444443 334677777754

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

Probab=88.99  E-value=2.1  Score=23.24  Aligned_cols=30  Identities=23%  Similarity=0.308  Sum_probs=14.0

Q ss_pred             cCChhHHHHHHHHHHHCCCCcCHhhHHHHH
Q 039342           71 AGLVDESKEQFQEIKSSGILPSVMCYCMLL  100 (248)
Q Consensus        71 ~g~~~~a~~~~~~m~~~~~~p~~~~~~~li  100 (248)
                      .|..+++..++++|.+.|+..+...|..++
T Consensus        15 ~GlI~~~~~~l~~l~~~g~~is~~l~~~~L   44 (48)
T PF11848_consen   15 RGLISEVKPLLDRLQQAGFRISPKLIEEIL   44 (48)
T ss_pred             cCChhhHHHHHHHHHHcCcccCHHHHHHHH
Confidence            344444444455554444444444444433

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

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=88.91  E-value=17  Score=32.76  Aligned_cols=81  Identities=17%  Similarity=0.293  Sum_probs=51.6

Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHH
Q 039342           32 AFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDD  111 (248)
Q Consensus        32 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~  111 (248)
                      .+.+.|++++|..-|-+-... +.|     .-+|.-|....++..--.+++.+.+.|+. +...-..|+.+|.+.++.++
T Consensus       377 ~Ly~Kgdf~~A~~qYI~tI~~-le~-----s~Vi~kfLdaq~IknLt~YLe~L~~~gla-~~dhttlLLncYiKlkd~~k  449 (933)
T KOG2114|consen  377 YLYGKGDFDEATDQYIETIGF-LEP-----SEVIKKFLDAQRIKNLTSYLEALHKKGLA-NSDHTTLLLNCYIKLKDVEK  449 (933)
T ss_pred             HHHhcCCHHHHHHHHHHHccc-CCh-----HHHHHHhcCHHHHHHHHHHHHHHHHcccc-cchhHHHHHHHHHHhcchHH
Confidence            344678888887776664321 222     23556666666666667777777777765 55566777788887777766


Q ss_pred             HHHHHHHH
Q 039342          112 AYGLLDEM  119 (248)
Q Consensus       112 a~~~~~~m  119 (248)
                      -.++.+..
T Consensus       450 L~efI~~~  457 (933)
T KOG2114|consen  450 LTEFISKC  457 (933)
T ss_pred             HHHHHhcC
Confidence            65555543

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=88.84  E-value=13  Score=31.07  Aligned_cols=131  Identities=8%  Similarity=0.085  Sum_probs=84.5

Q ss_pred             CchHHHHHHHHHHHHcCC-CCC----HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH--HHhcCCh
Q 039342            2 GLYKECQAILSRMSESGV-ARN----SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSV--YCFAGLV   74 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~-~~~----~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~--~~~~g~~   74 (248)
                      |++.+|+++|.++-+..- .|.    ...-+.+|++|... +.+.....+....+.  .| ...|-.+..+  +.+.+++
T Consensus        20 ~~~~esEkifskI~~e~~~~~f~lkeEvl~grilnAffl~-nld~Me~~l~~l~~~--~~-~s~~l~LF~~L~~Y~~k~~   95 (549)
T PF07079_consen   20 KKFQESEKIFSKIYDEKESSPFLLKEEVLGGRILNAFFLN-NLDLMEKQLMELRQQ--FG-KSAYLPLFKALVAYKQKEY   95 (549)
T ss_pred             hhhhHHHHHHHHHHHHhhcchHHHHHHHHhhHHHHHHHHh-hHHHHHHHHHHHHHh--cC-CchHHHHHHHHHHHHhhhH
Confidence            578899999999865422 111    23456677887755 355555555555433  23 2345555444  4578899


Q ss_pred             hHHHHHHHHHHHC--CCC------------cCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC----chHHhHHHHhc
Q 039342           75 DESKEQFQEIKSS--GIL------------PSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRIS----NIHQVTGQMIK  136 (248)
Q Consensus        75 ~~a~~~~~~m~~~--~~~------------p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~----~~~~~~~~~l~  136 (248)
                      ++|.+.+....+.  +-.            +|-.-=+..+.++...|++.++..+++++...=.+    -+..+|+.++.
T Consensus        96 ~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~yd~~vl  175 (549)
T PF07079_consen   96 RKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMYDRAVL  175 (549)
T ss_pred             HHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHHHHHHH
Confidence            9999999888754  322            22233356677888999999999999998765433    56667776543

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>KOG4077 consensus Cytochrome c oxidase, subunit Va/COX6 [Energy production and conversion]

Probab=88.58  E-value=4.5  Score=27.18  Aligned_cols=43  Identities=14%  Similarity=0.266  Sum_probs=22.3

Q ss_pred             HHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 039342           78 KEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMH  120 (248)
Q Consensus        78 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~  120 (248)
                      .+-++.+....+.|++.+...-+++|-+.+++..|.++|+-+.
T Consensus        69 rkglN~l~~yDlVP~pkvIEaaLRA~RRvNDfa~aVRilE~iK  111 (149)
T KOG4077|consen   69 RKGLNNLFDYDLVPSPKVIEAALRACRRVNDFATAVRILEAIK  111 (149)
T ss_pred             HHHHHhhhccccCCChHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            3344444444555555555555555555555555555555443

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=88.27  E-value=13  Score=30.45  Aligned_cols=190  Identities=15%  Similarity=0.147  Sum_probs=114.7

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHH--hcCCHHHHHHHHHHHHHcCCCCCHHHH--HHHHHHHHhcCChhH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFR--QGGRFEEAIKAYVEMEKVRCDPNERTL--EAVLSVYCFAGLVDE   76 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~--~~~~~~~a~~~~~~m~~~~~~p~~~t~--~~ll~~~~~~g~~~~   76 (248)
                      +||-..|.++-.+-.+. +.-|....-.++.+-.  -.|+++.|.+-|+.|...   |...-.  ..|.-.--+.|..+.
T Consensus        97 AGda~lARkmt~~~~~l-lssDqepLIhlLeAQaal~eG~~~~Ar~kfeAMl~d---PEtRllGLRgLyleAqr~Garea  172 (531)
T COG3898          97 AGDASLARKMTARASKL-LSSDQEPLIHLLEAQAALLEGDYEDARKKFEAMLDD---PETRLLGLRGLYLEAQRLGAREA  172 (531)
T ss_pred             cCchHHHHHHHHHHHhh-hhccchHHHHHHHHHHHHhcCchHHHHHHHHHHhcC---hHHHHHhHHHHHHHHHhcccHHH
Confidence            46666777666554321 2234455555555443  469999999999999752   333222  234444457788888


Q ss_pred             HHHHHHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC-chHHhH-HH-Hhcc--cccccchHHHHHH
Q 039342           77 SKEQFQEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRIS-NIHQVT-GQ-MIKG--EFDDESNWQMVEY  150 (248)
Q Consensus        77 a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-~~~~~~-~~-~l~~--~~~~~~~~~~a~~  150 (248)
                      |..+-+..-+.  .| -...+.+.+...+..|+|+.|+++++.-++..+. ++..-- .. ++.+  ...-..+...+..
T Consensus       173 Ar~yAe~Aa~~--Ap~l~WA~~AtLe~r~~~gdWd~AlkLvd~~~~~~vie~~~aeR~rAvLLtAkA~s~ldadp~~Ar~  250 (531)
T COG3898         173 ARHYAERAAEK--APQLPWAARATLEARCAAGDWDGALKLVDAQRAAKVIEKDVAERSRAVLLTAKAMSLLDADPASARD  250 (531)
T ss_pred             HHHHHHHHHhh--ccCCchHHHHHHHHHHhcCChHHHHHHHHHHHHHHhhchhhHHHHHHHHHHHHHHHHhcCChHHHHH
Confidence            88887776554  34 3578899999999999999999999987654332 222111 11 1111  0111122233333


Q ss_pred             HHHHHHhcCCCCCHHHH-HHHHHHHHhcCchHHHHHHHHHHHHCCCCCC
Q 039342          151 VFDKLNCEGYGLGMRFY-NALLEALWCLGLRERAARVLDEATKRGLFPE  198 (248)
Q Consensus       151 ~~~~m~~~~~~p~~~~~-~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  198 (248)
                      .-.  ...+..||..-- ...-+++.+.|+..++-.+++.+=+..-.|+
T Consensus       251 ~A~--~a~KL~pdlvPaav~AAralf~d~~~rKg~~ilE~aWK~ePHP~  297 (531)
T COG3898         251 DAL--EANKLAPDLVPAAVVAARALFRDGNLRKGSKILETAWKAEPHPD  297 (531)
T ss_pred             HHH--HHhhcCCccchHHHHHHHHHHhccchhhhhhHHHHHHhcCCChH
Confidence            222  233455554432 2345789999999999999999877655554

>PF04097 Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic96 is a component of the nuclear pore complex

Probab=87.97  E-value=1.7  Score=38.02  Aligned_cols=36  Identities=8%  Similarity=0.142  Sum_probs=21.2

Q ss_pred             cchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHHHcC
Q 039342          199 LFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMG  237 (248)
Q Consensus       199 ~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~~~~  237 (248)
                      ..|+..|+.-.-...+...|++++|.   +.+.+.++-|
T Consensus       500 ~~t~~~Ll~L~~ff~~~~~g~~~~AL---~~i~~L~liP  535 (613)
T PF04097_consen  500 RETFQLLLDLAEFFDLYHAGQYEQAL---DIIEKLDLIP  535 (613)
T ss_dssp             HHHHHHHHHHHHHHHHHHTT-HHHHH---HHHHHTT-S-
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHHH---HHHHhCCCCC
Confidence            45666666665566777888888864   4555555666

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.

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

Probab=87.87  E-value=2.9  Score=22.65  Aligned_cols=38  Identities=11%  Similarity=0.152  Sum_probs=30.5

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 039342           30 IEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSV   67 (248)
Q Consensus        30 i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   67 (248)
                      +....+.|-.+++..++++|.+.|+..+...|..++..
T Consensus         9 L~~Ak~~GlI~~~~~~l~~l~~~g~~is~~l~~~~L~~   46 (48)
T PF11848_consen    9 LLLAKRRGLISEVKPLLDRLQQAGFRISPKLIEEILRR   46 (48)
T ss_pred             HHHHHHcCChhhHHHHHHHHHHcCcccCHHHHHHHHHH
Confidence            33445677788899999999999999999888887764

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

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=87.49  E-value=13  Score=33.30  Aligned_cols=92  Identities=17%  Similarity=0.266  Sum_probs=51.4

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHH----HHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHH
Q 039342           25 SFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLS----VYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLL  100 (248)
Q Consensus        25 ~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~----~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li  100 (248)
                      ....-|...++...++-|..+-+.   .+..+  .+...+..    -+.+.|++++|..-|-+-... +.|+     -+|
T Consensus       336 ~le~kL~iL~kK~ly~~Ai~LAk~---~~~d~--d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~-le~s-----~Vi  404 (933)
T KOG2114|consen  336 DLETKLDILFKKNLYKVAINLAKS---QHLDE--DTLAEIHRKYGDYLYGKGDFDEATDQYIETIGF-LEPS-----EVI  404 (933)
T ss_pred             cHHHHHHHHHHhhhHHHHHHHHHh---cCCCH--HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHccc-CChH-----HHH
Confidence            344556666777777777665443   22222  23333333    345677777777666544332 2222     245


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHCCCCch
Q 039342          101 AVYAKSNRWDDAYGLLDEMHTNRISNI  127 (248)
Q Consensus       101 ~~~~~~~~~~~a~~~~~~m~~~~~~~~  127 (248)
                      .-|....++..--..++.+.+.|+...
T Consensus       405 ~kfLdaq~IknLt~YLe~L~~~gla~~  431 (933)
T KOG2114|consen  405 KKFLDAQRIKNLTSYLEALHKKGLANS  431 (933)
T ss_pred             HHhcCHHHHHHHHHHHHHHHHcccccc
Confidence            555666667777777777777776443

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=87.44  E-value=7.6  Score=26.88  Aligned_cols=83  Identities=13%  Similarity=0.052  Sum_probs=44.6

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHCCC-----CchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHH
Q 039342           95 CYCMLLAVYAKSNRWDDAYGLLDEMHTNRI-----SNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNA  169 (248)
Q Consensus        95 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-----~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~  169 (248)
                      ..|+++......+++.....+++.+.--..     ..+...|..++.+.......--.+..+|.-|++.+..++..-|..
T Consensus        41 fiN~iL~hl~~~~nf~~~v~~L~~l~~l~~~~~~~~~~~ssf~~if~SlsnSsSaK~~~~~Lf~~Lk~~~~~~t~~dy~~  120 (145)
T PF13762_consen   41 FINCILNHLASYQNFSGVVSILEHLHFLNTDNIIGWLDNSSFHIIFKSLSNSSSAKLTSLTLFNFLKKNDIEFTPSDYSC  120 (145)
T ss_pred             HHHHHHHHHHHccchHHHHHHHHHHHHhhHHHHhhhcccchHHHHHHHHccChHHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            355555555555666666666555521110     123344555555532222224455566666666666667777777


Q ss_pred             HHHHHHhc
Q 039342          170 LLEALWCL  177 (248)
Q Consensus       170 li~~~~~~  177 (248)
                      +|.++.+.
T Consensus       121 li~~~l~g  128 (145)
T PF13762_consen  121 LIKAALRG  128 (145)
T ss_pred             HHHHHHcC
Confidence            77766655

>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=87.12  E-value=8.5  Score=27.12  Aligned_cols=103  Identities=15%  Similarity=0.074  Sum_probs=59.7

Q ss_pred             HhHHHHHH---HHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHH-HHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHH
Q 039342           24 DSFNAVIE---AFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAV-LSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCML   99 (248)
Q Consensus        24 ~~y~~li~---~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l-l~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l   99 (248)
                      .+.+.||.   .-.+.++.+++..+++-++-.  .|.......+ -..+.+.|+|++|..+|+++.+..  |....-..|
T Consensus         8 ~iv~gLie~~~~al~~~~~~D~e~lL~ALrvL--RP~~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~~--~~~p~~kAL   83 (160)
T PF09613_consen    8 EIVGGLIEVLSVALRLGDPDDAEALLDALRVL--RPEFPELDLFDGWLHIVRGDWDDALRLLRELEERA--PGFPYAKAL   83 (160)
T ss_pred             HHHHHHHHHHHHHHccCChHHHHHHHHHHHHh--CCCchHHHHHHHHHHHHhCCHHHHHHHHHHHhccC--CCChHHHHH
Confidence            33444444   445678999999999998754  4555443322 345678899999999999987653  444444445


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHCCCCchHHh
Q 039342          100 LAVYAKSNRWDDAYGLLDEMHTNRISNIHQV  130 (248)
Q Consensus       100 i~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~  130 (248)
                      +..|.....-..=...-++..+.+-.|+...
T Consensus        84 lA~CL~~~~D~~Wr~~A~evle~~~d~~a~~  114 (160)
T PF09613_consen   84 LALCLYALGDPSWRRYADEVLESGADPDARA  114 (160)
T ss_pred             HHHHHHHcCChHHHHHHHHHHhcCCChHHHH
Confidence            5444433322222222334445554444443

>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=87.09  E-value=0.26  Score=33.89  Aligned_cols=77  Identities=14%  Similarity=0.188  Sum_probs=52.4

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      +.++.....++.+...+...+....+.++..|++.++.+...++++..  .++     -...++..|-+.|.++.+.-++
T Consensus        21 ~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~~--~~y-----d~~~~~~~c~~~~l~~~a~~Ly   93 (143)
T PF00637_consen   21 NQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKTS--NNY-----DLDKALRLCEKHGLYEEAVYLY   93 (143)
T ss_dssp             T-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTSS--SSS------CTHHHHHHHTTTSHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcccc--ccc-----CHHHHHHHHHhcchHHHHHHHH
Confidence            345555667777777666677999999999999998888888887721  122     2245667777777777777666


Q ss_pred             HHHH
Q 039342           82 QEIK   85 (248)
Q Consensus        82 ~~m~   85 (248)
                      .++.
T Consensus        94 ~~~~   97 (143)
T PF00637_consen   94 SKLG   97 (143)
T ss_dssp             HCCT
T ss_pred             HHcc
Confidence            6543

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.

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=87.02  E-value=2.7  Score=22.35  Aligned_cols=23  Identities=22%  Similarity=0.315  Sum_probs=11.8

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHC
Q 039342          100 LAVYAKSNRWDDAYGLLDEMHTN  122 (248)
Q Consensus       100 i~~~~~~~~~~~a~~~~~~m~~~  122 (248)
                      -.+|...|+.+.|.+++++....
T Consensus         6 A~ayie~Gd~e~Ar~lL~evl~~   28 (44)
T TIGR03504         6 ARAYIEMGDLEGARELLEEVIEE   28 (44)
T ss_pred             HHHHHHcCChHHHHHHHHHHHHc
Confidence            34555555555555555555443

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.

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=86.90  E-value=13  Score=29.05  Aligned_cols=148  Identities=9%  Similarity=0.041  Sum_probs=80.8

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHH
Q 039342           31 EAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWD  110 (248)
Q Consensus        31 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~  110 (248)
                      ......|+..+|..+|+......- -+...--.+..+|...|+.+.|..++..+...--.........-|..+.+.....
T Consensus       142 ~~~~~~e~~~~a~~~~~~al~~~~-~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~~~~~~l~a~i~ll~qaa~~~  220 (304)
T COG3118         142 KELIEAEDFGEAAPLLKQALQAAP-ENSEAKLLLAECLLAAGDVEAAQAILAALPLQAQDKAAHGLQAQIELLEQAAATP  220 (304)
T ss_pred             hhhhhccchhhHHHHHHHHHHhCc-ccchHHHHHHHHHHHcCChHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHhcCC
Confidence            345667888888888888765432 2234556678888888888888888888764321122222223344444444444


Q ss_pred             HHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHH-HHhc-CCCCCHHHHHHHHHHHHhcCchHHH
Q 039342          111 DAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDK-LNCE-GYGLGMRFYNALLEALWCLGLRERA  183 (248)
Q Consensus       111 ~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~-m~~~-~~~p~~~~~~~li~~~~~~g~~~~a  183 (248)
                      +...+-.+.-..   |++.-...-+.-.+...|+.+.|.+.+-. +.+. |.. |...-..+++.+.-.|..|.+
T Consensus       221 ~~~~l~~~~aad---Pdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~d~~~~-d~~~Rk~lle~f~~~g~~Dp~  291 (304)
T COG3118         221 EIQDLQRRLAAD---PDDVEAALALADQLHLVGRNEAALEHLLALLRRDRGFE-DGEARKTLLELFEAFGPADPL  291 (304)
T ss_pred             CHHHHHHHHHhC---CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccccc-CcHHHHHHHHHHHhcCCCCHH
Confidence            444444444333   43333322222224445555666554444 4333 443 555566777777766654443

>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]

Probab=86.83  E-value=18  Score=30.71  Aligned_cols=164  Identities=10%  Similarity=0.047  Sum_probs=106.4

Q ss_pred             CCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHH
Q 039342           21 RNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLL  100 (248)
Q Consensus        21 ~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li  100 (248)
                      .|-...-+++..+..+..+.-+..+-.+|..-|  -+-..|-.++.+|... .-+.-..+|+++.+..+  +.....--+
T Consensus        64 l~d~~l~~~~~~f~~n~k~~~veh~c~~~l~~~--e~kmal~el~q~y~en-~n~~l~~lWer~ve~df--nDvv~~ReL  138 (711)
T COG1747          64 LDDSCLVTLLTIFGDNHKNQIVEHLCTRVLEYG--ESKMALLELLQCYKEN-GNEQLYSLWERLVEYDF--NDVVIGREL  138 (711)
T ss_pred             ccchHHHHHHHHhccchHHHHHHHHHHHHHHhc--chHHHHHHHHHHHHhc-CchhhHHHHHHHHHhcc--hhHHHHHHH
Confidence            355666778888888888888888888887654  4556778888888887 56677888888877643  344444444


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHCCCC-----chHHhHHHHhcccccccchHHHHHHHHHHHHhc-CCCCCHHHHHHHHHHH
Q 039342          101 AVYAKSNRWDDAYGLLDEMHTNRIS-----NIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCE-GYGLGMRFYNALLEAL  174 (248)
Q Consensus       101 ~~~~~~~~~~~a~~~~~~m~~~~~~-----~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~-~~~p~~~~~~~li~~~  174 (248)
                      ..+...++.+.+...|......-++     .-...|..+..-   -+.+.+....+...++.. |..--...+.-+-.-|
T Consensus       139 a~~yEkik~sk~a~~f~Ka~yrfI~~~q~~~i~evWeKL~~~---i~dD~D~fl~l~~kiqt~lg~~~~~Vl~qdv~~~Y  215 (711)
T COG1747         139 ADKYEKIKKSKAAEFFGKALYRFIPRRQNAAIKEVWEKLPEL---IGDDKDFFLRLQKKIQTKLGEGRGSVLMQDVYKKY  215 (711)
T ss_pred             HHHHHHhchhhHHHHHHHHHHHhcchhhhhhHHHHHHHHHHh---ccccHHHHHHHHHHHHHhhccchHHHHHHHHHHHh
Confidence            4444447777777777776543322     122233333331   134445555665555544 5555566677777888


Q ss_pred             HhcCchHHHHHHHHHHHH
Q 039342          175 WCLGLRERAARVLDEATK  192 (248)
Q Consensus       175 ~~~g~~~~a~~~~~~m~~  192 (248)
                      ....++++|.+++..+.+
T Consensus       216 s~~eN~~eai~Ilk~il~  233 (711)
T COG1747         216 SENENWTEAIRILKHILE  233 (711)
T ss_pred             ccccCHHHHHHHHHHHhh
Confidence            888999999999886654

>PHA02875 ankyrin repeat protein; Provisional

Probab=86.20  E-value=5.2  Score=33.01  Aligned_cols=70  Identities=19%  Similarity=0.103  Sum_probs=40.4

Q ss_pred             HHHHHHHHcCCCCCHHh--HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHH--HHHHHHHHHHhcCChhHHHHHHH
Q 039342            9 AILSRMSESGVARNSDS--FNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNER--TLEAVLSVYCFAGLVDESKEQFQ   82 (248)
Q Consensus         9 ~~~~~m~~~g~~~~~~~--y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~--t~~~ll~~~~~~g~~~~a~~~~~   82 (248)
                      ++++.+.+.|..|+...  ..+.+..++..|+.+-    .+.+.+.|..|+..  .....+...++.|+.+.+..+++
T Consensus        16 ~iv~~Ll~~g~~~n~~~~~g~tpL~~A~~~~~~~~----v~~Ll~~ga~~~~~~~~~~t~L~~A~~~g~~~~v~~Ll~   89 (413)
T PHA02875         16 DIARRLLDIGINPNFEIYDGISPIKLAMKFRDSEA----IKLLMKHGAIPDVKYPDIESELHDAVEEGDVKAVEELLD   89 (413)
T ss_pred             HHHHHHHHCCCCCCccCCCCCCHHHHHHHcCCHHH----HHHHHhCCCCccccCCCcccHHHHHHHCCCHHHHHHHHH
Confidence            34455556677666532  3445666677787754    44555566665532  12234556667788877665554

>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

Probab=84.65  E-value=9.4  Score=29.83  Aligned_cols=71  Identities=18%  Similarity=-0.001  Sum_probs=51.3

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHH-----HCCCCchHHhH
Q 039342           60 TLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMH-----TNRISNIHQVT  131 (248)
Q Consensus        60 t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~-----~~~~~~~~~~~  131 (248)
                      +++..-+.|..+|.+.+|.++.++..... +.+...|-.++..+...|+--.|.+-++++.     +-|+..+....
T Consensus       281 llgkva~~yle~g~~neAi~l~qr~ltld-pL~e~~nk~lm~~la~~gD~is~~khyerya~vleaelgi~vddsie  356 (361)
T COG3947         281 LLGKVARAYLEAGKPNEAIQLHQRALTLD-PLSEQDNKGLMASLATLGDEISAIKHYERYAEVLEAELGIDVDDSIE  356 (361)
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHhhcC-hhhhHHHHHHHHHHHHhccchhhhhHHHHHHHHHHHHhCCCcchhHH
Confidence            56677788888999999998888877653 3367778888888888888777777666653     33555555443

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=84.63  E-value=11  Score=26.20  Aligned_cols=51  Identities=10%  Similarity=0.161  Sum_probs=31.4

Q ss_pred             HhcCChhHHHHHHHHHHHCCCCcCH---hhHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           69 CFAGLVDESKEQFQEIKSSGILPSV---MCYCMLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        69 ~~~g~~~~a~~~~~~m~~~~~~p~~---~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      ...++++++..+++.|+-.  .|..   .++...  -+...|+|++|.++|++..+.+
T Consensus        21 L~~~d~~D~e~lLdALrvL--rP~~~e~d~~dg~--l~i~rg~w~eA~rvlr~l~~~~   74 (153)
T TIGR02561        21 LRSADPYDAQAMLDALRVL--RPNLKELDMFDGW--LLIARGNYDEAARILRELLSSA   74 (153)
T ss_pred             HhcCCHHHHHHHHHHHHHh--CCCccccchhHHH--HHHHcCCHHHHHHHHHhhhccC
Confidence            4567777777777777653  3432   233332  3456677777777777776654

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=84.34  E-value=3.2  Score=22.10  Aligned_cols=24  Identities=17%  Similarity=0.326  Sum_probs=15.7

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHC
Q 039342           64 VLSVYCFAGLVDESKEQFQEIKSS   87 (248)
Q Consensus        64 ll~~~~~~g~~~~a~~~~~~m~~~   87 (248)
                      +-.+|...|+.+.|.++++++...
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~~   28 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIEE   28 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHc
Confidence            455666777777777777766644

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.

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=83.97  E-value=17  Score=27.78  Aligned_cols=174  Identities=15%  Similarity=0.084  Sum_probs=108.6

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHHC-CCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHH
Q 039342           56 PNERTLEAVLSVYCFAGLVDESKEQFQEIKSS-GILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQ  133 (248)
Q Consensus        56 p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~-~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~  133 (248)
                      |-...|+.-+.. .+.|++++|.+.|+.+... ...| ...+--.++.++-+.++.+.|+..+++....--.....-|..
T Consensus        33 p~~~LY~~g~~~-L~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~~n~dY~~  111 (254)
T COG4105          33 PASELYNEGLTE-LQKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTHPNADYAY  111 (254)
T ss_pred             CHHHHHHHHHHH-HhcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCCCChhHHH
Confidence            444566665554 4679999999999999854 2222 456677778888899999999999999876532222222222


Q ss_pred             Hhcc---cc---cccchHHHHHHHHHHHHh---c----CCCCCHHHH------------HHHHHHHHhcCchHHHHHHHH
Q 039342          134 MIKG---EF---DDESNWQMVEYVFDKLNC---E----GYGLGMRFY------------NALLEALWCLGLRERAARVLD  188 (248)
Q Consensus       134 ~l~~---~~---~~~~~~~~a~~~~~~m~~---~----~~~p~~~~~------------~~li~~~~~~g~~~~a~~~~~  188 (248)
                      .|.+   ..   ...++...+..-+..+.+   .    ...||...-            -.+-+-|.+.|.+-.|..-++
T Consensus       112 YlkgLs~~~~i~~~~rDq~~~~~A~~~f~~~i~ryPnS~Ya~dA~~~i~~~~d~LA~~Em~IaryY~kr~~~~AA~nR~~  191 (254)
T COG4105         112 YLKGLSYFFQIDDVTRDQSAARAAFAAFKELVQRYPNSRYAPDAKARIVKLNDALAGHEMAIARYYLKRGAYVAAINRFE  191 (254)
T ss_pred             HHHHHHHhccCCccccCHHHHHHHHHHHHHHHHHCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHH
Confidence            2222   11   123344444444444433   2    334444331            134467889999999999999


Q ss_pred             HHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          189 EATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       189 ~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      +|.+. .+-+..+...|.+  +..+|-..|-.++|.+.-+-+...
T Consensus       192 ~v~e~-y~~t~~~~eaL~~--l~eaY~~lgl~~~a~~~~~vl~~N  233 (254)
T COG4105         192 EVLEN-YPDTSAVREALAR--LEEAYYALGLTDEAKKTAKVLGAN  233 (254)
T ss_pred             HHHhc-cccccchHHHHHH--HHHHHHHhCChHHHHHHHHHHHhc
Confidence            99987 4445555555543  337777788777777765555444

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=83.76  E-value=13  Score=27.82  Aligned_cols=55  Identities=15%  Similarity=0.230  Sum_probs=26.8

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHH
Q 039342           28 AVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQE   83 (248)
Q Consensus        28 ~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~   83 (248)
                      ..++.+.+.+..++++...++-.+.+ +-|..+-..++..+|-.|+|++|..-++-
T Consensus         6 ~t~seLL~~~sL~dai~~a~~qVkak-Ptda~~RhflfqLlcvaGdw~kAl~Ql~l   60 (273)
T COG4455           6 DTISELLDDNSLQDAIGLARDQVKAK-PTDAGGRHFLFQLLCVAGDWEKALAQLNL   60 (273)
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHhcC-CccccchhHHHHHHhhcchHHHHHHHHHH
Confidence            34445555555555555555443332 22333334455555555555555544433

>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=83.54  E-value=2.2  Score=19.52  Aligned_cols=20  Identities=25%  Similarity=0.154  Sum_probs=9.6

Q ss_pred             HHHHHHHhcCCHHHHHHHHH
Q 039342           98 MLLAVYAKSNRWDDAYGLLD  117 (248)
Q Consensus        98 ~li~~~~~~~~~~~a~~~~~  117 (248)
                      .+-.++...|++++|..+++
T Consensus         6 ~la~~~~~~G~~~eA~~~l~   25 (26)
T PF07721_consen    6 ALARALLAQGDPDEAERLLR   25 (26)
T ss_pred             HHHHHHHHcCCHHHHHHHHh
Confidence            34444455555555554443

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

>PF11846 DUF3366: Domain of unknown function (DUF3366); InterPro: IPR021797 This domain is functionally uncharacterised

Probab=83.44  E-value=10  Score=27.56  Aligned_cols=60  Identities=12%  Similarity=-0.046  Sum_probs=34.2

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHH-CCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 039342           63 AVLSVYCFAGLVDESKEQFQEIKS-SGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTN  122 (248)
Q Consensus        63 ~ll~~~~~~g~~~~a~~~~~~m~~-~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  122 (248)
                      ..+......++.+......+...+ ....|++.+|..++.++...|+.++|.+...++..-
T Consensus       113 ~~l~~~~~~~~~~~l~~~~~~a~~~l~~~P~~~~~~~~a~~l~~~G~~~eA~~~~~~~~~l  173 (193)
T PF11846_consen  113 ALLLLARLPPDPEMLEAYIEWAERLLRRRPDPNVYQRYALALALLGDPEEARQWLARARRL  173 (193)
T ss_pred             HHHHhhcCCCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            333333344444444444444332 234567777777777777777777777777766543

This domain is found in bacteria. This presumed domain is about 200 amino acids in length.

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=83.39  E-value=7.7  Score=34.25  Aligned_cols=85  Identities=15%  Similarity=0.105  Sum_probs=45.3

Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHH
Q 039342           24 DSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVY  103 (248)
Q Consensus        24 ~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~  103 (248)
                      -+.+--+.-+..-|+..+|.++-.+.+    -||-..|-.=+.+++..++|++-+++-+..+      ++.-|.-.+.+|
T Consensus       685 lSl~dTv~~li~~g~~k~a~ql~~~Fk----ipdKr~~wLk~~aLa~~~kweeLekfAkskk------sPIGy~PFVe~c  754 (829)
T KOG2280|consen  685 LSLHDTVTTLILIGQNKRAEQLKSDFK----IPDKRLWWLKLTALADIKKWEELEKFAKSKK------SPIGYLPFVEAC  754 (829)
T ss_pred             CcHHHHHHHHHHccchHHHHHHHHhcC----CcchhhHHHHHHHHHhhhhHHHHHHHHhccC------CCCCchhHHHHH
Confidence            344445555555566666655555544    3555666666666666666555433332222      234455556666


Q ss_pred             HhcCCHHHHHHHHHH
Q 039342          104 AKSNRWDDAYGLLDE  118 (248)
Q Consensus       104 ~~~~~~~~a~~~~~~  118 (248)
                      .+.|+.++|.+.+-+
T Consensus       755 ~~~~n~~EA~KYipr  769 (829)
T KOG2280|consen  755 LKQGNKDEAKKYIPR  769 (829)
T ss_pred             HhcccHHHHhhhhhc
Confidence            666666666655553

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=83.37  E-value=3.8  Score=19.80  Aligned_cols=27  Identities=19%  Similarity=0.167  Sum_probs=14.2

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHH
Q 039342           60 TLEAVLSVYCFAGLVDESKEQFQEIKS   86 (248)
Q Consensus        60 t~~~ll~~~~~~g~~~~a~~~~~~m~~   86 (248)
                      +|..+-.+|...|++++|...|++..+
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            444555555555555555555555543

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 ....

>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=83.16  E-value=16  Score=26.87  Aligned_cols=79  Identities=11%  Similarity=0.092  Sum_probs=53.9

Q ss_pred             HHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHC---CCCchHHhHHHHhcccccccc
Q 039342           67 VYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTN---RISNIHQVTGQMIKGEFDDES  143 (248)
Q Consensus        67 ~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~---~~~~~~~~~~~~l~~~~~~~~  143 (248)
                      -+.+.|+ +.|.+.|-.+...+..-++...-.|...|. ..+.+++..++.+..+.   +-.++...+.++... +...+
T Consensus       116 ~Wsr~~d-~~A~~~fL~~E~~~~l~t~elq~aLAtyY~-krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~-~~~~~  192 (203)
T PF11207_consen  116 HWSRFGD-QEALRRFLQLEGTPELETAELQYALATYYT-KRDPEKTIQLLLRALELSNPDDNFNPEILKSLASI-YQKLK  192 (203)
T ss_pred             HhhccCc-HHHHHHHHHHcCCCCCCCHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHH-HHHhc
Confidence            3445454 677888888887766656666666666666 67888999988877543   335777888887766 55556


Q ss_pred             hHHHH
Q 039342          144 NWQMV  148 (248)
Q Consensus       144 ~~~~a  148 (248)
                      +++.|
T Consensus       193 ~~e~A  197 (203)
T PF11207_consen  193 NYEQA  197 (203)
T ss_pred             chhhh
Confidence            65555

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=83.01  E-value=8  Score=28.88  Aligned_cols=77  Identities=12%  Similarity=0.092  Sum_probs=57.2

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHC--CCCchHHhHHHHhcc
Q 039342           60 TLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTN--RISNIHQVTGQMIKG  137 (248)
Q Consensus        60 t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~--~~~~~~~~~~~~l~~  137 (248)
                      |.+..++.+.+.+.++++....++-.+.+ +.+..+-..+++.+|-.|+|++|..-++-.-+-  ...+-..+|..++..
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            45667788888999999999887766653 236677888999999999999998877755332  234556677777764

>PF11846 DUF3366: Domain of unknown function (DUF3366); InterPro: IPR021797 This domain is functionally uncharacterised

Probab=82.87  E-value=9.1  Score=27.85  Aligned_cols=31  Identities=3%  Similarity=-0.169  Sum_probs=14.9

Q ss_pred             chHHhHHHHhcccccccchHHHHHHHHHHHHh
Q 039342          126 NIHQVTGQMIKGEFDDESNWQMVEYVFDKLNC  157 (248)
Q Consensus       126 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  157 (248)
                      |+..++...+.. +...|+.++|.++..++..
T Consensus       142 P~~~~~~~~a~~-l~~~G~~~eA~~~~~~~~~  172 (193)
T PF11846_consen  142 PDPNVYQRYALA-LALLGDPEEARQWLARARR  172 (193)
T ss_pred             CCHHHHHHHHHH-HHHcCCHHHHHHHHHHHHH
Confidence            444444444433 4444555555555555444

This domain is found in bacteria. This presumed domain is about 200 amino acids in length.

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=81.79  E-value=25  Score=28.09  Aligned_cols=184  Identities=15%  Similarity=0.120  Sum_probs=93.9

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC----CCCHHHHHHHHHHHHhcCChhHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRC----DPNERTLEAVLSVYCFAGLVDES   77 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~----~p~~~t~~~ll~~~~~~g~~~~a   77 (248)
                      |+|+...+........  .++...|.++...  +.++.+++...++...+.-.    ......|........+...+.+.
T Consensus        12 ~~Wd~l~~~~~~~~~~--~~~~~~~~al~~l--~~~~~~~~~~~i~~~r~~~~~~l~~~~~~s~~~~y~~l~~lq~L~El   87 (352)
T PF02259_consen   12 GDWDLLEEYLSQSNED--SPEYSFYRALLAL--RQGDYDEAKKYIEKARQLLLDELSALSSESYQRAYPSLVKLQQLVEL   87 (352)
T ss_pred             CChhhHHHHHhhccCC--ChhHHHHHHHHHH--hCccHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHhHHHHH
Confidence            5566644444444321  2355566666555  88999999888888754311    11223333333333333334444


Q ss_pred             HHHHHHHHHCCCCcCHhhHHHHHHHHHh-----cCCHHHHHHHH---HHHHH--CCCCchHHhHHHHhcccccccchHHH
Q 039342           78 KEQFQEIKSSGILPSVMCYCMLLAVYAK-----SNRWDDAYGLL---DEMHT--NRISNIHQVTGQMIKGEFDDESNWQM  147 (248)
Q Consensus        78 ~~~~~~m~~~~~~p~~~~~~~li~~~~~-----~~~~~~a~~~~---~~m~~--~~~~~~~~~~~~~l~~~~~~~~~~~~  147 (248)
                      .++.+-.....  .+......++..+..     .++++.-..++   .-+..  ........++..+... +.+.|.++.
T Consensus        88 ee~~~~~~~~~--~~~~~~~~l~~~W~~Rl~~~~~~~~~~~~il~~R~~~l~~~~~~~~~~~~~l~~a~~-aRk~g~~~~  164 (352)
T PF02259_consen   88 EEIIELKSNLS--QNPQDLKSLLKRWRSRLPNMQDDFSVWEPILSLRRLVLSLILLPEELAETWLKFAKL-ARKAGNFQL  164 (352)
T ss_pred             HHHHHHHHhhc--ccHHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHH-HHHCCCcHH
Confidence            44433332110  011222222222211     11111111111   11111  1111223344444444 888999999


Q ss_pred             HHHHHHHHHhcCCCC---CHHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          148 VEYVFDKLNCEGYGL---GMRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       148 a~~~~~~m~~~~~~p---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                      |...+..+...+..+   ++...-.-.+.+...|+..+|...+++..+
T Consensus       165 A~~~l~~~~~~~~~~~~~~~~v~~e~akllw~~g~~~~Ai~~L~~~~~  212 (352)
T PF02259_consen  165 ALSALNRLFQLNPSSESLLPRVFLEYAKLLWAQGEQEEAIQKLRELLK  212 (352)
T ss_pred             HHHHHHHHhccCCcccCCCcchHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            999999888754222   345555667788889999999999988776

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>PF11663 Toxin_YhaV: Toxin with endonuclease activity YhaV; InterPro: IPR021679 YhaV causes reversible bacteriostasis and is part of a toxin-antitoxin system in Escherichia coli along with PrlF

Probab=81.78  E-value=1.8  Score=29.34  Aligned_cols=29  Identities=21%  Similarity=0.341  Sum_probs=15.8

Q ss_pred             CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 039342           37 GRFEEAIKAYVEMEKVRCDPNERTLEAVLSV   67 (248)
Q Consensus        37 ~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   67 (248)
                      |.-..|..+|+.|.++|-+||.  |+.|+..
T Consensus       109 gsk~DaY~VF~kML~~G~pPdd--W~~Ll~~  137 (140)
T PF11663_consen  109 GSKTDAYAVFRKMLERGNPPDD--WDALLKE  137 (140)
T ss_pred             ccCCcHHHHHHHHHhCCCCCcc--HHHHHHH
Confidence            3334455666666666666653  5555543

The toxicity of YhaV is counteracted by PrlF by the formation of a tight complex which binds to the promoter of the prlF-yhaV operon. In vitro, YhaV also has endonuclease activity [].

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=81.57  E-value=4.3  Score=19.22  Aligned_cols=24  Identities=25%  Similarity=0.324  Sum_probs=16.4

Q ss_pred             HHHHHHhcCchHHHHHHHHHHHHC
Q 039342          170 LLEALWCLGLRERAARVLDEATKR  193 (248)
Q Consensus       170 li~~~~~~g~~~~a~~~~~~m~~~  193 (248)
                      +-.++.+.|++++|.++|+++.+.
T Consensus         6 ~a~~~~~~g~~~~A~~~~~~~~~~   29 (33)
T PF13174_consen    6 LARCYYKLGDYDEAIEYFQRLIKR   29 (33)
T ss_dssp             HHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHH
Confidence            445566677777887777776653

>cd00280 TRFH Telomeric Repeat binding Factor or TTAGGG Repeat binding Factor, central (dimerization) domain Homology; TRFH

Probab=81.35  E-value=18  Score=26.21  Aligned_cols=64  Identities=19%  Similarity=0.240  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHHcCCCCC--HHHHHH-----HHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHh
Q 039342           39 FEEAIKAYVEMEKVRCDPN--ERTLEA-----VLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAK  105 (248)
Q Consensus        39 ~~~a~~~~~~m~~~~~~p~--~~t~~~-----ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~  105 (248)
                      .+.|+.+|+...+.--.|.  ...-..     .+-.|.+.|.+++|.+++++..+.   |+......-+....+
T Consensus        85 LESAl~v~~~I~~E~~~~~~lhe~i~~lik~~aV~VCm~~g~Fk~A~eiLkr~~~d---~~~~~~r~kL~~II~  155 (200)
T cd00280          85 LESALMVLESIEKEFSLPETLHEEIRKLIKEQAVAVCMENGEFKKAEEVLKRLFSD---PESQKLRMKLLMIIR  155 (200)
T ss_pred             HHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHhcC---CCchhHHHHHHHHHH
Confidence            3566666666654432221  111111     223566666666666666666542   344433444433333

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.

>cd00280 TRFH Telomeric Repeat binding Factor or TTAGGG Repeat binding Factor, central (dimerization) domain Homology; TRFH

Probab=81.25  E-value=18  Score=26.19  Aligned_cols=67  Identities=12%  Similarity=0.151  Sum_probs=46.3

Q ss_pred             hHHHHHHHHHHHHcCCCCC--HH-----hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCC
Q 039342            4 YKECQAILSRMSESGVARN--SD-----SFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGL   73 (248)
Q Consensus         4 ~~~a~~~~~~m~~~g~~~~--~~-----~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~   73 (248)
                      ++.|+.+|+.+.+.--.|.  ..     .=-..+..|.+.|.+++|.+++++..+   .|+......-+....+.++
T Consensus        85 LESAl~v~~~I~~E~~~~~~lhe~i~~lik~~aV~VCm~~g~Fk~A~eiLkr~~~---d~~~~~~r~kL~~II~~Kd  158 (200)
T cd00280          85 LESALMVLESIEKEFSLPETLHEEIRKLIKEQAVAVCMENGEFKKAEEVLKRLFS---DPESQKLRMKLLMIIREKD  158 (200)
T ss_pred             HHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHhc---CCCchhHHHHHHHHHHccc
Confidence            5789999999986543331  11     223345679999999999999999876   4666666666665555544

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.

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=81.18  E-value=2.8  Score=20.67  Aligned_cols=22  Identities=27%  Similarity=0.212  Sum_probs=18.9

Q ss_pred             CHHHHHHHHHHHHhcCchHHHH
Q 039342          163 GMRFYNALLEALWCLGLRERAA  184 (248)
Q Consensus       163 ~~~~~~~li~~~~~~g~~~~a~  184 (248)
                      +...|+.+-..|...|++++|.
T Consensus        12 n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen   12 NAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             CHHHHHHHHHHHHHCcCHHhhc
Confidence            6788888999999999998885

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=80.24  E-value=19  Score=25.91  Aligned_cols=128  Identities=12%  Similarity=0.168  Sum_probs=58.9

Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCCCHHHH-HHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHh-hHHHHHH--HHHhcCCH
Q 039342           34 RQGGRFEEAIKAYVEMEKVRCDPNERTL-EAVLSVYCFAGLVDESKEQFQEIKSSGILPSVM-CYCMLLA--VYAKSNRW  109 (248)
Q Consensus        34 ~~~~~~~~a~~~~~~m~~~~~~p~~~t~-~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~-~~~~li~--~~~~~~~~  109 (248)
                      ++.+..++|+.-|..+.+.|..-=+..- --.-......|+...|...|++.-...-.|-.. -..-|=.  .+..+|.+
T Consensus        69 A~~~k~d~Alaaf~~lektg~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt~~P~~~rd~ARlraa~lLvD~gsy  148 (221)
T COG4649          69 AQENKTDDALAAFTDLEKTGYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRDLARLRAAYLLVDNGSY  148 (221)
T ss_pred             HHcCCchHHHHHHHHHHhcCCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhccCCCcchhhHHHHHHHHHHHhccccH
Confidence            4455566666666666665543211110 111223445666666666666665443233222 1111111  23355666


Q ss_pred             HHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCC
Q 039342          110 DDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGL  162 (248)
Q Consensus       110 ~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p  162 (248)
                      +....-.+.+-..+-+. ..+-...+--..-+.|++..+...|..+......|
T Consensus       149 ~dV~srvepLa~d~n~m-R~sArEALglAa~kagd~a~A~~~F~qia~Da~ap  200 (221)
T COG4649         149 DDVSSRVEPLAGDGNPM-RHSAREALGLAAYKAGDFAKAKSWFVQIANDAQAP  200 (221)
T ss_pred             HHHHHHhhhccCCCChh-HHHHHHHHhHHHHhccchHHHHHHHHHHHccccCc
Confidence            66666665554433222 22222222211334566666666666665543333

>PF07163 Pex26: Pex26 protein; InterPro: IPR010797 This family consists of Pex26 and related mammalian proteins

Probab=80.17  E-value=24  Score=27.47  Aligned_cols=88  Identities=6%  Similarity=-0.081  Sum_probs=50.0

Q ss_pred             HHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcc----ccc
Q 039342           65 LSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKG----EFD  140 (248)
Q Consensus        65 l~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~----~~~  140 (248)
                      |.+++..++|.++....-+--+.--..-..+....|-.|++.++...+.++-..-....-.-...-|..+..-    .+.
T Consensus        90 IQALAEmnrWreVLsWvlqyYq~pEklPpkIleLCILLysKv~Ep~amlev~~~WL~~p~Nq~lp~y~~vaELyLl~VLl  169 (309)
T PF07163_consen   90 IQALAEMNRWREVLSWVLQYYQVPEKLPPKILELCILLYSKVQEPAAMLEVASAWLQDPSNQSLPEYGTVAELYLLHVLL  169 (309)
T ss_pred             HHHHHHHhhHHHHHHHHHHHhcCcccCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhCcccCCchhhHHHHHHHHHHHHh
Confidence            6778888888777665544433322223556677777788888888777777665443221112223333322    234


Q ss_pred             ccchHHHHHHHH
Q 039342          141 DESNWQMVEYVF  152 (248)
Q Consensus       141 ~~~~~~~a~~~~  152 (248)
                      -.|.+++|+++.
T Consensus       170 PLG~~~eAeelv  181 (309)
T PF07163_consen  170 PLGHFSEAEELV  181 (309)
T ss_pred             ccccHHHHHHHH
Confidence            456666666654

Pex26 is a type II peroxisomal membrane protein that recruits Pex6-Pex1 complexes to peroxisomes []. Mutations in Pex26 can lead to human disorders [].; GO: 0032403 protein complex binding, 0045046 protein import into peroxisome membrane, 0005779 integral to peroxisomal membrane

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	248
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	2e-09
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	2e-08
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	4e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-06

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 56.7 bits (135), Expect = 2e-09
 Identities = 25/193 (12%), Positives = 55/193 (28%), Gaps = 9/193 (4%)

Query: 2   GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYV-EMEKVRCDPNERT 60
           G +KE   +L  + ++G+  +  S+ A ++   +  +    I+  + +M +         
Sbjct: 179 GAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALF 238

Query: 61  LEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMH 120
              +LS    A ++    +          LP  +    LL      +       L   + 
Sbjct: 239 TAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGRVSYPKLHLPLK 298

Query: 121 TNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR 180
           T +     Q+          + ++   V  V             R     L   W   L 
Sbjct: 299 TLQCLFEKQLH--------MELASRVCVVSVEKPTLPSKEVKHARKTLKTLRDQWEKALC 350

Query: 181 ERAARVLDEATKR 193
                  +   + 
Sbjct: 351 RALRETKNRLERE 363

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 53.7 bits (127), Expect = 2e-08
 Identities = 18/210 (8%), Positives = 61/210 (29%), Gaps = 3/210 (1%)

Query: 9   AILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVY 68
            +     ++  +   +    +++        +       +  + +    ++ L A     
Sbjct: 78  CLEDCTRQAPESPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFKCC 137

Query: 69  CFAGLVDESKEQFQEIKS---SGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRIS 125
                +  +               L ++  Y  ++  +A+   + +   +L  +    ++
Sbjct: 138 LLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLT 197

Query: 126 NIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAAR 185
                    ++     + +   +E   ++++ EG  L   F   LL       + +   +
Sbjct: 198 PDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHK 257

Query: 186 VLDEATKRGLFPELFRHNKLVWSVDVHRMW 215
           V    +     P     +KL+  V      
Sbjct: 258 VKPTFSLPPQLPPPVNTSKLLRDVYAKDGR 287

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 52.5 bits (124), Expect = 4e-08
 Identities = 24/223 (10%), Positives = 66/223 (29%), Gaps = 14/223 (6%)

Query: 10  ILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYC 69
           +     +       D +NAV+  + + G F+E +     ++     P+  +  A L    
Sbjct: 152 VHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMG 211

Query: 70  FAGLVDESKEQ-FQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIH 128
                  + E+  +++   G+    +   +LL+   ++      + +             
Sbjct: 212 RQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPP 271

Query: 129 QVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLD 188
             T ++++  +  +      +        +                      E A+RV  
Sbjct: 272 VNTSKLLRDVYAKDGRVSYPKLHLPLKTLQCLFEKQL-------------HMELASRVCV 318

Query: 189 EATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMY 231
            + ++   P     +       +   WE     A+    N++ 
Sbjct: 319 VSVEKPTLPSKEVKHARKTLKTLRDQWEKALCRALRETKNRLE 361

>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 = 46.0 bits (108), Expect = 7e-06
 Identities = 36/223 (16%), Positives = 67/223 (30%), Gaps = 65/223 (29%)

Query: 4   YKECQAILSRMSESGVARN-SDSFNAVIEAF----------RQGGRFEEAIKAYVEMEKV 52
           Y+ C  +L          N  ++      AF          R     +  + A      +
Sbjct: 243 YENCLLVL---------LNVQNA--KAWNAFNLSCKILLTTRFKQVTD-FLSAATTTH-I 289

Query: 53  RCDPNERTLEAVLSVYCFAGLVDESKEQFQ---EIKSSGILPSVMCYC--MLLAVYAKS- 106
             D +  TL             DE K       + +    LP  +       L++ A+S 
Sbjct: 290 SLDHHSMTLTP-----------DEVKSLLLKYLDCRPQD-LPREVLTTNPRRLSIIAESI 337

Query: 107 ----NRWDD-AYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYG 161
                 WD+  +   D++ T   S+++ +     +  FD  S       VF         
Sbjct: 338 RDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLS-------VFPP------- 383

Query: 162 LGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNK 204
                   LL  +W   ++     V+++  K  L   + +  K
Sbjct: 384 -SAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSL---VEKQPK 422

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	248
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.91
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.88
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.88
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.87
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.71
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.69
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.67
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.67
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.67
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.63
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.62
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.62
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.59
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.58
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.57
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.57
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.57
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.57
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.57
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.56
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.56
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.56
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.55
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.54
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.53
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.53
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.51
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.51
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.5
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.5
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.49
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.47
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.46
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.45
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.45
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.44
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.44
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.43
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.42
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.41
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.38
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.37
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.36
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.36
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.35
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.32
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.29
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.29
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.27
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.27
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.24
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.23
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.23
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.2
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.17
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.17
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.17
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.16
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.15
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.15
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.14
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.12
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.1
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.1
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.07
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.07
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.07
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.06
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.04
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.04
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.04
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	99.01
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.96
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	98.96
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	98.95
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.95
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.94
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	98.92
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.9
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	98.87
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.84
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.83
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	98.83
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	98.83
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.81
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.78
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.78
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.77
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.76
4g1t_A	472	Interferon-induced protein with tetratricopeptide	98.76
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.75
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.75
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	98.75
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.71
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.71
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.7
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.7
4g1t_A	472	Interferon-induced protein with tetratricopeptide	98.68
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.68
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	98.65
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.65
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.63
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.62
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.61
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.61
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.6
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.6
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.6
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.59
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.59
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.56
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.55
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.54
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.51
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.51
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.5
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.49
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.49
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	98.45
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	98.45
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.44
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.43
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.43
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.43
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.42
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	98.39
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.38
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.38
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.35
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.35
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.34
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.34
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.33
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.33
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.32
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.32
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.29
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.29
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.28
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.27
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.26
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	98.26
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.25
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.25
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.24
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.24
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	98.22
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.19
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.18
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.13
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.13
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.11
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.11
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.08
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.07
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.05
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.05
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.05
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	98.04
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.04
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.04
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.03
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.03
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.02
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.0
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.0
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.98
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.97
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	97.94
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.92
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.91
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	97.89
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	97.88
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.86
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	97.85
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.85
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	97.84
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.84
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	97.83
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	97.79
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.79
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	97.77
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.74
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.72
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	97.7
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.68
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.55
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.54
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.52
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.5
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	97.47
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.46
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	97.46
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.4
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.39
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.3
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	97.27
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.14
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.14
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.14
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	97.13
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.08
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	97.06
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.88
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	96.8
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.79
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	96.75
2l6j_A	111	TPR repeat-containing protein associated with HSP;	96.69
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	96.51
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	96.45
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	96.42
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	96.34
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.27
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	96.27
1pc2_A	152	Mitochondria fission protein; unknown function; NM	96.11
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.09
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	95.93
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	95.67
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	95.64
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	95.4
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	95.28
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	95.27
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	95.21
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	95.04
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	94.88
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	94.84
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	94.7
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	94.57
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	94.53
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	94.5
1pc2_A	152	Mitochondria fission protein; unknown function; NM	94.46
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	94.43
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	93.62
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	93.05
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	92.01
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	91.78
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	91.19
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	90.54
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	90.04
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	88.87
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	88.54
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	86.6
3t8k_A	186	Uncharacterized protein; structural genomics, PSI-	86.11
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	85.97
3kea_A	285	K1L; tropism, ANK repeat, viral protein; 2.30A {Va	85.38
1wdy_A	285	2-5A-dependent ribonuclease; hydrolase, RNA-bindin	84.77
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	84.75
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	84.69
1k1a_A	241	B-cell lymphoma 3-encoded protein; BCL-3, NF-kappa	84.01
3jxi_A	260	Vanilloid receptor-related osmotically activated p	83.07
1k1a_A	241	B-cell lymphoma 3-encoded protein; BCL-3, NF-kappa	82.95
3esl_A	202	Checkpoint serine/threonine-protein kinase BUB1; m	82.91
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	81.91
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	81.73
2p58_C	116	Putative type III secretion protein YSCG; type III	81.58

>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=2.3e-40  Score=273.00  Aligned_cols=207  Identities=11%  Similarity=0.088  Sum_probs=179.2

Q ss_pred             Cch-HHHHHHHHHHHHcCCCCCH-HhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCC------
Q 039342            2 GLY-KECQAILSRMSESGVARNS-DSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGL------   73 (248)
Q Consensus         2 g~~-~~a~~~~~~m~~~g~~~~~-~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~------   73 (248)
                      |+. ..+..+++++++.+..+.+ ..++.+|.+|++.|++++|+++|++|.+.|++||..|||+||.+|++.+.      
T Consensus         3 G~~~s~~e~L~~~~~~k~~~~spe~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~   82 (501)
T 4g26_A            3 GHMASPSENLSRKAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSP   82 (501)
T ss_dssp             ---------------------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSC
T ss_pred             ccccchHHHHHHHHHHhcccCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhh
Confidence            444 4455666778888776654 46899999999999999999999999999999999999999999998765      


Q ss_pred             ---hhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHH
Q 039342           74 ---VDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEY  150 (248)
Q Consensus        74 ---~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  150 (248)
                         ++.|.++|++|.+.|+.||..||++||.+|++.|++++|.++|++|.+.|+.|+..+|+.+|.+ +.+.|+++.|.+
T Consensus        83 ~~~l~~A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~-~~~~g~~~~A~~  161 (501)
T 4g26_A           83 NPGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFG-FCRKGDADKAYE  161 (501)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHH-HHHTTCHHHHHH
T ss_pred             cchHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHH-HHHCCCHHHHHH
Confidence               6889999999999999999999999999999999999999999999999999999999999999 778899999999


Q ss_pred             HHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhh
Q 039342          151 VFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSV  209 (248)
Q Consensus       151 ~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~  209 (248)
                      +|++|.+.|+.||..||++||++|++.|++++|.+++++|.+.|+.|+..||+.++..+
T Consensus       162 l~~~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F  220 (501)
T 4g26_A          162 VDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWF  220 (501)
T ss_dssp             HHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHH
T ss_pred             HHHHHHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999998444

>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=8.5e-37  Score=251.73  Aligned_cols=176  Identities=15%  Similarity=0.136  Sum_probs=170.4

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCC---------HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGR---------FEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFA   71 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~---------~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~   71 (248)
                      +|++++|+++|++|.+.|++||..|||+||.+|++.+.         ++.|.++|++|.+.|+.||..||+++|.+|++.
T Consensus        39 ~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~  118 (501)
T 4g26_A           39 KGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAK  118 (501)
T ss_dssp             SCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhc
Confidence            58999999999999999999999999999999998765         688999999999999999999999999999999


Q ss_pred             CChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHH
Q 039342           72 GLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYV  151 (248)
Q Consensus        72 g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  151 (248)
                      |++++|.++|++|.+.|+.||..||+++|.+|++.|++++|.++|++|.+.|+.|+..+|+.+|.+ +.+.|++++|.++
T Consensus       119 g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~-~~~~g~~d~A~~l  197 (501)
T 4g26_A          119 DDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKV-SMDTKNADKVYKT  197 (501)
T ss_dssp             TCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHH-HHHTTCHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHH-HhhCCCHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999999 8888999999999


Q ss_pred             HHHHHhcCCCCCHHHHHHHHHHHHhc
Q 039342          152 FDKLNCEGYGLGMRFYNALLEALWCL  177 (248)
Q Consensus       152 ~~~m~~~~~~p~~~~~~~li~~~~~~  177 (248)
                      +++|.+.|..|+..||+.++..|+..
T Consensus       198 l~~Mr~~g~~ps~~T~~~l~~~F~s~  223 (501)
T 4g26_A          198 LQRLRDLVRQVSKSTFDMIEEWFKSE  223 (501)
T ss_dssp             HHHHHHHTSSBCHHHHHHHHHHHHSH
T ss_pred             HHHHHHhCCCcCHHHHHHHHHHHhcC
Confidence            99999999999999999999999864

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.91  E-value=3.5e-24  Score=183.52  Aligned_cols=150  Identities=15%  Similarity=0.119  Sum_probs=126.8

Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHH---HcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHH
Q 039342           23 SDSFNAVIEAFRQGGRFEEAIKAYVEME---KVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCML   99 (248)
Q Consensus        23 ~~~y~~li~~~~~~~~~~~a~~~~~~m~---~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l   99 (248)
                      ..|||+||++||+.|++++|.++|++|.   +.|+.||..|||+||++||+.|++++|.++|++|.+.|+.||.+|||+|
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            4589999999999999999999998886   4589999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcCC-HHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCC------HHHHHHHHH
Q 039342          100 LAVYAKSNR-WDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLG------MRFYNALLE  172 (248)
Q Consensus       100 i~~~~~~~~-~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~------~~~~~~li~  172 (248)
                      |.++++.|+ .++|.++|++|.+.|+.|+..+|++++.+ ..+    +.+.+..+.+ ..++.|+      ..+...|.+
T Consensus       207 I~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~-~eR----~~vL~~Vrkv-~P~f~p~~~~~~~~~t~~LL~d  280 (1134)
T 3spa_A          207 LQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSE-EDR----ATVLKAVHKV-KPTFSLPPQLPPPVNTSKLLRD  280 (1134)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCH-HHH----HHHHHHHGGG-CCCCCCCCCCCCCCCCCTTTHH
T ss_pred             HHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccCh-hhH----HHHHHHHHHh-CcccCCCCCCcccccchHHHHH
Confidence            999999998 57899999999999999999999999865 222    3333333333 3355554      556666777


Q ss_pred             HHHhcC
Q 039342          173 ALWCLG  178 (248)
Q Consensus       173 ~~~~~g  178 (248)
                      .|.+.+
T Consensus       281 l~s~d~  286 (1134)
T 3spa_A          281 VYAKDG  286 (1134)
T ss_dssp             HHCCCS
T ss_pred             HHccCC
Confidence            777655

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.88  E-value=2.9e-23  Score=177.88  Aligned_cols=137  Identities=10%  Similarity=0.071  Sum_probs=117.9

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHH---CCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHH
Q 039342           57 NERTLEAVLSVYCFAGLVDESKEQFQEIKS---SGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQ  133 (248)
Q Consensus        57 ~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~---~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~  133 (248)
                      -..|||++|++||+.|++++|.++|++|.+   .|+.||..|||+||++|++.|++++|.++|++|.+.|+.||..||+.
T Consensus       126 ~~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYnt  205 (1134)
T 3spa_A          126 QQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAA  205 (1134)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHH
Confidence            456899999999999999999999998864   48999999999999999999999999999999999999999999999


Q ss_pred             HhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCC
Q 039342          134 MIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPE  198 (248)
Q Consensus       134 ~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  198 (248)
                      +|.+++..+...+.|.++|++|.+.|+.||..+|+++++++.+.+-++.+    +++ ..++.|+
T Consensus       206 LI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~~vL~~V----rkv-~P~f~p~  265 (1134)
T 3spa_A          206 ALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAV----HKV-KPTFSLP  265 (1134)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHHHHHHHH----GGG-CCCCCCC
T ss_pred             HHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHHHHHHHH----HHh-CcccCCC
Confidence            99985554444689999999999999999999999999877765433333    333 3455554

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.88  E-value=1.4e-20  Score=158.85  Aligned_cols=221  Identities=12%  Similarity=-0.005  Sum_probs=124.6

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|.++|+++.+.+. .+..+|+.++.++.+.|++++|.++++++.+.. +.+..+|+.+..+|.+.|++++|.++|
T Consensus       319 g~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~  396 (597)
T 2xpi_A          319 SRFIDVLAITTKILEIDP-YNLDVYPLHLASLHESGEKNKLYLISNDLVDRH-PEKAVTWLAVGIYYLCVNKISEARRYF  396 (597)
T ss_dssp             TCHHHHHHHHHHHHHHCT-TCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHcCc-ccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHhccHHHHHHHH
Confidence            555666666665554332 244445555555555555555555555544321 345566666666666666666666666


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCC
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYG  161 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~  161 (248)
                      +++.+.. +.+..+|+.++.+|.+.|++++|+++|+++.+.+ +.+..++..+... +...|+++.|..+|+.+.+....
T Consensus       397 ~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~-~~~~g~~~~A~~~~~~~~~~~~~  473 (597)
T 2xpi_A          397 SKSSTMD-PQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLF-QGTHLPYLFLGMQ-HMQLGNILLANEYLQSSYALFQY  473 (597)
T ss_dssp             HHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-TTCSHHHHHHHHH-HHHHTCHHHHHHHHHHHHHHCCC
T ss_pred             HHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHH-HHHcCCHHHHHHHHHHHHHhCCC
Confidence            6665532 1245566666666666666666666666665543 1233444444433 55556666666666666654322


Q ss_pred             CCHHHHHHHHHHHHhcCchHHHHHHHHHHHHC----CCCCC--cchhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          162 LGMRFYNALLEALWCLGLRERAARVLDEATKR----GLFPE--LFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       162 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~--~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                       +..+|+.+...|.+.|++++|.++|+++.+.    +..|+  ..+|..+.     ..|.+.|++++|.+.++++.+.
T Consensus       474 -~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~-----~~~~~~g~~~~A~~~~~~~~~~  545 (597)
T 2xpi_A          474 -DPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLG-----HAYRKLKMYDAAIDALNQGLLL  545 (597)
T ss_dssp             -CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHH-----HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             -ChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHH-----HHHHHhcCHHHHHHHHHHHHHh
Confidence             4566666666666666666666666666543    55555  34444444     5555566666666666666554

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.87  E-value=4.7e-20  Score=155.57  Aligned_cols=225  Identities=10%  Similarity=-0.031  Sum_probs=193.3

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|.++|+++.+.. +.+..+|+.+...|.+.|++++|.++|+++.+.. +.+..+|+.++.+|.+.|++++|.++|
T Consensus       353 g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~  430 (597)
T 2xpi_A          353 GEKNKLYLISNDLVDRH-PEKAVTWLAVGIYYLCVNKISEARRYFSKSSTMD-PQFGPAWIGFAHSFAIEGEHDQAISAY  430 (597)
T ss_dssp             TCHHHHHHHHHHHHHHC-TTSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            78999999999998644 3578999999999999999999999999998753 356889999999999999999999999


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhc---
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCE---  158 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~---  158 (248)
                      +++.+.+ +.+..+|+.+..+|.+.|++++|.++|+++.+... .+..++..+... +...|++++|..+|+++.+.   
T Consensus       431 ~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~-~~~~g~~~~A~~~~~~~~~~~~~  507 (597)
T 2xpi_A          431 TTAARLF-QGTHLPYLFLGMQHMQLGNILLANEYLQSSYALFQ-YDPLLLNELGVV-AFNKSDMQTAINHFQNALLLVKK  507 (597)
T ss_dssp             HHHHHTT-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCC-CCHHHHHHHHHH-HHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhC-ccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CChHHHHHHHHH-HHHhCCHHHHHHHHHHHHHhhhc
Confidence            9998764 34788999999999999999999999999987642 345566666665 77889999999999999876   


Q ss_pred             -CCCCC--HHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHHH
Q 039342          159 -GYGLG--MRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFM  235 (248)
Q Consensus       159 -~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~~  235 (248)
                       +..|+  ..+|..+..+|.+.|++++|.++|+++.+.+ +.+..+|..+.     ..|.+.|++++|.+.++++.+.  
T Consensus       508 ~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~-----~~~~~~g~~~~A~~~~~~~l~~--  579 (597)
T 2xpi_A          508 TQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLS-TNDANVHTAIA-----LVYLHKKIPGLAITHLHESLAI--  579 (597)
T ss_dssp             SCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-SCCHHHHHHHH-----HHHHHTTCHHHHHHHHHHHHHH--
T ss_pred             cccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHH-----HHHHHhCCHHHHHHHHHHHHhc--
Confidence             77888  7899999999999999999999999998764 33566666666     7888999999999999998875  


Q ss_pred             cCCC
Q 039342          236 MGED  239 (248)
Q Consensus       236 ~~~~  239 (248)
                      .|+.
T Consensus       580 ~p~~  583 (597)
T 2xpi_A          580 SPNE  583 (597)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            5543

>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=99.71  E-value=6.9e-15  Score=117.70  Aligned_cols=216  Identities=15%  Similarity=0.094  Sum_probs=167.9

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|.+.|+++.+... .+..+|+.+...+.+.|++++|.+.|+++.+.+ +-+...|..+-..+...|++++|...|
T Consensus       149 g~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~  226 (388)
T 1w3b_A          149 GRLEEAKACYLKAIETQP-NFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAY  226 (388)
T ss_dssp             SCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHH
T ss_pred             cCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            677788888877766432 246778888888888888888888888876654 345667777788888888888888888


Q ss_pred             HHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchH-HhHHHHhcccccccchHHHHHHHHHHHHhcC
Q 039342           82 QEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIH-QVTGQMIKGEFDDESNWQMVEYVFDKLNCEG  159 (248)
Q Consensus        82 ~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~  159 (248)
                      ++..+.  .| +..++..+...|.+.|++++|...|+++.+..  |+. ..+..+... +...|+++.|...++.+.+..
T Consensus       227 ~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~-~~~~g~~~~A~~~~~~al~~~  301 (388)
T 1w3b_A          227 LRALSL--SPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ--PHFPDAYCNLANA-LKEKGSVAEAEDCYNTALRLC  301 (388)
T ss_dssp             HHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC--SSCHHHHHHHHHH-HHHHSCHHHHHHHHHHHHHHC
T ss_pred             HHHHhh--CcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCCHHHHHHHHHH-HHHcCCHHHHHHHHHHHHhhC
Confidence            877664  34 57889999999999999999999999998765  433 344444443 777889999999999988774


Q ss_pred             CCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCC-cchhhhHHhhhhhhccccchHHHHHHHHHHHHHH
Q 039342          160 YGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPE-LFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYE  232 (248)
Q Consensus       160 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~  232 (248)
                       +.+..+++.+...+.+.|++++|.+.++++.+.  .|+ ..++..+.     ..+.+.|++++|...++++.+
T Consensus       302 -p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~-----~~~~~~g~~~~A~~~~~~a~~  367 (388)
T 1w3b_A          302 -PTHADSLNNLANIKREQGNIEEAVRLYRKALEV--FPEFAAAHSNLA-----SVLQQQGKLQEALMHYKEAIR  367 (388)
T ss_dssp             -TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTS--CTTCHHHHHHHH-----HHHHTTTCCHHHHHHHHHHHT
T ss_pred             -cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCcHHHHHHHH-----HHHHHcCCHHHHHHHHHHHHh
Confidence             447889999999999999999999999998764  454 44555555     778889999999999998876

>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=99.69  E-value=1.5e-14  Score=115.69  Aligned_cols=185  Identities=12%  Similarity=0.029  Sum_probs=75.1

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|.+.|+++.+.. +.+..+|..+..++.+.|++++|.+.|+++.+.+ +-+...+..+-..+...|++++|.+.|
T Consensus        81 g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~  158 (388)
T 1w3b_A           81 GQLQEAIEHYRHALRLK-PDFIDGYINLAAALVAAGDMEGAVQAYVSALQYN-PDLYCVRSDLGNLLKALGRLEEAKACY  158 (388)
T ss_dssp             TCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHC-TTCTHHHHHHHHHHHTTSCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcC-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHH
Confidence            34444444444443321 1123334444444444444444444444443321 111223333344444444455555555


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCC
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYG  161 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~  161 (248)
                      +++.+.. +.+..+|..+...+.+.|++++|...|+++.+..  |+.......+...+...++++.|...++....... 
T Consensus       159 ~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p-  234 (388)
T 1w3b_A          159 LKAIETQ-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD--PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSP-  234 (388)
T ss_dssp             HHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCT-
T ss_pred             HHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCc-
Confidence            4444321 1134455555555555555555555555554332  22111111111112223333333333333322211 


Q ss_pred             CCHHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          162 LGMRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       162 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                      -+..++..+...+.+.|++++|.+.|+++.+
T Consensus       235 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  265 (388)
T 1w3b_A          235 NHAVVHGNLACVYYEQGLIDLAIDTYRRAIE  265 (388)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            1234444555555555555555555555544

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.67  E-value=1.5e-14  Score=111.58  Aligned_cols=216  Identities=16%  Similarity=0.116  Sum_probs=164.9

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCChhHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN-ERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      |+++.|+..++.   . -+|+..++..+...+...++.++|.+.++++...+..|+ ...+..+-..+.+.|++++|.+.
T Consensus        48 g~~~~al~~~~~---~-~~~~~~a~~~la~~~~~~~~~~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~  123 (291)
T 3mkr_A           48 RKYGVVLDEIKP---S-SAPELQAVRMFAEYLASHSRRDAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRT  123 (291)
T ss_dssp             TCHHHHHHHSCT---T-SCHHHHHHHHHHHHHHCSTTHHHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CCHHHHHHHhcc---c-CChhHHHHHHHHHHHcCCCcHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            667777765543   1 346788999999999999999999999999988876564 45556666899999999999999


Q ss_pred             HHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHH--HhcccccccchHHHHHHHHHHHHhc
Q 039342           81 FQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQ--MIKGEFDDESNWQMVEYVFDKLNCE  158 (248)
Q Consensus        81 ~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~--~l~~~~~~~~~~~~a~~~~~~m~~~  158 (248)
                      +++      ..+...+..+...+.+.|++++|...|+++.+..  |+......  .........++++.|..+|+++.+.
T Consensus       124 l~~------~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~--p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~  195 (291)
T 3mkr_A          124 LHQ------GDSLECMAMTVQILLKLDRLDLARKELKKMQDQD--EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADK  195 (291)
T ss_dssp             HTT------CCSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH
T ss_pred             HhC------CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHh
Confidence            987      3578899999999999999999999999998775  54432221  1112233568899999999999987


Q ss_pred             CCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCC-CcchhhhHHhhhhhhccccchHHHH-HHHHHHHHHHHHHc
Q 039342          159 GYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFP-ELFRHNKLVWSVDVHRMWEGGAYTA-ISVWLNKMYEMFMM  236 (248)
Q Consensus       159 ~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~~~~~~g~~~~-~~~~~~~m~~~~~~  236 (248)
                       .+.+...++.+..++.+.|++++|.+.|++..+.  .| +..++..+.     ..+...|+.++ +.+++++..+.  .
T Consensus       196 -~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~--~p~~~~~l~~l~-----~~~~~~g~~~eaa~~~~~~~~~~--~  265 (291)
T 3mkr_A          196 -CSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDK--DSGHPETLINLV-----VLSQHLGKPPEVTNRYLSQLKDA--H  265 (291)
T ss_dssp             -SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHH-----HHHHHTTCCHHHHHHHHHHHHHH--C
T ss_pred             -CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHH-----HHHHHcCCCHHHHHHHHHHHHHh--C
Confidence             3458889999999999999999999999998764  34 334455554     45556776654 56787777655  5


Q ss_pred             CCC
Q 039342          237 GED  239 (248)
Q Consensus       237 ~~~  239 (248)
                      |+.
T Consensus       266 P~~  268 (291)
T 3mkr_A          266 RSH  268 (291)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            543

>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=99.67  E-value=2.5e-14  Score=116.42  Aligned_cols=227  Identities=12%  Similarity=0.068  Sum_probs=177.9

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|.++|+++.+.. +.+...|..+...+.+.|++++|.+.|+++.+.+ +.+...+..+..+|.+.|++++|.+.
T Consensus        39 ~g~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~  116 (450)
T 2y4t_A           39 AGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLK-MDFTAARLQRGHLLLKQGKLDEAEDD  116 (450)
T ss_dssp             TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHH
Confidence            489999999999998753 3478899999999999999999999999998765 45678899999999999999999999


Q ss_pred             HHHHHHCCCCcC-H---hhHHHHHH------------HHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccch
Q 039342           81 FQEIKSSGILPS-V---MCYCMLLA------------VYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESN  144 (248)
Q Consensus        81 ~~~m~~~~~~p~-~---~~~~~li~------------~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~  144 (248)
                      |+++.+..  |+ .   ..+..+..            .+.+.|++++|+..|+++.+..  |+.......+...+...|+
T Consensus       117 ~~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~  192 (450)
T 2y4t_A          117 FKKVLKSN--PSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVC--VWDAELRELRAECFIKEGE  192 (450)
T ss_dssp             HHHHHTSC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHhcC--CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHCCC
Confidence            99998753  43 3   56665544            4889999999999999998754  4443333333344778889


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHh--------hhhhhcccc
Q 039342          145 WQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVW--------SVDVHRMWE  216 (248)
Q Consensus       145 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~--------~~~~~~~~~  216 (248)
                      ++.|...++.+.+... .+..++..+...|...|++++|.+.|+++.+.  .|+.......+.        ......+.+
T Consensus       193 ~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~p~~~~~~~~~~~~~~~~~~~~~~~~~~~  269 (450)
T 2y4t_A          193 PRKAISDLKAASKLKN-DNTEAFYKISTLYYQLGDHELSLSEVRECLKL--DQDHKRCFAHYKQVKKLNKLIESAEELIR  269 (450)
T ss_dssp             GGGGHHHHHHHHHHHC-SCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCChHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999887642 36788999999999999999999999998864  555443222210        001366778


Q ss_pred             chHHHHHHHHHHHHHHHHHcCC
Q 039342          217 GGAYTAISVWLNKMYEMFMMGE  238 (248)
Q Consensus       217 ~g~~~~~~~~~~~m~~~~~~~~  238 (248)
                      .|++++|...++++.+.  .|+
T Consensus       270 ~g~~~~A~~~~~~~l~~--~p~  289 (450)
T 2y4t_A          270 DGRYTDATSKYESVMKT--EPS  289 (450)
T ss_dssp             HTCHHHHHHHHHHHHHH--CCS
T ss_pred             cCCHHHHHHHHHHHHhc--CCc
Confidence            89999999999998874  454

>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=99.67  E-value=3.2e-14  Score=115.77  Aligned_cols=115  Identities=12%  Similarity=0.066  Sum_probs=56.4

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH----HHHHHHHH-----------
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNE----RTLEAVLS-----------   66 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~----~t~~~ll~-----------   66 (248)
                      |++++|.+.|+++.+.+. .+...|..+...|.+.|++++|.+.|+++.+.  .|+.    ..+..+..           
T Consensus        74 g~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~a  150 (450)
T 2y4t_A           74 GKSKAALPDLTKVIQLKM-DFTAARLQRGHLLLKQGKLDEAEDDFKKVLKS--NPSENEEKEAQSQLIKSDEMQRLRSQA  150 (450)
T ss_dssp             TCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhcCC-CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCChhhHHHHHHHHHHHHHHHHHHHH
Confidence            556666666666555432 23555666666666666666666666665543  2322    23333322           


Q ss_pred             -HHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 039342           67 -VYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMH  120 (248)
Q Consensus        67 -~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~  120 (248)
                       .+.+.|++++|...|+++.+.. +.+..++..+...|.+.|++++|...|+++.
T Consensus       151 ~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  204 (450)
T 2y4t_A          151 LNAFGSGDYTAAIAFLDKILEVC-VWDAELRELRAECFIKEGEPRKAISDLKAAS  204 (450)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCGGGGHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence             2444555555555555544321 1133444444444445555555554444443

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.63  E-value=3.3e-14  Score=112.77  Aligned_cols=222  Identities=12%  Similarity=-0.001  Sum_probs=171.1

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|.+.|+++.+... .+..+|..+...+.+.|++++|.+.|++..+.. +.+..+|..+..+|.+.|++++|.+.|
T Consensus        79 g~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~  156 (365)
T 4eqf_A           79 GDLPVTILFMEAAILQDP-GDAEAWQFLGITQAENENEQAAIVALQRCLELQ-PNNLKALMALAVSYTNTSHQQDACEAL  156 (365)
T ss_dssp             TCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhCc-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHccccHHHHHHHH
Confidence            789999999999987543 468899999999999999999999999997764 456889999999999999999999999


Q ss_pred             HHHHHCCCCcC-----------HhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCc-hHHhHHHHhcccccccchHHHHH
Q 039342           82 QEIKSSGILPS-----------VMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISN-IHQVTGQMIKGEFDDESNWQMVE  149 (248)
Q Consensus        82 ~~m~~~~~~p~-----------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~  149 (248)
                      ++..+..  |+           ...+..+...+.+.|++++|...|++..+..... +...+..+... +...|+++.|.
T Consensus       157 ~~al~~~--p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~-~~~~g~~~~A~  233 (365)
T 4eqf_A          157 KNWIKQN--PKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLGVL-FHLSGEFNRAI  233 (365)
T ss_dssp             HHHHHHC--HHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHHHH-HHHHTCHHHHH
T ss_pred             HHHHHhC--ccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHHHH-HHHCCCHHHHH
Confidence            9988642  32           2233445788999999999999999998765221 34445444443 67789999999


Q ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCC-cchhhhHHhhhhhhccccchHHHHHHHHHH
Q 039342          150 YVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPE-LFRHNKLVWSVDVHRMWEGGAYTAISVWLN  228 (248)
Q Consensus       150 ~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~~~~~~g~~~~~~~~~~  228 (248)
                      ..++...+... .+..++..+..+|...|++++|...|++..+.  .|+ ..++..+.     ..+...|++++|...++
T Consensus       234 ~~~~~al~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~-----~~~~~~g~~~~A~~~~~  305 (365)
T 4eqf_A          234 DAFNAALTVRP-EDYSLWNRLGATLANGDRSEEAVEAYTRALEI--QPGFIRSRYNLG-----ISCINLGAYREAVSNFL  305 (365)
T ss_dssp             HHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHH-----HHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCchHHHHHHH-----HHHHHCCCHHHHHHHHH
Confidence            99999887643 36788999999999999999999999998775  444 34444444     67788999999999999


Q ss_pred             HHHHHHHc
Q 039342          229 KMYEMFMM  236 (248)
Q Consensus       229 ~m~~~~~~  236 (248)
                      +..+..-.
T Consensus       306 ~al~~~~~  313 (365)
T 4eqf_A          306 TALSLQRK  313 (365)
T ss_dssp             HHHHHHHC
T ss_pred             HHHHhCcc
Confidence            98877533

>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=99.62  E-value=1.9e-13  Score=108.23  Aligned_cols=222  Identities=11%  Similarity=0.004  Sum_probs=166.3

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|...|+++.+... .+...|..+...+.+.|++++|.+.|++..+.. +.+..++..+...|...|++++|.+.+
T Consensus        78 g~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~  155 (368)
T 1fch_A           78 GDLPNAVLLFEAAVQQDP-KHMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSFTNESLQRQACEIL  155 (368)
T ss_dssp             TCHHHHHHHHHHHHHSCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            788899999998887542 467788888888999999999999999887664 457788888888999999999999999


Q ss_pred             HHHHHCCCCcCHhhHHH---------------HHHHHHhcCCHHHHHHHHHHHHHCCCCc-hHHhHHHHhcccccccchH
Q 039342           82 QEIKSSGILPSVMCYCM---------------LLAVYAKSNRWDDAYGLLDEMHTNRISN-IHQVTGQMIKGEFDDESNW  145 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~---------------li~~~~~~~~~~~a~~~~~~m~~~~~~~-~~~~~~~~l~~~~~~~~~~  145 (248)
                      +++.+.... +...+..               .+..+...|++++|...|+++.+..... +...+..+... +...|++
T Consensus       156 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~-~~~~g~~  233 (368)
T 1fch_A          156 RDWLRYTPA-YAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVL-FNLSGEY  233 (368)
T ss_dssp             HHHHHTSTT-TGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHH-HHHTTCH
T ss_pred             HHHHHhCcC-cHHHHHHHHHHhhhhcccHHHHHHHHHhhcccHHHHHHHHHHHHHhCcCcccHHHHHHHHHH-HHHcCCH
Confidence            888875322 2222221               2344448888999999999887654221 23444444433 6778899


Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCC-cchhhhHHhhhhhhccccchHHHHHH
Q 039342          146 QMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPE-LFRHNKLVWSVDVHRMWEGGAYTAIS  224 (248)
Q Consensus       146 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~~~~~~g~~~~~~  224 (248)
                      +.|...++...+... .+..++..+...+...|++++|...|++..+.  .|+ ...+..+.     ..+.+.|++++|.
T Consensus       234 ~~A~~~~~~al~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~~~~~~~~~~l~-----~~~~~~g~~~~A~  305 (368)
T 1fch_A          234 DKAVDCFTAALSVRP-NDYLLWNKLGATLANGNQSEEAVAAYRRALEL--QPGYIRSRYNLG-----ISCINLGAHREAV  305 (368)
T ss_dssp             HHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHH-----HHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHHHhCc-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCcHHHHHHHH-----HHHHHCCCHHHHH
Confidence            999999999887642 35778999999999999999999999998764  343 33444444     6778899999999


Q ss_pred             HHHHHHHHHHH
Q 039342          225 VWLNKMYEMFM  235 (248)
Q Consensus       225 ~~~~~m~~~~~  235 (248)
                      ..+++..+..-
T Consensus       306 ~~~~~al~~~~  316 (368)
T 1fch_A          306 EHFLEALNMQR  316 (368)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHhCC
Confidence            99998887643

>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=99.62  E-value=2.9e-13  Score=105.37  Aligned_cols=222  Identities=12%  Similarity=0.009  Sum_probs=167.2

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC-ChhHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAG-LVDESKE   79 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g-~~~~a~~   79 (248)
                      .|++++|.++|+++.+... .+...+..+...+...|++++|..+++++.+.. +.+...|..+...+...| ++++|.+
T Consensus        35 ~g~~~~A~~~~~~~l~~~p-~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~A~~  112 (330)
T 3hym_B           35 NCDFKMCYKLTSVVMEKDP-FHASCLPVHIGTLVELNKANELFYLSHKLVDLY-PSNPVSWFAVGCYYLMVGHKNEHARR  112 (330)
T ss_dssp             TTCHHHHHHHHHHHHHHCT-TCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSTHHHHHHHHHHHHSCSCHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHcCC-CChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhhhhHHHHHH
Confidence            3789999999999876543 356677778888889999999999999987753 345678888888999999 8999999


Q ss_pred             HHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcC
Q 039342           80 QFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEG  159 (248)
Q Consensus        80 ~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~  159 (248)
                      .|++..+.. +.+...|..+...+...|++++|...+++..+..... ...+..+ ...+...|+++.|...++...+..
T Consensus       113 ~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~-~~~~~~l-~~~~~~~~~~~~A~~~~~~al~~~  189 (330)
T 3hym_B          113 YLSKATTLE-KTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMKGC-HLPMLYI-GLEYGLTNNSKLAERFFSQALSIA  189 (330)
T ss_dssp             HHHHHHTTC-TTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTC-SHHHHHH-HHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHhC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhcccc-HHHHHHH-HHHHHHHhhHHHHHHHHHHHHHhC
Confidence            999988653 2256788889999999999999999999887664221 2222223 333667788899999999887764


Q ss_pred             CCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCC--------CCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHH
Q 039342          160 YGLGMRFYNALLEALWCLGLRERAARVLDEATKRG--------LFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMY  231 (248)
Q Consensus       160 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g--------~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~  231 (248)
                      . .+...+..+...+...|++++|...+++..+..        .+.+...+..+.     ..+...|++++|...+++..
T Consensus       190 ~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la-----~~~~~~g~~~~A~~~~~~a~  263 (330)
T 3hym_B          190 P-EDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLG-----HVCRKLKKYAEALDYHRQAL  263 (330)
T ss_dssp             T-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHH-----HHHHHTTCHHHHHHHHHHHH
T ss_pred             C-CChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHH-----HHHHHhcCHHHHHHHHHHHH
Confidence            3 357788888899999999999999998876521        122233444444     66778889999988888877


Q ss_pred             HH
Q 039342          232 EM  233 (248)
Q Consensus       232 ~~  233 (248)
                      +.
T Consensus       264 ~~  265 (330)
T 3hym_B          264 VL  265 (330)
T ss_dssp             HH
T ss_pred             hh
Confidence            65

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.59  E-value=5.9e-13  Score=99.98  Aligned_cols=213  Identities=12%  Similarity=0.077  Sum_probs=165.5

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCCC----HHHHHHHHHHHHhcCCh
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVR--CDPN----ERTLEAVLSVYCFAGLV   74 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~--~~p~----~~t~~~ll~~~~~~g~~   74 (248)
                      .|++++|.+.|++..+..  .+...|..+...+...|++++|.+.+++..+..  ..|+    ..+|..+...|.+.|++
T Consensus        18 ~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~   95 (258)
T 3uq3_A           18 ARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFARIGNAYHKLGDL   95 (258)
T ss_dssp             TTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             hccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHHHHHHcccH
Confidence            378899999999888766  778889999999999999999999998886542  2223    57888888899999999


Q ss_pred             hHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHH
Q 039342           75 DESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDK  154 (248)
Q Consensus        75 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  154 (248)
                      ++|.+.|++..+.  .|+.       ..+.+.|++++|...+++.....  |........+...+...|+++.|...++.
T Consensus        96 ~~A~~~~~~a~~~--~~~~-------~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~A~~~~~~  164 (258)
T 3uq3_A           96 KKTIEYYQKSLTE--HRTA-------DILTKLRNAEKELKKAEAEAYVN--PEKAEEARLEGKEYFTKSDWPNAVKAYTE  164 (258)
T ss_dssp             HHHHHHHHHHHHH--CCCH-------HHHHHHHHHHHHHHHHHHHHHCC--HHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhc--Cchh-------HHHHHHhHHHHHHHHHHHHHHcC--cchHHHHHHHHHHHHHhcCHHHHHHHHHH
Confidence            9999999888874  3442       34666788889999998887654  55554444444447778999999999999


Q ss_pred             HHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCC-cchhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          155 LNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPE-LFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       155 m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      ..+.... +..++..+...+...|++++|...+++..+.  .|+ ...+..+.     ..+...|++++|...+++..+.
T Consensus       165 a~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~~~~~~~~~~l~-----~~~~~~g~~~~A~~~~~~a~~~  236 (258)
T 3uq3_A          165 MIKRAPE-DARGYSNRAAALAKLMSFPEAIADCNKAIEK--DPNFVRAYIRKA-----TAQIAVKEYASALETLDAARTK  236 (258)
T ss_dssp             HHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHH-----HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHhcCcc-cHHHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CHHHHHHHHHHH-----HHHHHHhhHHHHHHHHHHHHHh
Confidence            8876533 6788999999999999999999999998775  343 33344443     6778889999999999888776


Q ss_pred             H
Q 039342          234 F  234 (248)
Q Consensus       234 ~  234 (248)
                      .
T Consensus       237 ~  237 (258)
T 3uq3_A          237 D  237 (258)
T ss_dssp             H
T ss_pred             C
Confidence            4

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=99.58  E-value=5.3e-13  Score=103.74  Aligned_cols=220  Identities=10%  Similarity=-0.022  Sum_probs=170.7

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|.++|+++.+... .+...|..+...+.+.|++++|.+.+++..+.. +.+..++..+...|...|++++|.+.
T Consensus        34 ~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~  111 (327)
T 3cv0_A           34 LANLAEAALAFEAVCQAAP-EREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHNANAALAS  111 (327)
T ss_dssp             TTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             hccHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            3789999999999987543 478889999999999999999999999997764 45778899999999999999999999


Q ss_pred             HHHHHHCCCCcCHhhHHHH--------------HH-HHHhcCCHHHHHHHHHHHHHCCCCchH-HhHHHHhcccccccch
Q 039342           81 FQEIKSSGILPSVMCYCML--------------LA-VYAKSNRWDDAYGLLDEMHTNRISNIH-QVTGQMIKGEFDDESN  144 (248)
Q Consensus        81 ~~~m~~~~~~p~~~~~~~l--------------i~-~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~~l~~~~~~~~~  144 (248)
                      +++..+.... +...+..+              .. .+...|++++|...+++..+..  |+. ..+..+.. .+...|+
T Consensus       112 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~la~-~~~~~~~  187 (327)
T 3cv0_A          112 LRAWLLSQPQ-YEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMN--PNDAQLHASLGV-LYNLSNN  187 (327)
T ss_dssp             HHHHHHTSTT-TTTC--------------------CCTTSHHHHHHHHHHHHHHHHHS--TTCHHHHHHHHH-HHHHTTC
T ss_pred             HHHHHHhCCc-cHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhC--CCCHHHHHHHHH-HHHHhcc
Confidence            9999875321 23333333              22 3778889999999999998765  333 33333333 3677889


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCC-cchhhhHHhhhhhhccccchHHHHH
Q 039342          145 WQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPE-LFRHNKLVWSVDVHRMWEGGAYTAI  223 (248)
Q Consensus       145 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~~~~~~g~~~~~  223 (248)
                      ++.|...++...+... .+..++..+...+...|++++|.+.+++..+.  .|+ ...+..+.     ..+...|++++|
T Consensus       188 ~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~l~-----~~~~~~g~~~~A  259 (327)
T 3cv0_A          188 YDSAAANLRRAVELRP-DDAQLWNKLGATLANGNRPQEALDAYNRALDI--NPGYVRVMYNMA-----VSYSNMSQYDLA  259 (327)
T ss_dssp             HHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHH-----HHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHH-----HHHHHhccHHHH
Confidence            9999999999887643 35788999999999999999999999998764  343 33444444     677889999999


Q ss_pred             HHHHHHHHHHH
Q 039342          224 SVWLNKMYEMF  234 (248)
Q Consensus       224 ~~~~~~m~~~~  234 (248)
                      ...+++..+..
T Consensus       260 ~~~~~~a~~~~  270 (327)
T 3cv0_A          260 AKQLVRAIYMQ  270 (327)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHhC
Confidence            99999888764

>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=99.57  E-value=9.7e-13  Score=102.39  Aligned_cols=220  Identities=10%  Similarity=-0.070  Sum_probs=174.2

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcC-CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGG-RFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~-~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      |++++|..+|+++.+... .+...|..+...+...| ++++|.+.|++..+.. +.+...|..+...+...|++++|.+.
T Consensus        70 ~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~  147 (330)
T 3hym_B           70 NKANELFYLSHKLVDLYP-SNPVSWFAVGCYYLMVGHKNEHARRYLSKATTLE-KTYGPAWIAYGHSFAVESEHDQAMAA  147 (330)
T ss_dssp             TCHHHHHHHHHHHHHHCT-TSTHHHHHHHHHHHHSCSCHHHHHHHHHHHHTTC-TTCTHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHhCc-CCHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHccCHHHHHHH
Confidence            789999999999987542 46788999999999999 9999999999997654 34567899999999999999999999


Q ss_pred             HHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcC-
Q 039342           81 FQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEG-  159 (248)
Q Consensus        81 ~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~-  159 (248)
                      +++..+.. +.+...+..+...|...|++++|...+++..+..  |+.......+...+...|+++.|...++...+.. 
T Consensus       148 ~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~  224 (330)
T 3hym_B          148 YFTAAQLM-KGCHLPMLYIGLEYGLTNNSKLAERFFSQALSIA--PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIK  224 (330)
T ss_dssp             HHHHHHHT-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHhc-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhh
Confidence            99998753 2245677789999999999999999999998764  4443333333334777889999999998887642 


Q ss_pred             -------CCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHH
Q 039342          160 -------YGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYE  232 (248)
Q Consensus       160 -------~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~  232 (248)
                             ...+..++..+...+...|++++|...+++..+.. +.+...+..+.     ..+...|++++|...+++..+
T Consensus       225 ~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~-~~~~~~~~~la-----~~~~~~g~~~~A~~~~~~al~  298 (330)
T 3hym_B          225 AIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQALVLI-PQNASTYSAIG-----YIHSLMGNFENAVDYFHTALG  298 (330)
T ss_dssp             TTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCSHHHHHHH-----HHHHHHTCHHHHHHHHHTTTT
T ss_pred             hccccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhhC-ccchHHHHHHH-----HHHHHhccHHHHHHHHHHHHc
Confidence                   13346788999999999999999999999987642 22334444444     677889999999998887654

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.57  E-value=1.6e-12  Score=95.58  Aligned_cols=204  Identities=11%  Similarity=-0.013  Sum_probs=153.6

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHH
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLA  101 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~  101 (248)
                      +...|..+...+...|++++|.+.+++..+.. +.+...+..+...|...|++++|.+.+++..+.. +.+..++..+..
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~   84 (225)
T 2vq2_A            7 VSNIKTQLAMEYMRGQDYRQATASIEDALKSD-PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYGW   84 (225)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHHH
Confidence            56778888889999999999999999887654 3457788888899999999999999999887653 236778888889


Q ss_pred             HHHhc-CCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCch
Q 039342          102 VYAKS-NRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR  180 (248)
Q Consensus       102 ~~~~~-~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~  180 (248)
                      .+... |++++|...+++..+.+..|........+...+...|+++.|...++...+.... +...+..+...+...|++
T Consensus        85 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~~~~  163 (225)
T 2vq2_A           85 FLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQPQ-FPPAFKELARTKMLAGQL  163 (225)
T ss_dssp             HHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHTCH
T ss_pred             HHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CchHHHHHHHHHHHcCCH
Confidence            99999 9999999999998874344544433333333467788899999999888776432 577788888899999999


Q ss_pred             HHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          181 ERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       181 ~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      ++|.+.+++..+..-..+...+..+.     ..+...|+.+++..+++.+.+.
T Consensus       164 ~~A~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~a~~~~~~~~~~  211 (225)
T 2vq2_A          164 GDADYYFKKYQSRVEVLQADDLLLGW-----KIAKALGNAQAAYEYEAQLQAN  211 (225)
T ss_dssp             HHHHHHHHHHHHHHCSCCHHHHHHHH-----HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHH-----HHHHhcCcHHHHHHHHHHHHHh
Confidence            99999999877642112333333332     5566788888888888887654

>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=99.57  E-value=1.7e-12  Score=97.46  Aligned_cols=201  Identities=9%  Similarity=-0.050  Sum_probs=161.7

Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHH
Q 039342           23 SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAV  102 (248)
Q Consensus        23 ~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~  102 (248)
                      ...|..+...+...|++++|.+.|++..+.. +.+...+..+...|.+.|++++|.+.+++..+.. +.+...+..+...
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~  114 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTEMEPKLADEEYRKALASD-SRNARVLNNYGGF  114 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHH
Confidence            5678888899999999999999999987764 4567889999999999999999999999988753 2367889999999


Q ss_pred             HHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHH
Q 039342          103 YAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRER  182 (248)
Q Consensus       103 ~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~  182 (248)
                      |...|++++|...+++..+.+..|........+...+...|+++.|...++...+... .+...+..+...+...|++++
T Consensus       115 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~la~~~~~~g~~~~  193 (252)
T 2ho1_A          115 LYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLNR-NQPSVALEMADLLYKEREYVP  193 (252)
T ss_dssp             HHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCS-CCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCc-ccHHHHHHHHHHHHHcCCHHH
Confidence            9999999999999999987444565544444444446778899999999999887653 257788899999999999999


Q ss_pred             HHHHHHHHHHCCCCCC-cchhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          183 AARVLDEATKRGLFPE-LFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       183 a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      |...+++..+.  .|+ ...+..+.     ..+...|+.++|.+.++++.+.
T Consensus       194 A~~~~~~~~~~--~~~~~~~~~~~~-----~~~~~~g~~~~A~~~~~~~~~~  238 (252)
T 2ho1_A          194 ARQYYDLFAQG--GGQNARSLLLGI-----RLAKVFEDRDTAASYGLQLKRL  238 (252)
T ss_dssp             HHHHHHHHHTT--SCCCHHHHHHHH-----HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHh--CcCcHHHHHHHH-----HHHHHccCHHHHHHHHHHHHHH
Confidence            99999998764  333 33333333     5677889999999999998775

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.57  E-value=2e-13  Score=105.22  Aligned_cols=219  Identities=11%  Similarity=0.087  Sum_probs=164.2

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|+++.|+..++........+.......+.++|...|+++.|...++.    .-+|+..++..+...+.+.++.++|.+.
T Consensus        12 ~g~y~~ai~~~~~~~~~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~----~~~~~~~a~~~la~~~~~~~~~~~A~~~   87 (291)
T 3mkr_A           12 IGSYQQCINEAQRVKPSSPERDVERDVFLYRAYLAQRKYGVVLDEIKP----SSAPELQAVRMFAEYLASHSRRDAIVAE   87 (291)
T ss_dssp             TTCHHHHHHHHHHSCCCSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCT----TSCHHHHHHHHHHHHHHCSTTHHHHHHH
T ss_pred             HHHHHHHHHHHHhcccCCchhhHHHHHHHHHHHHHCCCHHHHHHHhcc----cCChhHHHHHHHHHHHcCCCcHHHHHHH
Confidence            388999999888765433222234667788999999999999986654    2467788999999999999999999999


Q ss_pred             HHHHHHCCCCcC-HhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcC
Q 039342           81 FQEIKSSGILPS-VMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEG  159 (248)
Q Consensus        81 ~~~m~~~~~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~  159 (248)
                      ++++...+..|+ ...+..+-..+...|++++|++.+++      +.+...+..+... +...|+++.|...++.+.+..
T Consensus        88 l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~-~~~~g~~~~A~~~l~~~~~~~  160 (291)
T 3mkr_A           88 LDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQI-LLKLDRLDLARKELKKMQDQD  160 (291)
T ss_dssp             HHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHH-HHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHH-HHHCCCHHHHHHHHHHHHhhC
Confidence            999988776664 55666677899999999999999997      2333444444443 777899999999999998875


Q ss_pred             CCCCHHHH---HHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHHHc
Q 039342          160 YGLGMRFY---NALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMM  236 (248)
Q Consensus       160 ~~p~~~~~---~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~~~  236 (248)
                        |+....   ...+..+...|++++|..+|+++.+. .+.+...++.+.     ..+.+.|++++|...+++..+.  .
T Consensus       161 --p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~-~p~~~~~~~~la-----~~~~~~g~~~eA~~~l~~al~~--~  230 (291)
T 3mkr_A          161 --EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADK-CSPTLLLLNGQA-----ACHMAQGRWEAAEGVLQEALDK--D  230 (291)
T ss_dssp             --TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH-SCCCHHHHHHHH-----HHHHHTTCHHHHHHHHHHHHHH--C
T ss_pred             --cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHh-CCCcHHHHHHHH-----HHHHHcCCHHHHHHHHHHHHHh--C
Confidence              443221   23344455569999999999999876 233444444444     6788999999999999998765  5


Q ss_pred             CCCC
Q 039342          237 GEDL  240 (248)
Q Consensus       237 ~~~~  240 (248)
                      |+.+
T Consensus       231 p~~~  234 (291)
T 3mkr_A          231 SGHP  234 (291)
T ss_dssp             TTCH
T ss_pred             CCCH
Confidence            5443

>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=99.57  E-value=2.1e-12  Score=96.92  Aligned_cols=193  Identities=14%  Similarity=0.079  Sum_probs=158.3

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|.+.|+++.+.. +.+...|..+...+...|++++|.+.+++..+.. +.+...+..+...|...|++++|.++
T Consensus        50 ~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~  127 (252)
T 2ho1_A           50 RGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTEMEPKLADEEYRKALASD-SRNARVLNNYGGFLYEQKRYEEAYQR  127 (252)
T ss_dssp             TTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHHhHHHHHHHH
Confidence            378999999999988754 2468899999999999999999999999997764 34778899999999999999999999


Q ss_pred             HHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCch-HHhHHHHhcccccccchHHHHHHHHHHHHhc
Q 039342           81 FQEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNI-HQVTGQMIKGEFDDESNWQMVEYVFDKLNCE  158 (248)
Q Consensus        81 ~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  158 (248)
                      +++..+.+..| +...+..+...+...|++++|...+++..+..  |. ...+..+.. .+...|+++.|...++...+.
T Consensus       128 ~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~la~-~~~~~g~~~~A~~~~~~~~~~  204 (252)
T 2ho1_A          128 LLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN--RNQPSVALEMAD-LLYKEREYVPARQYYDLFAQG  204 (252)
T ss_dssp             HHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--SCCHHHHHHHHH-HHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--cccHHHHHHHHH-HHHHcCCHHHHHHHHHHHHHh
Confidence            99998743445 56788899999999999999999999988765  33 333333333 367788999999999998876


Q ss_pred             CCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcch
Q 039342          159 GYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFR  201 (248)
Q Consensus       159 ~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t  201 (248)
                      .. .+...+..+...+...|+.++|.++++++.+.  .|+...
T Consensus       205 ~~-~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~--~p~~~~  244 (252)
T 2ho1_A          205 GG-QNARSLLLGIRLAKVFEDRDTAASYGLQLKRL--YPGSLE  244 (252)
T ss_dssp             SC-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTSHH
T ss_pred             Cc-CcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH--CCCCHH
Confidence            43 46778888999999999999999999998774  455433

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.56  E-value=4.4e-12  Score=93.16  Aligned_cols=198  Identities=13%  Similarity=0.033  Sum_probs=159.5

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc-CChhHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFA-GLVDESKE   79 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~-g~~~~a~~   79 (248)
                      .|++++|.+.|++..+... .+...|..+...+...|++++|.+.+++..+.. +.+..++..+...+... |++++|..
T Consensus        21 ~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~~A~~   98 (225)
T 2vq2_A           21 GQDYRQATASIEDALKSDP-KNELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYGWFLCGRLNRPAESMA   98 (225)
T ss_dssp             TTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCCHHHHHH
T ss_pred             HhhHHHHHHHHHHHHHhCc-cchHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCcHHHHHH
Confidence            3889999999999887542 468899999999999999999999999997764 45778899999999999 99999999


Q ss_pred             HHHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhc
Q 039342           80 QFQEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCE  158 (248)
Q Consensus        80 ~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  158 (248)
                      .+++..+.+..| +...+..+...+...|++++|...+++..+..  |+.......+...+...|+++.|...++...+.
T Consensus        99 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  176 (225)
T 2vq2_A           99 YFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQ--PQFPPAFKELARTKMLAGQLGDADYYFKKYQSR  176 (225)
T ss_dssp             HHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            999998843334 36788999999999999999999999998764  443333333333377788999999999998876


Q ss_pred             CCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhh
Q 039342          159 GYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNK  204 (248)
Q Consensus       159 ~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~  204 (248)
                      ....+...+..+...+...|+.+.+..+++.+.+.  .|+...+..
T Consensus       177 ~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~--~p~~~~~~~  220 (225)
T 2vq2_A          177 VEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQAN--FPYSEELQT  220 (225)
T ss_dssp             HCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHh--CCCCHHHHH
Confidence            54246777888888899999999999999998754  465444433

>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=99.56  E-value=6.9e-13  Score=105.02  Aligned_cols=222  Identities=10%  Similarity=-0.009  Sum_probs=166.8

Q ss_pred             CchHHHHH-HHHHHHHcCC-CC--CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHH
Q 039342            2 GLYKECQA-ILSRMSESGV-AR--NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDES   77 (248)
Q Consensus         2 g~~~~a~~-~~~~m~~~g~-~~--~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a   77 (248)
                      |++++|.+ .|++..+... .|  +...+..+-..+.+.|++++|...|+++.+.. +.+..++..+..++.+.|++++|
T Consensus        39 ~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A  117 (368)
T 1fch_A           39 SDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLA  117 (368)
T ss_dssp             -------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHH
Confidence            45566666 5654433211 11  45678889999999999999999999998764 45778999999999999999999


Q ss_pred             HHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHH--------------Hhcccccccc
Q 039342           78 KEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQ--------------MIKGEFDDES  143 (248)
Q Consensus        78 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~--------------~l~~~~~~~~  143 (248)
                      .+.|++..+.. +.+..++..+...|...|++++|...++++.+............              .+...+ ..|
T Consensus       118 ~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~  195 (368)
T 1fch_A          118 ISALRRCLELK-PDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLL-SDS  195 (368)
T ss_dssp             HHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHH-HHH
T ss_pred             HHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHhhhhcccHHHHHHHHHh-hcc
Confidence            99999998764 33778999999999999999999999999987653221111110              222323 778


Q ss_pred             hHHHHHHHHHHHHhcCCCC-CHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCC-cchhhhHHhhhhhhccccchHHH
Q 039342          144 NWQMVEYVFDKLNCEGYGL-GMRFYNALLEALWCLGLRERAARVLDEATKRGLFPE-LFRHNKLVWSVDVHRMWEGGAYT  221 (248)
Q Consensus       144 ~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~~~~~~g~~~  221 (248)
                      +++.|...++.+.+..... +..++..+...+.+.|++++|...+++..+.  .|+ ...+..+.     ..+...|+++
T Consensus       196 ~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~~~~~~~~~~l~-----~~~~~~g~~~  268 (368)
T 1fch_A          196 LFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSV--RPNDYLLWNKLG-----ATLANGNQSE  268 (368)
T ss_dssp             HHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHH-----HHHHHTTCHH
T ss_pred             cHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CcCCHHHHHHHH-----HHHHHcCCHH
Confidence            9999999999988764332 5888999999999999999999999998764  343 34444444     6778899999


Q ss_pred             HHHHHHHHHHHH
Q 039342          222 AISVWLNKMYEM  233 (248)
Q Consensus       222 ~~~~~~~~m~~~  233 (248)
                      +|...+++..+.
T Consensus       269 ~A~~~~~~al~~  280 (368)
T 1fch_A          269 EAVAAYRRALEL  280 (368)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh
Confidence            999999988775

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.56  E-value=7.5e-13  Score=97.62  Aligned_cols=199  Identities=12%  Similarity=0.024  Sum_probs=148.7

Q ss_pred             CCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHH
Q 039342           20 ARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCML   99 (248)
Q Consensus        20 ~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l   99 (248)
                      +++...+..+-..+.+.|++++|...|++..+.. +.+...+..+-.++.+.|++++|...|++..+.. +.+...+..+
T Consensus         2 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~l   79 (217)
T 2pl2_A            2 QTAEQNPLRLGVQLYALGRYDAALTLFERALKEN-PQDPEALYWLARTQLKLGLVNPALENGKTLVART-PRYLGGYMVL   79 (217)
T ss_dssp             --CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHH
Confidence            4677888999999999999999999999987654 4567888899999999999999999999988753 2256788889


Q ss_pred             HHHHHhc-----------CCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHH
Q 039342          100 LAVYAKS-----------NRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYN  168 (248)
Q Consensus       100 i~~~~~~-----------~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~  168 (248)
                      -..+...           |++++|+..|++..+..  |+.......+...+...|++++|...+++..+..  .+...+.
T Consensus        80 g~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~--P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~  155 (217)
T 2pl2_A           80 SEAYVALYRQAEDRERGKGYLEQALSVLKDAERVN--PRYAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRS  155 (217)
T ss_dssp             HHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHH
T ss_pred             HHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhC--cccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHH
Confidence            9999999           99999999999988764  5554444444444778899999999999998887  6888899


Q ss_pred             HHHHHHHhcCchHHHHHHHHHHHHCCCCCC-cchhhhHHhhhhhhccccchHHHHHHHHHHHHH
Q 039342          169 ALLEALWCLGLRERAARVLDEATKRGLFPE-LFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMY  231 (248)
Q Consensus       169 ~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~  231 (248)
                      .+-.++...|++++|...|++..+.  .|+ ...+..+.     ..+...|+.++|...+++-.
T Consensus       156 ~la~~~~~~g~~~~A~~~~~~al~~--~P~~~~~~~~la-----~~~~~~g~~~~A~~~~~~~~  212 (217)
T 2pl2_A          156 ALAELYLSMGRLDEALAQYAKALEQ--APKDLDLRVRYA-----SALLLKGKAEEAARAAALEH  212 (217)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHH--STTCHHHHHHHH-----HHHTC---------------
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHHHHHH-----HHHHHccCHHHHHHHHHHHh
Confidence            9999999999999999999998764  454 23333333     66788999999888777543

>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=99.55  E-value=2e-15  Score=120.54  Aligned_cols=191  Identities=16%  Similarity=0.182  Sum_probs=57.1

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|.+.++++..      +.+|..+..++.+.|++++|.+.|.+      .+|..+|..++.++...|++++|..++
T Consensus        17 ~~ld~A~~fae~~~~------~~vWs~La~A~l~~g~~~eAIdsfik------a~D~~~y~~V~~~ae~~g~~EeAi~yl   84 (449)
T 1b89_A           17 GNLDRAYEFAERCNE------PAVWSQLAKAQLQKGMVKEAIDSYIK------ADDPSSYMEVVQAANTSGNWEELVKYL   84 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cCHHHHHHHHHhCCC------hHHHHHHHHHHHHcCCHHHHHHHHHc------CCCHHHHHHHHHHHHhCCCHHHHHHHH
Confidence            678888888888833      35899999999999999999999865      367778999999999999999999977


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCC
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYG  161 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~  161 (248)
                      +..++.  .+++.+.+.++.+|.+.|+++++.++++       .|+..++..+-.. |...|.|+.|...|..+      
T Consensus        85 ~~ark~--~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~-~~~~g~yeeA~~~Y~~a------  148 (449)
T 1b89_A           85 QMARKK--ARESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDR-CYDEKMYDAAKLLYNNV------  148 (449)
T ss_dssp             --------------------------CHHHHTTTTT-------CC-----------------CTTTHHHHHHHT------
T ss_pred             HHHHHh--CccchhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHH-HHHcCCHHHHHHHHHHh------
Confidence            776664  4557788889999999999988888885       2566667666666 77778888888888765      


Q ss_pred             CCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhh-------------------------cccc
Q 039342          162 LGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVH-------------------------RMWE  216 (248)
Q Consensus       162 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~-------------------------~~~~  216 (248)
                         ..|..+..++.+.|+++.|.+.+.++      .+..+|..++.+|...                         .|.+
T Consensus       149 ---~n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~~~ad~l~~lv~~Yek  219 (449)
T 1b89_A          149 ---SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHADELEELINYYQD  219 (449)
T ss_dssp             ---TCHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTTTTTCHHHHHHHHHHHHH
T ss_pred             ---hhHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHHHHhCHhhHHHHHHHHHH
Confidence               35777778888888888877777776      2455666666444433                         3666


Q ss_pred             chHHHHHHHHHHH
Q 039342          217 GGAYTAISVWLNK  229 (248)
Q Consensus       217 ~g~~~~~~~~~~~  229 (248)
                      .|+++++..+++.
T Consensus       220 ~G~~eEai~lLe~  232 (449)
T 1b89_A          220 RGYFEELITMLEA  232 (449)
T ss_dssp             TTCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHH
Confidence            7777776665544

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.54  E-value=2.2e-12  Score=106.44  Aligned_cols=85  Identities=8%  Similarity=0.094  Sum_probs=73.0

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|.+.|+++.+..  |+...|..+..++.+.|++++|.+.++++.+.+ +.+...|..+..+|.+.|++++|...
T Consensus        19 ~g~~~~A~~~~~~al~~~--p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~   95 (514)
T 2gw1_A           19 NKKYDDAIKYYNWALELK--EDPVFYSNLSACYVSVGDLKKVVEMSTKALELK-PDYSKVLLRRASANEGLGKFADAMFD   95 (514)
T ss_dssp             TSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             hccHHHHHHHHHHHHhcC--ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC-hHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence            388999999999998755  789999999999999999999999999988765 45667888999999999999999999


Q ss_pred             HHHHHHCC
Q 039342           81 FQEIKSSG   88 (248)
Q Consensus        81 ~~~m~~~~   88 (248)
                      |+++.+.+
T Consensus        96 ~~~~~~~~  103 (514)
T 2gw1_A           96 LSVLSLNG  103 (514)
T ss_dssp             HHHHHHSS
T ss_pred             HHHHHhcC
Confidence            98886553

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.53  E-value=1.1e-11  Score=97.31  Aligned_cols=226  Identities=11%  Similarity=0.046  Sum_probs=174.1

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|.+.|++..+... .+...|..+...+...|++++|...+++..+.. +-+...+..+...+.+.|++++|...
T Consensus        16 ~g~~~~A~~~~~~~l~~~p-~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~   93 (359)
T 3ieg_A           16 AGQLADALSQFHAAVDGDP-DNYIAYYRRATVFLAMGKSKAALPDLTKVIALK-MDFTAARLQRGHLLLKQGKLDEAEDD   93 (359)
T ss_dssp             TTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhhCc-ccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCcchHHHHHHHHHHHcCChHHHHHH
Confidence            3899999999999987543 468899999999999999999999999998763 34678899999999999999999999


Q ss_pred             HHHHHHCCCC--cCHhhHHHH------------HHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHH
Q 039342           81 FQEIKSSGIL--PSVMCYCML------------LAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQ  146 (248)
Q Consensus        81 ~~~m~~~~~~--p~~~~~~~l------------i~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~  146 (248)
                      |++..+....  .+...+..+            ...+...|++++|...+++..+..  |+.......+...+...|+++
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~  171 (359)
T 3ieg_A           94 FKKVLKSNPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVC--VWDAELRELRAECFIKEGEPR  171 (359)
T ss_dssp             HHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--CCchHHHHHHHHHHHHCCCHH
Confidence            9999876320  134445444            578889999999999999998764  444434444444477789999


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcch-hhhHHh-------hhhhhccccch
Q 039342          147 MVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFR-HNKLVW-------SVDVHRMWEGG  218 (248)
Q Consensus       147 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t-~~~li~-------~~~~~~~~~~g  218 (248)
                      .|...++...+.. +.+..++..+...+...|++++|.+.+++..+.  .|+... +..+..       ......+.+.|
T Consensus       172 ~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~  248 (359)
T 3ieg_A          172 KAISDLKAASKLK-SDNTEAFYKISTLYYQLGDHELSLSEVRECLKL--DQDHKRCFAHYKQVKKLNKLIESAEELIRDG  248 (359)
T ss_dssp             HHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CccchHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            9999999988764 336788999999999999999999999998764  344322 111100       01124467788


Q ss_pred             HHHHHHHHHHHHHHH
Q 039342          219 AYTAISVWLNKMYEM  233 (248)
Q Consensus       219 ~~~~~~~~~~~m~~~  233 (248)
                      ++++|...+++..+.
T Consensus       249 ~~~~A~~~~~~~~~~  263 (359)
T 3ieg_A          249 RYTDATSKYESVMKT  263 (359)
T ss_dssp             CHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHhc
Confidence            999999988887765

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.53  E-value=3e-12  Score=101.43  Aligned_cols=201  Identities=11%  Similarity=-0.025  Sum_probs=161.4

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHH
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLA  101 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~  101 (248)
                      +...|..+...+.+.|++++|.+.|+++.+.. +.+..+|..+..+|.+.|++++|.+.|++..+.. +.+..+|..+..
T Consensus        64 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~  141 (365)
T 4eqf_A           64 DWPGAFEEGLKRLKEGDLPVTILFMEAAILQD-PGDAEAWQFLGITQAENENEQAAIVALQRCLELQ-PNNLKALMALAV  141 (365)
T ss_dssp             TCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHH
Confidence            45568899999999999999999999998764 4578899999999999999999999999998753 235789999999


Q ss_pred             HHHhcCCHHHHHHHHHHHHHCCCCchHHhHHH----------HhcccccccchHHHHHHHHHHHHhcCCC-CCHHHHHHH
Q 039342          102 VYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQ----------MIKGEFDDESNWQMVEYVFDKLNCEGYG-LGMRFYNAL  170 (248)
Q Consensus       102 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~----------~l~~~~~~~~~~~~a~~~~~~m~~~~~~-p~~~~~~~l  170 (248)
                      .|...|++++|...|++..+..  |+......          .+...+...|+++.|...++...+.... ++..++..+
T Consensus       142 ~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l  219 (365)
T 4eqf_A          142 SYTNTSHQQDACEALKNWIKQN--PKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGL  219 (365)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC--HHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHH
T ss_pred             HHHccccHHHHHHHHHHHHHhC--ccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHH
Confidence            9999999999999999998754  43322221          1233477889999999999999887433 268899999


Q ss_pred             HHHHHhcCchHHHHHHHHHHHHCCCCCC-cchhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          171 LEALWCLGLRERAARVLDEATKRGLFPE-LFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       171 i~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      ...+...|++++|.+.|++..+.  .|+ ..++..+.     ..+...|++++|...+++..+.
T Consensus       220 ~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~-----~~~~~~g~~~~A~~~~~~al~~  276 (365)
T 4eqf_A          220 GVLFHLSGEFNRAIDAFNAALTV--RPEDYSLWNRLG-----ATLANGDRSEEAVEAYTRALEI  276 (365)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHH-----HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHH-----HHHHHcCCHHHHHHHHHHHHhc
Confidence            99999999999999999998874  343 34444444     7788899999999999988775

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.51  E-value=1.5e-11  Score=96.64  Aligned_cols=151  Identities=9%  Similarity=-0.036  Sum_probs=79.1

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC----CHHHHHHH------------H
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDP----NERTLEAV------------L   65 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p----~~~t~~~l------------l   65 (248)
                      |++++|.+.|++..+... .+...|..+...+.+.|++++|.+.+++..+.  .|    +...+..+            .
T Consensus        51 ~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~a  127 (359)
T 3ieg_A           51 GKSKAALPDLTKVIALKM-DFTAARLQRGHLLLKQGKLDEAEDDFKKVLKS--NPSEQEEKEAESQLVKADEMQRLRSQA  127 (359)
T ss_dssp             TCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHhCC-CcchHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCcccChHHHHHHHHHHHHHHHHHHHH
Confidence            566666666666655331 24566666666666666666666666666543  23    22223222            3


Q ss_pred             HHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchH
Q 039342           66 SVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNW  145 (248)
Q Consensus        66 ~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~  145 (248)
                      ..+...|++++|.+.+++..+.. +.+...+..+...+...|++++|...+++..+..  |+.......+...+...|++
T Consensus       128 ~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~la~~~~~~~~~  204 (359)
T 3ieg_A          128 LDAFDGADYTAAITFLDKILEVC-VWDAELRELRAECFIKEGEPRKAISDLKAASKLK--SDNTEAFYKISTLYYQLGDH  204 (359)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC--SCCHHHHHHHHHHHHHHTCH
T ss_pred             HHHHHccCHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCH
Confidence            45556666666666666655432 1244555556666666666666666666655432  22222222222224444555


Q ss_pred             HHHHHHHHHHHhc
Q 039342          146 QMVEYVFDKLNCE  158 (248)
Q Consensus       146 ~~a~~~~~~m~~~  158 (248)
                      +.|...++...+.
T Consensus       205 ~~A~~~~~~a~~~  217 (359)
T 3ieg_A          205 ELSLSEVRECLKL  217 (359)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhh
Confidence            5555555555443

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.51  E-value=2.1e-12  Score=106.62  Aligned_cols=221  Identities=10%  Similarity=-0.073  Sum_probs=174.3

Q ss_pred             CchHHHHHHHHHHHH-----cCC--------CCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 039342            2 GLYKECQAILSRMSE-----SGV--------ARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVY   68 (248)
Q Consensus         2 g~~~~a~~~~~~m~~-----~g~--------~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~   68 (248)
                      |++++|.+.|+++.+     ..-        +.+...|..+...+...|++++|...+++..+.+  |+...+..+...+
T Consensus       203 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~--~~~~~~~~l~~~~  280 (514)
T 2gw1_A          203 ESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTGIFKFLKNDPLGAHEDIKKAIELF--PRVNSYIYMALIM  280 (514)
T ss_dssp             THHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--ccHHHHHHHHHHH
Confidence            789999999999877     311        2346688889999999999999999999998765  4488899999999


Q ss_pred             HhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHH
Q 039342           69 CFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMV  148 (248)
Q Consensus        69 ~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  148 (248)
                      ...|++++|.+.+++..+.. +.+..++..+...+...|++++|...+++..+.... +...+..+... +...|+++.|
T Consensus       281 ~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~-~~~~~~~~~A  357 (514)
T 2gw1_A          281 ADRNDSTEYYNYFDKALKLD-SNNSSVYYHRGQMNFILQNYDQAGKDFDKAKELDPE-NIFPYIQLACL-AYRENKFDDC  357 (514)
T ss_dssp             HTSSCCTTGGGHHHHHHTTC-TTCTHHHHHHHHHHHHTTCTTHHHHHHHHHHHTCSS-CSHHHHHHHHH-TTTTTCHHHH
T ss_pred             HHCCCHHHHHHHHHHHhhcC-cCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhChh-hHHHHHHHHHH-HHHcCCHHHH
Confidence            99999999999999998763 236778999999999999999999999999876522 22334444333 7788999999


Q ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCC-CCC----cchhhhHHhhhhhhcccc---chHH
Q 039342          149 EYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGL-FPE----LFRHNKLVWSVDVHRMWE---GGAY  220 (248)
Q Consensus       149 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~-~p~----~~t~~~li~~~~~~~~~~---~g~~  220 (248)
                      ...++...+... .+..++..+...+.+.|++++|...++++.+..- .++    ...+..+.     ..+..   .|++
T Consensus       358 ~~~~~~~~~~~~-~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~-----~~~~~~~~~~~~  431 (514)
T 2gw1_A          358 ETLFSEAKRKFP-EAPEVPNFFAEILTDKNDFDKALKQYDLAIELENKLDGIYVGIAPLVGKA-----TLLTRNPTVENF  431 (514)
T ss_dssp             HHHHHHHHHHST-TCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSSSCSSCSHHHHHHH-----HHHHTSCCTTHH
T ss_pred             HHHHHHHHHHcc-cCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccchHHHHHHHHHHHH-----HHHhhhhhcCCH
Confidence            999999887643 2567888999999999999999999998875311 111    11344444     66677   8999


Q ss_pred             HHHHHHHHHHHHH
Q 039342          221 TAISVWLNKMYEM  233 (248)
Q Consensus       221 ~~~~~~~~~m~~~  233 (248)
                      ++|...+++..+.
T Consensus       432 ~~A~~~~~~a~~~  444 (514)
T 2gw1_A          432 IEATNLLEKASKL  444 (514)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999988765

>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=99.50  E-value=1.1e-12  Score=101.95  Aligned_cols=224  Identities=9%  Similarity=-0.048  Sum_probs=167.2

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHH--------------HH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAV--------------LS   66 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l--------------l~   66 (248)
                      .|++++|.+.|++..+.. +.+...|..+...+...|++++|.+.+++..+..- .+...+..+              ..
T Consensus        68 ~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  145 (327)
T 3cv0_A           68 NEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHNANAALASLRAWLLSQP-QYEQLGSVNLQADVDIDDLNVQSED  145 (327)
T ss_dssp             TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTST-TTTTC--------------------
T ss_pred             cCCHHHHHHHHHHHHhcC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-ccHHHHHHHhHHHHHHHHHHHHHHh
Confidence            378999999999998754 24688999999999999999999999999976532 122222222              22


Q ss_pred             -HHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchH
Q 039342           67 -VYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNW  145 (248)
Q Consensus        67 -~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~  145 (248)
                       .+...|++++|.+.+++..+.. +.+...+..+...+.+.|++++|...+++..+..  |+.......+...+...|++
T Consensus       146 ~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~  222 (327)
T 3cv0_A          146 FFFAAPNEYRECRTLLHAALEMN-PNDAQLHASLGVLYNLSNNYDSAAANLRRAVELR--PDDAQLWNKLGATLANGNRP  222 (327)
T ss_dssp             CCTTSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHcccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHcCCH
Confidence             3778899999999999998753 2367889999999999999999999999998764  44333333333336678899


Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCc--------chhhhHHhhhhhhccccc
Q 039342          146 QMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPEL--------FRHNKLVWSVDVHRMWEG  217 (248)
Q Consensus       146 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~--------~t~~~li~~~~~~~~~~~  217 (248)
                      +.|...++...+... .+..++..+...+...|++++|.+.+++..+..  |+.        ...+...+..+...+...
T Consensus       223 ~~A~~~~~~a~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  299 (327)
T 3cv0_A          223 QEALDAYNRALDINP-GYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQ--VGGTTPTGEASREATRSMWDFFRMLLNVM  299 (327)
T ss_dssp             HHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH--TTSCC-----CCTHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CccccccccchhhcCHHHHHHHHHHHHhc
Confidence            999999999887643 357889999999999999999999999987642  220        011233334444778889


Q ss_pred             hHHHHHHHHHHHHHH
Q 039342          218 GAYTAISVWLNKMYE  232 (248)
Q Consensus       218 g~~~~~~~~~~~m~~  232 (248)
                      |+.++|...+++..+
T Consensus       300 g~~~~A~~~~~~~l~  314 (327)
T 3cv0_A          300 NRPDLVELTYAQNVE  314 (327)
T ss_dssp             TCHHHHHHHTTCCSH
T ss_pred             CCHHHHHHHHHHHHH
Confidence            999999888765443

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.50  E-value=4.4e-12  Score=94.44  Aligned_cols=185  Identities=14%  Similarity=0.113  Sum_probs=84.4

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|.+.|++..+.. +.+...|..+...+.+.|++++|.+.+++..+.. +.+...+..+...|...|++++|.+.+
T Consensus        37 ~~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~  114 (243)
T 2q7f_A           37 GDYEKAAEAFTKAIEEN-KEDAIPYINFANLLSSVNELERALAFYDKALELD-SSAATAYYGAGNVYVVKEMYKEAKDMF  114 (243)
T ss_dssp             -----CCTTHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             hCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CcchHHHHHHHHHHHHhccHHHHHHHH
Confidence            44455555555554422 1234455555555555555555555555554432 224445555555555555555555555


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCC
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYG  161 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~  161 (248)
                      ++..+.. +.+...+..+...+.+.|++++|...+++..+..  |+.......+...+...|+++.|...++...+... 
T Consensus       115 ~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-  190 (243)
T 2q7f_A          115 EKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVELN--ENDTEARFQFGMCLANEGMLDEALSQFAAVTEQDP-  190 (243)
T ss_dssp             HHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHCT-
T ss_pred             HHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-
Confidence            5554432 1234445555555555555555555555554432  21111111111223344445555555555444321 


Q ss_pred             CCHHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          162 LGMRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       162 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                      .+..++..+...+...|++++|.+.+++..+
T Consensus       191 ~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  221 (243)
T 2q7f_A          191 GHADAFYNAGVTYAYKENREKALEMLDKAID  221 (243)
T ss_dssp             TCHHHHHHHHHHHHHTTCTTHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHccCHHHHHHHHHHHHc
Confidence            1344455555555555555555555555443

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.49  E-value=5.8e-12  Score=95.55  Aligned_cols=223  Identities=9%  Similarity=-0.089  Sum_probs=158.2

Q ss_pred             CchHHHHHHHHHHHHcCC---CCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHH
Q 039342            2 GLYKECQAILSRMSESGV---ARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESK   78 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~---~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~   78 (248)
                      |++++|.+.|+++.+...   +.+...|..+...+...|++++|.+.|++..+.. +.+..+|..+...|...|++++|.
T Consensus        19 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~   97 (275)
T 1xnf_A           19 LQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAY   97 (275)
T ss_dssp             HHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             chHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHccCHHHHH
Confidence            688999999999987532   1256789999999999999999999999998764 356889999999999999999999


Q ss_pred             HHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhc
Q 039342           79 EQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCE  158 (248)
Q Consensus        79 ~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  158 (248)
                      +.|++..+.. +.+...+..+...|.+.|++++|...|++..+..  |+.......+.. +...++++.|...++.....
T Consensus        98 ~~~~~al~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~--~~~~~~~~~~~~-~~~~~~~~~A~~~~~~~~~~  173 (275)
T 1xnf_A           98 EAFDSVLELD-PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD--PNDPFRSLWLYL-AEQKLDEKQAKEVLKQHFEK  173 (275)
T ss_dssp             HHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHH-HHHHHCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcC-ccccHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CCChHHHHHHHH-HHHhcCHHHHHHHHHHHHhc
Confidence            9999998753 2257889999999999999999999999998754  443333222222 34557888898888766654


Q ss_pred             CCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          159 GYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       159 ~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      .. ++...+. +...+...++.++|.+.+.+..+.  .|+........+..+...+...|++++|...+++..+.
T Consensus       174 ~~-~~~~~~~-~~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  244 (275)
T 1xnf_A          174 SD-KEQWGWN-IVEFYLGNISEQTLMERLKADATD--NTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVAN  244 (275)
T ss_dssp             SC-CCSTHHH-HHHHHTTSSCHHHHHHHHHHHCCS--HHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             CC-cchHHHH-HHHHHHHhcCHHHHHHHHHHHhcc--cccccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHhC
Confidence            22 2333333 555666666677777777765432  12110011222222335666777777777777766543

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.47  E-value=9.3e-12  Score=91.72  Aligned_cols=183  Identities=12%  Similarity=0.069  Sum_probs=140.9

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc---------
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFA---------   71 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~---------   71 (248)
                      .|++++|...|++..+... .+...|..+-..+.+.|++++|...+++..+.. +-+...+..+-.++.+.         
T Consensus        18 ~g~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~~~~~~~~~   95 (217)
T 2pl2_A           18 LGRYDAALTLFERALKENP-QDPEALYWLARTQLKLGLVNPALENGKTLVART-PRYLGGYMVLSEAYVALYRQAEDRER   95 (217)
T ss_dssp             TTCHHHHHHHHHHHHTTSS-SCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHTCSSHHH
T ss_pred             cCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHhhhhhhhhcc
Confidence            3889999999999887542 468899999999999999999999999998764 44678888999999999         


Q ss_pred             --CChhHHHHHHHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHH
Q 039342           72 --GLVDESKEQFQEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMV  148 (248)
Q Consensus        72 --g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  148 (248)
                        |++++|...|++..+.  .| +...+..+-..+...|++++|+..|++..+..  .+...+..+-.. +...|++++|
T Consensus        96 ~~g~~~~A~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~la~~-~~~~g~~~~A  170 (217)
T 2pl2_A           96 GKGYLEQALSVLKDAERV--NPRYAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRSALAEL-YLSMGRLDEA  170 (217)
T ss_dssp             HHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHH-HHHHTCHHHH
T ss_pred             cccCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHHHHHHH-HHHcCCHHHH
Confidence              9999999999999875  34 57788999999999999999999999998877  444444444444 7778999999


Q ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHH
Q 039342          149 EYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEAT  191 (248)
Q Consensus       149 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  191 (248)
                      ...++...+.... +...+..+...+...|++++|.+.+++..
T Consensus       171 ~~~~~~al~~~P~-~~~~~~~la~~~~~~g~~~~A~~~~~~~~  212 (217)
T 2pl2_A          171 LAQYAKALEQAPK-DLDLRVRYASALLLKGKAEEAARAAALEH  212 (217)
T ss_dssp             HHHHHHHHHHSTT-CHHHHHHHHHHHTC---------------
T ss_pred             HHHHHHHHHhCCC-ChHHHHHHHHHHHHccCHHHHHHHHHHHh
Confidence            9999998886433 67788889999999999999999998754

>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=99.46  E-value=1.9e-10  Score=87.49  Aligned_cols=214  Identities=7%  Similarity=-0.070  Sum_probs=167.9

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHh----cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----cC
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQ----GGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCF----AG   72 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~----~g   72 (248)
                      .|++++|.+.|++..+.   -+...+..+-..|..    .+++++|.+.|++..+.+   +...+..+-..|..    .+
T Consensus        19 ~~~~~~A~~~~~~a~~~---~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~   92 (273)
T 1ouv_A           19 EKDFTQAKKYFEKACDL---KENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCHLLGNLYYSGQGVSQ   92 (273)
T ss_dssp             TTCHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCC
T ss_pred             CCCHHHHHHHHHHHHHC---CCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHhCCCCccc
Confidence            37899999999999872   356788888889999    999999999999998876   77888889999999    99


Q ss_pred             ChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHh----cCCHHHHHHHHHHHHHCCCCchHHhHHHHhccccc----ccch
Q 039342           73 LVDESKEQFQEIKSSGILPSVMCYCMLLAVYAK----SNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFD----DESN  144 (248)
Q Consensus        73 ~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~----~~~~  144 (248)
                      ++++|.+.|++..+.+   +...+..+-..|..    .+++++|+..|++..+.+  +. ..+..+-.. +.    ..++
T Consensus        93 ~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~--~~-~a~~~lg~~-~~~~~~~~~~  165 (273)
T 1ouv_A           93 NTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN--DG-DGCTILGSL-YDAGRGTPKD  165 (273)
T ss_dssp             CHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT--CH-HHHHHHHHH-HHHTSSSCCC
T ss_pred             CHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC--cH-HHHHHHHHH-HHcCCCCCCC
Confidence            9999999999998875   67888899999999    999999999999998876  22 222222211 22    3788


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh----cCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHH
Q 039342          145 WQMVEYVFDKLNCEGYGLGMRFYNALLEALWC----LGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAY  220 (248)
Q Consensus       145 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~  220 (248)
                      ++.|...++...+.+   +...+..+-..|..    .+++++|.+.|++..+.+-   ...+..+-.. ...+....++.
T Consensus       166 ~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~---~~a~~~l~~~-~~~g~~~~~~~  238 (273)
T 1ouv_A          166 LKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELEN---GGGCFNLGAM-QYNGEGVTRNE  238 (273)
T ss_dssp             HHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTTC---HHHHHHHHHH-HHTTSSSSCCS
T ss_pred             HHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCCC---HHHHHHHHHH-HHcCCCcccCH
Confidence            999999999988775   45778888889999    9999999999999887643   2233333311 11233337888


Q ss_pred             HHHHHHHHHHHHHH
Q 039342          221 TAISVWLNKMYEMF  234 (248)
Q Consensus       221 ~~~~~~~~~m~~~~  234 (248)
                      ++|..++++-.+.+
T Consensus       239 ~~A~~~~~~a~~~~  252 (273)
T 1ouv_A          239 KQAIENFKKGCKLG  252 (273)
T ss_dssp             TTHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcC
Confidence            89999888877664

>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=99.45  E-value=1.2e-11  Score=102.86  Aligned_cols=221  Identities=11%  Similarity=-0.039  Sum_probs=168.4

Q ss_pred             CchHHHHHHHHHHHHcCCCCC--------HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCC
Q 039342            2 GLYKECQAILSRMSESGVARN--------SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGL   73 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~--------~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~   73 (248)
                      |++++|.++|+++.+..  |+        ..+|..+-..+...|++++|.+.+++..+.  .|+...+..+...+.+.|+
T Consensus       216 ~~~~~A~~~~~~~l~~~--p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~  291 (537)
T 3fp2_A          216 DLLTKSTDMYHSLLSAN--TVDDPLRENAALALCYTGIFHFLKNNLLDAQVLLQESINL--HPTPNSYIFLALTLADKEN  291 (537)
T ss_dssp             HHHHHHHHHHHHHHC----CCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCHHHHHHHHHHTCCSSC
T ss_pred             HHHHHHHHHHHHHHHHC--CCcchhhHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc--CCCchHHHHHHHHHHHhcC
Confidence            47889999999987644  33        335777778889999999999999999875  4668899999999999999


Q ss_pred             hhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchH-HhHHHHhcccccccchHHHHHHHH
Q 039342           74 VDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIH-QVTGQMIKGEFDDESNWQMVEYVF  152 (248)
Q Consensus        74 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~  152 (248)
                      +++|.+.+++..+.. +.+..+|..+...+...|++++|...|++..+..  |+. ..+..+. ..+...|+++.|...+
T Consensus       292 ~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~la-~~~~~~g~~~~A~~~~  367 (537)
T 3fp2_A          292 SQEFFKFFQKAVDLN-PEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLN--PENVYPYIQLA-CLLYKQGKFTESEAFF  367 (537)
T ss_dssp             CHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCSHHHHHHH-HHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHhccC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC--CCCHHHHHHHH-HHHHHcCCHHHHHHHH
Confidence            999999999998753 2367889999999999999999999999998764  333 3333333 3367789999999999


Q ss_pred             HHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCc-chhhhHH-hhhhhhccccc----------hHH
Q 039342          153 DKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPEL-FRHNKLV-WSVDVHRMWEG----------GAY  220 (248)
Q Consensus       153 ~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~t~~~li-~~~~~~~~~~~----------g~~  220 (248)
                      +...+... .+...+..+...+...|++++|.+.|++..+..  |+. ..+..+. .......+...          |++
T Consensus       368 ~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  444 (537)
T 3fp2_A          368 NETKLKFP-TLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLE--EVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKF  444 (537)
T ss_dssp             HHHHHHCT-TCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH--HHCSSCSSTTHHHHHHHHHHHHHHTC----CCHHHH
T ss_pred             HHHHHhCC-CChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcC--CcchhhHHHHHHHHHHHHHHHHHhhccchhhhHhHH
Confidence            99888743 356788899999999999999999999987532  211 1111110 11111234445          999


Q ss_pred             HHHHHHHHHHHHH
Q 039342          221 TAISVWLNKMYEM  233 (248)
Q Consensus       221 ~~~~~~~~~m~~~  233 (248)
                      ++|...+++..+.
T Consensus       445 ~~A~~~~~~a~~~  457 (537)
T 3fp2_A          445 NAAIKLLTKACEL  457 (537)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999988775

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.45  E-value=2e-11  Score=92.50  Aligned_cols=231  Identities=7%  Similarity=-0.050  Sum_probs=171.1

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC--CCHHHHHHHHHHHHhcCChhHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCD--PNERTLEAVLSVYCFAGLVDESK   78 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~--p~~~t~~~ll~~~~~~g~~~~a~   78 (248)
                      .|++++|.+.|++..+... .+...|..+...+...|++++|.+.+++..+..-.  .....|..+-..+.+.|++++|.
T Consensus        16 ~~~~~~A~~~~~~~l~~~p-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~~~~~~~~~A~   94 (272)
T 3u4t_A           16 NNNYAEAIEVFNKLEAKKY-NSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKILMKKGQDSLAI   94 (272)
T ss_dssp             TTCHHHHHHHHHHHHHTTC-CCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             hcCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHcccHHHHH
Confidence            3899999999999987542 35668999999999999999999999999874322  22445889999999999999999


Q ss_pred             HHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHh-HHHHhcccccccchHHHHHHHHHHHHh
Q 039342           79 EQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQV-TGQMIKGEFDDESNWQMVEYVFDKLNC  157 (248)
Q Consensus        79 ~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~m~~  157 (248)
                      +.|++..+.. +.+..++..+-..|...|++++|+..|++..+..  |+... +..+-...+. .++++.|...++...+
T Consensus        95 ~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~l~~~~~~-~~~~~~A~~~~~~a~~  170 (272)
T 3u4t_A           95 QQYQAAVDRD-TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPT--TTDPKVFYELGQAYYY-NKEYVKADSSFVKVLE  170 (272)
T ss_dssp             HHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSS--CCCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcC--CCcHHHHHHHHHHHHH-HHHHHHHHHHHHHHHH
Confidence            9999998753 2256789999999999999999999999887653  44333 3333213233 3489999999999887


Q ss_pred             cCCCCCHHHHHHHHHHHHhcCc---hHHHHHHHHHHHHCC-CCCCcc-hhhhHHhhhhhhccccchHHHHHHHHHHHHHH
Q 039342          158 EGYGLGMRFYNALLEALWCLGL---RERAARVLDEATKRG-LFPELF-RHNKLVWSVDVHRMWEGGAYTAISVWLNKMYE  232 (248)
Q Consensus       158 ~~~~p~~~~~~~li~~~~~~g~---~~~a~~~~~~m~~~g-~~p~~~-t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~  232 (248)
                      .... +...+..+...+...|+   +++|...+++..+.. -.|+.. ....-.+..+-..|...|++++|...+++..+
T Consensus       171 ~~p~-~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~  249 (272)
T 3u4t_A          171 LKPN-IYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKYKDELIEANEYIAYYYTINRDKVKADAAWKNILA  249 (272)
T ss_dssp             HSTT-CHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hCcc-chHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            6433 46777778888888888   888998888876531 123321 11112222333667789999999999998877


Q ss_pred             HHHcCCC
Q 039342          233 MFMMGED  239 (248)
Q Consensus       233 ~~~~~~~  239 (248)
                      .  .|+.
T Consensus       250 ~--~p~~  254 (272)
T 3u4t_A          250 L--DPTN  254 (272)
T ss_dssp             H--CTTC
T ss_pred             c--CccH
Confidence            5  4543

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.44  E-value=4.4e-12  Score=94.45  Aligned_cols=202  Identities=7%  Similarity=-0.041  Sum_probs=144.0

Q ss_pred             CCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHH
Q 039342           21 RNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLL  100 (248)
Q Consensus        21 ~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li  100 (248)
                      .....|..+-..+...|++++|...|++..+.. +.+...+..+...+.+.|++++|.+.+++..+.. +.+...+..+.
T Consensus        21 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la   98 (243)
T 2q7f_A           21 MASMTGGQQMGRGSEFGDYEKAAEAFTKAIEEN-KEDAIPYINFANLLSSVNELERALAFYDKALELD-SSAATAYYGAG   98 (243)
T ss_dssp             ---------------------CCTTHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CcchHHHHHHH
Confidence            456778888889999999999999999998753 4568889999999999999999999999988753 23678899999


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCch
Q 039342          101 AVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR  180 (248)
Q Consensus       101 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~  180 (248)
                      ..+...|++++|...+++..+.... +...+..+. ..+...|+++.|...++...+... .+...+..+...+.+.|++
T Consensus        99 ~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~a-~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~  175 (243)
T 2q7f_A           99 NVYVVKEMYKEAKDMFEKALRAGME-NGDLFYMLG-TVLVKLEQPKLALPYLQRAVELNE-NDTEARFQFGMCLANEGML  175 (243)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHTCC-SHHHHHHHH-HHHHHTSCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHhccHHHHHHHHHHHHHhCCC-CHHHHHHHH-HHHHHhccHHHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHcCCH
Confidence            9999999999999999999876522 223333333 336778899999999999887643 3677888999999999999


Q ss_pred             HHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          181 ERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       181 ~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      ++|.+.+++..+.. +.+..++..+.     ..+...|++++|...+++..+.
T Consensus       176 ~~A~~~~~~~~~~~-~~~~~~~~~la-----~~~~~~~~~~~A~~~~~~~~~~  222 (243)
T 2q7f_A          176 DEALSQFAAVTEQD-PGHADAFYNAG-----VTYAYKENREKALEMLDKAIDI  222 (243)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHH-----HHHHHTTCTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC-cccHHHHHHHH-----HHHHHccCHHHHHHHHHHHHcc
Confidence            99999999987652 22233344444     6778899999999999988775

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.44  E-value=1.4e-10  Score=90.05  Aligned_cols=221  Identities=10%  Similarity=0.024  Sum_probs=166.8

Q ss_pred             HHHHHHHHHHHHcCCCCCHHhHHHHHHHHH-------hcCCH-------HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 039342            5 KECQAILSRMSESGVARNSDSFNAVIEAFR-------QGGRF-------EEAIKAYVEMEKVRCDPNERTLEAVLSVYCF   70 (248)
Q Consensus         5 ~~a~~~~~~m~~~g~~~~~~~y~~li~~~~-------~~~~~-------~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~   70 (248)
                      ++|..+|++..+.. +-++..|..+...+.       +.|++       ++|..+|++..+.--+-+...|..+...+.+
T Consensus        33 ~~a~~~~~~al~~~-p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~~  111 (308)
T 2ond_A           33 KRVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEES  111 (308)
T ss_dssp             HHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCcccHHHHHHHHHHHHh
Confidence            67888999887643 346788888888776       35886       8999999998863123355689999999999


Q ss_pred             cCChhHHHHHHHHHHHCCCCcC-Hh-hHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHH
Q 039342           71 AGLVDESKEQFQEIKSSGILPS-VM-CYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMV  148 (248)
Q Consensus        71 ~g~~~~a~~~~~~m~~~~~~p~-~~-~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  148 (248)
                      .|++++|.++|++..+.  .|+ .. .|..+...+.+.|++++|..+|++..+... ++...+.......+...|+++.|
T Consensus       112 ~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p-~~~~~~~~~a~~~~~~~~~~~~A  188 (308)
T 2ond_A          112 RMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDAR-TRHHVYVTAALMEYYCSKDKSVA  188 (308)
T ss_dssp             TTCHHHHHHHHHHHHTS--SSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTT-CCTHHHHHHHHHHHHTSCCHHHH
T ss_pred             cCCHHHHHHHHHHHHhc--cccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHHHcCCHHHH
Confidence            99999999999999874  454 33 899999999999999999999999987642 22233332222112236889999


Q ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCC-CCCCcchhhhHHhhhhhhccccchHHHHHHHHH
Q 039342          149 EYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRG-LFPELFRHNKLVWSVDVHRMWEGGAYTAISVWL  227 (248)
Q Consensus       149 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~  227 (248)
                      ..+|+...+... -+...|..++..+.+.|+.++|..+|++..... +.|+.   ..-+|......+.+.|+.+.+..++
T Consensus       189 ~~~~~~al~~~p-~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~---~~~l~~~~~~~~~~~g~~~~a~~~~  264 (308)
T 2ond_A          189 FKIFELGLKKYG-DIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEK---SGEIWARFLAFESNIGDLASILKVE  264 (308)
T ss_dssp             HHHHHHHHHHHT-TCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGG---CHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             HHHHHHHHHhCC-CcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHH---HHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            999998877633 267888999999999999999999999998863 56642   1222333335566789999999998


Q ss_pred             HHHHHH
Q 039342          228 NKMYEM  233 (248)
Q Consensus       228 ~~m~~~  233 (248)
                      ++..+.
T Consensus       265 ~~a~~~  270 (308)
T 2ond_A          265 KRRFTA  270 (308)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            888766

>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=99.43  E-value=2.8e-11  Score=100.55  Aligned_cols=219  Identities=12%  Similarity=0.062  Sum_probs=164.0

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|.+.|++..+..  |+...|..+...+...|++++|.+.+++..+.. +.+..+|..+...+...|++++|.+.|
T Consensus       257 ~~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~  333 (537)
T 3fp2_A          257 NNLLDAQVLLQESINLH--PTPNSYIFLALTLADKENSQEFFKFFQKAVDLN-PEYPPTYYHRGQMYFILQDYKNAKEDF  333 (537)
T ss_dssp             TCHHHHHHHHHHHHHHC--CCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHhcC--CCchHHHHHHHHHHHhcCHHHHHHHHHHHhccC-CCCHHHHHHHHHHHHhcCCHHHHHHHH
Confidence            78899999999988743  567888888899999999999999999987654 356788889999999999999999999


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcC--
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEG--  159 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~--  159 (248)
                      ++..+.. +.+...+..+...+...|++++|...+++..+..  |+.......+...+...|+++.|...++...+..  
T Consensus       334 ~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~  410 (537)
T 3fp2_A          334 QKAQSLN-PENVYPYIQLACLLYKQGKFTESEAFFNETKLKF--PTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEV  410 (537)
T ss_dssp             HHHHHHC-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCc
Confidence            9988753 2246788889999999999999999999987764  4333233333333667788899999988876542  


Q ss_pred             ---CCCCHHHHHHHHHHHHhc----------CchHHHHHHHHHHHHCCCCCC-cchhhhHHhhhhhhccccchHHHHHHH
Q 039342          160 ---YGLGMRFYNALLEALWCL----------GLRERAARVLDEATKRGLFPE-LFRHNKLVWSVDVHRMWEGGAYTAISV  225 (248)
Q Consensus       160 ---~~p~~~~~~~li~~~~~~----------g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~~~~~~g~~~~~~~  225 (248)
                         .......+......+...          |++++|...|++..+.  .|+ ...+..+.     ..+.+.|+.++|..
T Consensus       411 ~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~--~p~~~~~~~~l~-----~~~~~~g~~~~A~~  483 (537)
T 3fp2_A          411 QEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACEL--DPRSEQAKIGLA-----QLKLQMEKIDEAIE  483 (537)
T ss_dssp             CSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHH--CTTCHHHHHHHH-----HHHHHTTCHHHHHH
T ss_pred             chhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHh--CCCCHHHHHHHH-----HHHHHhccHHHHHH
Confidence               112223344455667777          9999999999988764  343 33333343     66778889999888


Q ss_pred             HHHHHHHH
Q 039342          226 WLNKMYEM  233 (248)
Q Consensus       226 ~~~~m~~~  233 (248)
                      .+++..+.
T Consensus       484 ~~~~al~~  491 (537)
T 3fp2_A          484 LFEDSAIL  491 (537)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHh
Confidence            88877665

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.42  E-value=1.6e-11  Score=94.71  Aligned_cols=212  Identities=12%  Similarity=0.052  Sum_probs=155.7

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHc-------CCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHC------C
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKV-------RCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSS------G   88 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~-------~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~------~   88 (248)
                      +..+|..+...+...|++++|..++++..+.       .-+.....+..+...|...|++++|...+++..+.      +
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            4678888999999999999999999998663       23345577888899999999999999999988753      2


Q ss_pred             CCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHC------CCCchHHhHHHHhcccccccchHHHHHHHHHHHHhc---
Q 039342           89 ILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTN------RISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCE---  158 (248)
Q Consensus        89 ~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~------~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~---  158 (248)
                      -.| ...++..+...|...|++++|...+++..+.      +..|........+...+...|+++.|...++...+.   
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            223 4578889999999999999999999988754      333444444444444477888999999999887764   


Q ss_pred             ---CCCC-CHHHHHHHHHHHHhcCchHHHHHHHHHHHHCC-------CCCC-----------------------------
Q 039342          159 ---GYGL-GMRFYNALLEALWCLGLRERAARVLDEATKRG-------LFPE-----------------------------  198 (248)
Q Consensus       159 ---~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-------~~p~-----------------------------  198 (248)
                         +..| ...++..+...+...|++++|.+.+++..+..       ..+.                             
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               2233 34567888899999999999999999877420       0000                             


Q ss_pred             -------cchhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          199 -------LFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       199 -------~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                             .......++..+...|.+.|++++|.+.+++..+.
T Consensus       266 ~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l  307 (311)
T 3nf1_A          266 WYKACKVDSPTVTTTLKNLGALYRRQGKFEAAETLEEAAMRS  307 (311)
T ss_dssp             --------CHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHhhcCCCCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                   01112233334447788999999999999887665

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.41  E-value=2e-11  Score=94.08  Aligned_cols=192  Identities=10%  Similarity=0.085  Sum_probs=148.6

Q ss_pred             CCchHHHHHHHHHHHHc-------CCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHc------C-CCCCHHHHHHHHH
Q 039342            1 GGLYKECQAILSRMSES-------GVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKV------R-CDPNERTLEAVLS   66 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~-------g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~------~-~~p~~~t~~~ll~   66 (248)
                      .|++++|..+|++..+.       ..+.....+..+-..|...|++++|...+++..+.      + -+....++..+..
T Consensus        40 ~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~  119 (311)
T 3nf1_A           40 QGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGKDHPAVAATLNNLAV  119 (311)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHH
Confidence            37899999999988763       23345678899999999999999999999998654      2 2334577888999


Q ss_pred             HHHhcCChhHHHHHHHHHHHC------CCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHC------CCCchHHhHHH
Q 039342           67 VYCFAGLVDESKEQFQEIKSS------GILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTN------RISNIHQVTGQ  133 (248)
Q Consensus        67 ~~~~~g~~~~a~~~~~~m~~~------~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~------~~~~~~~~~~~  133 (248)
                      .|...|++++|.+.+++..+.      +-.| ....+..+...+...|++++|+..+++..+.      +..|.......
T Consensus       120 ~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~  199 (311)
T 3nf1_A          120 LYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTKLGPDDPNVAKTKN  199 (311)
T ss_dssp             HHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTSCTTCHHHHHHHH
T ss_pred             HHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence            999999999999999998753      2223 4567888999999999999999999998764      33455444444


Q ss_pred             HhcccccccchHHHHHHHHHHHHhc------------------------------------------------CCCCCHH
Q 039342          134 MIKGEFDDESNWQMVEYVFDKLNCE------------------------------------------------GYGLGMR  165 (248)
Q Consensus       134 ~l~~~~~~~~~~~~a~~~~~~m~~~------------------------------------------------~~~p~~~  165 (248)
                      .+...+...|+++.|...+++..+.                                                ....+..
T Consensus       200 ~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  279 (311)
T 3nf1_A          200 NLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEEREECKGKQKDGTSFGEYGGWYKACKVDSPTVTT  279 (311)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHHHC-------CCSCCCC---------CHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHhcCchhhHHHHHHHHHHHhhcCCCCchHHH
Confidence            4444477889999999999887753                                                1122456


Q ss_pred             HHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          166 FYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       166 ~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                      ++..+...|.+.|++++|.++|++..+
T Consensus       280 ~~~~la~~~~~~g~~~~A~~~~~~al~  306 (311)
T 3nf1_A          280 TLKNLGALYRRQGKFEAAETLEEAAMR  306 (311)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            788899999999999999999998654

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.38  E-value=3.8e-11  Score=91.02  Aligned_cols=210  Identities=12%  Similarity=0.000  Sum_probs=154.3

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|.+.|++..+... .+...|..+...+...|++++|.+.|++..+.. +.+...+..+...|.+.|++++|.+.|
T Consensus        57 ~~~~~A~~~~~~al~~~~-~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~  134 (275)
T 1xnf_A           57 GLRALARNDFSQALAIRP-DMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD-PTYNYAHLNRGIALYYGGRDKLAQDDL  134 (275)
T ss_dssp             TCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHcCC-CcHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-ccccHHHHHHHHHHHHhccHHHHHHHH
Confidence            789999999999987543 468899999999999999999999999998764 346788999999999999999999999


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCC
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYG  161 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~  161 (248)
                      ++..+.  .|+.......+..+...|++++|...+++.....  |+......+... +...+..+.+...+....+....
T Consensus       135 ~~a~~~--~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~~~~~~  209 (275)
T 1xnf_A          135 LAFYQD--DPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKS--DKEQWGWNIVEF-YLGNISEQTLMERLKADATDNTS  209 (275)
T ss_dssp             HHHHHH--CTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHS--CCCSTHHHHHHH-HTTSSCHHHHHHHHHHHCCSHHH
T ss_pred             HHHHHh--CCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhcC--CcchHHHHHHHH-HHHhcCHHHHHHHHHHHhccccc
Confidence            999875  4555555566666678899999999998876653  222222223333 44445567888888776554221


Q ss_pred             --C-CHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHH
Q 039342          162 --L-GMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWL  227 (248)
Q Consensus       162 --p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~  227 (248)
                        | +..++..+...+.+.|++++|...|++..+.  .|+..  ....     ..+...|+++++..-+
T Consensus       210 ~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~~--~~~~-----~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          210 LAEHLSETNFYLGKYYLSLGDLDSATALFKLAVAN--NVHNF--VEHR-----YALLELSLLGQDQDDL  269 (275)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CCTTC--HHHH-----HHHHHHHHHHHC----
T ss_pred             ccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHhC--CchhH--HHHH-----HHHHHHHHHHhhHHHH
Confidence              1 2577889999999999999999999998875  45321  1112     3345677777765544

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.37  E-value=7.6e-11  Score=88.34  Aligned_cols=193  Identities=11%  Similarity=0.028  Sum_probs=156.0

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCC--CCcC----Hhh
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSG--ILPS----VMC   95 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~--~~p~----~~~   95 (248)
                      ....|..+-..+...|++++|...|++..+..  .+...|..+..+|...|++++|.+.+++..+..  ..|+    ..+
T Consensus         4 ~a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~   81 (258)
T 3uq3_A            4 MADKEKAEGNKFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKS   81 (258)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHH
Confidence            35678888999999999999999999998887  888999999999999999999999999987642  1112    578


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHH
Q 039342           96 YCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALW  175 (248)
Q Consensus        96 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  175 (248)
                      |..+...+...|++++|...|++..+..  |....        +...++++.+...++....... .+...+..+...+.
T Consensus        82 ~~~l~~~~~~~~~~~~A~~~~~~a~~~~--~~~~~--------~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~~~~~  150 (258)
T 3uq3_A           82 FARIGNAYHKLGDLKKTIEYYQKSLTEH--RTADI--------LTKLRNAEKELKKAEAEAYVNP-EKAEEARLEGKEYF  150 (258)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHH--------HHHHHHHHHHHHHHHHHHHCCH-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHhcC--chhHH--------HHHHhHHHHHHHHHHHHHHcCc-chHHHHHHHHHHHH
Confidence            9999999999999999999999998754  33222        3445778999999998887532 25667888999999


Q ss_pred             hcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          176 CLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       176 ~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      ..|++++|.+.+++..+.. +.+...+..+.     ..+...|++++|...+++..+.
T Consensus       151 ~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~-----~~~~~~~~~~~A~~~~~~al~~  202 (258)
T 3uq3_A          151 TKSDWPNAVKAYTEMIKRA-PEDARGYSNRA-----AALAKLMSFPEAIADCNKAIEK  202 (258)
T ss_dssp             HTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH-----HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHhcC-cccHHHHHHHH-----HHHHHhCCHHHHHHHHHHHHHh
Confidence            9999999999999988642 22333344443     6778899999999999988775

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.36  E-value=5.9e-11  Score=97.64  Aligned_cols=214  Identities=9%  Similarity=-0.072  Sum_probs=165.4

Q ss_pred             hHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCH-HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHH
Q 039342            4 YKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRF-EEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQ   82 (248)
Q Consensus         4 ~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~-~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~   82 (248)
                      ++++.+.+++..... +.+...|..+-..+...|++ ++|.+.|++..+.. +-+...|..+-.+|.+.|++++|.+.|+
T Consensus        84 ~~~al~~l~~~~~~~-~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~  161 (474)
T 4abn_A           84 MEKTLQQMEEVLGSA-QVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLE-PELVEAWNQLGEVYWKKGDVTSAHTCFS  161 (474)
T ss_dssp             HHHHHHHHHHHHTTC-CCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccC-chhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            556667777655432 24788899999999999999 99999999997764 3457899999999999999999999999


Q ss_pred             HHHHCCCCcCHhhHHHHHHHHHhc---------CCHHHHHHHHHHHHHCCCCchHHhHHHHhccccccc--------chH
Q 039342           83 EIKSSGILPSVMCYCMLLAVYAKS---------NRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDE--------SNW  145 (248)
Q Consensus        83 ~m~~~~~~p~~~~~~~li~~~~~~---------~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~--------~~~  145 (248)
                      +..+.  .|+...+..+-..|...         |++++|+..|++..+..  |+.......+...+...        +++
T Consensus       162 ~al~~--~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~~~~~~~~~g~~  237 (474)
T 4abn_A          162 GALTH--CKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD--VLDGRSWYILGNAYLSLYFNTGQNPKIS  237 (474)
T ss_dssp             HHHTT--CCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHTTCCHHHH
T ss_pred             HHHhh--CCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHHHHhhccccchH
Confidence            99876  47778899999999999         99999999999988764  44433333333335455        889


Q ss_pred             HHHHHHHHHHHhcCCC--CCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcc-hhhhHHhhhhhhccccchHHHH
Q 039342          146 QMVEYVFDKLNCEGYG--LGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELF-RHNKLVWSVDVHRMWEGGAYTA  222 (248)
Q Consensus       146 ~~a~~~~~~m~~~~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~-t~~~li~~~~~~~~~~~g~~~~  222 (248)
                      +.|...|+...+....  -+...|..+-.+|...|++++|.+.|++..+.  .|+.. .+..+-     ..+...|++++
T Consensus       238 ~~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~~~a~~~l~-----~~~~~lg~~~e  310 (474)
T 4abn_A          238 QQALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAAL--DPAWPEPQQREQ-----QLLEFLSRLTS  310 (474)
T ss_dssp             HHHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHH-----HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHH-----HHHHHHHHHHH
Confidence            9999999998886431  37888999999999999999999999998764  45422 222232     55667788888


Q ss_pred             HHHHHHHH
Q 039342          223 ISVWLNKM  230 (248)
Q Consensus       223 ~~~~~~~m  230 (248)
                      +...+.++
T Consensus       311 Ai~~~~~~  318 (474)
T 4abn_A          311 LLESKGKT  318 (474)
T ss_dssp             HHHHTTTC
T ss_pred             HHHHhccc
Confidence            77654443

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.36  E-value=3.5e-10  Score=80.68  Aligned_cols=171  Identities=18%  Similarity=0.175  Sum_probs=138.6

Q ss_pred             CCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHH
Q 039342           21 RNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLL  100 (248)
Q Consensus        21 ~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li  100 (248)
                      -++..|..+-..|.+.|++++|.+.|++..+.. +-+...+..+..+|.+.|++++|...++...... +.+...+..+-
T Consensus         3 e~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~   80 (184)
T 3vtx_A            3 ETTTIYMDIGDKKRTKGDFDGAIRAYKKVLKAD-PNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLD-TTSAEAYYILG   80 (184)
T ss_dssp             -CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-chhHHHHHHHH
Confidence            367889999999999999999999999987764 3467888999999999999999999999987653 22567788888


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCch
Q 039342          101 AVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR  180 (248)
Q Consensus       101 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~  180 (248)
                      ..+...++++.|...+.+..+..  |+.......+...+...|++++|...+++..+.... +..+|..+-.+|.+.|++
T Consensus        81 ~~~~~~~~~~~a~~~~~~a~~~~--~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p~-~~~~~~~lg~~~~~~g~~  157 (184)
T 3vtx_A           81 SANFMIDEKQAAIDALQRAIALN--TVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKPG-FIRAYQSIGLAYEGKGLR  157 (184)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC--ccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcch-hhhHHHHHHHHHHHCCCH
Confidence            88999999999999999887654  444444444444477788999999999988876533 677888999999999999


Q ss_pred             HHHHHHHHHHHHCCCCCC
Q 039342          181 ERAARVLDEATKRGLFPE  198 (248)
Q Consensus       181 ~~a~~~~~~m~~~g~~p~  198 (248)
                      ++|.+.|++..+.  .|+
T Consensus       158 ~~A~~~~~~al~~--~p~  173 (184)
T 3vtx_A          158 DEAVKYFKKALEK--EEK  173 (184)
T ss_dssp             HHHHHHHHHHHHT--THH
T ss_pred             HHHHHHHHHHHhC--Ccc
Confidence            9999999988764  454

>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=99.35  E-value=3.3e-11  Score=91.47  Aligned_cols=156  Identities=10%  Similarity=0.060  Sum_probs=115.7

Q ss_pred             CchHHHHHHHHHHHH-------cCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHc------CC-CCCHHHHHHHHHH
Q 039342            2 GLYKECQAILSRMSE-------SGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKV------RC-DPNERTLEAVLSV   67 (248)
Q Consensus         2 g~~~~a~~~~~~m~~-------~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~------~~-~p~~~t~~~ll~~   67 (248)
                      |++++|++.|++..+       ...+....+|..+-..|...|++++|...+++..+.      +- +....++..+...
T Consensus        15 ~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~   94 (283)
T 3edt_B           15 VPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVL   94 (283)
T ss_dssp             SCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHH
Confidence            556666666665543       222335778999999999999999999999998654      22 2345678889999


Q ss_pred             HHhcCChhHHHHHHHHHHHC------CCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHC------CCCchHHhHHHH
Q 039342           68 YCFAGLVDESKEQFQEIKSS------GILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTN------RISNIHQVTGQM  134 (248)
Q Consensus        68 ~~~~g~~~~a~~~~~~m~~~------~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~------~~~~~~~~~~~~  134 (248)
                      |...|++++|.+.+++..+.      .-.| ...++..+...|...|++++|...+++..+.      +-.|........
T Consensus        95 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~  174 (283)
T 3edt_B           95 YGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKTKNN  174 (283)
T ss_dssp             HHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHH
T ss_pred             HHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHH
Confidence            99999999999999988753      1123 4678889999999999999999999998765      223444433334


Q ss_pred             hcccccccchHHHHHHHHHHHHh
Q 039342          135 IKGEFDDESNWQMVEYVFDKLNC  157 (248)
Q Consensus       135 l~~~~~~~~~~~~a~~~~~~m~~  157 (248)
                      +...+...|+++.|...+++..+
T Consensus       175 la~~~~~~g~~~~A~~~~~~~l~  197 (283)
T 3edt_B          175 LASCYLKQGKYQDAETLYKEILT  197 (283)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHH
Confidence            44447778889999998887765

>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=99.32  E-value=4.5e-10  Score=89.69  Aligned_cols=214  Identities=9%  Similarity=-0.055  Sum_probs=160.9

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCC-HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGR-FEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~-~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      |++++|++.|++..+... -+...|+.+-..+.+.|+ +++|++.|++..+.. +-+...|+.+-.++.+.|++++|...
T Consensus       111 g~~~~Al~~~~~al~l~P-~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~-P~~~~a~~~~g~~~~~~g~~~eAl~~  188 (382)
T 2h6f_A          111 ERSERAFKLTRDAIELNA-ANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRRVLVEWLRDPSQELEF  188 (382)
T ss_dssp             CCCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHH
T ss_pred             CChHHHHHHHHHHHHhCc-cCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHccCHHHHHHH
Confidence            789999999999987542 368899999999999996 999999999998765 34778999999999999999999999


Q ss_pred             HHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchH-HhHHHHhcccccc-cchHHHH-----HHHHH
Q 039342           81 FQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIH-QVTGQMIKGEFDD-ESNWQMV-----EYVFD  153 (248)
Q Consensus        81 ~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~~l~~~~~~-~~~~~~a-----~~~~~  153 (248)
                      |++..+... -+...|..+-.++.+.|++++|+..|++..+..  |+. ..++.+-.. +.. .+..+.|     ...++
T Consensus       189 ~~kal~ldP-~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~--P~~~~a~~~lg~~-l~~l~~~~~eA~~~~el~~~~  264 (382)
T 2h6f_A          189 IADILNQDA-KNYHAWQHRQWVIQEFKLWDNELQYVDQLLKED--VRNNSVWNQRYFV-ISNTTGYNDRAVLEREVQYTL  264 (382)
T ss_dssp             HHHHHHHCT-TCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC--TTCHHHHHHHHHH-HHHTTCSCSHHHHHHHHHHHH
T ss_pred             HHHHHHhCc-cCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhC--CCCHHHHHHHHHH-HHHhcCcchHHHHHHHHHHHH
Confidence            999987532 267899999999999999999999999998765  433 333333222 323 4443444     46677


Q ss_pred             HHHhcCCCCCHHHHHHHHHHHHhcC--chHHHHHHHHHHHHCCCCCC-cchhhhHHhhhhhhccccc--------h-HHH
Q 039342          154 KLNCEGYGLGMRFYNALLEALWCLG--LRERAARVLDEATKRGLFPE-LFRHNKLVWSVDVHRMWEG--------G-AYT  221 (248)
Q Consensus       154 ~m~~~~~~p~~~~~~~li~~~~~~g--~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~~~~~~--------g-~~~  221 (248)
                      ........ +...|+.+...+...|  ++++|.+.+.++ +  ..|+ ...+..+.     ..|.+.        + ..+
T Consensus       265 ~Al~l~P~-~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~--~~p~~~~al~~La-----~~~~~~~~~~~~~~~~~~~  335 (382)
T 2h6f_A          265 EMIKLVPH-NESAWNYLKGILQDRGLSKYPNLLNQLLDL-Q--PSHSSPYLIAFLV-----DIYEDMLENQCDNKEDILN  335 (382)
T ss_dssp             HHHHHSTT-CHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-T--TTCCCHHHHHHHH-----HHHHHHHHTTCSSHHHHHH
T ss_pred             HHHHHCCC-CHHHHHHHHHHHHccCccchHHHHHHHHHh-c--cCCCCHHHHHHHH-----HHHHHHhcccccchHHHHH
Confidence            76665433 5678888888888888  689999999887 2  3444 33444444     333343        3 358


Q ss_pred             HHHHHHHHH
Q 039342          222 AISVWLNKM  230 (248)
Q Consensus       222 ~~~~~~~~m  230 (248)
                      +|..+++++
T Consensus       336 ~A~~~~~~l  344 (382)
T 2h6f_A          336 KALELCEIL  344 (382)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            888888876

>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=99.29  E-value=4.9e-10  Score=79.42  Aligned_cols=165  Identities=14%  Similarity=0.079  Sum_probs=124.3

Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHH
Q 039342           23 SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAV  102 (248)
Q Consensus        23 ~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~  102 (248)
                      ...|..+...+...|++++|.+.+++..+.. +.+...+..+...+...|++++|.+.+++..+.. +.+...+..+...
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~   85 (186)
T 3as5_A            8 QVYYRDKGISHAKAGRYSQAVMLLEQVYDAD-AFDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLT   85 (186)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHTTTCCTT-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHH
Confidence            4567778888889999999999998886543 3567888889999999999999999999987653 2367788888899


Q ss_pred             HHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHH
Q 039342          103 YAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRER  182 (248)
Q Consensus       103 ~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~  182 (248)
                      +...|++++|...+++..+..  |+.......+...+...|+++.|...++...+... .+...+..+...+...|++++
T Consensus        86 ~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~la~~~~~~~~~~~  162 (186)
T 3as5_A           86 YVQVQKYDLAVPLLIKVAEAN--PINFNVRFRLGVALDNLGRFDEAIDSFKIALGLRP-NEGKVHRAIAFSYEQMGRHEE  162 (186)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHhcCHHHHHHHHHHHHhcC--cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcCc-cchHHHHHHHHHHHHcCCHHH
Confidence            999999999999999887653  33222222222335567777888888877766542 356677778888888888888


Q ss_pred             HHHHHHHHHH
Q 039342          183 AARVLDEATK  192 (248)
Q Consensus       183 a~~~~~~m~~  192 (248)
                      |.+.+++..+
T Consensus       163 A~~~~~~~~~  172 (186)
T 3as5_A          163 ALPHFKKANE  172 (186)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            8888887664

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.29  E-value=2.4e-09  Score=83.02  Aligned_cols=184  Identities=10%  Similarity=0.030  Sum_probs=143.4

Q ss_pred             hHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC-HH-HHHHHHHHHHhcCChhHHHHHH
Q 039342            4 YKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN-ER-TLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         4 ~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~-t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      .++|..+|++..+.-.+-+...|..+...+.+.|++++|.++|++..+.  .|+ .. .|..+...+.+.|++++|..+|
T Consensus        80 ~~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~  157 (308)
T 2ond_A           80 SDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIF  157 (308)
T ss_dssp             HHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS--SSSCTHHHHHHHHHHHHHHHCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc--cccCccHHHHHHHHHHHHhcCHHHHHHHH
Confidence            3899999999887312235679999999999999999999999999874  454 33 8999999999999999999999


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHH-hcCCHHHHHHHHHHHHHCCCCchHH-hHHHHhcccccccchHHHHHHHHHHHHhcC
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYA-KSNRWDDAYGLLDEMHTNRISNIHQ-VTGQMIKGEFDDESNWQMVEYVFDKLNCEG  159 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~-~~~~~~~a~~~~~~m~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~  159 (248)
                      ++..+.. +++...|........ ..|+.++|..+|++..+..  |+.. .+..+. ......|+++.|..+|+......
T Consensus       158 ~~a~~~~-p~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~~~-~~~~~~g~~~~A~~~~~~al~~~  233 (308)
T 2ond_A          158 KKAREDA-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY--GDIPEYVLAYI-DYLSHLNEDNNTRVLFERVLTSG  233 (308)
T ss_dssp             HHHHTST-TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH--TTCHHHHHHHH-HHHHTTCCHHHHHHHHHHHHHSS
T ss_pred             HHHHhcC-CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCcHHHHHHHH-HHHHHCCCHHHHHHHHHHHHhcc
Confidence            9998764 234445544433322 3699999999999987653  4433 333333 33667789999999999999873


Q ss_pred             -CCC--CHHHHHHHHHHHHhcCchHHHHHHHHHHHHC
Q 039342          160 -YGL--GMRFYNALLEALWCLGLRERAARVLDEATKR  193 (248)
Q Consensus       160 -~~p--~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  193 (248)
                       ..|  ....|..++....+.|+.+.|..+++++.+.
T Consensus       234 ~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~~a~~~  270 (308)
T 2ond_A          234 SLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             SSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence             455  4678889999999999999999999998764

>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=99.27  E-value=5.8e-09  Score=79.17  Aligned_cols=177  Identities=10%  Similarity=0.031  Sum_probs=147.0

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHh----cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----cCC
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQ----GGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCF----AGL   73 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~----~g~   73 (248)
                      |++++|.+.|++..+.+   +...+..+-..|..    .+++++|.+.|++..+.+   +...+..+-..|.+    .++
T Consensus        56 ~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~  129 (273)
T 1ouv_A           56 KNLKKAASFYAKACDLN---YSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRD  129 (273)
T ss_dssp             CCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCC
T ss_pred             CCHHHHHHHHHHHHHCC---CHHHHHHHHHHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccC
Confidence            68999999999998865   78889999999999    999999999999998875   77888899999999    999


Q ss_pred             hhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHh----cCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccc----cchH
Q 039342           74 VDESKEQFQEIKSSGILPSVMCYCMLLAVYAK----SNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDD----ESNW  145 (248)
Q Consensus        74 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~----~~~~  145 (248)
                      +++|.+.|++..+.+   +...+..+-..|..    .+++++|+..|++..+.+..   ..+..+-.. +..    .+++
T Consensus       130 ~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~~~---~a~~~lg~~-~~~g~~~~~~~  202 (273)
T 1ouv_A          130 FKKAVEYFTKACDLN---DGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLKDS---PGCFNAGNM-YHHGEGATKNF  202 (273)
T ss_dssp             HHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCH---HHHHHHHHH-HHHTCSSCCCH
T ss_pred             HHHHHHHHHHHHhcC---cHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCH---HHHHHHHHH-HHcCCCCCccH
Confidence            999999999998876   56677788888887    89999999999999887532   222222221 333    7899


Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh----cCchHHHHHHHHHHHHCC
Q 039342          146 QMVEYVFDKLNCEGYGLGMRFYNALLEALWC----LGLRERAARVLDEATKRG  194 (248)
Q Consensus       146 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g  194 (248)
                      +.|...++...+.+.   ...+..+-..|..    .+++++|.+.|++..+.|
T Consensus       203 ~~A~~~~~~a~~~~~---~~a~~~l~~~~~~g~~~~~~~~~A~~~~~~a~~~~  252 (273)
T 1ouv_A          203 KEALARYSKACELEN---GGGCFNLGAMQYNGEGVTRNEKQAIENFKKGCKLG  252 (273)
T ss_dssp             HHHHHHHHHHHHTTC---HHHHHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhCCC---HHHHHHHHHHHHcCCCcccCHHHHHHHHHHHHHcC
Confidence            999999999888753   5677788888888    999999999999987764

>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=99.27  E-value=6.1e-11  Score=94.93  Aligned_cols=160  Identities=15%  Similarity=0.112  Sum_probs=74.8

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|++.++..++.  .+++.+.+.++.+|.+.|+++++.++++       .|+..+|+.+...|...|++++|...|
T Consensus        75 g~~EeAi~yl~~ark~--~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~g~yeeA~~~Y  145 (449)
T 1b89_A           75 GNWEELVKYLQMARKK--ARESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLY  145 (449)
T ss_dssp             ------------------------------------CHHHHTTTTT-------CC----------------CTTTHHHHH
T ss_pred             CCHHHHHHHHHHHHHh--CccchhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            5566666655544442  2445666667777777777766666653       366667777777777777777777777


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCC
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYG  161 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~  161 (248)
                      +.+         ..|..+..++.+.|++++|.+.+.+.      .+..+|..++.+ |...|+|+.|......     +.
T Consensus       146 ~~a---------~n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~a-Cv~~~ef~lA~~~~l~-----L~  204 (449)
T 1b89_A          146 NNV---------SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFA-CVDGKEFRLAQMCGLH-----IV  204 (449)
T ss_dssp             HHT---------TCHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHH-HHHTTCHHHHHHTTTT-----TT
T ss_pred             HHh---------hhHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHH-HHHcCcHHHHHHHHHH-----HH
Confidence            754         37777777777788888877777776      245666666666 6667777777544332     22


Q ss_pred             CCHHHHHHHHHHHHhcCchHHHHHHHHHHH
Q 039342          162 LGMRFYNALLEALWCLGLRERAARVLDEAT  191 (248)
Q Consensus       162 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  191 (248)
                      ..+.-...++..|.+.|++++|..+++...
T Consensus       205 ~~ad~l~~lv~~Yek~G~~eEai~lLe~aL  234 (449)
T 1b89_A          205 VHADELEELINYYQDRGYFEELITMLEAAL  234 (449)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             hCHhhHHHHHHHHHHCCCHHHHHHHHHHHh
Confidence            233334567788888888998888888755

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.24  E-value=3.7e-09  Score=88.06  Aligned_cols=221  Identities=11%  Similarity=0.032  Sum_probs=163.0

Q ss_pred             HHHHHHHHHHHHcCCCCCHHhHHHHHHHHHh-------cCCHH-------HHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 039342            5 KECQAILSRMSESGVARNSDSFNAVIEAFRQ-------GGRFE-------EAIKAYVEMEKVRCDPNERTLEAVLSVYCF   70 (248)
Q Consensus         5 ~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~-------~~~~~-------~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~   70 (248)
                      ++|..+|++..... +-+...|..+...+.+       .|+++       +|.++|++..+.-.+-+...|..+...+.+
T Consensus       255 ~~a~~~y~~al~~~-p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~  333 (530)
T 2ooe_A          255 KRVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEES  333 (530)
T ss_dssp             HHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHHHhCcccHHHHHHHHHHHHh
Confidence            36667788776542 2467888888888876       79987       899999998753234468889999999999


Q ss_pred             cCChhHHHHHHHHHHHCCCCcC--HhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHH
Q 039342           71 AGLVDESKEQFQEIKSSGILPS--VMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMV  148 (248)
Q Consensus        71 ~g~~~~a~~~~~~m~~~~~~p~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  148 (248)
                      .|++++|.++|++..+.  .|+  ...|......+.+.|++++|..+|++..+..-. +...+.......+...|+++.|
T Consensus       334 ~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~~~-~~~~~~~~a~~~~~~~~~~~~A  410 (530)
T 2ooe_A          334 RMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDART-RHHVYVTAALMEYYCSKDKSVA  410 (530)
T ss_dssp             TTCHHHHHHHHHHHHHS--SSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTC-CTHHHHHHHHHHHHHTCCHHHH
T ss_pred             cCCHHHHHHHHHHHhCc--cccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhccCC-chHHHHHHHHHHHHHcCChhHH
Confidence            99999999999999885  454  258999999999999999999999999875321 1222222111113357888999


Q ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCC-CCCCcchhhhHHhhhhhhccccchHHHHHHHHH
Q 039342          149 EYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRG-LFPELFRHNKLVWSVDVHRMWEGGAYTAISVWL  227 (248)
Q Consensus       149 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g-~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~  227 (248)
                      ..+|+...+... -+...+..++..+.+.|+.++|..+|++....+ ..|+.   ...+|...+.-..+.|+.+.+..+.
T Consensus       411 ~~~~e~al~~~p-~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~~~~---~~~lw~~~~~~e~~~G~~~~~~~~~  486 (530)
T 2ooe_A          411 FKIFELGLKKYG-DIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEK---SGEIWARFLAFESNIGDLASILKVE  486 (530)
T ss_dssp             HHHHHHHHHHHT-TCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSCGGG---CHHHHHHHHHHHHHSSCHHHHHHHH
T ss_pred             HHHHHHHHHHCC-CCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCCHHH---HHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            999998877532 257889999999999999999999999988763 23321   2223333334556678899988888


Q ss_pred             HHHHHH
Q 039342          228 NKMYEM  233 (248)
Q Consensus       228 ~~m~~~  233 (248)
                      +++.+.
T Consensus       487 ~r~~~~  492 (530)
T 2ooe_A          487 KRRFTA  492 (530)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            887765

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.23  E-value=9.3e-11  Score=94.23  Aligned_cols=233  Identities=10%  Similarity=-0.037  Sum_probs=163.7

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCH----HhHHHHHHHHHhcCCHHHHHHHHHHHHHc----C-CCCCHHHHHHHHHHHHhc
Q 039342            1 GGLYKECQAILSRMSESGVARNS----DSFNAVIEAFRQGGRFEEAIKAYVEMEKV----R-CDPNERTLEAVLSVYCFA   71 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~----~~y~~li~~~~~~~~~~~a~~~~~~m~~~----~-~~p~~~t~~~ll~~~~~~   71 (248)
                      .|++++|.+.|++..+.+.. +.    ..|..+-..|...|++++|.+.+++..+.    + -+.....+..+-..|...
T Consensus        61 ~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~  139 (411)
T 4a1s_A           61 AGDCRAGVAFFQAAIQAGTE-DLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGNLGNTLKVM  139 (411)
T ss_dssp             TTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             hCcHHHHHHHHHHHHHhccc-ChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHC
Confidence            38999999999998875432 22    57888999999999999999999987543    1 123446778888899999


Q ss_pred             CChhHHHHHHHHHHHC----CCCc-CHhhHHHHHHHHHhcCC-----------------HHHHHHHHHHHHHC----CCC
Q 039342           72 GLVDESKEQFQEIKSS----GILP-SVMCYCMLLAVYAKSNR-----------------WDDAYGLLDEMHTN----RIS  125 (248)
Q Consensus        72 g~~~~a~~~~~~m~~~----~~~p-~~~~~~~li~~~~~~~~-----------------~~~a~~~~~~m~~~----~~~  125 (248)
                      |++++|...+++..+.    +-.| ...++..+-..|...|+                 +++|+..+++..+.    +-.
T Consensus       140 g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~  219 (411)
T 4a1s_A          140 GRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQENLKLMRDLGDR  219 (411)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTCH
T ss_pred             CCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHcCCH
Confidence            9999999999887643    2122 34578888899999999                 99999998876432    222


Q ss_pred             chHHhHHHHhcccccccchHHHHHHHHHHHHhcCCC-CC----HHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcc
Q 039342          126 NIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYG-LG----MRFYNALLEALWCLGLRERAARVLDEATKRGLFPELF  200 (248)
Q Consensus       126 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~-p~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  200 (248)
                      +........+...+...|+++.|...+++..+.... ++    ..++..+...+...|++++|.+.+++..+..-.....
T Consensus       220 ~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~  299 (411)
T 4a1s_A          220 GAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGER  299 (411)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCH
Confidence            333333333334467788899999998877653111 11    3377888899999999999999999876421111111


Q ss_pred             hhhhHHhhhhhhccccchHHHHHHHHHHHHHHHH
Q 039342          201 RHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMF  234 (248)
Q Consensus       201 t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~  234 (248)
                      .....++..+...+...|++++|...+++..+..
T Consensus       300 ~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~  333 (411)
T 4a1s_A          300 EVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIA  333 (411)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence            1122233333467788899999999888876653

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.23  E-value=1.5e-09  Score=77.39  Aligned_cols=167  Identities=10%  Similarity=-0.021  Sum_probs=131.5

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHh
Q 039342           56 PNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMI  135 (248)
Q Consensus        56 p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l  135 (248)
                      -++..|..+-..|.+.|++++|.+.|++..+.. +-+..++..+...|.+.|++++|...+.+.....  |+.......+
T Consensus         3 e~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~   79 (184)
T 3vtx_A            3 ETTTIYMDIGDKKRTKGDFDGAIRAYKKVLKAD-PNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLD--TTSAEAYYIL   79 (184)
T ss_dssp             -CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCCHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--chhHHHHHHH
Confidence            367789999999999999999999999988753 2267889999999999999999999999987765  3333333333


Q ss_pred             cccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCC-cchhhhHHhhhhhhcc
Q 039342          136 KGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPE-LFRHNKLVWSVDVHRM  214 (248)
Q Consensus       136 ~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~~~  214 (248)
                      ...+...++++.+...+......... +...+..+-..+.+.|++++|.+.|++..+.  .|+ ...|..+-     ..|
T Consensus        80 ~~~~~~~~~~~~a~~~~~~a~~~~~~-~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~~lg-----~~~  151 (184)
T 3vtx_A           80 GSANFMIDEKQAAIDALQRAIALNTV-YADAYYKLGLVYDSMGEHDKAIEAYEKTISI--KPGFIRAYQSIG-----LAY  151 (184)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHH-----HHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCcc-chHHHHHHHHHHHHhCCchhHHHHHHHHHHh--cchhhhHHHHHH-----HHH
Confidence            33366678889999999888776433 5778889999999999999999999998764  443 23344333     678


Q ss_pred             ccchHHHHHHHHHHHHHHH
Q 039342          215 WEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       215 ~~~g~~~~~~~~~~~m~~~  233 (248)
                      .+.|++++|...+++-.+.
T Consensus       152 ~~~g~~~~A~~~~~~al~~  170 (184)
T 3vtx_A          152 EGKGLRDEAVKYFKKALEK  170 (184)
T ss_dssp             HHTTCHHHHHHHHHHHHHT
T ss_pred             HHCCCHHHHHHHHHHHHhC
Confidence            8999999999999887653

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.20  E-value=4.6e-10  Score=87.05  Aligned_cols=233  Identities=12%  Similarity=-0.034  Sum_probs=161.9

Q ss_pred             CCchHHHHHHHHHHHHcCCCCC----HHhHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCC-CCHHHHHHHHHHHHhc
Q 039342            1 GGLYKECQAILSRMSESGVARN----SDSFNAVIEAFRQGGRFEEAIKAYVEMEKV----RCD-PNERTLEAVLSVYCFA   71 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~----~~~y~~li~~~~~~~~~~~a~~~~~~m~~~----~~~-p~~~t~~~ll~~~~~~   71 (248)
                      .|++++|...|++..+.... +    ...|..+...+...|++++|.+.+++..+.    +-. ....++..+...|...
T Consensus        18 ~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~   96 (338)
T 3ro2_A           18 SGDCRAGVSFFEAAVQVGTE-DLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTLKVL   96 (338)
T ss_dssp             TTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHT
T ss_pred             hccHHHHHHHHHHHHhhCcc-cHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHHHHc
Confidence            38999999999998875422 2    467888999999999999999999886432    212 2256778888899999


Q ss_pred             CChhHHHHHHHHHHHC----CCCc-CHhhHHHHHHHHHhcCC--------------------HHHHHHHHHHHHHC----
Q 039342           72 GLVDESKEQFQEIKSS----GILP-SVMCYCMLLAVYAKSNR--------------------WDDAYGLLDEMHTN----  122 (248)
Q Consensus        72 g~~~~a~~~~~~m~~~----~~~p-~~~~~~~li~~~~~~~~--------------------~~~a~~~~~~m~~~----  122 (248)
                      |++++|...+++..+.    +-.+ ...++..+...+...|+                    +++|...+++..+.    
T Consensus        97 g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a~~~~~~~  176 (338)
T 3ro2_A           97 GNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDLYEENLSLVTAL  176 (338)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHhc
Confidence            9999999999887542    1111 14478888889999999                    99999998876432    


Q ss_pred             CCCchHHhHHHHhcccccccchHHHHHHHHHHHHhc----CCC-CCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCC
Q 039342          123 RISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCE----GYG-LGMRFYNALLEALWCLGLRERAARVLDEATKRGLFP  197 (248)
Q Consensus       123 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~----~~~-p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  197 (248)
                      +..+........+...+...|+++.|...++...+.    +.. ....++..+...+...|++++|.+.+++..+..-..
T Consensus       177 ~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~  256 (338)
T 3ro2_A          177 GDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQL  256 (338)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhh
Confidence            222333333333334466778899999988876543    111 123477888889999999999999999876421111


Q ss_pred             CcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHH
Q 039342          198 ELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMF  234 (248)
Q Consensus       198 ~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~  234 (248)
                      +........+..+...+...|++++|...+++..+..
T Consensus       257 ~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~  293 (338)
T 3ro2_A          257 KDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIA  293 (338)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             cchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence            1111122233333366788899999999888876653

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.17  E-value=7.2e-10  Score=91.19  Aligned_cols=182  Identities=12%  Similarity=-0.010  Sum_probs=150.4

Q ss_pred             Cch-HHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc---------
Q 039342            2 GLY-KECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFA---------   71 (248)
Q Consensus         2 g~~-~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~---------   71 (248)
                      |++ ++|++.|++..+... -+...|..+-..|.+.|++++|.+.|++..+.  .|+...+..+-..|...         
T Consensus       116 g~~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~lg~~~~~~~~~~~~~~~  192 (474)
T 4abn_A          116 PDYSPEAEVLLSKAVKLEP-ELVEAWNQLGEVYWKKGDVTSAHTCFSGALTH--CKNKVSLQNLSMVLRQLQTDSGDEHS  192 (474)
T ss_dssp             SSCCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTT--CCCHHHHHHHHHHHTTCCCSCHHHHH
T ss_pred             cccHHHHHHHHHHHHhhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCHHHHHHHHHHHHHhccCChhhhh
Confidence            788 999999999887542 35889999999999999999999999999876  47788999999999999         


Q ss_pred             CChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhc--------CCHHHHHHHHHHHHHCCCCc---hHHhHHHHhccccc
Q 039342           72 GLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKS--------NRWDDAYGLLDEMHTNRISN---IHQVTGQMIKGEFD  140 (248)
Q Consensus        72 g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~--------~~~~~a~~~~~~m~~~~~~~---~~~~~~~~l~~~~~  140 (248)
                      |++++|.+.|++..+.. +-+...|..+-.+|...        |++++|+..|++..+..  |   +.......+...+.
T Consensus       193 g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~~~~lg~~~~  269 (474)
T 4abn_A          193 RHVMDSVRQAKLAVQMD-VLDGRSWYILGNAYLSLYFNTGQNPKISQQALSAYAQAEKVD--RKASSNPDLHLNRATLHK  269 (474)
T ss_dssp             HHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHC--GGGGGCHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhC--CCcccCHHHHHHHHHHHH
Confidence            99999999999998753 22678899999999998        99999999999998764  5   44444444444477


Q ss_pred             ccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHH
Q 039342          141 DESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEA  190 (248)
Q Consensus       141 ~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m  190 (248)
                      ..|+++.|...|++..+.... +...+..+-..+...|++++|.+.+.++
T Consensus       270 ~~g~~~~A~~~~~~al~l~p~-~~~a~~~l~~~~~~lg~~~eAi~~~~~~  318 (474)
T 4abn_A          270 YEESYGEALEGFSQAAALDPA-WPEPQQREQQLLEFLSRLTSLLESKGKT  318 (474)
T ss_dssp             HTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             HcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            889999999999998876533 5667888889999999999998766543

>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=99.17  E-value=7.7e-10  Score=83.81  Aligned_cols=159  Identities=12%  Similarity=0.006  Sum_probs=119.2

Q ss_pred             HhcCCHHHHHHHHHHHHHc-------CCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHC------CCCc-CHhhHHHH
Q 039342           34 RQGGRFEEAIKAYVEMEKV-------RCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSS------GILP-SVMCYCML   99 (248)
Q Consensus        34 ~~~~~~~~a~~~~~~m~~~-------~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~------~~~p-~~~~~~~l   99 (248)
                      ...|++++|...+++..+.       .-+....++..+-..|...|++++|...+++..+.      +-.| ...++..+
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            4567777777777766442       22334678889999999999999999999998754      2223 45789999


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHC------CCCchHHhHHHHhcccccccchHHHHHHHHHHHHhc------CCCC-CHHH
Q 039342          100 LAVYAKSNRWDDAYGLLDEMHTN------RISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCE------GYGL-GMRF  166 (248)
Q Consensus       100 i~~~~~~~~~~~a~~~~~~m~~~------~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~------~~~p-~~~~  166 (248)
                      -..|...|++++|...+++..+.      .-.|........+...+...|+++.|...+++..+.      +-.| ...+
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            99999999999999999988654      222444444444444477889999999999888765      2233 3567


Q ss_pred             HHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          167 YNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       167 ~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                      +..+...+...|++++|.+.+++..+
T Consensus       172 ~~~la~~~~~~g~~~~A~~~~~~~l~  197 (283)
T 3edt_B          172 KNNLASCYLKQGKYQDAETLYKEILT  197 (283)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            88899999999999999999998764

>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=99.17  E-value=3e-09  Score=75.25  Aligned_cols=151  Identities=13%  Similarity=0.073  Sum_probs=124.2

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|.+.|+++.+.. +.+...|..+...+...|++++|.+.+++..+.. +.+...+..+...+...|++++|.+.+
T Consensus        22 ~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~   99 (186)
T 3as5_A           22 GRYSQAVMLLEQVYDAD-AFDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLTYVQVQKYDLAVPLL   99 (186)
T ss_dssp             TCHHHHHHHHTTTCCTT-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHhC-ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHH
Confidence            78999999999887643 2468889999999999999999999999997763 456788899999999999999999999


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchH-HhHHHHhcccccccchHHHHHHHHHHHHhc
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIH-QVTGQMIKGEFDDESNWQMVEYVFDKLNCE  158 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  158 (248)
                      ++..+.. +.+...+..+...+...|++++|...+++..+..  |+. ..+..+.. .+...|+++.|...++...+.
T Consensus       100 ~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~la~-~~~~~~~~~~A~~~~~~~~~~  173 (186)
T 3as5_A          100 IKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIALGLR--PNEGKVHRAIAF-SYEQMGRHEEALPHFKKANEL  173 (186)
T ss_dssp             HHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHH-HHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC--ccchHHHHHHHH-HHHHcCCHHHHHHHHHHHHHc
Confidence            9988753 3467888999999999999999999999988765  333 33333333 366788999999999887654

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.16  E-value=1.2e-09  Score=87.26  Aligned_cols=234  Identities=11%  Similarity=-0.056  Sum_probs=161.7

Q ss_pred             CCchHHHHHHHHHHHHcCCCCC----HHhHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHhc
Q 039342            1 GGLYKECQAILSRMSESGVARN----SDSFNAVIEAFRQGGRFEEAIKAYVEMEKV----RCDP-NERTLEAVLSVYCFA   71 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~----~~~y~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p-~~~t~~~ll~~~~~~   71 (248)
                      .|++++|...|++..+.+.. +    ...|..+-..+...|++++|...+++..+.    +-.| ...++..+...|...
T Consensus        22 ~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~  100 (406)
T 3sf4_A           22 SGDCRAGVSFFEAAVQVGTE-DLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTLKVL  100 (406)
T ss_dssp             TTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             hccHHHHHHHHHHHHhcCcc-cHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHc
Confidence            38899999999998875422 2    367888999999999999999999886432    2222 245777888899999


Q ss_pred             CChhHHHHHHHHHHHC----CCCc-CHhhHHHHHHHHHhcCC--------------------HHHHHHHHHHHHH----C
Q 039342           72 GLVDESKEQFQEIKSS----GILP-SVMCYCMLLAVYAKSNR--------------------WDDAYGLLDEMHT----N  122 (248)
Q Consensus        72 g~~~~a~~~~~~m~~~----~~~p-~~~~~~~li~~~~~~~~--------------------~~~a~~~~~~m~~----~  122 (248)
                      |++++|...+++..+.    +-.+ ...++..+-..|...|+                    +++|...+++..+    .
T Consensus       101 g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~  180 (406)
T 3sf4_A          101 GNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAAVDFYEENLSLVTAL  180 (406)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHHhc
Confidence            9999999999887643    1111 24578888889999999                    9999999887643    2


Q ss_pred             CCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCC-CCC----HHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCC
Q 039342          123 RISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGY-GLG----MRFYNALLEALWCLGLRERAARVLDEATKRGLFP  197 (248)
Q Consensus       123 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~-~p~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  197 (248)
                      +..|........+...+...|+++.|...+++..+... .++    ..++..+...+...|++++|...+++..+..-..
T Consensus       181 ~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~  260 (406)
T 3sf4_A          181 GDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQL  260 (406)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             cCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhC
Confidence            32333333333334446778889999998887764311 112    3477888889999999999999999876421111


Q ss_pred             CcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHHH
Q 039342          198 ELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFM  235 (248)
Q Consensus       198 ~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~~  235 (248)
                      ........++..+...+...|++++|...+++..+..-
T Consensus       261 ~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~  298 (406)
T 3sf4_A          261 KDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQ  298 (406)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             cCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHH
Confidence            11111122233333667788999999998888766543

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.15  E-value=4.4e-09  Score=79.50  Aligned_cols=190  Identities=10%  Similarity=-0.030  Sum_probs=138.7

Q ss_pred             CchHHHHHHHHHHHHcCCCCC--HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHH
Q 039342            2 GLYKECQAILSRMSESGVARN--SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKE   79 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~--~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~   79 (248)
                      |++++|.+.|++..+.+..|+  ...|..+-..+...|++++|.+.|++..+.. +.+...+..+...|...|++++|.+
T Consensus        51 ~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~  129 (272)
T 3u4t_A           51 AKYDLAQKDIETYFSKVNATKAKSADFEYYGKILMKKGQDSLAIQQYQAAVDRD-TTRLDMYGQIGSYFYNKGNFPLAIQ  129 (272)
T ss_dssp             TCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHH
T ss_pred             hhHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHccCHHHHHH
Confidence            789999999999987432222  3458999999999999999999999997764 3456789999999999999999999


Q ss_pred             HHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHH-hHHHHhcccccccch---HHHHHHHHHHH
Q 039342           80 QFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQ-VTGQMIKGEFDDESN---WQMVEYVFDKL  155 (248)
Q Consensus        80 ~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~-~~~~~l~~~~~~~~~---~~~a~~~~~~m  155 (248)
                      .|++..+.. +.+...|..+-..+...+++++|...|++..+..  |+.. .+..+... +...++   ++.|...++..
T Consensus       130 ~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~--p~~~~~~~~~~~~-~~~~~~~~~~~~A~~~~~~a  205 (272)
T 3u4t_A          130 YMEKQIRPT-TTDPKVFYELGQAYYYNKEYVKADSSFVKVLELK--PNIYIGYLWRARA-NAAQDPDTKQGLAKPYYEKL  205 (272)
T ss_dssp             HHGGGCCSS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHH-HHHHSTTCSSCTTHHHHHHH
T ss_pred             HHHHHhhcC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC--ccchHHHHHHHHH-HHHcCcchhhHHHHHHHHHH
Confidence            999988762 2256667777624444569999999999998764  4332 22222221 222233   55666666665


Q ss_pred             Hhc-CCCCC------HHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCC
Q 039342          156 NCE-GYGLG------MRFYNALLEALWCLGLRERAARVLDEATKRGLFPE  198 (248)
Q Consensus       156 ~~~-~~~p~------~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  198 (248)
                      .+. .-.|+      ..+|..+-..|...|++++|.+.|++..+.  .|+
T Consensus       206 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~  253 (272)
T 3u4t_A          206 IEVCAPGGAKYKDELIEANEYIAYYYTINRDKVKADAAWKNILAL--DPT  253 (272)
T ss_dssp             HHHHGGGGGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT
T ss_pred             HHHHhcccccchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--Ccc
Confidence            543 12233      257888889999999999999999998864  465

>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=99.15  E-value=2.5e-08  Score=85.82  Aligned_cols=164  Identities=14%  Similarity=0.056  Sum_probs=138.3

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCc-CHhhHHHHH
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILP-SVMCYCMLL  100 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li  100 (248)
                      ++..|+.+-..+.+.|++++|.+.|++..+.. +-+...|..+-.+|.+.|++++|.+.|++..+.  .| +...|..+-
T Consensus         8 ~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~-P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l--~P~~~~a~~nLg   84 (723)
T 4gyw_A            8 HADSLNNLANIKREQGNIEEAVRLYRKALEVF-PEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTFADAYSNMG   84 (723)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHH
Confidence            47789999999999999999999999987753 335788999999999999999999999998875  34 578999999


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCch
Q 039342          101 AVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR  180 (248)
Q Consensus       101 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~  180 (248)
                      .+|.+.|++++|++.|++..+..  |+.......+...+...|++++|...|++..+.... +...+..+...+...|++
T Consensus        85 ~~l~~~g~~~~A~~~~~kAl~l~--P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~-~~~a~~~L~~~l~~~g~~  161 (723)
T 4gyw_A           85 NTLKEMQDVQGALQCYTRAIQIN--PAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPD-FPDAYCNLAHCLQIVCDW  161 (723)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSC-CHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-ChHHHhhhhhHHHhcccH
Confidence            99999999999999999988754  555444333444477889999999999998886533 577899999999999999


Q ss_pred             HHHHHHHHHHH
Q 039342          181 ERAARVLDEAT  191 (248)
Q Consensus       181 ~~a~~~~~~m~  191 (248)
                      ++|.+.+++..
T Consensus       162 ~~A~~~~~kal  172 (723)
T 4gyw_A          162 TDYDERMKKLV  172 (723)
T ss_dssp             TTHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999888765

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.14  E-value=3.8e-10  Score=90.62  Aligned_cols=232  Identities=11%  Similarity=-0.050  Sum_probs=160.8

Q ss_pred             CchHHHHHHHHHHHHc----CC-CCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHc----C-CCCCHHHHHHHHHHHHhc
Q 039342            2 GLYKECQAILSRMSES----GV-ARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKV----R-CDPNERTLEAVLSVYCFA   71 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~----g~-~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~----~-~~p~~~t~~~ll~~~~~~   71 (248)
                      |++++|.+.|++..+.    +- +.....|..+-..|...|++++|.+.+++..+.    + -+....++..+-..|...
T Consensus       100 g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~  179 (411)
T 4a1s_A          100 GDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAK  179 (411)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHc
Confidence            7889999999887542    11 234568888999999999999999999987543    1 122345778888899999


Q ss_pred             CC-----------------hhHHHHHHHHHHHC----CCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCC----CC
Q 039342           72 GL-----------------VDESKEQFQEIKSS----GILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNR----IS  125 (248)
Q Consensus        72 g~-----------------~~~a~~~~~~m~~~----~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~----~~  125 (248)
                      |+                 +++|.+.+++..+.    +-.| ...++..+-..|...|++++|...+++..+..    ..
T Consensus       180 g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~  259 (411)
T 4a1s_A          180 GKHLGQRNPGKFGDDVKEALTRAVEFYQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDR  259 (411)
T ss_dssp             HHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCH
T ss_pred             CcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCc
Confidence            99                 99999998886542    2222 34578889999999999999999999875432    11


Q ss_pred             chHHhHHHHhcccccccchHHHHHHHHHHHHhcCC----C-CCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcc
Q 039342          126 NIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGY----G-LGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELF  200 (248)
Q Consensus       126 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~----~-p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  200 (248)
                      +........+...+...|+++.|...+++..+...    . ....++..+...+...|++++|.+.+++..+..-.....
T Consensus       260 ~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~  339 (411)
T 4a1s_A          260 AAERRANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDR  339 (411)
T ss_dssp             HHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCH
T ss_pred             HHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCh
Confidence            11111222333347778899999999987765311    1 125678888899999999999999999876421111111


Q ss_pred             hhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          201 RHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       201 t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      ......+..+...|...|+.++|...+++..+.
T Consensus       340 ~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  372 (411)
T 4a1s_A          340 IGEARACWSLGNAHSAIGGHERALKYAEQHLQL  372 (411)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            112222223336778889999999888776554

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.12  E-value=4.8e-09  Score=83.68  Aligned_cols=230  Identities=8%  Similarity=-0.062  Sum_probs=161.6

Q ss_pred             CCchHHHHHHHHHHHHc----CCCC-CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHc--CC----CCCHHHHHHHHHHHH
Q 039342            1 GGLYKECQAILSRMSES----GVAR-NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKV--RC----DPNERTLEAVLSVYC   69 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~----g~~~-~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~--~~----~p~~~t~~~ll~~~~   69 (248)
                      .|++++|.+.|++..+.    +-.+ ...+|..+-..|...|+++.|...+++..+.  ..    +....+++.+-..|.
T Consensus       116 ~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~  195 (383)
T 3ulq_A          116 QREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHSLFATNFL  195 (383)
T ss_dssp             TTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHHHHHHHHH
Confidence            38899999999998653    1122 3568889999999999999999999987543  11    112467888889999


Q ss_pred             hcCChhHHHHHHHHHHHC----CCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHC----CCCchHHhHHHHhccccc
Q 039342           70 FAGLVDESKEQFQEIKSS----GILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTN----RISNIHQVTGQMIKGEFD  140 (248)
Q Consensus        70 ~~g~~~~a~~~~~~m~~~----~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~~~~~~~~~~l~~~~~  140 (248)
                      ..|++++|.+.|++..+.    +-.+ ...++..+-..|...|++++|+..+++..+.    +..|........+...+.
T Consensus       196 ~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~  275 (383)
T 3ulq_A          196 DLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLITQIHY  275 (383)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHH
Confidence            999999999999887643    2111 2357888999999999999999999988662    332444333333334477


Q ss_pred             ccchHHHHHHHHHHHHhc----CCCCCHHHHHHHHHHHHhcCc---hHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhc
Q 039342          141 DESNWQMVEYVFDKLNCE----GYGLGMRFYNALLEALWCLGL---RERAARVLDEATKRGLFPELFRHNKLVWSVDVHR  213 (248)
Q Consensus       141 ~~~~~~~a~~~~~~m~~~----~~~p~~~~~~~li~~~~~~g~---~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~  213 (248)
                      ..|+++.|...+++..+.    +-......+..+-..+...|+   +++|..++++.   +..|+..    -+...+...
T Consensus       276 ~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~---~~~~~~~----~~~~~la~~  348 (383)
T 3ulq_A          276 KLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESK---MLYADLE----DFAIDVAKY  348 (383)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHT---TCHHHHH----HHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHC---cCHHHHH----HHHHHHHHH
Confidence            788899999998876553    222223345677778888888   66777776654   3333321    122233377


Q ss_pred             cccchHHHHHHHHHHHHHHHHHcC
Q 039342          214 MWEGGAYTAISVWLNKMYEMFMMG  237 (248)
Q Consensus       214 ~~~~g~~~~~~~~~~~m~~~~~~~  237 (248)
                      |...|++++|...+++..+..-.-
T Consensus       349 y~~~g~~~~A~~~~~~al~~~~~i  372 (383)
T 3ulq_A          349 YHERKNFQKASAYFLKVEQVRQLI  372 (383)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHTSC
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHh
Confidence            889999999999999887765544

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.10  E-value=7.8e-10  Score=85.76  Aligned_cols=232  Identities=11%  Similarity=-0.051  Sum_probs=160.0

Q ss_pred             CchHHHHHHHHHHHHc----CCCC-CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-CCC----HHHHHHHHHHHHhc
Q 039342            2 GLYKECQAILSRMSES----GVAR-NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRC-DPN----ERTLEAVLSVYCFA   71 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~----g~~~-~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~----~~t~~~ll~~~~~~   71 (248)
                      |++++|.+.|++..+.    +-.| ....+..+-..+...|++++|.+.+++..+..- .++    ..++..+...|...
T Consensus        57 g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~  136 (338)
T 3ro2_A           57 HDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAK  136 (338)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHc
Confidence            7889999999876532    2222 356888899999999999999999998754311 122    34778888899999


Q ss_pred             CC--------------------hhHHHHHHHHHHHC----CCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHC----
Q 039342           72 GL--------------------VDESKEQFQEIKSS----GILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTN----  122 (248)
Q Consensus        72 g~--------------------~~~a~~~~~~m~~~----~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----  122 (248)
                      |+                    +++|.+.+++..+.    +-.| ...++..+...+...|++++|...+++..+.    
T Consensus       137 ~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~  216 (338)
T 3ro2_A          137 GKSFGCPGPQDTGEFPEDVRNALQAAVDLYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEF  216 (338)
T ss_dssp             HHTSSSSSCC----CCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHH
T ss_pred             CcccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhc
Confidence            99                    99999998876532    2122 2457888889999999999999999987543    


Q ss_pred             CCCchHHhHHHHhcccccccchHHHHHHHHHHHHhc----CCCC-CHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCC
Q 039342          123 RISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCE----GYGL-GMRFYNALLEALWCLGLRERAARVLDEATKRGLFP  197 (248)
Q Consensus       123 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~----~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  197 (248)
                      +..+........+...+...|+++.|...+++..+.    +..+ ...++..+...+...|++++|...+++..+..-..
T Consensus       217 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~  296 (338)
T 3ro2_A          217 GDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQEL  296 (338)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhc
Confidence            222222222222333366778899999998876543    1111 15567888899999999999999999876421111


Q ss_pred             CcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          198 ELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       198 ~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      ........++..+...+...|++++|...+++..+.
T Consensus       297 ~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~  332 (338)
T 3ro2_A          297 KDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEI  332 (338)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHC
T ss_pred             CCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHH
Confidence            111112223333447788899999999999887654

>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=99.10  E-value=3.3e-08  Score=72.89  Aligned_cols=152  Identities=11%  Similarity=-0.007  Sum_probs=90.1

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHH
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLA  101 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~  101 (248)
                      ++..|...-..+.+.|++++|.+.|++..+..-+++...+..+-.++.+.|++++|.+.|++..+... -+...|..+-.
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            45666666666777777777777777766654335666666666777777777777777777665421 14456666777


Q ss_pred             HHHhcCCHHHHHHHHHHHHHCCCCchHHh-------HHHHhcccccccchHHHHHHHHHHHHhcCCCCC---HHHHHHHH
Q 039342          102 VYAKSNRWDDAYGLLDEMHTNRISNIHQV-------TGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLG---MRFYNALL  171 (248)
Q Consensus       102 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~~-------~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~---~~~~~~li  171 (248)
                      .|...|++++|+..+++..+..  |+...       ....+...+...|+++.|...++...+.  .|+   ...+..+-
T Consensus        85 ~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~l~  160 (228)
T 4i17_A           85 AYRDMKNNQEYIATLTEGIKAV--PGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDV--TSKKWKTDALYSLG  160 (228)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--SCHHHHHHHHHHHH
T ss_pred             HHHHcccHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhc--CCCcccHHHHHHHH
Confidence            7777777777777777766543  33221       1111222244556667777777666554  333   34455555


Q ss_pred             HHHHhcC
Q 039342          172 EALWCLG  178 (248)
Q Consensus       172 ~~~~~~g  178 (248)
                      ..+...|
T Consensus       161 ~~~~~~~  167 (228)
T 4i17_A          161 VLFYNNG  167 (228)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            5554444

>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=99.07  E-value=1.8e-08  Score=67.13  Aligned_cols=130  Identities=15%  Similarity=0.154  Sum_probs=76.6

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHH
Q 039342           25 SFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYA  104 (248)
Q Consensus        25 ~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  104 (248)
                      .|..+...+...|++++|..+++++.+.+ +.+...+..+...+...|++++|..+++++.+.+ +.+...+..+...+.
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~   80 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYY   80 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHHH
Confidence            45556666666677777777776665543 2345566666666666777777777776665542 224556666666666


Q ss_pred             hcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhc
Q 039342          105 KSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCE  158 (248)
Q Consensus       105 ~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~  158 (248)
                      ..|++++|...++++.+.... +...+..+... +...|+++.|...++.+.+.
T Consensus        81 ~~~~~~~A~~~~~~~~~~~~~-~~~~~~~la~~-~~~~~~~~~A~~~~~~~~~~  132 (136)
T 2fo7_A           81 KQGDYDEAIEYYQKALELDPR-SAEAWYNLGNA-YYKQGDYDEAIEYYQKALEL  132 (136)
T ss_dssp             TTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH-HHTTTCHHHHHHHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHHhCCC-ChHHHHHHHHH-HHHHccHHHHHHHHHHHHcc
Confidence            777777777777666554311 12223233222 45566666777666666543

>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=99.07  E-value=1.4e-08  Score=81.09  Aligned_cols=196  Identities=13%  Similarity=0.050  Sum_probs=150.5

Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCC-hhHHHHHHHHHHHCCCCcCHhhHHHHHH
Q 039342           23 SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGL-VDESKEQFQEIKSSGILPSVMCYCMLLA  101 (248)
Q Consensus        23 ~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~-~~~a~~~~~~m~~~~~~p~~~~~~~li~  101 (248)
                      ...|+.+-..+.+.|++++|++.+++..+.. +-+...|+.+-.++.+.|+ +++|...|++..+... -+...|..+-.
T Consensus        97 ~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~-P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P-~~~~a~~~~g~  174 (382)
T 2h6f_A           97 RDVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQP-KNYQVWHHRRV  174 (382)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCC-CCHHHHHHHHH
Confidence            4678888889999999999999999998764 3467888999999999997 9999999999987632 26788999999


Q ss_pred             HHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHh-cCch
Q 039342          102 VYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWC-LGLR  180 (248)
Q Consensus       102 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~-~g~~  180 (248)
                      .+...|++++|+..|++..+..  |+.......+...+...|+++.|...++...+.... +...|+.+-.++.+ .|..
T Consensus       175 ~~~~~g~~~eAl~~~~kal~ld--P~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P~-~~~a~~~lg~~l~~l~~~~  251 (382)
T 2h6f_A          175 LVEWLRDPSQELEFIADILNQD--AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVR-NNSVWNQRYFVISNTTGYN  251 (382)
T ss_dssp             HHHHHTCCTTHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCSC
T ss_pred             HHHHccCHHHHHHHHHHHHHhC--ccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhcCcc
Confidence            9999999999999999998765  554443333333466778899999999999987655 67889999999999 6665


Q ss_pred             HHH-----HHHHHHHHHCCCCCCc-chhhhHHhhhhhhccccch--HHHHHHHHHHHH
Q 039342          181 ERA-----ARVLDEATKRGLFPEL-FRHNKLVWSVDVHRMWEGG--AYTAISVWLNKM  230 (248)
Q Consensus       181 ~~a-----~~~~~~m~~~g~~p~~-~t~~~li~~~~~~~~~~~g--~~~~~~~~~~~m  230 (248)
                      ++|     .+.+++..+.  .|+. ..|..+-     ..+...|  +++++...+.++
T Consensus       252 ~eA~~~~el~~~~~Al~l--~P~~~~a~~~l~-----~ll~~~g~~~~~~a~~~~~~~  302 (382)
T 2h6f_A          252 DRAVLEREVQYTLEMIKL--VPHNESAWNYLK-----GILQDRGLSKYPNLLNQLLDL  302 (382)
T ss_dssp             SHHHHHHHHHHHHHHHHH--STTCHHHHHHHH-----HHHTTTCGGGCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHH--CCCCHHHHHHHH-----HHHHccCccchHHHHHHHHHh
Confidence            777     4778877653  5542 2333333     3344445  577777766655

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.07  E-value=4.7e-08  Score=81.43  Aligned_cols=182  Identities=10%  Similarity=0.045  Sum_probs=139.0

Q ss_pred             HHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHhcCChhHHHHHHHH
Q 039342            6 ECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN--ERTLEAVLSVYCFAGLVDESKEQFQE   83 (248)
Q Consensus         6 ~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~--~~t~~~ll~~~~~~g~~~~a~~~~~~   83 (248)
                      +|.++|++..+.-.+.+...|..+...+.+.|++++|.++|++..+.  .|+  ...|......+.+.|++++|.++|++
T Consensus       304 ~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~  381 (530)
T 2ooe_A          304 EAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKK  381 (530)
T ss_dssp             HHHHHHHHHTTTTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--SSSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCc--cccCchHHHHHHHHHHHHhcCHHHHHHHHHH
Confidence            89999999875222346889999999999999999999999999874  554  35899999999999999999999999


Q ss_pred             HHHCCCCcCHhhHHHHHHH-HHhcCCHHHHHHHHHHHHHCCCCchH-HhHHHHhcccccccchHHHHHHHHHHHHhcCC-
Q 039342           84 IKSSGILPSVMCYCMLLAV-YAKSNRWDDAYGLLDEMHTNRISNIH-QVTGQMIKGEFDDESNWQMVEYVFDKLNCEGY-  160 (248)
Q Consensus        84 m~~~~~~p~~~~~~~li~~-~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~-  160 (248)
                      ..+.. +.+...|...... +...|+.++|..+|++..+..  |+. ..+..++.. ....|+.+.|..+|+.....+. 
T Consensus       382 Al~~~-~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~~--p~~~~~~~~~~~~-~~~~g~~~~Ar~~~~~al~~~~~  457 (530)
T 2ooe_A          382 AREDA-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY--GDIPEYVLAYIDY-LSHLNEDNNTRVLFERVLTSGSL  457 (530)
T ss_dssp             HHTCT-TCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHH--TTCHHHHHHHHHH-HTTTTCHHHHHHHHHHHHHSCCS
T ss_pred             HHhcc-CCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHHC--CCCHHHHHHHHHH-HHhCCCHhhHHHHHHHHHhccCC
Confidence            98752 1122333322222 336899999999999987653  543 344444433 6677899999999999988743 


Q ss_pred             CCC--HHHHHHHHHHHHhcCchHHHHHHHHHHHHC
Q 039342          161 GLG--MRFYNALLEALWCLGLRERAARVLDEATKR  193 (248)
Q Consensus       161 ~p~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  193 (248)
                      .|+  ...|...+......|+.+.+..++.++.+.
T Consensus       458 ~~~~~~~lw~~~~~~e~~~G~~~~~~~~~~r~~~~  492 (530)
T 2ooe_A          458 PPEKSGEIWARFLAFESNIGDLASILKVEKRRFTA  492 (530)
T ss_dssp             CGGGCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            333  457888888888999999999999988753

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.06  E-value=2.6e-09  Score=85.31  Aligned_cols=233  Identities=11%  Similarity=-0.057  Sum_probs=160.9

Q ss_pred             CchHHHHHHHHHHHHc----CCCC-CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-CCC----HHHHHHHHHHHHhc
Q 039342            2 GLYKECQAILSRMSES----GVAR-NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRC-DPN----ERTLEAVLSVYCFA   71 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~----g~~~-~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~----~~t~~~ll~~~~~~   71 (248)
                      |++++|...|++..+.    +-.| ...+|..+-..+...|++++|...+++..+..- .++    ..++..+-..|...
T Consensus        61 g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~  140 (406)
T 3sf4_A           61 HDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAK  140 (406)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHc
Confidence            7889999999876432    2222 356788889999999999999999988754310 122    45788888899999


Q ss_pred             CC--------------------hhHHHHHHHHHHHC----CCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHC----
Q 039342           72 GL--------------------VDESKEQFQEIKSS----GILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTN----  122 (248)
Q Consensus        72 g~--------------------~~~a~~~~~~m~~~----~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----  122 (248)
                      |+                    +++|.+.+++..+.    +-.| ...++..+-..|...|++++|...+++..+.    
T Consensus       141 g~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~  220 (406)
T 3sf4_A          141 GKSFGCPGPQDVGEFPEEVRDALQAAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEF  220 (406)
T ss_dssp             HHTCC-------CCCCHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHT
T ss_pred             CCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhc
Confidence            99                    99999998876532    2222 2457888899999999999999999987543    


Q ss_pred             CCCchHHhHHHHhcccccccchHHHHHHHHHHHHhc----CCCC-CHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCC
Q 039342          123 RISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCE----GYGL-GMRFYNALLEALWCLGLRERAARVLDEATKRGLFP  197 (248)
Q Consensus       123 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~----~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  197 (248)
                      +..+........+...+...|+++.|...++...+.    +..+ ...++..+...+...|++++|.+.+++..+..-..
T Consensus       221 ~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~  300 (406)
T 3sf4_A          221 GDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQEL  300 (406)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             CCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhc
Confidence            222222223333333467788999999998876643    2111 15677888999999999999999999876421111


Q ss_pred             CcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHH
Q 039342          198 ELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMF  234 (248)
Q Consensus       198 ~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~  234 (248)
                      +........+..+...+...|++++|...+++..+..
T Consensus       301 ~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~  337 (406)
T 3sf4_A          301 NDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEIS  337 (406)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence            1111112222333367788999999999888876653

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.04  E-value=4.6e-07  Score=74.70  Aligned_cols=111  Identities=10%  Similarity=0.055  Sum_probs=46.2

Q ss_pred             chHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHh----cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----cCCh
Q 039342            3 LYKECQAILSRMSESGVARNSDSFNAVIEAFRQ----GGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCF----AGLV   74 (248)
Q Consensus         3 ~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~----~g~~   74 (248)
                      +.++|.+.|++..+.|   ++..+..|-..|..    .+++++|.+.|++..+.|   +...+..+-..|..    .++.
T Consensus        94 ~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~d~  167 (490)
T 2xm6_A           94 DYAQAVIWYKKAALKG---LPQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQG---RDSGQQSMGDAYFEGDGVTRDY  167 (490)
T ss_dssp             CHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCH
T ss_pred             CHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCH
Confidence            3444444444444322   23333333333433    344444444444443332   22333333333333    3444


Q ss_pred             hHHHHHHHHHHHCCCCcCHhhHHHHHHHHHh----cCCHHHHHHHHHHHHHC
Q 039342           75 DESKEQFQEIKSSGILPSVMCYCMLLAVYAK----SNRWDDAYGLLDEMHTN  122 (248)
Q Consensus        75 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~  122 (248)
                      ++|.+.|++..+.|   +...+..+-..|..    .++.++|...|++..+.
T Consensus       168 ~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~  216 (490)
T 2xm6_A          168 VMAREWYSKAAEQG---NVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATS  216 (490)
T ss_dssp             HHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHC
Confidence            44444444444332   33344444444443    44444555554444443

>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=99.04  E-value=2.3e-08  Score=66.61  Aligned_cols=129  Identities=14%  Similarity=0.076  Sum_probs=71.5

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccc
Q 039342           60 TLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEF  139 (248)
Q Consensus        60 t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~  139 (248)
                      .|..+...+...|++++|..+++++.+.. +.+...+..+...+...|++++|...++++.+.... +...+..+.. .+
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~-~~   79 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPR-SAEAWYNLGN-AY   79 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHH-HH
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHCCC-chHHHHHHHH-HH
Confidence            34555566666666666666666665432 124455666666666666666666666666554311 1222222222 24


Q ss_pred             cccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          140 DDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       140 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                      ...|+++.|...++.+.+... .+...+..+...+...|++++|.+.++++.+
T Consensus        80 ~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  131 (136)
T 2fo7_A           80 YKQGDYDEAIEYYQKALELDP-RSAEAWYNLGNAYYKQGDYDEAIEYYQKALE  131 (136)
T ss_dssp             HTTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHHhCC-CChHHHHHHHHHHHHHccHHHHHHHHHHHHc
Confidence            455666666666666655432 2345555666666666666666666666544

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.04  E-value=5.5e-07  Score=74.22  Aligned_cols=181  Identities=13%  Similarity=0.043  Sum_probs=108.8

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHh----cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----cCC
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQ----GGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCF----AGL   73 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~----~g~   73 (248)
                      +++++|.+.|++..+.|   ++..+..+-..|..    .++.++|.+.|++..+.|   +...+..+-..|..    .++
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            46777777777776654   45566666666665    667777777777776654   45666666666666    677


Q ss_pred             hhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHh----cCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHH
Q 039342           74 VDESKEQFQEIKSSGILPSVMCYCMLLAVYAK----SNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVE  149 (248)
Q Consensus        74 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  149 (248)
                      .++|.+.|++..+.|   +...+..+-..|..    .++.++|...|++..+.+.......+..+........++++.|.
T Consensus       203 ~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~y~~g~~~~~d~~~A~  279 (490)
T 2xm6_A          203 DAISAQWYRKSATSG---DELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQGNSIAQFRLGYILEQGLAGAKEPLKAL  279 (490)
T ss_dssp             HHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHTTTSSCCHHHHH
T ss_pred             HHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCHHHHH
Confidence            777777777776654   44555666666654    56777777777776665432111111111111122245666777


Q ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHHHhc-----CchHHHHHHHHHHHHCC
Q 039342          150 YVFDKLNCEGYGLGMRFYNALLEALWCL-----GLRERAARVLDEATKRG  194 (248)
Q Consensus       150 ~~~~~m~~~~~~p~~~~~~~li~~~~~~-----g~~~~a~~~~~~m~~~g  194 (248)
                      ..|+...+.|   +...+..+-..|...     ++.++|...|++..+.|
T Consensus       280 ~~~~~a~~~~---~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~~  326 (490)
T 2xm6_A          280 EWYRKSAEQG---NSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQG  326 (490)
T ss_dssp             HHHHHHHTTT---CHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcC---CHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhcC
Confidence            7666665543   334455555555555     66666666666666543

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=99.01  E-value=5.9e-08  Score=74.46  Aligned_cols=146  Identities=12%  Similarity=0.030  Sum_probs=96.4

Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCC-cCHhhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 039342           42 AIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGIL-PSVMCYCMLLAVYAKSNRWDDAYGLLDEMH  120 (248)
Q Consensus        42 a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~-p~~~~~~~li~~~~~~~~~~~a~~~~~~m~  120 (248)
                      +...|++..+.+ .++..++..+..++...|++++|.+++.+....+-. -+...+..++..+.+.|+.+.|.+.+++|.
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            566677666554 456666667777788888888888888777655431 256677788888888888888888888887


Q ss_pred             HCCCCc-----hHHhHHHHhccc---ccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          121 TNRISN-----IHQVTGQMIKGE---FDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       121 ~~~~~~-----~~~~~~~~l~~~---~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                      +..  |     +..+...+..++   ....+.++.|..+|+++.+..  |+..+-..++.++...|++++|.+.++.+.+
T Consensus       164 ~~~--~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~~--p~~~~~~lLln~~~~~g~~~eAe~~L~~l~~  239 (310)
T 3mv2_B          164 NAI--EDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQTF--PTWKTQLGLLNLHLQQRNIAEAQGIVELLLS  239 (310)
T ss_dssp             HHS--CHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTTS--CSHHHHHHHHHHHHHHTCHHHHHHHHHHHHS
T ss_pred             hcC--ccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhC--CCcccHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            653  4     345554444431   222346778888888876543  4433334444477788888888888876543

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=98.96  E-value=1.7e-07  Score=69.03  Aligned_cols=138  Identities=12%  Similarity=-0.065  Sum_probs=111.7

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHh
Q 039342           56 PNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMI  135 (248)
Q Consensus        56 p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l  135 (248)
                      .|+..+...-..+.+.|++++|.+.|++..+....++...+..+-.++...|++++|+..|++..+..  |+.......+
T Consensus         5 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~l   82 (228)
T 4i17_A            5 TDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKN--YNLANAYIGK   82 (228)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT--CSHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhC--cchHHHHHHH
Confidence            46678888889999999999999999999876543677777779999999999999999999998765  5554444444


Q ss_pred             cccccccchHHHHHHHHHHHHhcCCCCCH-------HHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCC
Q 039342          136 KGEFDDESNWQMVEYVFDKLNCEGYGLGM-------RFYNALLEALWCLGLRERAARVLDEATKRGLFPE  198 (248)
Q Consensus       136 ~~~~~~~~~~~~a~~~~~~m~~~~~~p~~-------~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  198 (248)
                      ...+...|+++.|...++...+.... +.       ..|..+-..+...|++++|.+.|++..+.  .|+
T Consensus        83 ~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~p~  149 (228)
T 4i17_A           83 SAAYRDMKNNQEYIATLTEGIKAVPG-NATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDV--TSK  149 (228)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--SCH
T ss_pred             HHHHHHcccHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhc--CCC
Confidence            44477889999999999998876432 33       45777888889999999999999998764  554

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=98.96  E-value=2e-07  Score=73.91  Aligned_cols=232  Identities=11%  Similarity=-0.027  Sum_probs=151.1

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCH----HhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-CCCH----HHHHHHHHHHHhc
Q 039342            1 GGLYKECQAILSRMSESGVARNS----DSFNAVIEAFRQGGRFEEAIKAYVEMEKVRC-DPNE----RTLEAVLSVYCFA   71 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~----~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~~----~t~~~ll~~~~~~   71 (248)
                      .|++++|...+++........+.    ..++.+-..+...|++++|.+.+++..+..- .++.    .++..+-..+...
T Consensus        27 ~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~  106 (373)
T 1hz4_A           27 DGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFAQ  106 (373)
T ss_dssp             TTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHC
Confidence            37899999999987664322222    2566667788889999999999988754210 1222    3356677788999


Q ss_pred             CChhHHHHHHHHHHHC----CCC--c-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC--c-hH-HhHHHHhccccc
Q 039342           72 GLVDESKEQFQEIKSS----GIL--P-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRIS--N-IH-QVTGQMIKGEFD  140 (248)
Q Consensus        72 g~~~~a~~~~~~m~~~----~~~--p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~--~-~~-~~~~~~l~~~~~  140 (248)
                      |++++|...+++..+.    +..  | ....+..+-..+...|++++|...+++..+....  + .. ..+.. +...+.
T Consensus       107 G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~-la~~~~  185 (373)
T 1hz4_A          107 GFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAM-LIQCSL  185 (373)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHH-HHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHH-HHHHHH
Confidence            9999999999887642    222  3 2456677888899999999999999987654321  1 11 22222 223366


Q ss_pred             ccchHHHHHHHHHHHHhcCCCCC--HHHHH----HHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhcc
Q 039342          141 DESNWQMVEYVFDKLNCEGYGLG--MRFYN----ALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRM  214 (248)
Q Consensus       141 ~~~~~~~a~~~~~~m~~~~~~p~--~~~~~----~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~  214 (248)
                      ..|+++.|...+++.......++  .....    .....+...|++++|...+++.....  |....+....+..+...+
T Consensus       186 ~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~la~~~  263 (373)
T 1hz4_A          186 ARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPE--FANNHFLQGQWRNIARAQ  263 (373)
T ss_dssp             HHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCC--CTTCGGGHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCC--CCcchhhHHHHHHHHHHH
Confidence            77889999999988765421111  11111    23344778999999999998876532  211111111122233566


Q ss_pred             ccchHHHHHHHHHHHHHHHHH
Q 039342          215 WEGGAYTAISVWLNKMYEMFM  235 (248)
Q Consensus       215 ~~~g~~~~~~~~~~~m~~~~~  235 (248)
                      ...|+.++|...+++..+..-
T Consensus       264 ~~~g~~~~A~~~l~~a~~~~~  284 (373)
T 1hz4_A          264 ILLGEFEPAEIVLEELNENAR  284 (373)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHHHH
Confidence            778999999998888766543

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=98.95  E-value=6.9e-08  Score=76.87  Aligned_cols=225  Identities=7%  Similarity=-0.057  Sum_probs=155.3

Q ss_pred             CchHHHHHHHHHHHHcCC-CC----CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHc--CC---CC-CHHHHHHHHHHHHh
Q 039342            2 GLYKECQAILSRMSESGV-AR----NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKV--RC---DP-NERTLEAVLSVYCF   70 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~-~~----~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~--~~---~p-~~~t~~~ll~~~~~   70 (248)
                      |++++|.+.|++..+.-. .+    ...+|..+-..|...|+++.|...+++..+.  ..   .+ ...+++.+-..|..
T Consensus       115 g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~y~~  194 (378)
T 3q15_A          115 KEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIAGNYDD  194 (378)
T ss_dssp             TCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHHH
Confidence            789999999998865311 12    3567888889999999999999999887542  11   11 24677888899999


Q ss_pred             cCChhHHHHHHHHHHHC----CCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCC---CCchHHhHHHHhccccccc
Q 039342           71 AGLVDESKEQFQEIKSS----GILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNR---ISNIHQVTGQMIKGEFDDE  142 (248)
Q Consensus        71 ~g~~~~a~~~~~~m~~~----~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~---~~~~~~~~~~~l~~~~~~~  142 (248)
                      .|++++|.+.|++..+.    +-.+ ...++..+-..|...|++++|+..+++..+..   ..|........+...+...
T Consensus       195 ~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~  274 (378)
T 3q15_A          195 FKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKA  274 (378)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHT
T ss_pred             hCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHHHHHHHC
Confidence            99999999999887642    2222 24578888899999999999999999886610   1233332233333347778


Q ss_pred             chHHHHHHHHHHHHhcC----CCCCHHHHHHHHHHHHhcCc---hHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccc
Q 039342          143 SNWQMVEYVFDKLNCEG----YGLGMRFYNALLEALWCLGL---RERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMW  215 (248)
Q Consensus       143 ~~~~~a~~~~~~m~~~~----~~p~~~~~~~li~~~~~~g~---~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~  215 (248)
                      |+++.|...++...+..    -......+..+-..+...++   +++|..++++   .+..|+...    +...+...|.
T Consensus       275 g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~---~~~~~~~~~----~~~~la~~y~  347 (378)
T 3q15_A          275 GQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEK---KNLHAYIEA----CARSAAAVFE  347 (378)
T ss_dssp             TCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHH---TTCHHHHHH----HHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHh---CCChhHHHH----HHHHHHHHHH
Confidence            89999999998877642    22223455666666777777   6667766665   333333221    1122336788


Q ss_pred             cchHHHHHHHHHHHHHHH
Q 039342          216 EGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       216 ~~g~~~~~~~~~~~m~~~  233 (248)
                      ..|++++|...+++..+.
T Consensus       348 ~~g~~~~A~~~~~~al~~  365 (378)
T 3q15_A          348 SSCHFEQAAAFYRKVLKA  365 (378)
T ss_dssp             HTTCHHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHH
Confidence            899999999998877654

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.95  E-value=5.2e-08  Score=74.75  Aligned_cols=182  Identities=11%  Similarity=0.063  Sum_probs=134.3

Q ss_pred             HHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHhcCChhHHHHHHHHHH
Q 039342            7 CQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRC-DPNERTLEAVLSVYCFAGLVDESKEQFQEIK   85 (248)
Q Consensus         7 a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~   85 (248)
                      |+..|++..+.+ .++..++..+-.++...|++++|++++.+-...|- .-+...+..++..+.+.|+.+.|.+.++.|.
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            345566555444 45666667888899999999999999998766553 2356777888999999999999999999998


Q ss_pred             HCCCCc-----CHhhHHHHHHHHH--hcC--CHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHH
Q 039342           86 SSGILP-----SVMCYCMLLAVYA--KSN--RWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLN  156 (248)
Q Consensus        86 ~~~~~p-----~~~~~~~li~~~~--~~~--~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~  156 (248)
                      +.  .|     +..+...+..++.  ..|  +..+|..+|+++.+..  |+......++. ++...|++++|+..++.+.
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 NA--IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQTF--PTWKTQLGLLN-LHLQQRNIAEAQGIVELLL  238 (310)
T ss_dssp             HH--SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTTS--CSHHHHHHHHH-HHHHHTCHHHHHHHHHHHH
T ss_pred             hc--CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhC--CCcccHHHHHH-HHHHcCCHHHHHHHHHHHH
Confidence            75  45     3566666666633  334  8999999999987654  43222222222 4778899999999999776


Q ss_pred             hcC---------CCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCC
Q 039342          157 CEG---------YGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPE  198 (248)
Q Consensus       157 ~~~---------~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  198 (248)
                      +.-         -+-+..+...+|......|+  .|.+++.++++.  .|+
T Consensus       239 ~~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~~--~P~  285 (310)
T 3mv2_B          239 SDYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVKL--DHE  285 (310)
T ss_dssp             SHHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHHT--TCC
T ss_pred             HhcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHHh--CCC
Confidence            531         13366777788999999997  999999999885  676

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=98.94  E-value=2.8e-08  Score=85.55  Aligned_cols=165  Identities=12%  Similarity=0.033  Sum_probs=130.9

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHh
Q 039342           57 NERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMI  135 (248)
Q Consensus        57 ~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l  135 (248)
                      +...|+.+-..|.+.|++++|.+.|++..+.  .| +...|..+-.+|.+.|++++|+..|++..+..  |+.......+
T Consensus         8 ~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l--~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~--P~~~~a~~nL   83 (723)
T 4gyw_A            8 HADSLNNLANIKREQGNIEEAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRIS--PTFADAYSNM   83 (723)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHH
Confidence            3578999999999999999999999998875  34 57889999999999999999999999988764  5554444444


Q ss_pred             cccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCc-chhhhHHhhhhhhcc
Q 039342          136 KGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPEL-FRHNKLVWSVDVHRM  214 (248)
Q Consensus       136 ~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~t~~~li~~~~~~~~  214 (248)
                      ...+...|++++|.+.|++..+.... +...|+.+-.+|...|++++|.+.|++..+.  .|+. ..+..+.     ..+
T Consensus        84 g~~l~~~g~~~~A~~~~~kAl~l~P~-~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l--~P~~~~a~~~L~-----~~l  155 (723)
T 4gyw_A           84 GNTLKEMQDVQGALQCYTRAIQINPA-FADAHSNLASIHKDSGNIPEAIASYRTALKL--KPDFPDAYCNLA-----HCL  155 (723)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHH-----HHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHHhhhh-----hHH
Confidence            44477889999999999998876533 5788999999999999999999999998764  5652 3344444     566


Q ss_pred             ccchHHHHHHHHHHHHHHH
Q 039342          215 WEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       215 ~~~g~~~~~~~~~~~m~~~  233 (248)
                      ...|++++|.+.+++..+.
T Consensus       156 ~~~g~~~~A~~~~~kal~l  174 (723)
T 4gyw_A          156 QIVCDWTDYDERMKKLVSI  174 (723)
T ss_dssp             HHTTCCTTHHHHHHHHHHH
T ss_pred             HhcccHHHHHHHHHHHHHh
Confidence            6777777777766665543

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=98.92  E-value=9.8e-08  Score=75.65  Aligned_cols=229  Identities=14%  Similarity=0.073  Sum_probs=153.3

Q ss_pred             CchHHHHHHHHHHHHcCC-CCC----HHhHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCC--C-CHHHHHHHHHHHH
Q 039342            2 GLYKECQAILSRMSESGV-ARN----SDSFNAVIEAFRQGGRFEEAIKAYVEMEKV----RCD--P-NERTLEAVLSVYC   69 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~-~~~----~~~y~~li~~~~~~~~~~~a~~~~~~m~~~----~~~--p-~~~t~~~ll~~~~   69 (248)
                      |++++|.+.+++..+... .++    ..+++.+-..+...|++++|.+.+++..+.    +-.  | ....+..+-..+.
T Consensus        67 g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~  146 (373)
T 1hz4_A           67 GELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLW  146 (373)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHH
Confidence            788999999988754211 112    234667778889999999999999887543    222  3 2355667788899


Q ss_pred             hcCChhHHHHHHHHHHHCCC--Cc--CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCch-HHhHHH----Hhccccc
Q 039342           70 FAGLVDESKEQFQEIKSSGI--LP--SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNI-HQVTGQ----MIKGEFD  140 (248)
Q Consensus        70 ~~g~~~~a~~~~~~m~~~~~--~p--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~----~l~~~~~  140 (248)
                      ..|++++|...+++..+..-  .+  ...++..+-..+...|++++|...+++.......+. ...+..    .....+.
T Consensus       147 ~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  226 (373)
T 1hz4_A          147 AWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQ  226 (373)
T ss_dssp             HTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHH
Confidence            99999999999998765321  11  235678888889999999999999998865321111 111111    1111244


Q ss_pred             ccchHHHHHHHHHHHHhcCCCC---CHHHHHHHHHHHHhcCchHHHHHHHHHHHH----CCCCCCcchhhhHHhhhhhhc
Q 039342          141 DESNWQMVEYVFDKLNCEGYGL---GMRFYNALLEALWCLGLRERAARVLDEATK----RGLFPELFRHNKLVWSVDVHR  213 (248)
Q Consensus       141 ~~~~~~~a~~~~~~m~~~~~~p---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~----~g~~p~~~t~~~li~~~~~~~  213 (248)
                      ..|+++.+...++........+   ....+..+...+...|++++|...+++...    .|..++.    .-+...+...
T Consensus       227 ~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~----~~~~~~la~~  302 (373)
T 1hz4_A          227 MTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDL----NRNLLLLNQL  302 (373)
T ss_dssp             HTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH----HHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhH----HHHHHHHHHH
Confidence            6788999999988876543221   133567778899999999999999998754    2221111    1122223356


Q ss_pred             cccchHHHHHHHHHHHHHHHH
Q 039342          214 MWEGGAYTAISVWLNKMYEMF  234 (248)
Q Consensus       214 ~~~~g~~~~~~~~~~~m~~~~  234 (248)
                      +...|+.++|...+++-.+..
T Consensus       303 ~~~~g~~~~A~~~l~~al~~~  323 (373)
T 1hz4_A          303 YWQAGRKSDAQRVLLDALKLA  323 (373)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHHHh
Confidence            778889999988887766543

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.90  E-value=1.4e-07  Score=70.99  Aligned_cols=170  Identities=8%  Similarity=0.009  Sum_probs=122.4

Q ss_pred             CCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHHHhcCChhHHHHHHHHHHHCCC-Cc-CHhh
Q 039342           21 RNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN---ERTLEAVLSVYCFAGLVDESKEQFQEIKSSGI-LP-SVMC   95 (248)
Q Consensus        21 ~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~---~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~-~p-~~~~   95 (248)
                      .+...+-..-..+.+.|++++|...|++..+.. +-+   ...+..+-.+|.+.|++++|...|++..+... .| ....
T Consensus        13 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a   91 (261)
T 3qky_A           13 SSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYG-RTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQA   91 (261)
T ss_dssp             SSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGC-SCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHH
T ss_pred             CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHH
Confidence            456777778888899999999999999997753 122   57788888999999999999999999987521 12 2456


Q ss_pred             HHHHHHHHHh--------cCCHHHHHHHHHHHHHCCCCchHHhHH-----------------HHhcccccccchHHHHHH
Q 039342           96 YCMLLAVYAK--------SNRWDDAYGLLDEMHTNRISNIHQVTG-----------------QMIKGEFDDESNWQMVEY  150 (248)
Q Consensus        96 ~~~li~~~~~--------~~~~~~a~~~~~~m~~~~~~~~~~~~~-----------------~~l~~~~~~~~~~~~a~~  150 (248)
                      +..+-.++..        .|++++|+..|++..+..  |+.....                 ..+...+...|+++.|..
T Consensus        92 ~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  169 (261)
T 3qky_A           92 EYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRY--PNHELVDDATQKIRELRAKLARKQYEAARLYERRELYEAAAV  169 (261)
T ss_dssp             HHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHC--TTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHC--cCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHH
Confidence            6777778888        899999999999987654  3322111                 122233556778888888


Q ss_pred             HHHHHHhcCCCC--CHHHHHHHHHHHHhc----------CchHHHHHHHHHHHHC
Q 039342          151 VFDKLNCEGYGL--GMRFYNALLEALWCL----------GLRERAARVLDEATKR  193 (248)
Q Consensus       151 ~~~~m~~~~~~p--~~~~~~~li~~~~~~----------g~~~~a~~~~~~m~~~  193 (248)
                      .|+...+.....  ....+..+..+|...          |++++|...|++..+.
T Consensus       170 ~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~  224 (261)
T 3qky_A          170 TYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQI  224 (261)
T ss_dssp             HHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHH
Confidence            888877653221  244566666777655          7778888888887764

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=98.87  E-value=1.1e-07  Score=75.71  Aligned_cols=188  Identities=11%  Similarity=-0.003  Sum_probs=134.6

Q ss_pred             CchHHHHHHHHHHHHc----C--CCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-CCC----HHHHHHHHHHHHh
Q 039342            2 GLYKECQAILSRMSES----G--VARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRC-DPN----ERTLEAVLSVYCF   70 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~----g--~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~----~~t~~~ll~~~~~   70 (248)
                      |++++|.+.+.+..+.    +  ......+++.+-..|...|++++|.+.+++..+..- .++    ..++..+-..|..
T Consensus       157 ~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~  236 (383)
T 3ulq_A          157 KQTYFSMDYARQAYEIYKEHEAYNIRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNS  236 (383)
T ss_dssp             TCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHhCccchHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHH
Confidence            7888888888876542    1  111246788889999999999999999988754311 122    2478889999999


Q ss_pred             cCChhHHHHHHHHHHHC----CC-CcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCC---CchHHhHHHHhccccccc
Q 039342           71 AGLVDESKEQFQEIKSS----GI-LPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRI---SNIHQVTGQMIKGEFDDE  142 (248)
Q Consensus        71 ~g~~~~a~~~~~~m~~~----~~-~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~---~~~~~~~~~~l~~~~~~~  142 (248)
                      .|++++|.+.+++..+.    +. +....++..+-..|.+.|++++|...+++..+...   .|........+...+...
T Consensus       237 ~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~  316 (383)
T 3ulq_A          237 QSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSG  316 (383)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSS
T ss_pred             CCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCC
Confidence            99999999999988762    33 33467899999999999999999999998754321   122222223344446666


Q ss_pred             ch---HHHHHHHHHHHHhcCCCCC-HHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          143 SN---WQMVEYVFDKLNCEGYGLG-MRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       143 ~~---~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                      ++   ++.+..+++.   .+..|+ ...+..+-..|...|++++|.+.+++..+
T Consensus       317 ~~~~~~~~al~~~~~---~~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  367 (383)
T 3ulq_A          317 PDEEAIQGFFDFLES---KMLYADLEDFAIDVAKYYHERKNFQKASAYFLKVEQ  367 (383)
T ss_dssp             CCHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHH---CcCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            66   5555555554   344443 34677788999999999999999998764

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.84  E-value=4e-07  Score=69.86  Aligned_cols=167  Identities=9%  Similarity=0.038  Sum_probs=122.8

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHHC----CCCc-CHh
Q 039342           25 SFNAVIEAFRQGGRFEEAIKAYVEMEKV----RCDPN-ERTLEAVLSVYCFAGLVDESKEQFQEIKSS----GILP-SVM   94 (248)
Q Consensus        25 ~y~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p~-~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~~p-~~~   94 (248)
                      .|+.....|...|++++|.+.|.+..+.    |-+++ ..+|+.+-.+|.+.|++++|...+++..+.    |-.+ -..
T Consensus        39 ~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~  118 (292)
T 1qqe_A           39 LCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGAN  118 (292)
T ss_dssp             HHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            5677777888999999999999887443    32222 568899999999999999999999887643    2111 145


Q ss_pred             hHHHHHHHHHhc-CCHHHHHHHHHHHHHCC----CCch-HHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCH----
Q 039342           95 CYCMLLAVYAKS-NRWDDAYGLLDEMHTNR----ISNI-HQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGM----  164 (248)
Q Consensus        95 ~~~~li~~~~~~-~~~~~a~~~~~~m~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~----  164 (248)
                      +++.+-..|... |++++|+..|++..+..    ..+. ..++..+-. .+...|+++.|...++...+.......    
T Consensus       119 ~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~-~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  197 (292)
T 1qqe_A          119 FKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCAD-LKALDGQYIEASDIYSKLIKSSMGNRLSQWS  197 (292)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HHHHTTCHHHHHHHHHHHHHTTSSCTTTGGG
T ss_pred             HHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHH-HHHHhCCHHHHHHHHHHHHHHHhcCCcccHH
Confidence            788889999996 99999999999876432    1111 123333333 367788999999999998876433221    


Q ss_pred             --HHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          165 --RFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       165 --~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                        ..|..+..++...|++++|...|++..+
T Consensus       198 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  227 (292)
T 1qqe_A          198 LKDYFLKKGLCQLAATDAVAAARTLQEGQS  227 (292)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHGGGC
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence              2567788889999999999999998764

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.83  E-value=7.2e-07  Score=65.68  Aligned_cols=100  Identities=10%  Similarity=0.100  Sum_probs=66.6

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-C-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCH----hh
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCD-P-NERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSV----MC   95 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~-p-~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~----~~   95 (248)
                      +...+..+...+.+.|++++|...|+++.+..-. | ....+..+..+|.+.|++++|...|+++.+..  |+.    ..
T Consensus         3 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~--P~~~~~~~a   80 (225)
T 2yhc_A            3 PPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLN--PTHPNIDYV   80 (225)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCTTHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHC--cCCCcHHHH
Confidence            3455566667788889999999999988765311 1 13567777888888999999999998887642  322    13


Q ss_pred             HHHHHHHHHh------------------cCCHHHHHHHHHHHHHCC
Q 039342           96 YCMLLAVYAK------------------SNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        96 ~~~li~~~~~------------------~~~~~~a~~~~~~m~~~~  123 (248)
                      +-.+-.++..                  .|+.++|...|++..+..
T Consensus        81 ~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~  126 (225)
T 2yhc_A           81 MYMRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGY  126 (225)
T ss_dssp             HHHHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHC
Confidence            3333333332                  467778888888776543

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=98.83  E-value=4.7e-07  Score=81.56  Aligned_cols=158  Identities=17%  Similarity=0.215  Sum_probs=114.5

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|.++.++.      -+..+|..+-.++.+.|++++|.+.|.+.      -|...|..++.+|.+.|++++|.+.+
T Consensus      1090 ~nldrAiE~Aerv------n~p~vWsqLAKAql~~G~~kEAIdsYiKA------dD~say~eVa~~~~~lGkyEEAIeyL 1157 (1630)
T 1xi4_A         1090 GNLDRAYEFAERC------NEPAVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAANTSGNWEELVKYL 1157 (1630)
T ss_pred             hhHHHHHHHHHhc------CCHHHHHHHHHHHHhCCCHHHHHHHHHhc------CChHHHHHHHHHHHHcCCHHHHHHHH
Confidence            3445555554433      24677888888888888888888888552      56677888888888888888888888


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCC
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYG  161 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~  161 (248)
                      ...++..  +++...+.+..+|++.+++++...+.+       .++...+.. +..++...|++++|..+|...      
T Consensus      1158 ~mArk~~--~e~~Idt~LafaYAKl~rleele~fI~-------~~n~ad~~~-iGd~le~eg~YeeA~~~Y~kA------ 1221 (1630)
T 1xi4_A         1158 QMARKKA--RESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQ-VGDRCYDEKMYDAAKLLYNNV------ 1221 (1630)
T ss_pred             HHHHhhc--ccccccHHHHHHHHhhcCHHHHHHHHh-------CCCHHHHHH-HHHHHHhcCCHHHHHHHHHhh------
Confidence            8766543  444444558888888888876444431       234444554 334477788999999999874      


Q ss_pred             CCHHHHHHHHHHHHhcCchHHHHHHHHHH
Q 039342          162 LGMRFYNALLEALWCLGLRERAARVLDEA  190 (248)
Q Consensus       162 p~~~~~~~li~~~~~~g~~~~a~~~~~~m  190 (248)
                         ..|..+...+++.|+++.|.+.+++.
T Consensus      1222 ---~ny~rLA~tLvkLge~q~AIEaarKA 1247 (1630)
T 1xi4_A         1222 ---SNFGRLASTLVHLGEYQAAVDGARKA 1247 (1630)
T ss_pred             ---hHHHHHHHHHHHhCCHHHHHHHHHHh
Confidence               47999999999999999999998865

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=98.83  E-value=3.5e-07  Score=72.80  Aligned_cols=188  Identities=10%  Similarity=0.009  Sum_probs=133.9

Q ss_pred             CchHHHHHHHHHHHHc----C-CCC-CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCC-CCHHHHHHHHHHHHh
Q 039342            2 GLYKECQAILSRMSES----G-VAR-NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKV----RCD-PNERTLEAVLSVYCF   70 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~----g-~~~-~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~----~~~-p~~~t~~~ll~~~~~   70 (248)
                      |+++.|...+.+..+.    + ..+ ...+++.+-..|...|++++|.+.+++..+.    +-. ....++..+-.+|..
T Consensus       155 ~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~  234 (378)
T 3q15_A          155 KQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDR  234 (378)
T ss_dssp             TCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence            7788888888876542    1 111 3568888999999999999999999887542    111 123567788889999


Q ss_pred             cCChhHHHHHHHHHHHC----CCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC---chHHhHHHHhcccccccc
Q 039342           71 AGLVDESKEQFQEIKSS----GILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRIS---NIHQVTGQMIKGEFDDES  143 (248)
Q Consensus        71 ~g~~~~a~~~~~~m~~~----~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~---~~~~~~~~~l~~~~~~~~  143 (248)
                      .|++++|.+.|++..+.    +-+....++..+-..|.+.|++++|...+++..+....   |........+...+...+
T Consensus       235 ~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~  314 (378)
T 3q15_A          235 SGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETV  314 (378)
T ss_dssp             HTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSC
T ss_pred             CCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCC
Confidence            99999999999998761    22224678889999999999999999999998764321   222222234444456666


Q ss_pred             h---HHHHHHHHHHHHhcCCCCC-HHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          144 N---WQMVEYVFDKLNCEGYGLG-MRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       144 ~---~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                      +   ++.+...++.   .+..|+ ...+..+-..|...|++++|.+.|++..+
T Consensus       315 ~~~~~~~al~~~~~---~~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          315 DERKIHDLLSYFEK---KNLHAYIEACARSAAAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             CHHHHHHHHHHHHH---TTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHh---CCChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            6   5555555554   443333 34566788899999999999999998653

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=98.81  E-value=8.1e-07  Score=68.66  Aligned_cols=188  Identities=10%  Similarity=0.028  Sum_probs=134.1

Q ss_pred             CchHHHHHHHHHHHHc------CCCCCH----HhHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCCC-CHHHHHHHHH
Q 039342            2 GLYKECQAILSRMSES------GVARNS----DSFNAVIEAFRQGGRFEEAIKAYVEMEKV----RCDP-NERTLEAVLS   66 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~------g~~~~~----~~y~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p-~~~t~~~ll~   66 (248)
                      |++++|.+++++..+.      +..++.    ..|+.....|...|++++|.+.|.+..+.    +-.+ -..+|+.+..
T Consensus         5 ~~~~eA~~~~~~a~k~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~   84 (307)
T 2ifu_A            5 QKISEAHEHIAKAEKYLKTSFMKWKPDYDSAASEYAKAAVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGM   84 (307)
T ss_dssp             HHHHHHHHHHHHHHHHHCCCSSSCSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHccccccCCCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            6788999999877642      112442    36888888899999999999999887443    2111 1457888899


Q ss_pred             HHHhcCChhHHHHHHHHHHHC----CCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHC----CCCch-HHhHHHHhc
Q 039342           67 VYCFAGLVDESKEQFQEIKSS----GILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTN----RISNI-HQVTGQMIK  136 (248)
Q Consensus        67 ~~~~~g~~~~a~~~~~~m~~~----~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~~~-~~~~~~~l~  136 (248)
                      .|.+.|++++|...|++..+.    |-.+ ...+++.+-..|.. |++++|+..|++..+.    +..+. ..++..+- 
T Consensus        85 ~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg-  162 (307)
T 2ifu_A           85 MLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKAS-  162 (307)
T ss_dssp             HHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH-
T ss_pred             HHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHH-
Confidence            999999999999999887542    2111 24678888888988 9999999999987543    21111 22333333 


Q ss_pred             ccccccchHHHHHHHHHHHHhc----CCCCC-HHHHHHHHHHHHhcCchHHHHHHHHHHH
Q 039342          137 GEFDDESNWQMVEYVFDKLNCE----GYGLG-MRFYNALLEALWCLGLRERAARVLDEAT  191 (248)
Q Consensus       137 ~~~~~~~~~~~a~~~~~~m~~~----~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~  191 (248)
                      ..+...|+++.|...+++..+.    +..+. ...+..+...+...|++++|...|++..
T Consensus       163 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~al  222 (307)
T 2ifu_A          163 RLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRESY  222 (307)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            3367789999999999887653    22222 2356677778888899999999999987

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=98.78  E-value=1.5e-06  Score=63.35  Aligned_cols=179  Identities=10%  Similarity=-0.005  Sum_probs=130.1

Q ss_pred             HHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC----ChhHHHHH
Q 039342            5 KECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAG----LVDESKEQ   80 (248)
Q Consensus         5 ~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g----~~~~a~~~   80 (248)
                      .+|.+.|.+..+.|   ++..+..+-..|...+++++|.+.|++..+.|   +...+..+-..|.. +    ++++|.+.
T Consensus         3 ~eA~~~~~~aa~~g---~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~   75 (212)
T 3rjv_A            3 TEPGSQYQQQAEAG---DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQL   75 (212)
T ss_dssp             -CTTHHHHHHHHTT---CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHH
T ss_pred             chHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHH
Confidence            35778888887753   67788888888888999999999999998765   45677777777777 6    89999999


Q ss_pred             HHHHHHCCCCcCHhhHHHHHHHHHh----cCCHHHHHHHHHHHHHCCCCc-hHHhHHHHhcc---cccccchHHHHHHHH
Q 039342           81 FQEIKSSGILPSVMCYCMLLAVYAK----SNRWDDAYGLLDEMHTNRISN-IHQVTGQMIKG---EFDDESNWQMVEYVF  152 (248)
Q Consensus        81 ~~~m~~~~~~p~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~~-~~~~~~~~l~~---~~~~~~~~~~a~~~~  152 (248)
                      |++..+.|   +...+..|-..|..    .+++++|+..|++..+.+... ....+..+-..   .....++++.|...|
T Consensus        76 ~~~A~~~g---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~  152 (212)
T 3rjv_A           76 AEKAVEAG---SKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYF  152 (212)
T ss_dssp             HHHHHHTT---CHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHH
T ss_pred             HHHHHHCC---CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHH
Confidence            99988765   56677777777776    789999999999988777421 12222222111   122367889999999


Q ss_pred             HHHHhcCCCCCHHHHHHHHHHHHhc-C-----chHHHHHHHHHHHHCCC
Q 039342          153 DKLNCEGYGLGMRFYNALLEALWCL-G-----LRERAARVLDEATKRGL  195 (248)
Q Consensus       153 ~~m~~~~~~p~~~~~~~li~~~~~~-g-----~~~~a~~~~~~m~~~g~  195 (248)
                      +...+.+  ++...+..+-..|... |     +.++|...|+...+.|.
T Consensus       153 ~~A~~~~--~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g~  199 (212)
T 3rjv_A          153 KGSSSLS--RTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEGF  199 (212)
T ss_dssp             HHHHHTS--CTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHcC--CCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcCC
Confidence            9887762  2334566666666653 3     88999999988777663

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.78  E-value=2.7e-07  Score=70.86  Aligned_cols=188  Identities=7%  Similarity=0.033  Sum_probs=129.5

Q ss_pred             CchHHHHHHHHHHHHc----CCCCC-HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-CC----HHHHHHHHHHHHhc
Q 039342            2 GLYKECQAILSRMSES----GVARN-SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCD-PN----ERTLEAVLSVYCFA   71 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~----g~~~~-~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~-p~----~~t~~~ll~~~~~~   71 (248)
                      |++++|.+.|.+..+.    |-+++ ..+|+.+-..|.+.|++++|...+++..+.... .+    ..+++.+-..|...
T Consensus        51 g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~  130 (292)
T 1qqe_A           51 KELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILEND  130 (292)
T ss_dssp             TCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh
Confidence            7888888888876542    32222 568999999999999999999999887543111 11    45788889999996


Q ss_pred             -CChhHHHHHHHHHHHC----CCCcC-HhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHH------hHHHHhcccc
Q 039342           72 -GLVDESKEQFQEIKSS----GILPS-VMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQ------VTGQMIKGEF  139 (248)
Q Consensus        72 -g~~~~a~~~~~~m~~~----~~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~------~~~~~l~~~~  139 (248)
                       |++++|...|++..+.    +-.+. ..+++.+-..+.+.|++++|+..|++..+........      .+..+... +
T Consensus       131 lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~-~  209 (292)
T 1qqe_A          131 LHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLC-Q  209 (292)
T ss_dssp             TCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHH-H
T ss_pred             hcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHH-H
Confidence             9999999999987653    11111 3578899999999999999999999998765332211      23333222 5


Q ss_pred             cccchHHHHHHHHHHHHhcCCC-CC---HHHHHHHHHHHH--hcCchHHHHHHHHHH
Q 039342          140 DDESNWQMVEYVFDKLNCEGYG-LG---MRFYNALLEALW--CLGLRERAARVLDEA  190 (248)
Q Consensus       140 ~~~~~~~~a~~~~~~m~~~~~~-p~---~~~~~~li~~~~--~~g~~~~a~~~~~~m  190 (248)
                      ...|+++.|...++...+.... ++   ...+..++.++.  ..+++++|.+.|+.+
T Consensus       210 ~~~g~~~~A~~~~~~al~l~p~~~~~~~~~~l~~l~~~~~~~~~~~~~~A~~~~~~~  266 (292)
T 1qqe_A          210 LAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNF  266 (292)
T ss_dssp             HHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTS
T ss_pred             HHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHhccC
Confidence            5678899999999887653211 11   123444556664  345677777777654

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=98.77  E-value=3.7e-07  Score=76.66  Aligned_cols=155  Identities=9%  Similarity=-0.061  Sum_probs=110.2

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|.+.|++..+... -+...|..+-..+.+.|++++|.+.+++..+.. +-+...+..+-.+|.+.|++++|.+.
T Consensus         2 ~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~   79 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHRP-QDFVAWLMLADAELGMGDTTAGEMAVQRGLALH-PGHPEAVARLGRVRWTQQRHAEAAVL   79 (568)
T ss_dssp             --------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTS-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            4789999999999876432 357889999999999999999999999998764 34678899999999999999999999


Q ss_pred             HHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHH-hHHHHhccccccc---chHHHHHHHHHHHH
Q 039342           81 FQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQ-VTGQMIKGEFDDE---SNWQMVEYVFDKLN  156 (248)
Q Consensus        81 ~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~-~~~~~l~~~~~~~---~~~~~a~~~~~~m~  156 (248)
                      +++..+.. +.+...+..+-..|.+.|++++|.+.|++..+..  |+.. .+..+... +...   ++++.|...+++..
T Consensus        80 ~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~-~~~~~~~g~~~~A~~~~~~al  155 (568)
T 2vsy_A           80 LQQASDAA-PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLL--PEEPYITAQLLNW-RRRLCDWRALDVLSAQVRAAV  155 (568)
T ss_dssp             HHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHH-HHHTTCCTTHHHHHHHHHHHH
T ss_pred             HHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHH-HHHhhccccHHHHHHHHHHHH
Confidence            99988753 2257889999999999999999999999988764  4333 33333333 5556   88999999999888


Q ss_pred             hcCCC
Q 039342          157 CEGYG  161 (248)
Q Consensus       157 ~~~~~  161 (248)
                      +.+..
T Consensus       156 ~~~p~  160 (568)
T 2vsy_A          156 AQGVG  160 (568)
T ss_dssp             HHTCC
T ss_pred             hcCCc
Confidence            76543

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.76  E-value=6.3e-07  Score=65.18  Aligned_cols=165  Identities=12%  Similarity=0.008  Sum_probs=107.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC-HHHHHH----------------HHHHHHhcCChhHHHHHHHHHHHCC
Q 039342           26 FNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN-ERTLEA----------------VLSVYCFAGLVDESKEQFQEIKSSG   88 (248)
Q Consensus        26 y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~----------------ll~~~~~~g~~~~a~~~~~~m~~~~   88 (248)
                      +-..-..+.+.|++++|...|++..+..  |+ ...|..                +-.+|.+.|++++|...|++..+..
T Consensus         7 ~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~   84 (208)
T 3urz_A            7 MLQKVSAAIEAGQNGQAVSYFRQTIALN--IDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQKA   84 (208)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--HHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC
Confidence            3334455667888888888888876542  33 344555                7888999999999999999988753


Q ss_pred             CCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHh-HHHHhcccccc-cchHHHHHHHHHHHHhcCCCCCHHH
Q 039342           89 ILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQV-TGQMIKGEFDD-ESNWQMVEYVFDKLNCEGYGLGMRF  166 (248)
Q Consensus        89 ~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~-~~~~l~~~~~~-~~~~~~a~~~~~~m~~~~~~p~~~~  166 (248)
                       +-+...+..+-..+...|++++|+..|++..+..  |+... +..+-..++.. ....+.+...+....  ...|....
T Consensus        85 -p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~lg~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~a  159 (208)
T 3urz_A           85 -PNNVDCLEACAEMQVCRGQEKDALRMYEKILQLE--ADNLAANIFLGNYYYLTAEQEKKKLETDYKKLS--SPTKMQYA  159 (208)
T ss_dssp             -TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHHHHHHHHHHC-----CCCHHHHH
T ss_pred             -CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHh--CCCchhHH
Confidence             2267888999999999999999999999988764  44433 32222221111 123344444444432  22232233


Q ss_pred             HHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCc
Q 039342          167 YNALLEALWCLGLRERAARVLDEATKRGLFPEL  199 (248)
Q Consensus       167 ~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  199 (248)
                      +...-.++...|++++|...|++..+  +.|+.
T Consensus       160 ~~~~g~~~~~~~~~~~A~~~~~~al~--l~P~~  190 (208)
T 3urz_A          160 RYRDGLSKLFTTRYEKARNSLQKVIL--RFPST  190 (208)
T ss_dssp             HHHHHHHHHHHHTHHHHHHHHHHHTT--TSCCH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHH--hCCCH
Confidence            33345556668899999999999875  36764

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=98.76  E-value=2.3e-06  Score=69.78  Aligned_cols=220  Identities=10%  Similarity=-0.037  Sum_probs=140.4

Q ss_pred             CchHHHHHHHHHHHHcCCCC-CHHhHHHHHHH---HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----cCC
Q 039342            2 GLYKECQAILSRMSESGVAR-NSDSFNAVIEA---FRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCF----AGL   73 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~-~~~~y~~li~~---~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~----~g~   73 (248)
                      +++++|.+.|++..+..  | ++..+..+...   +...++.++|++.+++..+.+ +.+..++..+...+..    .|+
T Consensus       152 ~~y~~A~~~~~kal~~~--p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~-p~~~~~~~~l~~~~~~~~~~~~~  228 (472)
T 4g1t_A          152 NQNERAKVCFEKALEKK--PKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLN-PDNQYLKVLLALKLHKMREEGEE  228 (472)
T ss_dssp             THHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHC-SSCHHHHHHHHHHHHHCC-----
T ss_pred             ccHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcC-CcchHHHHHHHHHHHHHHhhhhH
Confidence            46889999999987643  4 34455444444   445677888998888876653 3455666665555544    467


Q ss_pred             hhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhccccc-------------
Q 039342           74 VDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFD-------------  140 (248)
Q Consensus        74 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~-------------  140 (248)
                      .++|.+++++..+.. +.+..++..+-..|...|++++|...+++..+..  |+.......+...+.             
T Consensus       229 ~~~a~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~lg~~y~~~~~~~~~~~~~~  305 (472)
T 4g1t_A          229 EGEGEKLVEEALEKA-PGVTDVLRSAAKFYRRKDEPDKAIELLKKALEYI--PNNAYLHCQIGCCYRAKVFQVMNLRENG  305 (472)
T ss_dssp             -CHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHHHHHHHHC----
T ss_pred             HHHHHHHHHHHHHhC-ccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHhC--CChHHHHHHHHHHHHHHHHHhhhHHHHH
Confidence            889999999887653 2367788999999999999999999999987654  443322221111111             


Q ss_pred             ------ccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhcc
Q 039342          141 ------DESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRM  214 (248)
Q Consensus       141 ------~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~  214 (248)
                            ..+.++.+...++...+.... +..++..+-..+...|++++|.+.|++..+....|...  ..+...+..-.+
T Consensus       306 ~~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~~~~~~~~--~~~~~~~~~~~~  382 (472)
T 4g1t_A          306 MYGKRKLLELIGHAVAHLKKADEANDN-LFRVCSILASLHALADQYEEAEYYFQKEFSKELTPVAK--QLLHLRYGNFQL  382 (472)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHCTT-TCCCHHHHHHHHHHTTCHHHHHHHHHHHHHSCCCHHHH--HHHHHHHHHHHH
T ss_pred             HHHHHHHHhhHHHHHHHHHHHhhcCCc-hhhhhhhHHHHHHHhccHHHHHHHHHHHHhcCCCChHH--HHHHHHHHHHHH
Confidence                  123456677777776665432 45567888899999999999999999988764333221  111111111123


Q ss_pred             ccchHHHHHHHHHHHH
Q 039342          215 WEGGAYTAISVWLNKM  230 (248)
Q Consensus       215 ~~~g~~~~~~~~~~~m  230 (248)
                      ...|+.++|...+++-
T Consensus       383 ~~~~~~~~Ai~~y~ka  398 (472)
T 4g1t_A          383 YQMKCEDKAIHHFIEG  398 (472)
T ss_dssp             HTSSCHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHH
Confidence            3567777777666554

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.75  E-value=1.3e-06  Score=65.59  Aligned_cols=155  Identities=11%  Similarity=0.099  Sum_probs=114.8

Q ss_pred             CCchHHHHHHHHHHHHcCCCCC---HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-C-CCHHHHHHHHHHHHh-----
Q 039342            1 GGLYKECQAILSRMSESGVARN---SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRC-D-PNERTLEAVLSVYCF-----   70 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~---~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~-~-p~~~t~~~ll~~~~~-----   70 (248)
                      .|++++|.+.|+++.+.... +   ...+..+-.++.+.|++++|...|++..+..- . .....+..+-.++.+     
T Consensus        28 ~g~~~~A~~~~~~~l~~~p~-~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~  106 (261)
T 3qky_A           28 QGKYDRAIEYFKAVFTYGRT-HEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAEYERAMCYYKLSPPY  106 (261)
T ss_dssp             TTCHHHHHHHHHHHGGGCSC-STTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCCCT
T ss_pred             hCCHHHHHHHHHHHHHhCCC-CcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHHhcccc
Confidence            38999999999999875421 2   67888889999999999999999999977531 1 224567777788888     


Q ss_pred             ---cCChhHHHHHHHHHHHCCCCcC-HhhH-----------------HHHHHHHHhcCCHHHHHHHHHHHHHCCCC-c-h
Q 039342           71 ---AGLVDESKEQFQEIKSSGILPS-VMCY-----------------CMLLAVYAKSNRWDDAYGLLDEMHTNRIS-N-I  127 (248)
Q Consensus        71 ---~g~~~~a~~~~~~m~~~~~~p~-~~~~-----------------~~li~~~~~~~~~~~a~~~~~~m~~~~~~-~-~  127 (248)
                         .|++++|...|++..+..  |+ ....                 ..+-..|.+.|++++|+..|++..+.... + .
T Consensus       107 ~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~  184 (261)
T 3qky_A          107 ELDQTDTRKAIEAFQLFIDRY--PNHELVDDATQKIRELRAKLARKQYEAARLYERRELYEAAAVTYEAVFDAYPDTPWA  184 (261)
T ss_dssp             TSCCHHHHHHHHHHHHHHHHC--TTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTH
T ss_pred             cccchhHHHHHHHHHHHHHHC--cCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCCchH
Confidence               999999999999998752  32 2333                 45577888999999999999999875422 1 1


Q ss_pred             HHhHHHHhccccc----------ccchHHHHHHHHHHHHhcC
Q 039342          128 HQVTGQMIKGEFD----------DESNWQMVEYVFDKLNCEG  159 (248)
Q Consensus       128 ~~~~~~~l~~~~~----------~~~~~~~a~~~~~~m~~~~  159 (248)
                      ...+..+... +.          ..++++.|...++...+..
T Consensus       185 ~~a~~~l~~~-~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~~  225 (261)
T 3qky_A          185 DDALVGAMRA-YIAYAEQSVRARQPERYRRAVELYERLLQIF  225 (261)
T ss_dssp             HHHHHHHHHH-HHHHHHTSCGGGHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHH-HHHhcccchhhcccchHHHHHHHHHHHHHHC
Confidence            2233333332 32          2388999999999988764

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.75  E-value=3.3e-07  Score=70.19  Aligned_cols=128  Identities=12%  Similarity=-0.011  Sum_probs=51.7

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhccc
Q 039342           60 TLEAVLSVYCFAGLVDESKEQFQEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGE  138 (248)
Q Consensus        60 t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~  138 (248)
                      .+..+-..+.+.|++++|...|++..+..  | +...+..+...+.+.|++++|...+++.....  |+...........
T Consensus       119 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~--p~~~~~~~~~~~~  194 (287)
T 3qou_A          119 LXAQQAMQLMQESNYTDALPLLXDAWQLS--NQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQD--QDTRYQGLVAQIE  194 (287)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHT--TSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGG--CSHHHHHHHHHHH
T ss_pred             hHHHHHHHHHhCCCHHHHHHHHHHHHHhC--CcchhHHHHHHHHHHHCCCHHHHHHHHHhCchhh--cchHHHHHHHHHH
Confidence            33344444444455555555544444321  2 33344444444444555555555444443222  2221111111111


Q ss_pred             ccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          139 FDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       139 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                      +...+..+.+...++....... .+...+..+-..+...|++++|...|.+..+
T Consensus       195 l~~~~~~~~a~~~l~~al~~~P-~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~  247 (287)
T 3qou_A          195 LLXQAADTPEIQQLQQQVAENP-EDAALATQLALQLHQVGRNEEALELLFGHLR  247 (287)
T ss_dssp             HHHHHTSCHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHhhcccCccHHHHHHHHhcCC-ccHHHHHHHHHHHHHcccHHHHHHHHHHHHh
Confidence            2222233333444444333321 1344444444555555555555555555443

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=98.75  E-value=1.9e-06  Score=73.60  Aligned_cols=225  Identities=8%  Similarity=0.058  Sum_probs=164.1

Q ss_pred             HHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHH-HHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHH
Q 039342            5 KECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAI-KAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQE   83 (248)
Q Consensus         5 ~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~-~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~   83 (248)
                      +++..+|++.... .+-+...|-.....+...|+.++|. ++|++... .++.+...|-..+...-+.|+++.|.++|+.
T Consensus       326 ~Rv~~~Ye~aL~~-~p~~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~-~~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek  403 (679)
T 4e6h_A          326 ARMTYVYMQAAQH-VCFAPEIWFNMANYQGEKNTDSTVITKYLKLGQQ-CIPNSAVLAFSLSEQYELNTKIPEIETTILS  403 (679)
T ss_dssp             HHHHHHHHHHHHH-TTTCHHHHHHHHHHHHHHSCCTTHHHHHHHHHHH-HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH-cCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHH-hCCCCHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence            3455667766543 2346778888888888899999996 99999875 3456666777888889999999999999999


Q ss_pred             HHHCC---------CCcC------------HhhHHHHHHHHHhcCCHHHHHHHHHHHHHC-CC-CchHHhHHHHhccccc
Q 039342           84 IKSSG---------ILPS------------VMCYCMLLAVYAKSNRWDDAYGLLDEMHTN-RI-SNIHQVTGQMIKGEFD  140 (248)
Q Consensus        84 m~~~~---------~~p~------------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~-~~~~~~~~~~l~~~~~  140 (248)
                      +.+..         -.|+            ..+|...+....+.|..+.|..+|.+..+. +. .+...+....+.  +.
T Consensus       404 ~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE--~~  481 (679)
T 4e6h_A          404 CIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCRRLKKLVTPDIYLENAYIE--YH  481 (679)
T ss_dssp             HHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHH--HT
T ss_pred             HHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHH--HH
Confidence            87631         0132            346888888888999999999999999876 32 222223233333  33


Q ss_pred             ccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHH
Q 039342          141 DESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAY  220 (248)
Q Consensus       141 ~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~  220 (248)
                      ..++.+.|..+|+...+. +.-+...+...++.....|+.+.|..+|++.....-.++   ....+|...+.--.+.|..
T Consensus       482 ~~~d~e~Ar~ife~~Lk~-~p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~~~~~~---~~~~lw~~~~~fE~~~G~~  557 (679)
T 4e6h_A          482 ISKDTKTACKVLELGLKY-FATDGEYINKYLDFLIYVNEESQVKSLFESSIDKISDSH---LLKMIFQKVIFFESKVGSL  557 (679)
T ss_dssp             TTSCCHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTTSSSTT---HHHHHHHHHHHHHHHTCCS
T ss_pred             hCCCHHHHHHHHHHHHHH-CCCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCHH---HHHHHHHHHHHHHHHcCCH
Confidence            345679999999988876 333566677888888889999999999999876532221   2445566655667788999


Q ss_pred             HHHHHHHHHHHHHHHcCCC
Q 039342          221 TAISVWLNKMYEMFMMGED  239 (248)
Q Consensus       221 ~~~~~~~~~m~~~~~~~~~  239 (248)
                      +.+..+.+++.+.  .|+.
T Consensus       558 ~~~~~v~~R~~~~--~P~~  574 (679)
T 4e6h_A          558 NSVRTLEKRFFEK--FPEV  574 (679)
T ss_dssp             HHHHHHHHHHHHH--STTC
T ss_pred             HHHHHHHHHHHHh--CCCC
Confidence            9999999999887  4543

>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=98.71  E-value=1.8e-06  Score=62.64  Aligned_cols=88  Identities=16%  Similarity=0.175  Sum_probs=44.3

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCC
Q 039342           29 VIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNR  108 (248)
Q Consensus        29 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~  108 (248)
                      +-..+...|++++|.+.|++.    +.|+...|..+..+|.+.|++++|.+.|++..+.. +.+...|..+-..|...|+
T Consensus        12 ~g~~~~~~~~~~~A~~~~~~a----~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~   86 (213)
T 1hh8_A           12 EGVLAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEK   86 (213)
T ss_dssp             HHHHHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHhCCHHHHHHHHHHH----cCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHccc
Confidence            334444555555555555443    23445555555555555555555555555544332 1234445555555555555


Q ss_pred             HHHHHHHHHHHHH
Q 039342          109 WDDAYGLLDEMHT  121 (248)
Q Consensus       109 ~~~a~~~~~~m~~  121 (248)
                      +++|+..|++..+
T Consensus        87 ~~~A~~~~~~al~   99 (213)
T 1hh8_A           87 YDLAIKDLKEALI   99 (213)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            5555555555544

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=98.71  E-value=2.4e-07  Score=79.59  Aligned_cols=170  Identities=9%  Similarity=-0.054  Sum_probs=130.7

Q ss_pred             CCchHHHHHHHHHHH--------HcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC
Q 039342            1 GGLYKECQAILSRMS--------ESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAG   72 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~--------~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g   72 (248)
                      .|++++|++.|++..        +.. +.+...|..+-..+.+.|++++|.+.|++..+.+ +-+...|..+-.+|.+.|
T Consensus       404 ~~~~~~A~~~~~~al~~~~~~~~~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g  481 (681)
T 2pzi_A          404 LSQPVQTLDSLRAARHGALDADGVDF-SESVELPLMEVRALLDLGDVAKATRKLDDLAERV-GWRWRLVWYRAVAELLTG  481 (681)
T ss_dssp             TCCHHHHHHHHHHHHTC-------CC-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHT
T ss_pred             ccCHHHHHHHHHHhhhhccccccccc-ccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccC-cchHHHHHHHHHHHHHcC
Confidence            378899999999987        322 3467889999999999999999999999997754 356788899999999999


Q ss_pred             ChhHHHHHHHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHH
Q 039342           73 LVDESKEQFQEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYV  151 (248)
Q Consensus        73 ~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  151 (248)
                      ++++|.+.|++..+..  | +...|..+-.+|.+.|++++ +..|++..+..  |+.......+...+...|++++|...
T Consensus       482 ~~~~A~~~~~~al~l~--P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~--P~~~~a~~~lg~~~~~~g~~~~A~~~  556 (681)
T 2pzi_A          482 DYDSATKHFTEVLDTF--PGELAPKLALAATAELAGNTDE-HKFYQTVWSTN--DGVISAAFGLARARSAEGDRVGAVRT  556 (681)
T ss_dssp             CHHHHHHHHHHHHHHS--TTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhC--CchHHHHHHHHHHHHHcCCHHHHHHH
Confidence            9999999999988753  4 56788999999999999999 99999988765  44433333333337778899999999


Q ss_pred             HHHHHhcCCCCC-HHHHHHHHHHHHhcCc
Q 039342          152 FDKLNCEGYGLG-MRFYNALLEALWCLGL  179 (248)
Q Consensus       152 ~~~m~~~~~~p~-~~~~~~li~~~~~~g~  179 (248)
                      |++..+.+  |+ ...+..+..++...++
T Consensus       557 ~~~al~l~--P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          557 LDEVPPTS--RHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             HHTSCTTS--TTHHHHHHHHHHHTC----
T ss_pred             HHhhcccC--cccHHHHHHHHHHHHccCC
Confidence            98776543  43 5566666677655444

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=98.70  E-value=5.9e-07  Score=75.45  Aligned_cols=153  Identities=10%  Similarity=-0.069  Sum_probs=110.3

Q ss_pred             cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHH
Q 039342           36 GGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGL  115 (248)
Q Consensus        36 ~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~  115 (248)
                      .|++++|.+.+++..+.. +-+...|..+-..|.+.|++++|.+.|++..+.. +.+...+..+-..|...|++++|...
T Consensus         2 ~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~   79 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHR-PQDFVAWLMLADAELGMGDTTAGEMAVQRGLALH-PGHPEAVARLGRVRWTQQRHAEAAVL   79 (568)
T ss_dssp             --------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTS-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            478899999999886543 3457889999999999999999999999998763 22578899999999999999999999


Q ss_pred             HHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhc---CchHHHHHHHHHHHH
Q 039342          116 LDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCL---GLRERAARVLDEATK  192 (248)
Q Consensus       116 ~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~---g~~~~a~~~~~~m~~  192 (248)
                      +++..+..  |+.......+...+...|++++|...+++..+.... +...+..+...+...   |+.++|.+.+++..+
T Consensus        80 ~~~al~~~--p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~  156 (568)
T 2vsy_A           80 LQQASDAA--PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPE-EPYITAQLLNWRRRLCDWRALDVLSAQVRAAVA  156 (568)
T ss_dssp             HHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHH
T ss_pred             HHHHHhcC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhhccccHHHHHHHHHHHHh
Confidence            99988764  444333333334477889999999999998876533 577888899999999   999999999999876


Q ss_pred             C
Q 039342          193 R  193 (248)
Q Consensus       193 ~  193 (248)
                      .
T Consensus       157 ~  157 (568)
T 2vsy_A          157 Q  157 (568)
T ss_dssp             H
T ss_pred             c
Confidence            4

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=98.70  E-value=2e-07  Score=65.94  Aligned_cols=161  Identities=7%  Similarity=0.009  Sum_probs=88.9

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHH-H
Q 039342           25 SFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAV-Y  103 (248)
Q Consensus        25 ~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~-~  103 (248)
                      .+...-..+.+.|++++|...|++..+.. +-+...+..+-..+.+.|++++|...++...+.  .|+...+...... +
T Consensus         8 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~--~p~~~~~~~~~~~~~   84 (176)
T 2r5s_A            8 QLLKQVSELLQQGEHAQALNVIQTLSDEL-QSRGDVKLAKADCLLETKQFELAQELLATIPLE--YQDNSYKSLIAKLEL   84 (176)
T ss_dssp             THHHHHHHHHHTTCHHHHHHHHHTSCHHH-HTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGG--GCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhc--cCChHHHHHHHHHHH
Confidence            34455566777778888887777765432 335566777777777788888888777776543  2333222221111 1


Q ss_pred             HhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCC-CHHHHHHHHHHHHhcCchHH
Q 039342          104 AKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGL-GMRFYNALLEALWCLGLRER  182 (248)
Q Consensus       104 ~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~  182 (248)
                      ...+...+|...+++..+..  |+.......+...+...|+++.|...++...+....+ +...+..+...+...|+.++
T Consensus        85 ~~~~~~~~a~~~~~~al~~~--P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~  162 (176)
T 2r5s_A           85 HQQAAESPELKRLEQELAAN--PDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNA  162 (176)
T ss_dssp             HHHHTSCHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCH
T ss_pred             HhhcccchHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCc
Confidence            12122233555666555432  4333222222223555666666666666666554332 24456666666666677666


Q ss_pred             HHHHHHHH
Q 039342          183 AARVLDEA  190 (248)
Q Consensus       183 a~~~~~~m  190 (248)
                      |...|++.
T Consensus       163 A~~~y~~a  170 (176)
T 2r5s_A          163 IASKYRRQ  170 (176)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            66666654

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=98.68  E-value=1.3e-06  Score=71.27  Aligned_cols=34  Identities=6%  Similarity=-0.240  Sum_probs=12.8

Q ss_pred             CcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHHHc
Q 039342          198 ELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMM  236 (248)
Q Consensus       198 ~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~~~  236 (248)
                      +..+|..+-     ..|...|++++|.+.+++-.+.+-.
T Consensus       429 ~~~~~~~LG-----~~~~~~g~~~~A~~~y~kALe~~~~  462 (472)
T 4g1t_A          429 DSEALHVLA-----FLQELNEKMQQADEDSERGLESGSL  462 (472)
T ss_dssp             CTTHHHHHH-----HHHHHHHHCC---------------
T ss_pred             CHHHHHHHH-----HHHHHcCCHHHHHHHHHHHHhcCCC
Confidence            455666555     5667788888888888877765543

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*

Probab=98.68  E-value=2.9e-06  Score=61.43  Aligned_cols=117  Identities=14%  Similarity=0.033  Sum_probs=96.4

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|.+.|++..    .|+...|..+-..+.+.|++++|.+.|++..+.. +.+...|..+-.+|.+.|++++|.+.|
T Consensus        20 ~~~~~A~~~~~~a~----~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~   94 (213)
T 1hh8_A           20 KDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKYDLAIKDL   94 (213)
T ss_dssp             TCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHc----CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcccHHHHHHHH
Confidence            78899999998774    5788899999999999999999999999987664 456788889999999999999999999


Q ss_pred             HHHHHCCC--------------Cc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           82 QEIKSSGI--------------LP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        82 ~~m~~~~~--------------~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      ++..+...              .| ....+..+-..|.+.|++++|...|++..+..
T Consensus        95 ~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  151 (213)
T 1hh8_A           95 KEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMK  151 (213)
T ss_dssp             HHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHcC
Confidence            99887421              12 22677888888888899999999888877654

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=98.65  E-value=3e-06  Score=76.55  Aligned_cols=184  Identities=14%  Similarity=0.193  Sum_probs=135.1

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |.+++|..+|++..     -.....+.++.   ..+++++|.++.++.      -+..+|..+-.++.+.|++++|.+.|
T Consensus      1063 glyEEAf~IYkKa~-----~~~~A~~VLie---~i~nldrAiE~Aerv------n~p~vWsqLAKAql~~G~~kEAIdsY 1128 (1630)
T 1xi4_A         1063 ELFEEAFAIFRKFD-----VNTSAVQVLIE---HIGNLDRAYEFAERC------NEPAVWSQLAKAQLQKGMVKEAIDSY 1128 (1630)
T ss_pred             CCHHHHHHHHHHcC-----CHHHHHHHHHH---HHhhHHHHHHHHHhc------CCHHHHHHHHHHHHhCCCHHHHHHHH
Confidence            67889999998852     22333344433   667899999888865      33678999999999999999999999


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCC
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYG  161 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~  161 (248)
                      .+-      -|...|..++.+|.+.|++++|.+.|..-++..  ++......+... +.+.++++......    +   .
T Consensus      1129 iKA------dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~Lafa-YAKl~rleele~fI----~---~ 1192 (1630)
T 1xi4_A         1129 IKA------DDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFA-LAKTNRLAELEEFI----N---G 1192 (1630)
T ss_pred             Hhc------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHH-HHhhcCHHHHHHHH----h---C
Confidence            553      367788999999999999999999999877655  222222234433 55556666544442    1   3


Q ss_pred             CCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHH
Q 039342          162 LGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNK  229 (248)
Q Consensus       162 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~  229 (248)
                      |+...|..+-..|...|++++|..+|...         ..|..+.     ..+.+.|++++|.+..++
T Consensus      1193 ~n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA-----~tLvkLge~q~AIEaarK 1246 (1630)
T 1xi4_A         1193 PNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLA-----STLVHLGEYQAAVDGARK 1246 (1630)
T ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHH-----HHHHHhCCHHHHHHHHHH
Confidence            56677778999999999999999999984         2455555     677777888887776654

>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=98.65  E-value=7.8e-06  Score=62.58  Aligned_cols=178  Identities=9%  Similarity=-0.012  Sum_probs=103.5

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHCC-CCcCH----hhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchH-----HhHHH
Q 039342           64 VLSVYCFAGLVDESKEQFQEIKSSG-ILPSV----MCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIH-----QVTGQ  133 (248)
Q Consensus        64 ll~~~~~~g~~~~a~~~~~~m~~~~-~~p~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~-----~~~~~  133 (248)
                      .+..+.+.|++++|.+++++..+.. ..|+.    ..+..+...+...+++++|+..|++..+.......     ..++.
T Consensus        81 ~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~  160 (293)
T 3u3w_A           81 QVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENA  160 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHH
T ss_pred             HHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHH
Confidence            3667778888888888888876532 22332    13334555666677888888888887763222111     12333


Q ss_pred             HhcccccccchHHHHHHHHHHHHh----c-CCCCC-HHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHh
Q 039342          134 MIKGEFDDESNWQMVEYVFDKLNC----E-GYGLG-MRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVW  207 (248)
Q Consensus       134 ~l~~~~~~~~~~~~a~~~~~~m~~----~-~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~  207 (248)
                      +- ..+...|+++.|...++...+    . +..+. ..+|..+...|.+.|++++|.+.+++..+..-..+...+...++
T Consensus       161 lg-~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~  239 (293)
T 3u3w_A          161 IA-NIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLY  239 (293)
T ss_dssp             HH-HHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHH
T ss_pred             HH-HHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHH
Confidence            33 236667778888888877663    1 22222 33677888888899999999988887653211111111112222


Q ss_pred             hhhhhccccch-HHHHHHHHHHHHHHHHHcCCCCCc
Q 039342          208 SVDVHRMWEGG-AYTAISVWLNKMYEMFMMGEDLPQ  242 (248)
Q Consensus       208 ~~~~~~~~~~g-~~~~~~~~~~~m~~~~~~~~~~~~  242 (248)
                      ..+-..+.+.| .+++|...+++-.+..-.-+...+
T Consensus       240 ~~lg~~~~~~g~~~~~A~~~~~~Al~i~~~~~~~~~  275 (293)
T 3u3w_A          240 YQRGECLRKLEYEEAEIEDAYKKASFFFDILEMHAY  275 (293)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCTGG
T ss_pred             HHHHHHHHHhCCcHHHHHHHHHHHHHHHHHhCCHHH
Confidence            22225566677 457788777776655444443333

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.63  E-value=1e-06  Score=67.49  Aligned_cols=167  Identities=7%  Similarity=-0.031  Sum_probs=130.5

Q ss_pred             CCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHH-
Q 039342           20 ARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCM-   98 (248)
Q Consensus        20 ~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~-   98 (248)
                      +.+...+..+-..+.+.|++++|.+.|++..+.. +-+...+..+...+.+.|++++|...+++..+.  .|+...... 
T Consensus       114 p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~--~p~~~~~~~~  190 (287)
T 3qou_A          114 PREEELXAQQAMQLMQESNYTDALPLLXDAWQLS-NQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQ--DQDTRYQGLV  190 (287)
T ss_dssp             CCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGG--GCSHHHHHHH
T ss_pred             CCchhhHHHHHHHHHhCCCHHHHHHHHHHHHHhC-CcchhHHHHHHHHHHHCCCHHHHHHHHHhCchh--hcchHHHHHH
Confidence            3456778888888999999999999999997764 346678889999999999999999999988764  355443332 


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCC-CHHHHHHHHHHHHhc
Q 039342           99 LLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGL-GMRFYNALLEALWCL  177 (248)
Q Consensus        99 li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~  177 (248)
                      ....+...++.+.|...+++..+..  |+.......+...+...|++++|...+....+..... +...+..+...+...
T Consensus       191 ~~~~l~~~~~~~~a~~~l~~al~~~--P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~  268 (287)
T 3qou_A          191 AQIELLXQAADTPEIQQLQQQVAEN--PEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAAL  268 (287)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHH
T ss_pred             HHHHHHhhcccCccHHHHHHHHhcC--CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHc
Confidence            3333667788888999999887765  5555444444444778899999999999998875432 367899999999999


Q ss_pred             CchHHHHHHHHHHH
Q 039342          178 GLRERAARVLDEAT  191 (248)
Q Consensus       178 g~~~~a~~~~~~m~  191 (248)
                      |+.++|...+++-.
T Consensus       269 g~~~~a~~~~r~al  282 (287)
T 3qou_A          269 GTGDALASXYRRQL  282 (287)
T ss_dssp             CTTCHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHH
Confidence            99999999888643

>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=98.62  E-value=7.8e-06  Score=62.58  Aligned_cols=165  Identities=10%  Similarity=-0.003  Sum_probs=119.1

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcC-CCCCH----HHHHHHHHHHHhcCChhHHHHHHHHHHHCCCC-cC----HhhHH
Q 039342           28 AVIEAFRQGGRFEEAIKAYVEMEKVR-CDPNE----RTLEAVLSVYCFAGLVDESKEQFQEIKSSGIL-PS----VMCYC   97 (248)
Q Consensus        28 ~li~~~~~~~~~~~a~~~~~~m~~~~-~~p~~----~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~-p~----~~~~~   97 (248)
                      ..+..+...|++++|.+++++..+.. ..|+.    ..+..+...+...|++++|...|++..+.... ++    ..+++
T Consensus        80 ~~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~  159 (293)
T 3u3w_A           80 DQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIEN  159 (293)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHH
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHH
Confidence            34678889999999999999987642 22332    23345666777888999999999999874222 22    23689


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHH----C-CCCchHHhHHHHhcccccccchHHHHHHHHHHHHhc----CCCCC-HHHH
Q 039342           98 MLLAVYAKSNRWDDAYGLLDEMHT----N-RISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCE----GYGLG-MRFY  167 (248)
Q Consensus        98 ~li~~~~~~~~~~~a~~~~~~m~~----~-~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~----~~~p~-~~~~  167 (248)
                      .+-..|...|++++|+..|++..+    . +..+.......-+...+...|+++.|...+++..+.    +..+. ..+|
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            999999999999999999999873    2 223333323333334477889999999988876542    33333 6788


Q ss_pred             HHHHHHHHhcCc-hHHHHHHHHHHHH
Q 039342          168 NALLEALWCLGL-RERAARVLDEATK  192 (248)
Q Consensus       168 ~~li~~~~~~g~-~~~a~~~~~~m~~  192 (248)
                      ..+-.++.+.|+ +++|.+.+++...
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            889999999994 6999999987653

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=98.61  E-value=4.9e-07  Score=62.18  Aligned_cols=123  Identities=11%  Similarity=0.022  Sum_probs=89.5

Q ss_pred             CchHHHHHHHHHHHHcCCCC-CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            2 GLYKECQAILSRMSESGVAR-NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~-~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      |++++|.+.+......  .| +...+-.+-..|.+.|++++|.+.|++..+.. +-+...|..+-.+|.+.|++++|...
T Consensus        11 ~~~e~ai~~~~~a~~~--~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~   87 (150)
T 4ga2_A           11 ADVERYIASVQGSTPS--PRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQ-ERDPKAHRFLGLLYELEENTDKAVEC   87 (150)
T ss_dssp             HHHHHHHHHHHHHSCS--HHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             ChHHHHHHHHHHhccc--CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCchHHHHHH
Confidence            5678888888776542  23 34456667788888899999999998887654 34677888888888999999999999


Q ss_pred             HHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHH-HHHHHHCCCCchHHhH
Q 039342           81 FQEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGL-LDEMHTNRISNIHQVT  131 (248)
Q Consensus        81 ~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~-~~~m~~~~~~~~~~~~  131 (248)
                      |++..+.  .| +...|..+-..|.+.|+.++|... +++..+..  |+....
T Consensus        88 ~~~al~~--~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~--P~~~~~  136 (150)
T 4ga2_A           88 YRRSVEL--NPTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKLF--PGSPAV  136 (150)
T ss_dssp             HHHHHHH--CTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHS--TTCHHH
T ss_pred             HHHHHHh--CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhC--cCCHHH
Confidence            9888765  34 567788888888888888766554 46655432  544433

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=98.61  E-value=1.2e-06  Score=75.21  Aligned_cols=157  Identities=10%  Similarity=-0.043  Sum_probs=124.2

Q ss_pred             HhcCCHHHHHHHHHHHH--------HcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHh
Q 039342           34 RQGGRFEEAIKAYVEME--------KVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAK  105 (248)
Q Consensus        34 ~~~~~~~~a~~~~~~m~--------~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~  105 (248)
                      ...|++++|.+.+++..        +. -+.+...+..+-.++.+.|++++|.+.|++..+.. +-+...|..+-.+|..
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~-~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~  479 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVD-FSESVELPLMEVRALLDLGDVAKATRKLDDLAERV-GWRWRLVWYRAVAELL  479 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------C-CTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccc-cccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccC-cchHHHHHHHHHHHHH
Confidence            77899999999999987        32 24456788888999999999999999999998753 2267789999999999


Q ss_pred             cCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHH
Q 039342          106 SNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAAR  185 (248)
Q Consensus       106 ~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~  185 (248)
                      .|++++|+..|++..+..  |+.......+...+...|++++ ...|++..+.+.. +...|..+-.++.+.|++++|.+
T Consensus       480 ~g~~~~A~~~~~~al~l~--P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~P~-~~~a~~~lg~~~~~~g~~~~A~~  555 (681)
T 2pzi_A          480 TGDYDSATKHFTEVLDTF--PGELAPKLALAATAELAGNTDE-HKFYQTVWSTNDG-VISAAFGLARARSAEGDRVGAVR  555 (681)
T ss_dssp             HTCHHHHHHHHHHHHHHS--TTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhCCc-hHHHHHHHHHHHHHcCCHHHHHH
Confidence            999999999999988764  4443333333333667778888 8888888776543 57788999999999999999999


Q ss_pred             HHHHHHHCCCCCC
Q 039342          186 VLDEATKRGLFPE  198 (248)
Q Consensus       186 ~~~~m~~~g~~p~  198 (248)
                      .|++..+.  .|+
T Consensus       556 ~~~~al~l--~P~  566 (681)
T 2pzi_A          556 TLDEVPPT--SRH  566 (681)
T ss_dssp             HHHTSCTT--STT
T ss_pred             HHHhhccc--Ccc
Confidence            99987543  454

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.60  E-value=1.9e-06  Score=56.30  Aligned_cols=99  Identities=18%  Similarity=0.245  Sum_probs=84.9

Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHH
Q 039342           23 SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAV  102 (248)
Q Consensus        23 ~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~  102 (248)
                      ...|..+...+...|++++|.+.++++.+.. +.+..++..+...+.+.|++++|..+++++.+.. +.+..++..+...
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~   86 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNA   86 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHH
Confidence            5788888899999999999999999987654 4567888899999999999999999999988653 2367788899999


Q ss_pred             HHhcCCHHHHHHHHHHHHHCC
Q 039342          103 YAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus       103 ~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      +...|++++|...+++..+..
T Consensus        87 ~~~~~~~~~A~~~~~~~~~~~  107 (125)
T 1na0_A           87 YYKQGDYDEAIEYYQKALELD  107 (125)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHhcCHHHHHHHHHHHHHhC
Confidence            999999999999999987654

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.60  E-value=4.2e-06  Score=60.77  Aligned_cols=159  Identities=9%  Similarity=0.052  Sum_probs=112.9

Q ss_pred             CCchHHHHHHHHHHHHcCCCC-CHHhHHH----------------HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVAR-NSDSFNA----------------VIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEA   63 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~-~~~~y~~----------------li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~   63 (248)
                      .|++++|...|++..+..  | +...|..                +-..+.+.|++++|...|++..+.. +-+...+..
T Consensus        17 ~g~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~   93 (208)
T 3urz_A           17 AGQNGQAVSYFRQTIALN--IDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQKA-PNNVDCLEA   93 (208)
T ss_dssp             TTCHHHHHHHHHHHHHHC--HHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhC--CCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC-CCCHHHHHH
Confidence            389999999999987743  4 3556666                8889999999999999999998764 346788999


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHCCCCc-CHhhHHHHHHHHHhcCC--HHHHHHHHHHHHHCCCCchHHhHHHHhccccc
Q 039342           64 VLSVYCFAGLVDESKEQFQEIKSSGILP-SVMCYCMLLAVYAKSNR--WDDAYGLLDEMHTNRISNIHQVTGQMIKGEFD  140 (248)
Q Consensus        64 ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~--~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~  140 (248)
                      +-.++...|++++|...|++..+..  | +..+|..+-..|...|+  .+.+...++....  ..|....+...-.+ ..
T Consensus        94 lg~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~lg~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~a~~~~g~~-~~  168 (208)
T 3urz_A           94 CAEMQVCRGQEKDALRMYEKILQLE--ADNLAANIFLGNYYYLTAEQEKKKLETDYKKLSS--PTKMQYARYRDGLS-KL  168 (208)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHHHHHHHHHHC---C--CCHHHHHHHHHHHH-HH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhC--CCchhHHHHHHHHH-HH
Confidence            9999999999999999999998753  4 56788888887766554  4455556655432  22222222221111 33


Q ss_pred             ccchHHHHHHHHHHHHhcCCCCCHHHHHH
Q 039342          141 DESNWQMVEYVFDKLNCEGYGLGMRFYNA  169 (248)
Q Consensus       141 ~~~~~~~a~~~~~~m~~~~~~p~~~~~~~  169 (248)
                      ..+++++|...|++..+.  .|+......
T Consensus       169 ~~~~~~~A~~~~~~al~l--~P~~~~~~~  195 (208)
T 3urz_A          169 FTTRYEKARNSLQKVILR--FPSTEAQKT  195 (208)
T ss_dssp             HHHTHHHHHHHHHHHTTT--SCCHHHHHH
T ss_pred             HccCHHHHHHHHHHHHHh--CCCHHHHHH
Confidence            467889999999987764  566554433

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.60  E-value=1.5e-06  Score=62.41  Aligned_cols=158  Identities=14%  Similarity=-0.010  Sum_probs=92.3

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCC-CCHHHHHHHHHHHHhcCChhH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKV----RCD-PNERTLEAVLSVYCFAGLVDE   76 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~----~~~-p~~~t~~~ll~~~~~~g~~~~   76 (248)
                      |++++|.++++.+.. ........++.+-..+...|++++|...+++..+.    +.. ....++..+-..|...|++++
T Consensus         6 g~~~~A~~~~~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~   84 (203)
T 3gw4_A            6 HDYALAERQAQALLA-HPATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNWDA   84 (203)
T ss_dssp             -CHHHHHHHHHHHHT-STTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             ccHHHHHHHHHHhcC-ChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHHH
Confidence            677777775544433 11234567777777777777777777777776441    111 223456666667777777777


Q ss_pred             HHHHHHHHHHC----CCCc--CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHH
Q 039342           77 SKEQFQEIKSS----GILP--SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEY  150 (248)
Q Consensus        77 a~~~~~~m~~~----~~~p--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  150 (248)
                      |.+.+++..+.    +-.|  ....+..+-..+...|++++|...+++..+..                           
T Consensus        85 A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~---------------------------  137 (203)
T 3gw4_A           85 ARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYA---------------------------  137 (203)
T ss_dssp             HHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH---------------------------
T ss_pred             HHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH---------------------------
Confidence            77777765432    2111  23456666667777777777777776653220                           


Q ss_pred             HHHHHHhcCCC-CCHHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          151 VFDKLNCEGYG-LGMRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       151 ~~~~m~~~~~~-p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                           ...+.. .-..++..+-..+...|++++|.+.+++..+
T Consensus       138 -----~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  175 (203)
T 3gw4_A          138 -----QQADDQVAIACAFRGLGDLAQQEKNLLEAQQHWLRARD  175 (203)
T ss_dssp             -----HHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             -----HhccchHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence                 000000 1123356666777777888877777776543

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.59  E-value=8e-06  Score=59.98  Aligned_cols=173  Identities=10%  Similarity=-0.073  Sum_probs=117.8

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCC-Cc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC-chH-HhHH
Q 039342           57 NERTLEAVLSVYCFAGLVDESKEQFQEIKSSGI-LP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRIS-NIH-QVTG  132 (248)
Q Consensus        57 ~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~-~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-~~~-~~~~  132 (248)
                      +...+-.+...+.+.|++++|...|+++.+... .| ....+..+..+|.+.|++++|+..|++..+..-. +.. ..+.
T Consensus         3 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~   82 (225)
T 2yhc_A            3 PPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMY   82 (225)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHH
Confidence            344555667788999999999999999986521 12 1357788889999999999999999999875422 111 1111


Q ss_pred             HHhcc-----------------cccccchHHHHHHHHHHHHhcCCCCCHHHH-----------------HHHHHHHHhcC
Q 039342          133 QMIKG-----------------EFDDESNWQMVEYVFDKLNCEGYGLGMRFY-----------------NALLEALWCLG  178 (248)
Q Consensus       133 ~~l~~-----------------~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~-----------------~~li~~~~~~g  178 (248)
                      .+-..                 .....++++.|...|+.+.+.... +....                 ..+...|.+.|
T Consensus        83 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~P~-~~~a~~a~~~l~~~~~~~~~~~~~~a~~~~~~~  161 (225)
T 2yhc_A           83 MRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGYPN-SQYTTDATKRLVFLKDRLAKYEYSVAEYYTERG  161 (225)
T ss_dssp             HHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTTCTT-CTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHCcC-ChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            11111                 122467899999999998876422 11111                 23456788999


Q ss_pred             chHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          179 LRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       179 ~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      ++++|...|+++.+.  .|+... ..-.+..+...+.+.|+.++|...++.+...
T Consensus       162 ~~~~A~~~~~~~l~~--~p~~~~-~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~  213 (225)
T 2yhc_A          162 AWVAVVNRVEGMLRD--YPDTQA-TRDALPLMENAYRQMQMNAQAEKVAKIIAAN  213 (225)
T ss_dssp             CHHHHHHHHHHHHHH--STTSHH-HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHH--CcCCCc-cHHHHHHHHHHHHHcCCcHHHHHHHHHHHhh
Confidence            999999999998875  454321 1122223347888999999999999877765

>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=98.59  E-value=7.1e-06  Score=56.67  Aligned_cols=99  Identities=10%  Similarity=0.057  Sum_probs=76.0

Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHH
Q 039342           23 SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAV  102 (248)
Q Consensus        23 ~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~  102 (248)
                      ...|..+-..+...|++++|...|++..+.. +.+...+..+..++...|++++|.+.+++..+.. +.+...|..+...
T Consensus        13 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~   90 (166)
T 1a17_A           13 AEELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAAS   90 (166)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHH
Confidence            4567777778888888988888888876653 3467778888888888888888888888877653 2356677788888


Q ss_pred             HHhcCCHHHHHHHHHHHHHCC
Q 039342          103 YAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus       103 ~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      +...|++++|...|++..+..
T Consensus        91 ~~~~~~~~~A~~~~~~a~~~~  111 (166)
T 1a17_A           91 NMALGKFRAALRDYETVVKVK  111 (166)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHhccHHHHHHHHHHHHHhC
Confidence            888888888888888776543

>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=98.56  E-value=6.4e-06  Score=62.81  Aligned_cols=192  Identities=9%  Similarity=-0.011  Sum_probs=126.7

Q ss_pred             CCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHH
Q 039342           21 RNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLL  100 (248)
Q Consensus        21 ~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li  100 (248)
                      .+...+..+-..+.+.|++++|...|++..+.. +-+...|..+-.+|.+.|++++|...+++..+.. +.+...+..+-
T Consensus         2 ~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg   79 (281)
T 2c2l_A            2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLG   79 (281)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHH
Confidence            356778888899999999999999999987753 3478889999999999999999999999988753 22677889999


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHCCCCchHH-----hHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHH
Q 039342          101 AVYAKSNRWDDAYGLLDEMHTNRISNIHQ-----VTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALW  175 (248)
Q Consensus       101 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~-----~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  175 (248)
                      .+|...|++++|...|++..+..  |+..     .....+.  .      ... .-+..........+......+ ..+ 
T Consensus        80 ~~~~~~g~~~~A~~~~~~al~l~--p~~~~~~~~~~~~~~~--~------~~~-~~~~~~~~~~~~~~~~i~~~l-~~l-  146 (281)
T 2c2l_A           80 QCQLEMESYDEAIANLQRAYSLA--KEQRLNFGDDIPSALR--I------AKK-KRWNSIEERRIHQESELHSYL-TRL-  146 (281)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHH--HHTTCCCCSHHHHHHH--H------HHH-HHHHHHHHTCCCCCCHHHHHH-HHH-
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC--ccchhhHHHHHHHHHH--H------HHH-HHHHHHHHHHHhhhHHHHHHH-HHH-
Confidence            99999999999999999876542  3221     1111111  0      111 112223333344444443333 333 


Q ss_pred             hcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccc-hHHHHHHHHHHHHHHH
Q 039342          176 CLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEG-GAYTAISVWLNKMYEM  233 (248)
Q Consensus       176 ~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~-g~~~~~~~~~~~m~~~  233 (248)
                      ..|+.++|.+.++...+.  .|+......-+    ...+.+. +.++++.++|++..+.
T Consensus       147 ~~~~~~~A~~~~~~al~~--~p~~~~~~~~l----~~~~~~~~~~~~~a~~~f~~a~~~  199 (281)
T 2c2l_A          147 IAAERERELEECQRNHEG--HEDDGHIRAQQ----ACIEAKHDKYMADMDELFSQVDEK  199 (281)
T ss_dssp             HHHHHHHHHTTTSGGGTT--TSCHHHHTHHH----HHHHHHHHHHHHHHHHHHHHSSCT
T ss_pred             HHHHHHHHHHHHHhhhcc--ccchhhhhhHH----HHHHHHHHHHHHHHHHHHHhhhcc
Confidence            368888998888776543  55532222222    1222333 6677788888776654

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=98.55  E-value=1.9e-05  Score=57.51  Aligned_cols=185  Identities=9%  Similarity=-0.015  Sum_probs=130.6

Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcC----CHHHHHHHH
Q 039342           41 EAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSN----RWDDAYGLL  116 (248)
Q Consensus        41 ~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~----~~~~a~~~~  116 (248)
                      +|++.|++..+.   -+...+..+-..|...+++++|.+.|++..+.|   +...+..|-..|.. +    +.++|+..|
T Consensus         4 eA~~~~~~aa~~---g~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~~   76 (212)
T 3rjv_A            4 EPGSQYQQQAEA---GDRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQLA   76 (212)
T ss_dssp             CTTHHHHHHHHT---TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHHH
T ss_pred             hHHHHHHHHHHC---CCHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHHH
Confidence            466777777665   467778888888999999999999999998876   56677777777777 6    899999999


Q ss_pred             HHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCC-CCHHHHHHHHHHHHh----cCchHHHHHHHHHHH
Q 039342          117 DEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYG-LGMRFYNALLEALWC----LGLRERAARVLDEAT  191 (248)
Q Consensus       117 ~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~-p~~~~~~~li~~~~~----~g~~~~a~~~~~~m~  191 (248)
                      ++..+.+...-...+..+........++++.|...|+...+.|.. .+...+..|-..|..    .++.++|...|++..
T Consensus        77 ~~A~~~g~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~  156 (212)
T 3rjv_A           77 EKAVEAGSKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSS  156 (212)
T ss_dssp             HHHHHTTCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHH
Confidence            999887643322222222222123367899999999998877642 126677888888888    889999999999988


Q ss_pred             HCCCCCCcchhhhHHhhhhhhccc--cchHHHHHHHHHHHHHHHHH
Q 039342          192 KRGLFPELFRHNKLVWSVDVHRMW--EGGAYTAISVWLNKMYEMFM  235 (248)
Q Consensus       192 ~~g~~p~~~t~~~li~~~~~~~~~--~~g~~~~~~~~~~~m~~~~~  235 (248)
                      +.+  .+...+..|-..+ ..+..  ...+.++|..+++.-.+.|.
T Consensus       157 ~~~--~~~~a~~~Lg~~y-~~g~gg~~~~d~~~A~~~~~~A~~~g~  199 (212)
T 3rjv_A          157 SLS--RTGYAEYWAGMMF-QQGEKGFIEPNKQKALHWLNVSCLEGF  199 (212)
T ss_dssp             HTS--CTTHHHHHHHHHH-HHCBTTTBCCCHHHHHHHHHHHHHHTC
T ss_pred             HcC--CCHHHHHHHHHHH-HcCCCCCCCCCHHHHHHHHHHHHHcCC
Confidence            762  2223333333211 12211  23388999999988777653

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.54  E-value=1.8e-06  Score=61.94  Aligned_cols=171  Identities=11%  Similarity=-0.027  Sum_probs=97.5

Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHH----CCCCc-CHhhHHHHHHHHHhcCC
Q 039342           34 RQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKS----SGILP-SVMCYCMLLAVYAKSNR  108 (248)
Q Consensus        34 ~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~----~~~~p-~~~~~~~li~~~~~~~~  108 (248)
                      ...|++++|.+.++.+.. ........+..+-..+...|++++|...+++..+    .+..| ...++..+-..+...|+
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            356777777774444432 1123456666667777777777777777766654    12222 23456666666667777


Q ss_pred             HHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCC--CHHHHHHHHHHHHhcCchHHHHHH
Q 039342          109 WDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGL--GMRFYNALLEALWCLGLRERAARV  186 (248)
Q Consensus       109 ~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p--~~~~~~~li~~~~~~g~~~~a~~~  186 (248)
                      +++|...+++..+..                                ...+-.|  ....+..+-..+...|++++|...
T Consensus        82 ~~~A~~~~~~al~~~--------------------------------~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~  129 (203)
T 3gw4_A           82 WDAARRCFLEERELL--------------------------------ASLPEDPLAASANAYEVATVALHFGDLAGARQE  129 (203)
T ss_dssp             HHHHHHHHHHHHHHH--------------------------------HHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH--------------------------------HHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHH
Confidence            777766666543220                                0111111  134567778888899999999999


Q ss_pred             HHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHHHHcC
Q 039342          187 LDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEMFMMG  237 (248)
Q Consensus       187 ~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~~~~~  237 (248)
                      +++..+..-..+...........+-..+...|++++|...+++-.+..-..
T Consensus       130 ~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~  180 (203)
T 3gw4_A          130 YEKSLVYAQQADDQVAIACAFRGLGDLAQQEKNLLEAQQHWLRARDIFAEL  180 (203)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhccchHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHc
Confidence            988653211111111112222333366778899999999888877665443

>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=98.51  E-value=3.1e-06  Score=59.53  Aligned_cols=119  Identities=13%  Similarity=0.140  Sum_probs=91.7

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH-HHhcCCh--hHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSV-YCFAGLV--DESK   78 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~-~~~~g~~--~~a~   78 (248)
                      |++++|...|.+..+.. +.+...|..+-..|...|++++|...|++..+.. +.+...+..+..+ +...|++  ++|.
T Consensus        24 ~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~l~~~~~~~~~~~A~  101 (177)
T 2e2e_A           24 QNPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLR-GENAELYAALATVLYYQASQHMTAQTR  101 (177)
T ss_dssp             ---CCCCHHHHHHHHHC-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-CSCHHHHHHHHHHHHHHTTTCCCHHHH
T ss_pred             cCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhcCCcchHHHH
Confidence            67778888888876643 2467888888889999999999999999887654 3466777777777 7788888  9999


Q ss_pred             HHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           79 EQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        79 ~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      ..+++..+.. +.+...+..+...|...|++++|...|++..+..
T Consensus       102 ~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~  145 (177)
T 2e2e_A          102 AMIDKALALD-SNEITALMLLASDAFMQANYAQAIELWQKVMDLN  145 (177)
T ss_dssp             HHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHhC-CCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhhC
Confidence            9999887653 2256778888888999999999999999887654

>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=98.51  E-value=7.4e-06  Score=56.58  Aligned_cols=117  Identities=8%  Similarity=-0.018  Sum_probs=94.1

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|...|.+..+... .+...|..+...+...|++++|.+.+++..+.. +.+...|..+..++.+.|++++|.+.
T Consensus        26 ~~~~~~A~~~~~~al~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~  103 (166)
T 1a17_A           26 AKDYENAIKFYSQAIELNP-SNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAALRD  103 (166)
T ss_dssp             TTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHhCC-CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhccHHHHHHH
Confidence            3789999999999877542 368889999999999999999999999987764 45678899999999999999999999


Q ss_pred             HHHHHHCCCCcCHhhH--HHHHHHHHhcCCHHHHHHHHHHHH
Q 039342           81 FQEIKSSGILPSVMCY--CMLLAVYAKSNRWDDAYGLLDEMH  120 (248)
Q Consensus        81 ~~~m~~~~~~p~~~~~--~~li~~~~~~~~~~~a~~~~~~m~  120 (248)
                      |++..+... .+...+  -.....+.+.|++++|+..+.+..
T Consensus       104 ~~~a~~~~p-~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~  144 (166)
T 1a17_A          104 YETVVKVKP-HDKDAKMKYQECNKIVKQKAFERAIAGDEHKR  144 (166)
T ss_dssp             HHHHHHHST-TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCC-CCHHHHHHHHHHHHHHHHHHHHHHHHcccchH
Confidence            999887532 234444  334444778899999999988754

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=98.50  E-value=1.3e-06  Score=61.66  Aligned_cols=149  Identities=11%  Similarity=0.110  Sum_probs=105.9

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH-HHhcCChhHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSV-YCFAGLVDESKE   79 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~-~~~~g~~~~a~~   79 (248)
                      .|++++|...|++..+.. +-+...+..+-..+.+.|++++|...++...+..  |+...+...... +...+....+..
T Consensus        19 ~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~--p~~~~~~~~~~~~~~~~~~~~~a~~   95 (176)
T 2r5s_A           19 QGEHAQALNVIQTLSDEL-QSRGDVKLAKADCLLETKQFELAQELLATIPLEY--QDNSYKSLIAKLELHQQAAESPELK   95 (176)
T ss_dssp             TTCHHHHHHHHHTSCHHH-HTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGG--CCHHHHHHHHHHHHHHHHTSCHHHH
T ss_pred             cCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhcc--CChHHHHHHHHHHHHhhcccchHHH
Confidence            388999999999876533 2367889999999999999999999999986543  355444332212 223334445788


Q ss_pred             HHHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCch-HHhHHHHhcccccccchHHHHHHHHHHH
Q 039342           80 QFQEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNI-HQVTGQMIKGEFDDESNWQMVEYVFDKL  155 (248)
Q Consensus        80 ~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~m  155 (248)
                      .+++..+.  .| +...+..+-..+...|++++|...|++..+....+. ...+..+... +...|+.+.+...|+..
T Consensus        96 ~~~~al~~--~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~-~~~~g~~~~A~~~y~~a  170 (176)
T 2r5s_A           96 RLEQELAA--NPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDI-LSALGQGNAIASKYRRQ  170 (176)
T ss_dssp             HHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHH-HHHHCSSCHHHHHHHHH
T ss_pred             HHHHHHHh--CCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHH-HHHhCCCCcHHHHHHHH
Confidence            88888764  35 578899999999999999999999999987753332 2334444333 56667777777777654

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.49  E-value=3.6e-05  Score=58.85  Aligned_cols=166  Identities=12%  Similarity=0.028  Sum_probs=102.3

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH-----HHHHHHHHHHHhcCChhHHHHHHHHHHHCCC---CcC--Hh
Q 039342           25 SFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNE-----RTLEAVLSVYCFAGLVDESKEQFQEIKSSGI---LPS--VM   94 (248)
Q Consensus        25 ~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-----~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~---~p~--~~   94 (248)
                      .+...+..+...|++++|.+.+.+..+..-..+.     ..+..+...+...|++++|...+++..+...   .+.  ..
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            3445566777888888888888776554322111     2233345556677788888888887764311   111  34


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHH---C-CCCchH--HhHHHHhcccccccchHHHHHHHHHHHHhc----CCCC-C
Q 039342           95 CYCMLLAVYAKSNRWDDAYGLLDEMHT---N-RISNIH--QVTGQMIKGEFDDESNWQMVEYVFDKLNCE----GYGL-G  163 (248)
Q Consensus        95 ~~~~li~~~~~~~~~~~a~~~~~~m~~---~-~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~----~~~p-~  163 (248)
                      +|+.+-..|...|++++|+..|++..+   . +..+..  .++..+-.. +...|+++.|...+++..+.    +..+ -
T Consensus       157 ~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~-y~~~~~y~~Al~~~~kal~~~~~~~~~~~~  235 (293)
T 2qfc_A          157 IENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKA-LYLDSRYEESLYQVNKAIEISCRINSMALI  235 (293)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHH-HHHTTCHHHHHHHHHHHHHHHHHTTBCSSH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHH-HHHHhhHHHHHHHHHHHHHHHHhcCcHHHH
Confidence            777888888888888888888887652   1 111111  233333333 66777788888877765432    1111 1


Q ss_pred             HHHHHHHHHHHHhcCchHHH-HHHHHHHH
Q 039342          164 MRFYNALLEALWCLGLRERA-ARVLDEAT  191 (248)
Q Consensus       164 ~~~~~~li~~~~~~g~~~~a-~~~~~~m~  191 (248)
                      ..+|..+-..|.+.|+.++| ...+++..
T Consensus       236 ~~~~~~lg~~y~~~g~~~~Ai~~~~~~Al  264 (293)
T 2qfc_A          236 GQLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence            56677777888888888888 66666543

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.49  E-value=1.1e-05  Score=53.53  Aligned_cols=109  Identities=9%  Similarity=0.057  Sum_probs=89.3

Q ss_pred             CCCC-HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHH
Q 039342           19 VARN-SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYC   97 (248)
Q Consensus        19 ~~~~-~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~   97 (248)
                      +.|+ ...|...-..|.+.|++++|.+.|++..+.. +.+...|..+-.+|.+.|++++|.+.|++..+.. +.+...|.
T Consensus         8 inP~~a~~~~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~   85 (126)
T 4gco_A            8 INPELAQEEKNKGNEYFKKGDYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDTCIRLD-SKFIKGYI   85 (126)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             HCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhh-hhhhHHHH
Confidence            3444 4577778888999999999999999987664 4578889999999999999999999999988753 22577899


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhH
Q 039342           98 MLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVT  131 (248)
Q Consensus        98 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~  131 (248)
                      .+-.+|...|++++|+..|++..+..  |+....
T Consensus        86 ~lg~~~~~~~~~~~A~~~~~~al~l~--P~~~~a  117 (126)
T 4gco_A           86 RKAACLVAMREWSKAQRAYEDALQVD--PSNEEA  117 (126)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHC--cCCHHH
Confidence            99999999999999999999987654  554433

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=98.45  E-value=0.00013  Score=59.50  Aligned_cols=212  Identities=8%  Similarity=-0.055  Sum_probs=90.4

Q ss_pred             chHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhc----CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH-H--HhcCChh
Q 039342            3 LYKECQAILSRMSESGVARNSDSFNAVIEAFRQG----GRFEEAIKAYVEMEKVRCDPNERTLEAVLSV-Y--CFAGLVD   75 (248)
Q Consensus         3 ~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~----~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~-~--~~~g~~~   75 (248)
                      +.++|.+.|....+.|. ++...+..+-..|...    +++++|.+.|++.. .|   +...+..+-.. +  ...++++
T Consensus       194 ~~~~A~~~~~~aa~~g~-~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa-~g---~~~a~~~Lg~~~~~~~~~~d~~  268 (452)
T 3e4b_A          194 QQAELLKQMEAGVSRGT-VTAQRVDSVARVLGDATLGTPDEKTAQALLEKIA-PG---YPASWVSLAQLLYDFPELGDVE  268 (452)
T ss_dssp             HHHHHHHHHHHHHHTTC-SCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHG-GG---STHHHHHHHHHHHHSGGGCCHH
T ss_pred             cHHHHHHHHHHHHHCCC-HHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHc-CC---CHHHHHHHHHHHHhCCCCCCHH
Confidence            44455555555544442 2333333333333332    35555555555544 22   12222223222 2  2345555


Q ss_pred             HHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcC-----CHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHH
Q 039342           76 ESKEQFQEIKSSGILPSVMCYCMLLAVYAKSN-----RWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEY  150 (248)
Q Consensus        76 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~-----~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  150 (248)
                      +|.+.|++..+.|   +...+..|-..|. .|     +.++|+..|++.. .|...-...+..+.........++++|..
T Consensus       269 ~A~~~~~~Aa~~g---~~~A~~~Lg~~y~-~G~g~~~d~~~A~~~~~~Aa-~g~~~A~~~Lg~~y~~G~g~~~d~~~A~~  343 (452)
T 3e4b_A          269 QMMKYLDNGRAAD---QPRAELLLGKLYY-EGKWVPADAKAAEAHFEKAV-GREVAADYYLGQIYRRGYLGKVYPQKALD  343 (452)
T ss_dssp             HHHHHHHHHHHTT---CHHHHHHHHHHHH-HCSSSCCCHHHHHHHHHTTT-TTCHHHHHHHHHHHHTTTTSSCCHHHHHH
T ss_pred             HHHHHHHHHHHCC---CHHHHHHHHHHHH-cCCCCCCCHHHHHHHHHHHh-CCCHHHHHHHHHHHHCCCCCCcCHHHHHH
Confidence            5555555555444   3334444444443 23     5555555555444 22111111111111110112335566666


Q ss_pred             HHHHHHhcCCCCCHHHHHHHHHHHHh----cCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHH
Q 039342          151 VFDKLNCEGYGLGMRFYNALLEALWC----LGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVW  226 (248)
Q Consensus       151 ~~~~m~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~  226 (248)
                      .|+...+.|..   .....+-..|..    ..+.++|...|+...+.|...-..... .+     ......++..++.++
T Consensus       344 ~~~~Aa~~g~~---~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~A~~~g~~~a~~~l~-~l-----~~~~~~~~~~~a~~~  414 (452)
T 3e4b_A          344 HLLTAARNGQN---SADFAIAQLFSQGKGTKPDPLNAYVFSQLAKAQDTPEANDLAT-QL-----EAPLTPAQRAEGQRL  414 (452)
T ss_dssp             HHHHHHTTTCT---THHHHHHHHHHSCTTBCCCHHHHHHHHHHHHTTCCHHHHHHHH-HH-----HTTCCHHHHHHHHHH
T ss_pred             HHHHHHhhChH---HHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHH-HH-----HHhCCHHHHHHHHHH
Confidence            66655554432   223333334432    335666666666655555322111111 11     333455666777777


Q ss_pred             HHHHHHH
Q 039342          227 LNKMYEM  233 (248)
Q Consensus       227 ~~~m~~~  233 (248)
                      .++.++.
T Consensus       415 ~~~~~~~  421 (452)
T 3e4b_A          415 VQQELAA  421 (452)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            7766555

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=98.45  E-value=7.6e-05  Score=60.87  Aligned_cols=213  Identities=11%  Similarity=0.023  Sum_probs=137.6

Q ss_pred             hHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcC---CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc----CChhH
Q 039342            4 YKECQAILSRMSESGVARNSDSFNAVIEAFRQGG---RFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFA----GLVDE   76 (248)
Q Consensus         4 ~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~---~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~----g~~~~   76 (248)
                      .+.+..++.....    .++..+..+-..|.+.|   +.++|++.|++..+.| .++...+..+-..|...    +++++
T Consensus       161 ~~~a~~~~~~a~~----~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g-~~~a~~~~~Lg~~y~~g~~~~~d~~~  235 (452)
T 3e4b_A          161 LDDVERICKAALN----TTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRG-TVTAQRVDSVARVLGDATLGTPDEKT  235 (452)
T ss_dssp             HHHHHHHHHHHTT----TCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT-CSCHHHHHHHHHHHTCGGGSSCCHHH
T ss_pred             HHHHHHHHHHHHc----CCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCCCCCHHH
Confidence            3444444444433    33447888888888899   8999999999998887 46666656666677554    78999


Q ss_pred             HHHHHHHHHHCCCCcCHhhHHHHHHH-H--HhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHH
Q 039342           77 SKEQFQEIKSSGILPSVMCYCMLLAV-Y--AKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFD  153 (248)
Q Consensus        77 a~~~~~~m~~~~~~p~~~~~~~li~~-~--~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  153 (248)
                      |.+.|++.. .|   +...+..+-.. +  ...++.++|+..|++..+.|...-......+.........++++|...|+
T Consensus       236 A~~~~~~aa-~g---~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~  311 (452)
T 3e4b_A          236 AQALLEKIA-PG---YPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAADQPRAELLLGKLYYEGKWVPADAKAAEAHFE  311 (452)
T ss_dssp             HHHHHHHHG-GG---STHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHHHH
T ss_pred             HHHHHHHHc-CC---CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence            999999877 33   45555555555 3  46889999999999998887322222222221111223448899999988


Q ss_pred             HHHhcCCCCCHHHHHHHHHHHHh----cCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHH
Q 039342          154 KLNCEGYGLGMRFYNALLEALWC----LGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNK  229 (248)
Q Consensus       154 ~m~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~  229 (248)
                      ...    .-+...+..+-..|..    ..+.++|...|++..+.|...-   ...|-.. ...|.....+.++|..+++.
T Consensus       312 ~Aa----~g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~~~A---~~~Lg~~-y~~G~g~~~d~~~A~~~~~~  383 (452)
T 3e4b_A          312 KAV----GREVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNGQNSA---DFAIAQL-FSQGKGTKPDPLNAYVFSQL  383 (452)
T ss_dssp             TTT----TTCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTTCTTH---HHHHHHH-HHSCTTBCCCHHHHHHHHHH
T ss_pred             HHh----CCCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhChHHH---HHHHHHH-HHhCCCCCCCHHHHHHHHHH
Confidence            766    3356666777777766    3489999999999888764322   2222211 11333334567777777765


Q ss_pred             HHHH
Q 039342          230 MYEM  233 (248)
Q Consensus       230 m~~~  233 (248)
                      -.+.
T Consensus       384 A~~~  387 (452)
T 3e4b_A          384 AKAQ  387 (452)
T ss_dssp             HHTT
T ss_pred             HHHC
Confidence            4443

>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=98.44  E-value=2.7e-06  Score=58.33  Aligned_cols=112  Identities=9%  Similarity=0.021  Sum_probs=89.0

Q ss_pred             HHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 039342            8 QAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSS   87 (248)
Q Consensus         8 ~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~   87 (248)
                      .+.|++..+.. +.+...+..+-..+.+.|++++|...|+...+.. +.+...|..+-.+|.+.|++++|.+.|++..+.
T Consensus         7 ~~~~~~al~~~-p~~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l   84 (148)
T 2vgx_A            7 GGTIAMLNEIS-SDTLEQLYSLAFNQYQSGXYEDAHXVFQALCVLD-HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVM   84 (148)
T ss_dssp             CCSHHHHTTCC-HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHcCC-HhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            34455554422 1246677788888999999999999999987654 457788888999999999999999999998875


Q ss_pred             CCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 039342           88 GILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTN  122 (248)
Q Consensus        88 ~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  122 (248)
                      . +.+...+..+-.+|...|++++|...|++..+.
T Consensus        85 ~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A           85 D-IXEPRFPFHAAECLLQXGELAEAESGLFLAQEL  118 (148)
T ss_dssp             S-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             C-CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            3 225678888999999999999999999988654

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=98.43  E-value=6.2e-06  Score=63.68  Aligned_cols=189  Identities=11%  Similarity=0.086  Sum_probs=125.1

Q ss_pred             cCCHHHHHHHHHHHHHc------CCCCCH----HHHHHHHHHHHhcCChhHHHHHHHHHHHC----CCCc-CHhhHHHHH
Q 039342           36 GGRFEEAIKAYVEMEKV------RCDPNE----RTLEAVLSVYCFAGLVDESKEQFQEIKSS----GILP-SVMCYCMLL  100 (248)
Q Consensus        36 ~~~~~~a~~~~~~m~~~------~~~p~~----~t~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~~p-~~~~~~~li  100 (248)
                      .|++++|.+++++..+.      +..++.    ..|+.....|...|++++|.+.|.+..+.    +-.+ -..+|+.+.
T Consensus         4 ~~~~~eA~~~~~~a~k~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg   83 (307)
T 2ifu_A            4 AQKISEAHEHIAKAEKYLKTSFMKWKPDYDSAASEYAKAAVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAG   83 (307)
T ss_dssp             HHHHHHHHHHHHHHHHHHCCCSSSCSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHccccccCCCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            45667777777765432      112443    35666778889999999999999887643    2111 245888999


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHC----CCCch-HHhHHHHhcccccccchHHHHHHHHHHHHhc----CCCC-CHHHHHHH
Q 039342          101 AVYAKSNRWDDAYGLLDEMHTN----RISNI-HQVTGQMIKGEFDDESNWQMVEYVFDKLNCE----GYGL-GMRFYNAL  170 (248)
Q Consensus       101 ~~~~~~~~~~~a~~~~~~m~~~----~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~----~~~p-~~~~~~~l  170 (248)
                      ..|.+.|++++|+..|++..+.    |-... ...+..+-.. +.. |+++.|...+++..+.    +-.+ ...+++.+
T Consensus        84 ~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~-~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~l  161 (307)
T 2ifu_A           84 MMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKL-MEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKA  161 (307)
T ss_dssp             HHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH-HTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHH
Confidence            9999999999999999886432    22222 2233333333 556 9999999999876543    1111 14678888


Q ss_pred             HHHHHhcCchHHHHHHHHHHHHC----CCCCCcc-hhhhHHhhhhhhccccchHHHHHHHHHHHHH
Q 039342          171 LEALWCLGLRERAARVLDEATKR----GLFPELF-RHNKLVWSVDVHRMWEGGAYTAISVWLNKMY  231 (248)
Q Consensus       171 i~~~~~~g~~~~a~~~~~~m~~~----g~~p~~~-t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~  231 (248)
                      -..+.+.|++++|...|++..+.    +..+... .+..+.     ..+...|++++|...+++..
T Consensus       162 g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g-----~~~~~~g~~~~A~~~~~~al  222 (307)
T 2ifu_A          162 SRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQV-----LVQLHRADYVAAQKCVRESY  222 (307)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH-----HHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHH-----HHHHHcCCHHHHHHHHHHHh
Confidence            99999999999999999987652    2111100 111111     34455689999988888766

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.43  E-value=7.9e-06  Score=54.09  Aligned_cols=102  Identities=12%  Similarity=0.041  Sum_probs=85.2

Q ss_pred             CCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHH
Q 039342           20 ARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCML   99 (248)
Q Consensus        20 ~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l   99 (248)
                      +.+...|..+-..+.+.|++++|.+.|++..+.. +.+...+..+...+...|++++|.+.+++..+.. +.+...+..+
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l   90 (133)
T 2lni_A           13 PDLALMVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTRK   90 (133)
T ss_dssp             SCHHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHHH
Confidence            3457788889999999999999999999987653 3467888889999999999999999999988753 2357788888


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHCC
Q 039342          100 LAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus       100 i~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      ...+.+.|++++|...|++..+..
T Consensus        91 a~~~~~~~~~~~A~~~~~~~~~~~  114 (133)
T 2lni_A           91 AAALEAMKDYTKAMDVYQKALDLD  114 (133)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHhC
Confidence            999999999999999999887653

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.43  E-value=1.5e-05  Score=51.83  Aligned_cols=101  Identities=19%  Similarity=0.206  Sum_probs=81.1

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|.+.|+++.+.. +.+...+..+...+.+.|++++|...++++.+.. +.+..++..+...|.+.|++++|...
T Consensus        22 ~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~   99 (125)
T 1na0_A           22 QGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEY   99 (125)
T ss_dssp             TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHH
Confidence            378999999999988754 2467889999999999999999999999997764 45778899999999999999999999


Q ss_pred             HHHHHHCCCCcCHhhHHHHHHHHH
Q 039342           81 FQEIKSSGILPSVMCYCMLLAVYA  104 (248)
Q Consensus        81 ~~~m~~~~~~p~~~~~~~li~~~~  104 (248)
                      |++..+.. +.+...+..+-..+.
T Consensus       100 ~~~~~~~~-~~~~~~~~~l~~~~~  122 (125)
T 1na0_A          100 YQKALELD-PNNAEAKQNLGNAKQ  122 (125)
T ss_dssp             HHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHhC-CCcHHHHHHHHHHHH
Confidence            99988653 124445555444443

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.42  E-value=9.7e-06  Score=55.76  Aligned_cols=100  Identities=11%  Similarity=-0.007  Sum_probs=84.4

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHH
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLA  101 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~  101 (248)
                      +...+..+-..+.+.|++++|...|++..+.. +-+...|..+-.+|.+.|++++|...|++..+.. +-+...|..+-.
T Consensus        35 ~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~-P~~~~~~~~lg~  112 (151)
T 3gyz_A           35 MMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYD-FYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALG-KNDYTPVFHTGQ  112 (151)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-SSCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-CCCcHHHHHHHH
Confidence            35577788888999999999999999987764 4567888899999999999999999999988753 225678889999


Q ss_pred             HHHhcCCHHHHHHHHHHHHHCC
Q 039342          102 VYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus       102 ~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      +|.+.|++++|...|++..+..
T Consensus       113 ~~~~lg~~~eA~~~~~~al~l~  134 (151)
T 3gyz_A          113 CQLRLKAPLKAKECFELVIQHS  134 (151)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC
Confidence            9999999999999999987754

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=98.39  E-value=2.1e-05  Score=67.27  Aligned_cols=198  Identities=9%  Similarity=-0.021  Sum_probs=140.1

Q ss_pred             CchHHHH-HHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC---------CCC------------HH
Q 039342            2 GLYKECQ-AILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRC---------DPN------------ER   59 (248)
Q Consensus         2 g~~~~a~-~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~---------~p~------------~~   59 (248)
                      |+.++|. ++|++.... .+.+...|-..+...-+.|+++.|.++|+.+.+...         .|+            ..
T Consensus       357 ~~~~~a~r~il~rAi~~-~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~  435 (679)
T 4e6h_A          357 NTDSTVITKYLKLGQQC-IPNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTY  435 (679)
T ss_dssp             SCCTTHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHH
Confidence            5667786 999988753 334667788888889999999999999999876410         142            34


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHC-CCCcCHhhHHHHHHHHHh-cCCHHHHHHHHHHHHHCCCCchHHhHH-HHhc
Q 039342           60 TLEAVLSVYCFAGLVDESKEQFQEIKSS-GILPSVMCYCMLLAVYAK-SNRWDDAYGLLDEMHTNRISNIHQVTG-QMIK  136 (248)
Q Consensus        60 t~~~ll~~~~~~g~~~~a~~~~~~m~~~-~~~p~~~~~~~li~~~~~-~~~~~~a~~~~~~m~~~~~~~~~~~~~-~~l~  136 (248)
                      .|...+....+.|..+.|.++|....+. +. ++...|-.....--+ .++.+.|..+|+...+.  .|+...+. ..+.
T Consensus       436 vWi~y~~~erR~~~l~~AR~vf~~A~~~~~~-~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~--~p~~~~~w~~y~~  512 (679)
T 4e6h_A          436 VYCVYMNTMKRIQGLAASRKIFGKCRRLKKL-VTPDIYLENAYIEYHISKDTKTACKVLELGLKY--FATDGEYINKYLD  512 (679)
T ss_dssp             HHHHHHHHHHHHHCHHHHHHHHHHHHHTGGG-SCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHH--HTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhcCC-CChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH--CCCchHHHHHHHH
Confidence            6888888888999999999999999875 21 122333322222223 35599999999998876  24333333 3333


Q ss_pred             ccccccchHHHHHHHHHHHHhcCCCC--CHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHH
Q 039342          137 GEFDDESNWQMVEYVFDKLNCEGYGL--GMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLV  206 (248)
Q Consensus       137 ~~~~~~~~~~~a~~~~~~m~~~~~~p--~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li  206 (248)
                       +....++.+.|..+|+........+  ....|...++.-.+.|+.+.+.++.+++.+.  .|+......++
T Consensus       513 -fe~~~~~~~~AR~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~--~P~~~~~~~f~  581 (679)
T 4e6h_A          513 -FLIYVNEESQVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEK--FPEVNKLEEFT  581 (679)
T ss_dssp             -HHHHHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHH--STTCCHHHHHH
T ss_pred             -HHHhCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCcHHHHHH
Confidence             2445678899999999987764422  3567888888889999999999999999875  45544444444

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.38  E-value=9.5e-06  Score=51.85  Aligned_cols=100  Identities=6%  Similarity=-0.041  Sum_probs=82.6

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCc--CHhhHHHH
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILP--SVMCYCML   99 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p--~~~~~~~l   99 (248)
                      +...|..+-..+.+.|++++|...+++..+.. +.+...+..+-.++.+.|++++|.+.|++..+.. +.  +...+..+
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~l   82 (112)
T 2kck_A            5 NPEEYYLEGVLQYDAGNYTESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYVINVI-EDEYNKDVWAAK   82 (112)
T ss_dssp             STTGGGGHHHHHHSSCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-CCTTCHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccchHHHHHHH
Confidence            45677788888899999999999999987654 3467788888899999999999999999988753 22  46788888


Q ss_pred             HHHHHhc-CCHHHHHHHHHHHHHCC
Q 039342          100 LAVYAKS-NRWDDAYGLLDEMHTNR  123 (248)
Q Consensus       100 i~~~~~~-~~~~~a~~~~~~m~~~~  123 (248)
                      ...+.+. |++++|.+.+++.....
T Consensus        83 ~~~~~~~~~~~~~A~~~~~~~~~~~  107 (112)
T 2kck_A           83 ADALRYIEGKEVEAEIAEARAKLEH  107 (112)
T ss_dssp             HHHHTTCSSCSHHHHHHHHHHGGGC
T ss_pred             HHHHHHHhCCHHHHHHHHHHHhhcc
Confidence            8999999 99999999999887654

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.38  E-value=6.5e-06  Score=54.16  Aligned_cols=101  Identities=10%  Similarity=0.044  Sum_probs=81.3

Q ss_pred             CCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHH
Q 039342           21 RNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLL  100 (248)
Q Consensus        21 ~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li  100 (248)
                      .+...|..+...+...|++++|.+.+++..+.. +.+...+..+...+...|++++|.+.+++..+.. +.+...+..+.
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~   87 (131)
T 2vyi_A           10 AEAERLKTEGNEQMKVENFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGRMG   87 (131)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHHHH
Confidence            356678888888889999999999999887653 3467788888888999999999999998887653 22567788888


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHCC
Q 039342          101 AVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus       101 ~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      ..+.+.|++++|...|++..+..
T Consensus        88 ~~~~~~~~~~~A~~~~~~~~~~~  110 (131)
T 2vyi_A           88 LALSSLNKHVEAVAYYKKALELD  110 (131)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHhCCHHHHHHHHHHHHhcC
Confidence            88899999999999998877653

>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=98.35  E-value=4.3e-05  Score=49.11  Aligned_cols=100  Identities=15%  Similarity=0.087  Sum_probs=83.4

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHH
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLA  101 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~  101 (248)
                      ++..|..+...+...|++++|...++...+.. +.+...+..+...+.+.|++++|...+++..+.. +.+...+..+..
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~   80 (118)
T 1elw_A            3 QVNELKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAA   80 (118)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC-cccHHHHHHHHH
Confidence            45677888888999999999999999987653 3467888888899999999999999999987753 225778888899


Q ss_pred             HHHhcCCHHHHHHHHHHHHHCC
Q 039342          102 VYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus       102 ~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      .+...|++++|...+++..+..
T Consensus        81 ~~~~~~~~~~A~~~~~~~~~~~  102 (118)
T 1elw_A           81 ALEFLNRFEEAKRTYEEGLKHE  102 (118)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHHHhhHHHHHHHHHHHHHcC
Confidence            9999999999999999887654

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.35  E-value=3.3e-05  Score=59.07  Aligned_cols=172  Identities=7%  Similarity=-0.030  Sum_probs=110.2

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCc-CH----hhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC---ch--H
Q 039342           59 RTLEAVLSVYCFAGLVDESKEQFQEIKSSGILP-SV----MCYCMLLAVYAKSNRWDDAYGLLDEMHTNRIS---NI--H  128 (248)
Q Consensus        59 ~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~---~~--~  128 (248)
                      ..+...+..+...|++++|.+.+++..+..... +.    ..+..+...+...|++++|+..+++..+....   +.  .
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            345566788899999999999998877643221 11    23444556677889999999999998753221   21  2


Q ss_pred             HhHHHHhcccccccchHHHHHHHHHHHHhc----CCCC--CHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchh
Q 039342          129 QVTGQMIKGEFDDESNWQMVEYVFDKLNCE----GYGL--GMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRH  202 (248)
Q Consensus       129 ~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~----~~~p--~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~  202 (248)
                      ..++.+- ..+...|+++.|...+++..+.    +-.+  ...++..+...|.+.|++++|.+.+++..+..-..+....
T Consensus       156 ~~~~~lg-~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~  234 (293)
T 2qfc_A          156 YIENAIA-NIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMAL  234 (293)
T ss_dssp             HHHHHHH-HHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSS
T ss_pred             HHHHHHH-HHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHH
Confidence            2333333 3377789999999999887632    2122  2258889999999999999999999987642111111111


Q ss_pred             hhHHhhhhhhccccchHHHHH-HHHHHHHH
Q 039342          203 NKLVWSVDVHRMWEGGAYTAI-SVWLNKMY  231 (248)
Q Consensus       203 ~~li~~~~~~~~~~~g~~~~~-~~~~~~m~  231 (248)
                      ...++..+-..|.+.|+.++| ...+++-.
T Consensus       235 ~~~~~~~lg~~y~~~g~~~~Ai~~~~~~Al  264 (293)
T 2qfc_A          235 IGQLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence            122222222566777877777 65555543

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=98.34  E-value=1.3e-06  Score=60.10  Aligned_cols=86  Identities=13%  Similarity=-0.054  Sum_probs=54.7

Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHH
Q 039342           34 RQGGRFEEAIKAYVEMEKVRCDPN-ERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDA  112 (248)
Q Consensus        34 ~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a  112 (248)
                      ...|++++|++.+......  .|+ ...+-.+-..|.+.|++++|.+.|++..+.. +-+..+|..+-..|.+.|++++|
T Consensus         8 ~~~~~~e~ai~~~~~a~~~--~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A   84 (150)
T 4ga2_A            8 RSKADVERYIASVQGSTPS--PRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQ-ERDPKAHRFLGLLYELEENTDKA   84 (150)
T ss_dssp             CCHHHHHHHHHHHHHHSCS--HHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHcChHHHHHHHHHHhccc--CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCchHHH
Confidence            3446667777766665432  222 2334456667777777777777777776542 12566777777777777777777


Q ss_pred             HHHHHHHHHC
Q 039342          113 YGLLDEMHTN  122 (248)
Q Consensus       113 ~~~~~~m~~~  122 (248)
                      +..|++..+.
T Consensus        85 ~~~~~~al~~   94 (150)
T 4ga2_A           85 VECYRRSVEL   94 (150)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            7777776654

>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=98.34  E-value=2.1e-05  Score=61.61  Aligned_cols=100  Identities=7%  Similarity=-0.060  Sum_probs=68.0

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC--------------HHHHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN--------------ERTLEAVLSVYCFAGLVDESKEQFQEIKSS   87 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~--------------~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~   87 (248)
                      +...|..+-..+.+.|++++|...|++..+..-...              ...|..+-.+|.+.|++++|...+++..+.
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            345667777777777888888888877765432111              466777777777777777777777777654


Q ss_pred             CCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 039342           88 GILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTN  122 (248)
Q Consensus        88 ~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  122 (248)
                      . +.+...|..+-.+|...|++++|+..|++..+.
T Consensus       226 ~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l  259 (336)
T 1p5q_A          226 D-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQL  259 (336)
T ss_dssp             C-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             C-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            2 225566777777777777777777777776654

>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=98.33  E-value=3.7e-05  Score=51.28  Aligned_cols=100  Identities=11%  Similarity=0.022  Sum_probs=86.0

Q ss_pred             CCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHH
Q 039342           21 RNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLL  100 (248)
Q Consensus        21 ~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li  100 (248)
                      .+...|..+-..+.+.|++++|...|+...+.. +.+...|..+-.++...|++++|...+++..+.. +.+...+..+-
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~   84 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLG   84 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-chhHHHHHHHH
Confidence            467889999999999999999999999987764 3467888999999999999999999999988753 22677889999


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHC
Q 039342          101 AVYAKSNRWDDAYGLLDEMHTN  122 (248)
Q Consensus       101 ~~~~~~~~~~~a~~~~~~m~~~  122 (248)
                      ..|...|++++|...|++..+.
T Consensus        85 ~~~~~~~~~~~A~~~~~~a~~~  106 (137)
T 3q49_B           85 QCQLEMESYDEAIANLQRAYSL  106 (137)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHH
Confidence            9999999999999999988654

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.33  E-value=2.4e-05  Score=51.35  Aligned_cols=106  Identities=8%  Similarity=-0.012  Sum_probs=86.7

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|.+.|++..+.. +.+...|..+...+...|++++|.+.++...+.. +.+...+..+...+.+.|++++|...
T Consensus        25 ~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~  102 (131)
T 2vyi_A           25 VENFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGRMGLALSSLNKHVEAVAY  102 (131)
T ss_dssp             TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHHHHHHHHHhCCHHHHHHH
Confidence            378999999999987654 2467889999999999999999999999987753 34578888999999999999999999


Q ss_pred             HHHHHHCCCCcCHhhHHHHHHHHHhcCCH
Q 039342           81 FQEIKSSGILPSVMCYCMLLAVYAKSNRW  109 (248)
Q Consensus        81 ~~~m~~~~~~p~~~~~~~li~~~~~~~~~  109 (248)
                      |++..+.. +.+...+..+...+.+.|+.
T Consensus       103 ~~~~~~~~-p~~~~~~~~l~~~~~~~~~~  130 (131)
T 2vyi_A          103 YKKALELD-PDNETYKSNLKIAELKLREA  130 (131)
T ss_dssp             HHHHHHHS-TTCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHhcC-ccchHHHHHHHHHHHHHhcC
Confidence            99988753 22566777777777776653

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.32  E-value=7.4e-05  Score=60.12  Aligned_cols=53  Identities=9%  Similarity=-0.065  Sum_probs=26.2

Q ss_pred             ccccchHHHHHHHHHHHHhc--CC--CC-CHHHHHHHHHHHHhcCchHHHHHHHHHHH
Q 039342          139 FDDESNWQMVEYVFDKLNCE--GY--GL-GMRFYNALLEALWCLGLRERAARVLDEAT  191 (248)
Q Consensus       139 ~~~~~~~~~a~~~~~~m~~~--~~--~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~  191 (248)
                      +...|+++.|..+++.....  +.  .| ...+|..+++.|...|++++|..++++..
T Consensus       145 ~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al  202 (434)
T 4b4t_Q          145 HYQKKQYKDSLALINDLLREFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAAR  202 (434)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHccChHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHH
Confidence            44445555555555444322  11  11 13345556666666666666666665543

>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=98.32  E-value=2.8e-05  Score=51.23  Aligned_cols=99  Identities=15%  Similarity=0.113  Sum_probs=82.7

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHH
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLA  101 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~  101 (248)
                      +...|...-..+.+.|++++|...|++..+.. +.+...|..+-.+|.+.|++++|...+++..+.. +.+...|..+-.
T Consensus         3 ~a~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~   80 (126)
T 3upv_A            3 KAEEARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKAT   80 (126)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHH
Confidence            34567777888899999999999999987664 4567889999999999999999999999988753 225778888999


Q ss_pred             HHHhcCCHHHHHHHHHHHHHC
Q 039342          102 VYAKSNRWDDAYGLLDEMHTN  122 (248)
Q Consensus       102 ~~~~~~~~~~a~~~~~~m~~~  122 (248)
                      ++...|++++|...|++..+.
T Consensus        81 ~~~~~~~~~~A~~~~~~al~~  101 (126)
T 3upv_A           81 AQIAVKEYASALETLDAARTK  101 (126)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHhCHHHHHHHHHHHHHh
Confidence            999999999999999987654

>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=98.29  E-value=3e-05  Score=60.67  Aligned_cols=117  Identities=14%  Similarity=0.043  Sum_probs=97.6

Q ss_pred             CchHHHHHHHHHHHHcCCCCC--------------HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARN--------------SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSV   67 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~--------------~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   67 (248)
                      |++++|...|++..+......              ...|..+-.+|.+.|++++|...+++..+.. +.+...|..+-.+
T Consensus       161 g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~  239 (336)
T 1p5q_A          161 GKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD-SNNEKGLSRRGEA  239 (336)
T ss_dssp             TCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHH
Confidence            789999999999887543221              5899999999999999999999999998764 4578899999999


Q ss_pred             HHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHH-HHHHHHHH
Q 039342           68 YCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDA-YGLLDEMH  120 (248)
Q Consensus        68 ~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a-~~~~~~m~  120 (248)
                      |...|++++|...|++..+.. +-+...+..+-..+.+.|+.++| ...++.|.
T Consensus       240 ~~~~g~~~~A~~~~~~al~l~-P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~~  292 (336)
T 1p5q_A          240 HLAVNDFELARADFQKVLQLY-PNNKAAKTQLAVCQQRIRRQLAREKKLYANMF  292 (336)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999998753 22567888999999999999888 45666664

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.29  E-value=3.1e-05  Score=52.36  Aligned_cols=99  Identities=10%  Similarity=0.020  Sum_probs=82.8

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHH
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLA  101 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~  101 (248)
                      +...+..+-..+.+.|++++|...|+...+.+ +.+...|..+-.+|.+.|++++|...|++..+.. +.+...+..+-.
T Consensus        17 ~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~   94 (142)
T 2xcb_A           17 TLEQLYALGFNQYQAGKWDDAQKIFQALCMLD-HYDARYFLGLGACRQSLGLYEQALQSYSYGALMD-INEPRFPFHAAE   94 (142)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHH
Confidence            34566677788889999999999999987764 4577888889999999999999999999988753 225677888899


Q ss_pred             HHHhcCCHHHHHHHHHHHHHC
Q 039342          102 VYAKSNRWDDAYGLLDEMHTN  122 (248)
Q Consensus       102 ~~~~~~~~~~a~~~~~~m~~~  122 (248)
                      +|...|++++|...|++..+.
T Consensus        95 ~~~~~g~~~~A~~~~~~al~~  115 (142)
T 2xcb_A           95 CHLQLGDLDGAESGFYSARAL  115 (142)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHh
Confidence            999999999999999987654

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.28  E-value=2.4e-05  Score=51.66  Aligned_cols=67  Identities=12%  Similarity=-0.009  Sum_probs=47.1

Q ss_pred             CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 039342           55 DPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTN  122 (248)
Q Consensus        55 ~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  122 (248)
                      +.+...+..+...+.+.|++++|.+.|++..+.. +.+...+..+...+...|++++|+..+++..+.
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~   79 (133)
T 2lni_A           13 PDLALMVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQL   79 (133)
T ss_dssp             SCHHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            3455667777777788888888888887776542 225666777777777777777777777776554

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.27  E-value=1.8e-05  Score=59.94  Aligned_cols=189  Identities=11%  Similarity=0.052  Sum_probs=126.2

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHH-------HHHHHhcCCHHHHHHHHHHHHHcCCCCC-----------------
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAV-------IEAFRQGGRFEEAIKAYVEMEKVRCDPN-----------------   57 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~l-------i~~~~~~~~~~~a~~~~~~m~~~~~~p~-----------------   57 (248)
                      ++.+.|++.|.+..+... -....|+.+       ...+.+.++..+++..+..-.+  +.|+                 
T Consensus        20 ~d~~~A~~~F~~a~~~dP-~~~Daw~g~~a~g~~~~~~L~~~~r~~~a~~~~~~~l~--l~p~~l~a~~~~~g~y~~~~~   96 (282)
T 4f3v_A           20 MSEARSLDLFTEITNYDE-SACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQ--ISMSTLNARIAIGGLYGDITY   96 (282)
T ss_dssp             TCHHHHHHHHHHHHHHCT-TCHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTT--CCGGGGCCEEECCTTTCCCEE
T ss_pred             CCHHHHHHHHHHHHHhCh-hhhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhc--CChhhhhhhhccCCccccccc
Confidence            688999999999987542 246788877       4555555555555554444332  2221                 


Q ss_pred             -----HHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCch-HHhH
Q 039342           58 -----ERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNI-HQVT  131 (248)
Q Consensus        58 -----~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~-~~~~  131 (248)
                           ....-.+...+...|++++|.++|+.+...+  |+....-.+-..+.+.+++++|+..|+...... .|. ..-.
T Consensus        97 ~v~~r~dl~LayA~~L~~~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~-d~~~~~~a  173 (282)
T 4f3v_A           97 PVTSPLAITMGFAACEAAQGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP-DKFLAGAA  173 (282)
T ss_dssp             ECSSHHHHHHHHHHHHHHHTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS-CHHHHHHH
T ss_pred             ccCCHhHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC-CcccHHHH
Confidence                 1233446677888999999999999887653  544455556668889999999999998543322 121 1112


Q ss_pred             HHHhcccccccchHHHHHHHHHHHHhcCCCCC--HHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCC
Q 039342          132 GQMIKGEFDDESNWQMVEYVFDKLNCEGYGLG--MRFYNALLEALWCLGLRERAARVLDEATKRGLFPE  198 (248)
Q Consensus       132 ~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  198 (248)
                      ...+-..+...|++++|...|++.......|.  .......-.++.+.|+.++|...|+++...  .|+
T Consensus       174 ~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~--~P~  240 (282)
T 4f3v_A          174 GVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTT--HPE  240 (282)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--SCC
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCc
Confidence            23333347778899999999998875433253  335566777888899999999999998764  454

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.26  E-value=6.8e-05  Score=50.49  Aligned_cols=100  Identities=12%  Similarity=0.027  Sum_probs=84.9

Q ss_pred             CCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC----HHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhH
Q 039342           21 RNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN----ERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCY   96 (248)
Q Consensus        21 ~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~----~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~   96 (248)
                      .+...+..+-..+.+.|++++|.+.|++..+.  .|+    ...|..+..+|.+.|++++|...+++..+.. +.+...+
T Consensus        26 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~  102 (148)
T 2dba_A           26 SSVEQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKD-GGDVKAL  102 (148)
T ss_dssp             CCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-SCCHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-ccCHHHH
Confidence            35778888999999999999999999998764  466    6788888899999999999999999987653 2257788


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           97 CMLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        97 ~~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      ..+-.++...|++++|...|++..+..
T Consensus       103 ~~~a~~~~~~~~~~~A~~~~~~al~~~  129 (148)
T 2dba_A          103 YRRSQALEKLGRLDQAVLDLQRCVSLE  129 (148)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHcC
Confidence            888999999999999999999887654

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=98.26  E-value=0.00014  Score=56.10  Aligned_cols=222  Identities=5%  Similarity=-0.114  Sum_probs=145.3

Q ss_pred             chHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcC--CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH----Hhc---CC
Q 039342            3 LYKECQAILSRMSESGVARNSDSFNAVIEAFRQGG--RFEEAIKAYVEMEKVRCDPNERTLEAVLSVY----CFA---GL   73 (248)
Q Consensus         3 ~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~--~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~----~~~---g~   73 (248)
                      .-++|+++++.+..... -+...||.==..+...+  +++++++.++.+...+- -+..+|+.--..+    .+.   ++
T Consensus        48 ~s~~aL~~t~~~L~~nP-~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nP-k~y~aW~~R~~iL~~~~~~l~~~~~  125 (306)
T 3dra_A           48 YSERALHITELGINELA-SHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDNE-KNYQIWNYRQLIIGQIMELNNNDFD  125 (306)
T ss_dssp             CSHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCT-TCCHHHHHHHHHHHHHHHHTTTCCC
T ss_pred             CCHHHHHHHHHHHHHCc-HHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHCc-ccHHHHHHHHHHHHHHHHhccccCC
Confidence            34688999988877442 24667888777888888  89999999999877642 3344555433333    444   78


Q ss_pred             hhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHH--HHHHHHHHHHHCCCCchHHh-HHHHhcccccc---cchHHH
Q 039342           74 VDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWD--DAYGLLDEMHTNRISNIHQV-TGQMIKGEFDD---ESNWQM  147 (248)
Q Consensus        74 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~--~a~~~~~~m~~~~~~~~~~~-~~~~l~~~~~~---~~~~~~  147 (248)
                      ++++.++++.+.+... -+-.+|+---..+.+.+.++  ++++.++++.+........- +...+......   ...++.
T Consensus       126 ~~~EL~~~~~~l~~~p-kny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~~N~sAW~~R~~ll~~l~~~~~~~~~~e  204 (306)
T 3dra_A          126 PYREFDILEAMLSSDP-KNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDLKNNSAWSHRFFLLFSKKHLATDNTIDE  204 (306)
T ss_dssp             THHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHSSGGGCCHHHHHH
T ss_pred             HHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhccccchhhhHHH
Confidence            8899999999887532 26677877777777778877  89999999987764433322 12222211211   112778


Q ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHH-HHHHHHHHHHCC-CCCCcchhhhHHhhhhhhccccchHHHHHHH
Q 039342          148 VEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRER-AARVLDEATKRG-LFPELFRHNKLVWSVDVHRMWEGGAYTAISV  225 (248)
Q Consensus       148 a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~-a~~~~~~m~~~g-~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~  225 (248)
                      +.+.++......+. |...|+..--.+.+.|+... +.++..++.+.+ ..|.    +.....++...+.+.|+.++|.+
T Consensus       205 El~~~~~aI~~~p~-n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~----s~~al~~la~~~~~~~~~~~A~~  279 (306)
T 3dra_A          205 ELNYVKDKIVKCPQ-NPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVT----SSFALETLAKIYTQQKKYNESRT  279 (306)
T ss_dssp             HHHHHHHHHHHCSS-CHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEES----CHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHhCCC-CccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCC----CHHHHHHHHHHHHccCCHHHHHH
Confidence            88888887777655 77888877777777776443 555666554432 1121    22233344466778888899999


Q ss_pred             HHHHHHH
Q 039342          226 WLNKMYE  232 (248)
Q Consensus       226 ~~~~m~~  232 (248)
                      .++.+.+
T Consensus       280 ~~~~l~~  286 (306)
T 3dra_A          280 VYDLLKS  286 (306)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            9888876

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.25  E-value=3.8e-05  Score=53.22  Aligned_cols=101  Identities=13%  Similarity=0.088  Sum_probs=84.2

Q ss_pred             CCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHH
Q 039342           21 RNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLL  100 (248)
Q Consensus        21 ~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li  100 (248)
                      .+...|..+-..+.+.|++++|.+.|++..+.. +-+...|..+-.+|.+.|++++|...|++..+.. +-+...|..+-
T Consensus         9 ~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg   86 (164)
T 3sz7_A            9 PESDKLKSEGNAAMARKEYSKAIDLYTQALSIA-PANPIYLSNRAAAYSASGQHEKAAEDAELATVVD-PKYSKAWSRLG   86 (164)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHH
Confidence            356678888889999999999999999987764 3477888889999999999999999999988753 22577888999


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHCC
Q 039342          101 AVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus       101 ~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      .+|...|++++|...|++..+..
T Consensus        87 ~~~~~~g~~~~A~~~~~~al~~~  109 (164)
T 3sz7_A           87 LARFDMADYKGAKEAYEKGIEAE  109 (164)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHccCHHHHHHHHHHHHHhC
Confidence            99999999999999999886543

>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=98.25  E-value=4.7e-05  Score=49.94  Aligned_cols=100  Identities=15%  Similarity=0.198  Sum_probs=81.9

Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCC--CcC----HhhH
Q 039342           23 SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGI--LPS----VMCY   96 (248)
Q Consensus        23 ~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~--~p~----~~~~   96 (248)
                      ...|..+-..+...|++++|...|++..+.. +.+...+..+...+...|++++|...+++..+...  .++    ..++
T Consensus         4 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~   82 (131)
T 1elr_A            4 ALKEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAY   82 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHH
Confidence            4677888888999999999999999987664 45678888889999999999999999998876421  112    6678


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           97 CMLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        97 ~~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      ..+...+...|++++|...|++..+..
T Consensus        83 ~~la~~~~~~~~~~~A~~~~~~~~~~~  109 (131)
T 1elr_A           83 ARIGNSYFKEEKYKDAIHFYNKSLAEH  109 (131)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHHhC
Confidence            888889999999999999999887754

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.24  E-value=4.3e-05  Score=50.65  Aligned_cols=94  Identities=7%  Similarity=0.003  Sum_probs=78.6

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|++.|++..+... .+...|..+-.+|.+.|++++|++.+++..+.+ +.+...|..+-.+|...|++++|.+.
T Consensus        26 ~g~~~~A~~~~~~al~~~p-~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~  103 (126)
T 4gco_A           26 KGDYPTAMRHYNEAVKRDP-ENAILYSNRAACLTKLMEFQRALDDCDTCIRLD-SKFIKGYIRKAACLVAMREWSKAQRA  103 (126)
T ss_dssp             TTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhCC-CCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhh-hhhhHHHHHHHHHHHHCCCHHHHHHH
Confidence            3899999999999877542 468899999999999999999999999987764 45678899999999999999999999


Q ss_pred             HHHHHHCCCCcC-HhhHHH
Q 039342           81 FQEIKSSGILPS-VMCYCM   98 (248)
Q Consensus        81 ~~~m~~~~~~p~-~~~~~~   98 (248)
                      |++..+.  .|+ ...+..
T Consensus       104 ~~~al~l--~P~~~~a~~~  120 (126)
T 4gco_A          104 YEDALQV--DPSNEEAREG  120 (126)
T ss_dssp             HHHHHHH--CTTCHHHHHH
T ss_pred             HHHHHHH--CcCCHHHHHH
Confidence            9998875  453 334433

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.24  E-value=0.00018  Score=57.92  Aligned_cols=190  Identities=6%  Similarity=-0.074  Sum_probs=131.2

Q ss_pred             CchHHHHHHHHHHHHcCCCC-C---------------HHhHHHHHHHHHhcCCHHHHHHHHHHHHHc-CCCCCHH----H
Q 039342            2 GLYKECQAILSRMSESGVAR-N---------------SDSFNAVIEAFRQGGRFEEAIKAYVEMEKV-RCDPNER----T   60 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~-~---------------~~~y~~li~~~~~~~~~~~a~~~~~~m~~~-~~~p~~~----t   60 (248)
                      |++++|.+.|..+.+..... +               ...+..+...|.+.|++++|.+.+...... +-.++..    +
T Consensus        18 ~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~   97 (434)
T 4b4t_Q           18 KQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFAKSKTVKVL   97 (434)
T ss_dssp             TCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccchHHHHHH
Confidence            78999999999987643221 1               124788999999999999999999887542 1122222    2


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHH----CCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHC----CCCchHHhH
Q 039342           61 LEAVLSVYCFAGLVDESKEQFQEIKS----SGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTN----RISNIHQVT  131 (248)
Q Consensus        61 ~~~ll~~~~~~g~~~~a~~~~~~m~~----~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~~~~~~~  131 (248)
                      .+.+-..+...|+.+.+.++++....    .+..+ -..++..+...|...|++++|..++++....    +-.+....+
T Consensus        98 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~  177 (434)
T 4b4t_Q           98 KTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDDKPSLVDV  177 (434)
T ss_dssp             HHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCSTHHHHH
T ss_pred             HHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcccchhHHHH
Confidence            22333344567889999999887753    23333 2467888999999999999999999987543    223333333


Q ss_pred             HHHhcccccccchHHHHHHHHHHHHhc----CCCCC--HHHHHHHHHHHHhcCchHHHHHHHHHHH
Q 039342          132 GQMIKGEFDDESNWQMVEYVFDKLNCE----GYGLG--MRFYNALLEALWCLGLRERAARVLDEAT  191 (248)
Q Consensus       132 ~~~l~~~~~~~~~~~~a~~~~~~m~~~----~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~m~  191 (248)
                      ...+...+...++++.|..+++.....    +..|.  ...+..+...+...|+++.|...|.+..
T Consensus       178 ~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~  243 (434)
T 4b4t_Q          178 HLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFESF  243 (434)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence            333444477889999999998876543    22222  3456677778888999999988887654

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=98.22  E-value=0.00082  Score=51.72  Aligned_cols=185  Identities=6%  Similarity=-0.086  Sum_probs=136.2

Q ss_pred             chHHHHHHHHHHHHcCCCCCHHhHHHHHHHH----Hhc---CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChh
Q 039342            3 LYKECQAILSRMSESGVARNSDSFNAVIEAF----RQG---GRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVD   75 (248)
Q Consensus         3 ~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~----~~~---~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~   75 (248)
                      +++++++.++.+..... .+..+|+.--..+    .+.   +++++++++++.+.+.. +-|...|+.---.+.+.|.++
T Consensus        84 ~~~eeL~~~~~~L~~nP-k~y~aW~~R~~iL~~~~~~l~~~~~~~~EL~~~~~~l~~~-pkny~aW~~R~~vl~~l~~~~  161 (306)
T 3dra_A           84 NLYDELDWCEEIALDNE-KNYQIWNYRQLIIGQIMELNNNDFDPYREFDILEAMLSSD-PKNHHVWSYRKWLVDTFDLHN  161 (306)
T ss_dssp             CHHHHHHHHHHHHHHCT-TCCHHHHHHHHHHHHHHHHTTTCCCTHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTT
T ss_pred             cHHHHHHHHHHHHHHCc-ccHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcccC
Confidence            78999999999887543 3566777655555    555   78999999999998765 568888888888888889888


Q ss_pred             --HHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCC------HHHHHHHHHHHHHCCCCchHHhHHHHhcccccccch-HH
Q 039342           76 --ESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNR------WDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESN-WQ  146 (248)
Q Consensus        76 --~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~------~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~-~~  146 (248)
                        ++.+.++.+.+.... |-..|+.--..+.+.+.      ++++++.+++.....  |............+...|. .+
T Consensus       162 ~~~EL~~~~~~i~~d~~-N~sAW~~R~~ll~~l~~~~~~~~~~eEl~~~~~aI~~~--p~n~SaW~y~~~ll~~~~~~~~  238 (306)
T 3dra_A          162 DAKELSFVDKVIDTDLK-NNSAWSHRFFLLFSKKHLATDNTIDEELNYVKDKIVKC--PQNPSTWNYLLGIHERFDRSIT  238 (306)
T ss_dssp             CHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHSSGGGCCHHHHHHHHHHHHHHHHHC--SSCHHHHHHHHHHHHHTTCCGG
T ss_pred             hHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhccccchhhhHHHHHHHHHHHHHhC--CCCccHHHHHHHHHHhcCCChH
Confidence              999999999876533 67778777666766666      889999999888765  4444433333333333333 44


Q ss_pred             HHHHHHHHHHhcC--CCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          147 MVEYVFDKLNCEG--YGLGMRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       147 ~a~~~~~~m~~~~--~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                      .+..+...+.+.+  -..+...+..+...+.+.|+.++|.++++.+.+
T Consensus       239 ~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A~~~~~~l~~  286 (306)
T 3dra_A          239 QLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNESRTVYDLLKS  286 (306)
T ss_dssp             GGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHh
Confidence            5556666655443  234778899999999999999999999999875

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.19  E-value=4.5e-05  Score=52.36  Aligned_cols=96  Identities=6%  Similarity=-0.075  Sum_probs=52.2

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Q 039342           95 CYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEAL  174 (248)
Q Consensus        95 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~  174 (248)
                      .+..+-..+.+.|++++|+..|++..+..  |+...+...+..++...|+++.|...|+...+.... +...|..+-.+|
T Consensus        38 ~~~~lg~~~~~~g~~~eA~~~~~~al~~~--P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P~-~~~~~~~lg~~~  114 (151)
T 3gyz_A           38 DIYSYAYDFYNKGRIEEAEVFFRFLCIYD--FYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKN-DYTPVFHTGQCQ  114 (151)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSS-CCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCCC-CcHHHHHHHHHH
Confidence            44444455555555555555555554432  333333333333344455555555555555544322 345566677777


Q ss_pred             HhcCchHHHHHHHHHHHHC
Q 039342          175 WCLGLRERAARVLDEATKR  193 (248)
Q Consensus       175 ~~~g~~~~a~~~~~~m~~~  193 (248)
                      ...|++++|...|++..+.
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            7777777777777776653

>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=98.18  E-value=2.6e-05  Score=54.68  Aligned_cols=122  Identities=11%  Similarity=0.053  Sum_probs=60.8

Q ss_pred             hcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHH-HHhcCCHHHHH
Q 039342           35 QGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAV-YAKSNRWDDAY  113 (248)
Q Consensus        35 ~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~-~~~~~~~~~a~  113 (248)
                      ..|++++|...++...+.. +.+...|..+-..|...|++++|...|++..+.. +.+...+..+... +...|++    
T Consensus        22 ~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~l~~~~~~~----   95 (177)
T 2e2e_A           22 SQQNPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLR-GENAELYAALATVLYYQASQH----   95 (177)
T ss_dssp             -----CCCCHHHHHHHHHC-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-CSCHHHHHHHHHHHHHHTTTC----
T ss_pred             hccCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhcCCc----
Confidence            3445555555555544332 2344455555555555555555555555554331 1133344444444 3344444    


Q ss_pred             HHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHC
Q 039342          114 GLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKR  193 (248)
Q Consensus       114 ~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  193 (248)
                                                    ..+.|...++...+.... +...+..+...+...|++++|...|++..+.
T Consensus        96 ------------------------------~~~~A~~~~~~al~~~p~-~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  144 (177)
T 2e2e_A           96 ------------------------------MTAQTRAMIDKALALDSN-EITALMLLASDAFMQANYAQAIELWQKVMDL  144 (177)
T ss_dssp             ------------------------------CCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             ------------------------------chHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHcccHHHHHHHHHHHHhh
Confidence                                          004444444444443221 3455666777777888888888888877664

>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=98.13  E-value=8e-05  Score=49.36  Aligned_cols=100  Identities=13%  Similarity=0.028  Sum_probs=76.9

Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCC--CCcC----HhhH
Q 039342           23 SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSG--ILPS----VMCY   96 (248)
Q Consensus        23 ~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~--~~p~----~~~~   96 (248)
                      ...+..+-..+.+.|++++|++.|++..+.. +-+...|..+-.+|.+.|++++|.+.+++..+..  ..++    ..+|
T Consensus         8 A~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~-p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~   86 (127)
T 4gcn_A            8 AIAEKDLGNAAYKQKDFEKAHVHYDKAIELD-PSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAM   86 (127)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHH
Confidence            3466777788899999999999999987654 3457788889999999999999999998876531  1111    2356


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           97 CMLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        97 ~~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      ..+-.++...|++++|++.|++..+..
T Consensus        87 ~~lg~~~~~~~~~~~A~~~~~kal~~~  113 (127)
T 4gcn_A           87 SRAGNAFQKQNDLSLAVQWFHRSLSEF  113 (127)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            677777888899999999998876543

>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=98.13  E-value=8.3e-05  Score=53.21  Aligned_cols=99  Identities=11%  Similarity=-0.024  Sum_probs=66.3

Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-CC---C-----------HHHHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 039342           23 SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRC-DP---N-----------ERTLEAVLSVYCFAGLVDESKEQFQEIKSS   87 (248)
Q Consensus        23 ~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p---~-----------~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~   87 (248)
                      ...+..+-..+.+.|++++|...|++..+..- .|   .           ...|..+-.+|.+.|++++|...+++..+.
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            34566666677777888888888877765321 11   0           256667777777777777777777777654


Q ss_pred             CCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 039342           88 GILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTN  122 (248)
Q Consensus        88 ~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  122 (248)
                      . +.+...+..+-.+|...|++++|...|++..+.
T Consensus       118 ~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~  151 (198)
T 2fbn_A          118 D-KNNVKALYKLGVANMYFGFLEEAKENLYKAASL  151 (198)
T ss_dssp             S-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             C-cccHHHHHHHHHHHHHcccHHHHHHHHHHHHHH
Confidence            2 225566777777777777777777777776554

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=98.11  E-value=1.3e-05  Score=52.29  Aligned_cols=85  Identities=15%  Similarity=0.140  Sum_probs=55.1

Q ss_pred             CchHHHHHHHHHHHHcCC--CCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHH
Q 039342            2 GLYKECQAILSRMSESGV--ARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKE   79 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~--~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~   79 (248)
                      |++++|+..|++..+.+.  +.+...|..+-..|.+.|++++|.+.|++..+.. +-+...+..+-.++.+.|++++|..
T Consensus         4 g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~   82 (117)
T 3k9i_A            4 GLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQF-PNHQALRVFYAMVLYNLGRYEQGVE   82 (117)
T ss_dssp             ---CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHcCCHHHHHH
Confidence            567777777777766431  2245567777777777777777777777776553 2345666677777777777777777


Q ss_pred             HHHHHHHC
Q 039342           80 QFQEIKSS   87 (248)
Q Consensus        80 ~~~~m~~~   87 (248)
                      .+++..+.
T Consensus        83 ~~~~al~~   90 (117)
T 3k9i_A           83 LLLKIIAE   90 (117)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHh
Confidence            77776543

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.11  E-value=9.7e-05  Score=46.95  Aligned_cols=85  Identities=19%  Similarity=0.177  Sum_probs=73.7

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHhc-CChhHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDP--NERTLEAVLSVYCFA-GLVDESK   78 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p--~~~t~~~ll~~~~~~-g~~~~a~   78 (248)
                      |++++|...|++..+... .+...|..+-..+...|++++|.+.+++..+.. +.  +...+..+..++.+. |++++|.
T Consensus        20 ~~~~~A~~~~~~a~~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~A~   97 (112)
T 2kck_A           20 GNYTESIDLFEKAIQLDP-EESKYWLMKGKALYNLERYEEAVDCYNYVINVI-EDEYNKDVWAAKADALRYIEGKEVEAE   97 (112)
T ss_dssp             CCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-CCTTCHHHHHHHHHHHTTCSSCSHHHH
T ss_pred             hhHHHHHHHHHHHHHhCc-CCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccchHHHHHHHHHHHHHHhCCHHHHH
Confidence            789999999999877542 467889999999999999999999999998764 23  588899999999999 9999999


Q ss_pred             HHHHHHHHCC
Q 039342           79 EQFQEIKSSG   88 (248)
Q Consensus        79 ~~~~~m~~~~   88 (248)
                      +.++...+..
T Consensus        98 ~~~~~~~~~~  107 (112)
T 2kck_A           98 IAEARAKLEH  107 (112)
T ss_dssp             HHHHHHGGGC
T ss_pred             HHHHHHhhcc
Confidence            9999998763

>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=98.08  E-value=0.00027  Score=45.23  Aligned_cols=86  Identities=12%  Similarity=0.125  Sum_probs=73.9

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|.+.|++..+... .+...|..+...+...|++++|...+++..+.. +.+...+..+..++.+.|++++|.+.
T Consensus        17 ~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~   94 (118)
T 1elw_A           17 VGNIDDALQCYSEAIKLDP-HNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEFLNRFEEAKRT   94 (118)
T ss_dssp             TTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHCC-CcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHHhhHHHHHHH
Confidence            4889999999999877542 368889999999999999999999999987764 34678889999999999999999999


Q ss_pred             HHHHHHCC
Q 039342           81 FQEIKSSG   88 (248)
Q Consensus        81 ~~~m~~~~   88 (248)
                      +++..+..
T Consensus        95 ~~~~~~~~  102 (118)
T 1elw_A           95 YEEGLKHE  102 (118)
T ss_dssp             HHHHHTTC
T ss_pred             HHHHHHcC
Confidence            99988753

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=98.07  E-value=0.0001  Score=52.74  Aligned_cols=119  Identities=11%  Similarity=0.049  Sum_probs=87.0

Q ss_pred             CCchHHHHHHHHHHHHcCCC-CC--------------HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVA-RN--------------SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVL   65 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~-~~--------------~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll   65 (248)
                      .|++++|.+.|.+..+.... |+              ...|..+-.+|.+.|++++|...++...+.. +.+...+..+-
T Consensus        51 ~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg  129 (198)
T 2fbn_A           51 KNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLG  129 (198)
T ss_dssp             TTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-cccHHHHHHHH
Confidence            37899999999998764321 11              2788889999999999999999999997764 45778889999


Q ss_pred             HHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHH-HHHHHHHH
Q 039342           66 SVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAY-GLLDEMHT  121 (248)
Q Consensus        66 ~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~-~~~~~m~~  121 (248)
                      .+|...|++++|...|++..+.. +-+...+..+-..+...++.+++. ..+..+..
T Consensus       130 ~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~f~  185 (198)
T 2fbn_A          130 VANMYFGFLEEAKENLYKAASLN-PNNLDIRNSYELCVNKLKEARKKDKLTFGGMFD  185 (198)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHC-----------
T ss_pred             HHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999988653 125667777777777777666665 44554433

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.05  E-value=6.4e-05  Score=51.19  Aligned_cols=139  Identities=13%  Similarity=0.056  Sum_probs=91.4

Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-CCC----HHHHHHHHHHHHhcCChhHHHHHHHHHHHC----CCCc-C
Q 039342           23 SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRC-DPN----ERTLEAVLSVYCFAGLVDESKEQFQEIKSS----GILP-S   92 (248)
Q Consensus        23 ~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~----~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~~p-~   92 (248)
                      ..++..+-..+...|++++|...+++..+..- .++    ..++..+-..+...|++++|.+.+++..+.    +-.+ .
T Consensus         9 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~   88 (164)
T 3ro3_A            9 GRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVE   88 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHH
Confidence            45677777888888999999888888754311 111    146777788888889999998888886542    1111 1


Q ss_pred             HhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 039342           93 VMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLE  172 (248)
Q Consensus        93 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~  172 (248)
                      ..++..+-..+...|++++|...+++..+...                ..++               .......+..+..
T Consensus        89 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~----------------~~~~---------------~~~~~~~~~~la~  137 (164)
T 3ro3_A           89 AQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQ----------------ELKD---------------RIGEGRACWSLGN  137 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH----------------HTTC---------------HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH----------------Hccc---------------hHhHHHHHHHHHH
Confidence            44677777778888888888888876543210                0000               0011344666777


Q ss_pred             HHHhcCchHHHHHHHHHHHH
Q 039342          173 ALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       173 ~~~~~g~~~~a~~~~~~m~~  192 (248)
                      .+...|++++|.+.+++..+
T Consensus       138 ~~~~~g~~~~A~~~~~~a~~  157 (164)
T 3ro3_A          138 AYTALGNHDQAMHFAEKHLE  157 (164)
T ss_dssp             HHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHccCHHHHHHHHHHHHH
Confidence            78888888888888887653

>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=98.05  E-value=2.1e-05  Score=59.96  Aligned_cols=179  Identities=7%  Similarity=-0.051  Sum_probs=113.7

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|...|.+..+... .+...|..+-..|.+.|++++|.+.+++..+.. +-+...+..+-.+|.+.|++++|...
T Consensus        17 ~g~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~   94 (281)
T 2c2l_A           17 GRKYPEAAACYGRAITRNP-LVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQCQLEMESYDEAIAN   94 (281)
T ss_dssp             TTCHHHHHHHHHHHHHHCS-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            4899999999999887542 378899999999999999999999999987653 34678888999999999999999999


Q ss_pred             HHHHHHCCCCcCH-hhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcC
Q 039342           81 FQEIKSSGILPSV-MCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEG  159 (248)
Q Consensus        81 ~~~m~~~~~~p~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~  159 (248)
                      |++..+..  |+. ..+...+....+.   ..+. -+..........+... ...+.. + ..|+++.|.+.++...+. 
T Consensus        95 ~~~al~l~--p~~~~~~~~~~~~~~~~---~~~~-~~~~~~~~~~~~~~~i-~~~l~~-l-~~~~~~~A~~~~~~al~~-  164 (281)
T 2c2l_A           95 LQRAYSLA--KEQRLNFGDDIPSALRI---AKKK-RWNSIEERRIHQESEL-HSYLTR-L-IAAERERELEECQRNHEG-  164 (281)
T ss_dssp             HHHHHHHH--HHTTCCCCSHHHHHHHH---HHHH-HHHHHHHTCCCCCCHH-HHHHHH-H-HHHHHHHHHTTTSGGGTT-
T ss_pred             HHHHHHhC--ccchhhHHHHHHHHHHH---HHHH-HHHHHHHHHHhhhHHH-HHHHHH-H-HHHHHHHHHHHHHhhhcc-
Confidence            99887532  211 1222222222211   1111 1122222333333322 222222 1 146677777766655443 


Q ss_pred             CCCCHHH-HHHHHHHHHhc-CchHHHHHHHHHHHH
Q 039342          160 YGLGMRF-YNALLEALWCL-GLRERAARVLDEATK  192 (248)
Q Consensus       160 ~~p~~~~-~~~li~~~~~~-g~~~~a~~~~~~m~~  192 (248)
                       .|+... ...+-..+.+. +.+++|.++|....+
T Consensus       165 -~p~~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~~  198 (281)
T 2c2l_A          165 -HEDDGHIRAQQACIEAKHDKYMADMDELFSQVDE  198 (281)
T ss_dssp             -TSCHHHHTHHHHHHHHHHHHHHHHHHHHHHHSSC
T ss_pred             -ccchhhhhhHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence             454433 33343444444 678899999988764

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.05  E-value=0.00011  Score=48.31  Aligned_cols=95  Identities=8%  Similarity=-0.041  Sum_probs=78.5

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCc-CHhhHHHHHHHH
Q 039342           25 SFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILP-SVMCYCMLLAVY  103 (248)
Q Consensus        25 ~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~  103 (248)
                      .+..+-..+.+.|++++|...|++..+.. +-+...|..+-.++.+.|++++|...|++..+..  | +...+..+-.++
T Consensus        19 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~--P~~~~~~~~la~~~   95 (121)
T 1hxi_A           19 NPMEEGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD--PKDIAVHAALAVSH   95 (121)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHH
Confidence            45556677889999999999999987754 3477888888889999999999999999988753  4 567888888999


Q ss_pred             HhcCCHHHHHHHHHHHHHC
Q 039342          104 AKSNRWDDAYGLLDEMHTN  122 (248)
Q Consensus       104 ~~~~~~~~a~~~~~~m~~~  122 (248)
                      ...|++++|+..|++..+.
T Consensus        96 ~~~g~~~~A~~~~~~al~~  114 (121)
T 1hxi_A           96 TNEHNANAALASLRAWLLS  114 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHC-
T ss_pred             HHcCCHHHHHHHHHHHHHh
Confidence            9999999999999987654

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=98.04  E-value=0.00011  Score=60.54  Aligned_cols=141  Identities=13%  Similarity=-0.012  Sum_probs=93.7

Q ss_pred             HHHhcCChhHHHHHHHHHHHC---CC---Cc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccc
Q 039342           67 VYCFAGLVDESKEQFQEIKSS---GI---LP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEF  139 (248)
Q Consensus        67 ~~~~~g~~~~a~~~~~~m~~~---~~---~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~  139 (248)
                      .+...|++++|..++++..+.   -+   .| ...+++.|...|...|++++|+.++++..+.                 
T Consensus       318 ~~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i-----------------  380 (490)
T 3n71_A          318 KARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDG-----------------  380 (490)
T ss_dssp             HHHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----------------
T ss_pred             HHHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH-----------------
Confidence            355788999999988877542   11   12 3467889999999999999999888765421                 


Q ss_pred             cccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHH---CCCCCCcchhhhHHhhhhhhcccc
Q 039342          140 DDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATK---RGLFPELFRHNKLVWSVDVHRMWE  216 (248)
Q Consensus       140 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~---~g~~p~~~t~~~li~~~~~~~~~~  216 (248)
                                  ++...-..-.-...+++.|-..|..+|++++|..++++..+   .-+-||-.. ..-+...+-..+.+
T Consensus       381 ------------~~~~lG~~Hp~~a~~l~nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~-~~~~~~~l~~~~~e  447 (490)
T 3n71_A          381 ------------YMKLYHHNNAQLGMAVMRAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPI-TKDLEAMRMQTEME  447 (490)
T ss_dssp             ------------HHHHSCTTCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHH-HHHHHHHHHHHHHH
T ss_pred             ------------HHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChH-HHHHHHHHHHHHHH
Confidence                        11111111111345678888889999999999998887542   222233222 22233455577788


Q ss_pred             chHHHHHHHHHHHHHHHHHcC
Q 039342          217 GGAYTAISVWLNKMYEMFMMG  237 (248)
Q Consensus       217 ~g~~~~~~~~~~~m~~~~~~~  237 (248)
                      .+.+.+++..+..++++-.+.
T Consensus       448 ~~~~~~ae~~~~~~~~~~~~~  468 (490)
T 3n71_A          448 LRMFRQNEFMYHKMREAALNN  468 (490)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHhcC
Confidence            889999999999998876554

>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=98.04  E-value=2.2e-05  Score=53.67  Aligned_cols=95  Identities=13%  Similarity=-0.024  Sum_probs=47.7

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Q 039342           95 CYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEAL  174 (248)
Q Consensus        95 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~  174 (248)
                      .+..+-..+.+.|++++|+..|++.....  |+...+...+...+...|+++.|...|+........ +...+..+-.++
T Consensus        23 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~-~~~~~~~lg~~~   99 (148)
T 2vgx_A           23 QLYSLAFNQYQSGXYEDAHXVFQALCVLD--HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDIX-EPRFPFHAAECL   99 (148)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHHHcC--cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC-CchHHHHHHHHH
Confidence            33344444444444444444444444332  222222222222233444445555555444443221 345566677777


Q ss_pred             HhcCchHHHHHHHHHHHH
Q 039342          175 WCLGLRERAARVLDEATK  192 (248)
Q Consensus       175 ~~~g~~~~a~~~~~~m~~  192 (248)
                      ...|++++|.+.|++..+
T Consensus       100 ~~~g~~~~A~~~~~~al~  117 (148)
T 2vgx_A          100 LQXGELAEAESGLFLAQE  117 (148)
T ss_dssp             HHTTCHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHH
Confidence            888888888888877654

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.04  E-value=9.6e-05  Score=49.89  Aligned_cols=85  Identities=14%  Similarity=0.138  Sum_probs=73.4

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|.+.|++..+... .+...|..+-.++.+.|++++|...|++..+.+ +-+...+..+-.+|...|++++|.+.
T Consensus        31 ~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~  108 (142)
T 2xcb_A           31 AGKWDDAQKIFQALCMLDH-YDARYFLGLGACRQSLGLYEQALQSYSYGALMD-INEPRFPFHAAECHLQLGDLDGAESG  108 (142)
T ss_dssp             TTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HccHHHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHH
Confidence            3899999999999887543 468889999999999999999999999998764 34667788899999999999999999


Q ss_pred             HHHHHHC
Q 039342           81 FQEIKSS   87 (248)
Q Consensus        81 ~~~m~~~   87 (248)
                      |+...+.
T Consensus       109 ~~~al~~  115 (142)
T 2xcb_A          109 FYSARAL  115 (142)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            9998764

>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=98.03  E-value=0.00024  Score=46.61  Aligned_cols=85  Identities=9%  Similarity=0.036  Sum_probs=74.0

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|.+.|++..+... .+...|..+-.++.+.|++++|...+++..+.. +-+...|..+-.++...|++++|...
T Consensus        17 ~~~~~~A~~~~~~al~~~p-~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~   94 (126)
T 3upv_A           17 KSDWPNAVKAYTEMIKRAP-EDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQIAVKEYASALET   94 (126)
T ss_dssp             TTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             hcCHHHHHHHHHHHHHhCC-CChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHhCHHHHHHH
Confidence            3899999999999887542 468899999999999999999999999997764 34578889999999999999999999


Q ss_pred             HHHHHHC
Q 039342           81 FQEIKSS   87 (248)
Q Consensus        81 ~~~m~~~   87 (248)
                      |++..+.
T Consensus        95 ~~~al~~  101 (126)
T 3upv_A           95 LDAARTK  101 (126)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            9998764

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.03  E-value=8e-05  Score=50.69  Aligned_cols=146  Identities=9%  Similarity=-0.099  Sum_probs=94.2

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHCCCC-cC----HhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHH
Q 039342           59 RTLEAVLSVYCFAGLVDESKEQFQEIKSSGIL-PS----VMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQ  133 (248)
Q Consensus        59 ~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~-p~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~  133 (248)
                      .++..+-..+...|++++|...+++..+..-. ++    ..++..+-..+...|++++|...+++..+...         
T Consensus        10 ~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~---------   80 (164)
T 3ro3_A           10 RAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLAR---------   80 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH---------
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH---------
Confidence            45677777888889999999988887643100 11    24677788888888888888888887653210         


Q ss_pred             HhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhc
Q 039342          134 MIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHR  213 (248)
Q Consensus       134 ~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~  213 (248)
                             ..++               .......+..+-..+...|++++|.+.+++..+..-..+........+..+...
T Consensus        81 -------~~~~---------------~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~  138 (164)
T 3ro3_A           81 -------QLKD---------------RAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNA  138 (164)
T ss_dssp             -------HTTC---------------HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             -------HhCC---------------cHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHH
Confidence                   0000               001134566777888889999999998887653211111112223333334477


Q ss_pred             cccchHHHHHHHHHHHHHHHHH
Q 039342          214 MWEGGAYTAISVWLNKMYEMFM  235 (248)
Q Consensus       214 ~~~~g~~~~~~~~~~~m~~~~~  235 (248)
                      +...|++++|...+++-.+..-
T Consensus       139 ~~~~g~~~~A~~~~~~a~~~~~  160 (164)
T 3ro3_A          139 YTALGNHDQAMHFAEKHLEISR  160 (164)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHHT
T ss_pred             HHHccCHHHHHHHHHHHHHHHH
Confidence            8899999999999998877643

>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=98.02  E-value=4.3e-05  Score=62.83  Aligned_cols=113  Identities=9%  Similarity=0.027  Sum_probs=87.5

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|.+.|++..+... .+...|..+-.+|.+.|++++|.+.+++..+.. +-+...|..+-.+|.+.|++++|.+.
T Consensus        19 ~g~~~~A~~~~~~Al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~~eA~~~   96 (477)
T 1wao_1           19 AKDYENAIKFYSQAIELNP-SNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAALRD   96 (477)
T ss_dssp             TTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             hCCHHHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            3789999999999877532 358899999999999999999999999988764 34678888999999999999999999


Q ss_pred             HHHHHHCCCCc-CHhhHHHHHHH--HHhcCCHHHHHHHHH
Q 039342           81 FQEIKSSGILP-SVMCYCMLLAV--YAKSNRWDDAYGLLD  117 (248)
Q Consensus        81 ~~~m~~~~~~p-~~~~~~~li~~--~~~~~~~~~a~~~~~  117 (248)
                      |++..+..  | +...+..+-.+  +.+.|++++|++.++
T Consensus        97 ~~~al~~~--p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           97 YETVVKVK--PHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHHHHS--TTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HHHHHHhC--CCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            99987652  3 33455555555  788899999999888

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.00  E-value=0.00031  Score=46.10  Aligned_cols=94  Identities=14%  Similarity=0.107  Sum_probs=71.3

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH---HHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcC----HhhHHHH
Q 039342           27 NAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNE---RTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPS----VMCYCML   99 (248)
Q Consensus        27 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~---~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~----~~~~~~l   99 (248)
                      ..+-..+.+.|++++|.+.|+...+..- .+.   ..+..+-.++.+.|++++|...|++..+..  |+    ...+..+
T Consensus         6 ~~~a~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~l   82 (129)
T 2xev_A            6 YNVAFDALKNGKYDDASQLFLSFLELYP-NGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRY--PTHDKAAGGLLKL   82 (129)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCS-SSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTSTTHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHCC-CCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHC--CCCcccHHHHHHH
Confidence            3455667788999999999998876531 122   467777888889999999999998887653  32    5567778


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHCC
Q 039342          100 LAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus       100 i~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      -.++...|++++|...|++..+..
T Consensus        83 a~~~~~~g~~~~A~~~~~~~~~~~  106 (129)
T 2xev_A           83 GLSQYGEGKNTEAQQTLQQVATQY  106 (129)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC
Confidence            888888999999999998887654

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.00  E-value=9.8e-05  Score=55.92  Aligned_cols=119  Identities=15%  Similarity=0.068  Sum_probs=59.4

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHhcCChhHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN--ERTLEAVLSVYCFAGLVDESKE   79 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~--~~t~~~ll~~~~~~g~~~~a~~   79 (248)
                      |++++|.++|+.+...+  |+......+-..+.+.+++++|+..|+...+.. .|.  ...+..+-.++.+.|++++|.+
T Consensus       116 g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~-d~~~~~~a~~~LG~al~~LG~~~eAl~  192 (282)
T 4f3v_A          116 GNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP-DKFLAGAAGVAHGVAAANLALFTEAER  192 (282)
T ss_dssp             TCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS-CHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             CCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC-CcccHHHHHHHHHHHHHHCCCHHHHHH
Confidence            55666666666555433  322233333445556666666666665332211 010  1244445555666666666666


Q ss_pred             HHHHHHHCCCCcC--HhhHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           80 QFQEIKSSGILPS--VMCYCMLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        80 ~~~~m~~~~~~p~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      .|++.......|.  .......-.++.+.|+.++|...|+++....
T Consensus       193 ~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~  238 (282)
T 4f3v_A          193 RLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTH  238 (282)
T ss_dssp             HHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            6666553322132  2234444455556666666666666665543

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=97.98  E-value=0.00011  Score=48.18  Aligned_cols=99  Identities=5%  Similarity=0.015  Sum_probs=78.8

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC--CCC----HHHHHHHHHHHHhcCCh
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRC--DPN----ERTLEAVLSVYCFAGLV   74 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~--~p~----~~t~~~ll~~~~~~g~~   74 (248)
                      .|++++|...|.+..+.. +.+...|..+...+...|++++|...+++..+...  .++    ..++..+..++.+.|++
T Consensus        17 ~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~   95 (131)
T 1elr_A           17 KKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEKY   95 (131)
T ss_dssp             TTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             hcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHHHHHHHHHHhccH
Confidence            378999999999987754 34678899999999999999999999999866531  233    77888899999999999


Q ss_pred             hHHHHHHHHHHHCCCCcCHhhHHHHHHH
Q 039342           75 DESKEQFQEIKSSGILPSVMCYCMLLAV  102 (248)
Q Consensus        75 ~~a~~~~~~m~~~~~~p~~~~~~~li~~  102 (248)
                      ++|.+.|++..+.  .|+......+-..
T Consensus        96 ~~A~~~~~~~~~~--~~~~~~~~~l~~~  121 (131)
T 1elr_A           96 KDAIHFYNKSLAE--HRTPDVLKKCQQA  121 (131)
T ss_dssp             HHHHHHHHHHHHH--CCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CCCHHHHHHHHHH
Confidence            9999999999875  3555555444433

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.97  E-value=5e-05  Score=62.43  Aligned_cols=120  Identities=13%  Similarity=0.043  Sum_probs=57.5

Q ss_pred             CchHHHHHHHHHHHHc-----CC-CC-CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHc---CCC---C-CHHHHHHHHHH
Q 039342            2 GLYKECQAILSRMSES-----GV-AR-NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKV---RCD---P-NERTLEAVLSV   67 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~-----g~-~~-~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~---~~~---p-~~~t~~~ll~~   67 (248)
                      |++++|+.++++..+.     |. .| ...+++.|...|...|++++|..++++..+-   -+.   | ...+++.|-..
T Consensus       323 g~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~  402 (490)
T 3n71_A          323 GLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMRAGLT  402 (490)
T ss_dssp             TCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            5555666555544321     11 11 2345566666666666666666655554221   111   1 12445555555


Q ss_pred             HHhcCChhHHHHHHHHHHH-----CCCC-c-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 039342           68 YCFAGLVDESKEQFQEIKS-----SGIL-P-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHT  121 (248)
Q Consensus        68 ~~~~g~~~~a~~~~~~m~~-----~~~~-p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  121 (248)
                      |...|++++|..++++..+     .|-. | ...+.+.+-.++...+.+++|+.+|.++++
T Consensus       403 ~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~  463 (490)
T 3n71_A          403 NWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMRE  463 (490)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6666666666655555432     1211 1 123344444455555555555555555543

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=97.94  E-value=0.00023  Score=47.28  Aligned_cols=99  Identities=11%  Similarity=0.006  Sum_probs=64.5

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHh
Q 039342           56 PNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMI  135 (248)
Q Consensus        56 p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l  135 (248)
                      .+...|..+-..+.+.|++++|...|+...+.. +.+...|..+-..+...|++++|...+++..+..  |         
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~--p---------   74 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD--G---------   74 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T---------
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC--c---------
Confidence            455666666677777777777777777666542 1245566666666666677776666666554332  1         


Q ss_pred             cccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          136 KGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       136 ~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                                                .+...+..+-.++...|++++|...|++..+
T Consensus        75 --------------------------~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           75 --------------------------QSVKAHFFLGQCQLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             --------------------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             --------------------------hhHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence                                      1345667777778888888888888887654

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=97.92  E-value=0.00057  Score=44.75  Aligned_cols=84  Identities=13%  Similarity=0.159  Sum_probs=70.2

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCH---HhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC----HHHHHHHHHHHHhcCC
Q 039342            1 GGLYKECQAILSRMSESGVARNS---DSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN----ERTLEAVLSVYCFAGL   73 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~---~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~----~~t~~~ll~~~~~~g~   73 (248)
                      .|++++|.+.|+...+.... +.   ..+..+-..+.+.|++++|...|+...+..  |+    ...+..+-.++.+.|+
T Consensus        15 ~~~~~~A~~~~~~~~~~~p~-~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~la~~~~~~g~   91 (129)
T 2xev_A           15 NGKYDDASQLFLSFLELYPN-GVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRY--PTHDKAAGGLLKLGLSQYGEGK   91 (129)
T ss_dssp             TTCHHHHHHHHHHHHHHCSS-STTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTSTTHHHHHHHHHHHHHHTTC
T ss_pred             hCCHHHHHHHHHHHHHHCCC-CcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHC--CCCcccHHHHHHHHHHHHHcCC
Confidence            38999999999998875432 23   577888889999999999999999997753  33    5678888899999999


Q ss_pred             hhHHHHHHHHHHHC
Q 039342           74 VDESKEQFQEIKSS   87 (248)
Q Consensus        74 ~~~a~~~~~~m~~~   87 (248)
                      +++|...|+...+.
T Consensus        92 ~~~A~~~~~~~~~~  105 (129)
T 2xev_A           92 NTEAQQTLQQVATQ  105 (129)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999999875

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.91  E-value=0.00044  Score=46.36  Aligned_cols=65  Identities=9%  Similarity=-0.065  Sum_probs=48.4

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcC----HhhHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 039342           56 PNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPS----VMCYCMLLAVYAKSNRWDDAYGLLDEMHTN  122 (248)
Q Consensus        56 p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  122 (248)
                      .+...+..+...+.+.|++++|.+.|++..+.  .|+    ...|..+-..|...|++++|+..+++..+.
T Consensus        26 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~   94 (148)
T 2dba_A           26 SSVEQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEK   94 (148)
T ss_dssp             CCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhh
Confidence            45667777788888888888888888887764  344    566777777777888888888877776544

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=97.89  E-value=0.00034  Score=48.31  Aligned_cols=100  Identities=8%  Similarity=-0.051  Sum_probs=77.3

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhc
Q 039342           57 NERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIK  136 (248)
Q Consensus        57 ~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~  136 (248)
                      +...+..+-..+.+.|++++|.+.|++..+.. +-+...|..+-.+|.+.|++++|+..|++..+..  |+.......+.
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg   86 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSKAIDLYTQALSIA-PANPIYLSNRAAAYSASGQHEKAAEDAELATVVD--PKYSKAWSRLG   86 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--CCCHHHHHHHH
Confidence            45677888889999999999999999988753 2267889999999999999999999999988765  44433333333


Q ss_pred             ccccccchHHHHHHHHHHHHhcC
Q 039342          137 GEFDDESNWQMVEYVFDKLNCEG  159 (248)
Q Consensus       137 ~~~~~~~~~~~a~~~~~~m~~~~  159 (248)
                      ..+...|+++.|...|+...+..
T Consensus        87 ~~~~~~g~~~~A~~~~~~al~~~  109 (164)
T 3sz7_A           87 LARFDMADYKGAKEAYEKGIEAE  109 (164)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHccCHHHHHHHHHHHHHhC
Confidence            33667788888888888877653

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=97.88  E-value=0.00027  Score=46.75  Aligned_cols=94  Identities=9%  Similarity=0.078  Sum_probs=73.7

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCCC----HHHHHHHHHHHHhcCCh
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVR--CDPN----ERTLEAVLSVYCFAGLV   74 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~--~~p~----~~t~~~ll~~~~~~g~~   74 (248)
                      .|++++|++.|++..+... -+...|+.+-.+|.+.|++++|++.+++..+.+  ..++    ..+|..+-.++...|++
T Consensus        21 ~~~~~~A~~~y~~Al~~~p-~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~~~~   99 (127)
T 4gcn_A           21 QKDFEKAHVHYDKAIELDP-SNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMSRAGNAFQKQNDL   99 (127)
T ss_dssp             TTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             cCCHHHHHHHHHHHHHhCC-CCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHHcCCH
Confidence            3899999999999887542 368889999999999999999999999986532  2222    24677778889999999


Q ss_pred             hHHHHHHHHHHHCCCCcCHhhHH
Q 039342           75 DESKEQFQEIKSSGILPSVMCYC   97 (248)
Q Consensus        75 ~~a~~~~~~m~~~~~~p~~~~~~   97 (248)
                      ++|.+.|++..+.  .|+..+..
T Consensus       100 ~~A~~~~~kal~~--~~~~~~~~  120 (127)
T 4gcn_A          100 SLAVQWFHRSLSE--FRDPELVK  120 (127)
T ss_dssp             HHHHHHHHHHHHH--SCCHHHHH
T ss_pred             HHHHHHHHHHHhh--CcCHHHHH
Confidence            9999999987764  45655443

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.86  E-value=3.6e-05  Score=50.16  Aligned_cols=87  Identities=10%  Similarity=-0.010  Sum_probs=64.3

Q ss_pred             hcCCHHHHHHHHHHHHHcC--CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHH
Q 039342           35 QGGRFEEAIKAYVEMEKVR--CDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDA  112 (248)
Q Consensus        35 ~~~~~~~a~~~~~~m~~~~--~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a  112 (248)
                      ..|++++|...|++..+.+  -+-+...+..+-.+|.+.|++++|...|++..+... -+...+..+-.++.+.|++++|
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~g~~~~A   80 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFP-NHQALRVFYAMVLYNLGRYEQG   80 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CchHHHHHHHHHHHHcCCHHHH
Confidence            3578888888888887654  123456777888888999999999999998876532 2567788888888999999999


Q ss_pred             HHHHHHHHHC
Q 039342          113 YGLLDEMHTN  122 (248)
Q Consensus       113 ~~~~~~m~~~  122 (248)
                      +..|++..+.
T Consensus        81 ~~~~~~al~~   90 (117)
T 3k9i_A           81 VELLLKIIAE   90 (117)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            9998887654

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=97.85  E-value=0.00018  Score=47.19  Aligned_cols=85  Identities=7%  Similarity=-0.048  Sum_probs=72.7

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|...|++..+... .+...|..+-.++...|++++|...|++..+.. +-+...+..+-.++.+.|++++|...
T Consensus        30 ~g~~~~A~~~~~~al~~~P-~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~~~~~la~~~~~~g~~~~A~~~  107 (121)
T 1hxi_A           30 LANLAEAALAFEAVCQKEP-EREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHNANAALAS  107 (121)
T ss_dssp             TTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            3889999999999987542 368889999999999999999999999987764 34677888999999999999999999


Q ss_pred             HHHHHHC
Q 039342           81 FQEIKSS   87 (248)
Q Consensus        81 ~~~m~~~   87 (248)
                      +++..+.
T Consensus       108 ~~~al~~  114 (121)
T 1hxi_A          108 LRAWLLS  114 (121)
T ss_dssp             HHHHHC-
T ss_pred             HHHHHHh
Confidence            9998764

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=97.85  E-value=0.00042  Score=56.57  Aligned_cols=121  Identities=8%  Similarity=-0.010  Sum_probs=81.9

Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC--------------HHHHHHHHHHHHhcCChhHHHHHHHHHHHCC
Q 039342           23 SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN--------------ERTLEAVLSVYCFAGLVDESKEQFQEIKSSG   88 (248)
Q Consensus        23 ~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~--------------~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~   88 (248)
                      ...|..+-..+.+.|++++|...|++..+..-...              ...|..+-.+|.+.|++++|...+++..+..
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            45677778888889999999999988866431111              5777888888888888888888888887653


Q ss_pred             CCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHH
Q 039342           89 ILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQ  146 (248)
Q Consensus        89 ~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~  146 (248)
                       +.+...|..+-.+|...|++++|+..|++..+..  |+.......+...+...++.+
T Consensus       348 -p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~--P~~~~a~~~l~~~~~~~~~~~  402 (457)
T 1kt0_A          348 -SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVN--PQNKAARLQISMCQKKAKEHN  402 (457)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC------CHHHHHHHHHHHHHHHH
T ss_pred             -CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHHHHHH
Confidence             2256778888888888888888888888877543  544433333333233333333

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=97.84  E-value=0.0058  Score=47.77  Aligned_cols=226  Identities=9%  Similarity=-0.085  Sum_probs=137.5

Q ss_pred             chHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcC-CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc-C-ChhHHHH
Q 039342            3 LYKECQAILSRMSESGVARNSDSFNAVIEAFRQGG-RFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFA-G-LVDESKE   79 (248)
Q Consensus         3 ~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~-~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~-g-~~~~a~~   79 (248)
                      .-++|+++++.+..... -+...|+.-=..+...| ++++++++++.+.... +-+..+|+.--..+.+. + +++++.+
T Consensus        69 ~se~AL~lt~~~L~~nP-~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~n-PKny~aW~hR~wlL~~l~~~~~~~EL~  146 (349)
T 3q7a_A           69 KSERALELTEIIVRMNP-AHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQN-LKSYQVWHHRLLLLDRISPQDPVSEIE  146 (349)
T ss_dssp             CSHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTT-CCCHHHHHHHHHHHHHHCCSCCHHHHH
T ss_pred             CCHHHHHHHHHHHHhCc-hhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHhcCCChHHHHH
Confidence            34678888888876442 24667777666777777 5999999999998765 45677887776666666 6 8899999


Q ss_pred             HHHHHHHCCCCcCHhhHHHHHHHHHhcCCHH--------HHHHHHHHHHHCCCCchHH-hHHHHhcccccc----cchHH
Q 039342           80 QFQEIKSSGILPSVMCYCMLLAVYAKSNRWD--------DAYGLLDEMHTNRISNIHQ-VTGQMIKGEFDD----ESNWQ  146 (248)
Q Consensus        80 ~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~--------~a~~~~~~m~~~~~~~~~~-~~~~~l~~~~~~----~~~~~  146 (248)
                      +++.+.+... -|-.+|+---..+.+.+.++        ++++.++++.+....-... .+...+......    ...++
T Consensus       147 ~~~k~L~~dp-kNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp~N~SAW~~R~~lL~~l~~~~~~~~~~~  225 (349)
T 3q7a_A          147 YIHGSLLPDP-KNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDGRNNSAWGWRWYLRVSRPGAETSSRSLQ  225 (349)
T ss_dssp             HHHHHTSSCT-TCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHTTSTTCCCCHHHHH
T ss_pred             HHHHHHHhCC-CCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhccccccchHHHH
Confidence            9999987532 26667776555555555555        8999999998876433222 222222221221    12357


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCch--------------------HHHHHHHHHHHHCCCCCCcchhhhHH
Q 039342          147 MVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLR--------------------ERAARVLDEATKRGLFPELFRHNKLV  206 (248)
Q Consensus       147 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~--------------------~~a~~~~~~m~~~g~~p~~~t~~~li  206 (248)
                      .+.+.++........ |...|+-+--.+.+.|+.                    ....+...++...+-..+...-+...
T Consensus       226 eELe~~~~aI~~~P~-n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~a  304 (349)
T 3q7a_A          226 DELIYILKSIHLIPH-NVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDIETVEAFGFPMPSDPLPEDTPLPVPLA  304 (349)
T ss_dssp             HHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC--------------CCCCC-CCCSSCCSCCHHH
T ss_pred             HHHHHHHHHHHhCCC-CHHHHHHHHHHHHhcCCCcccccccccccccccccccchhHHHHHHHHHhcccccccCCCcHHH
Confidence            777777777766544 677777666666665543                    22222222222211000001123334


Q ss_pred             hhhhhhccccchHHHHHHHHHHHHHH
Q 039342          207 WSVDVHRMWEGGAYTAISVWLNKMYE  232 (248)
Q Consensus       207 ~~~~~~~~~~~g~~~~~~~~~~~m~~  232 (248)
                      ..++...|.+.|+.++|.++++.+.+
T Consensus       305 l~~l~d~~~~~~~~~~a~~~~~~l~~  330 (349)
T 3q7a_A          305 LEYLADSFIEQNRVDDAAKVFEKLSS  330 (349)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHh
Confidence            45555777888888899998888754

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=97.84  E-value=0.00058  Score=47.01  Aligned_cols=104  Identities=14%  Similarity=0.071  Sum_probs=83.3

Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHHc-------C----------CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHH
Q 039342           23 SDSFNAVIEAFRQGGRFEEAIKAYVEMEKV-------R----------CDPNERTLEAVLSVYCFAGLVDESKEQFQEIK   85 (248)
Q Consensus        23 ~~~y~~li~~~~~~~~~~~a~~~~~~m~~~-------~----------~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~   85 (248)
                      +..+...-..+.+.|++++|...|.+..+.       .          -+.+...|..+-.+|.+.|++++|...++...
T Consensus        11 a~~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al   90 (162)
T 3rkv_A           11 VEALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVL   90 (162)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            456777778889999999999999988654       0          12234678888899999999999999999988


Q ss_pred             HCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHH
Q 039342           86 SSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQ  129 (248)
Q Consensus        86 ~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~  129 (248)
                      +.. +.+...|..+-.+|...|++++|...|++..+..  |+..
T Consensus        91 ~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~--p~~~  131 (162)
T 3rkv_A           91 KRE-ETNEKALFRRAKARIAAWKLDEAEEDLKLLLRNH--PAAA  131 (162)
T ss_dssp             HHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--GGGH
T ss_pred             hcC-CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhcC--CCCH
Confidence            753 2367789999999999999999999999887664  5544

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=97.83  E-value=0.0021  Score=53.01  Aligned_cols=205  Identities=12%  Similarity=0.015  Sum_probs=131.6

Q ss_pred             HHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHH
Q 039342            5 KECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEI   84 (248)
Q Consensus         5 ~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m   84 (248)
                      +++..+|++..... +.+...|-..+..+.+.|+++.|..++++....  +.+...+.    .|+...+.+..   ++.+
T Consensus       196 ~Rv~~~ye~al~~~-p~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~--P~~~~l~~----~y~~~~e~~~~---~~~l  265 (493)
T 2uy1_A          196 SRMHFIHNYILDSF-YYAEEVYFFYSEYLIGIGQKEKAKKVVERGIEM--SDGMFLSL----YYGLVMDEEAV---YGDL  265 (493)
T ss_dssp             HHHHHHHHHHHHHT-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCSSHHHH----HHHHHTTCTHH---HHHH
T ss_pred             HHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC--CCcHHHHH----HHHhhcchhHH---HHHH
Confidence            45677888877643 345788988899999999999999999999877  33333322    23332222222   3333


Q ss_pred             HHCC---------C---CcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHH--HHhcccccccchHHHHHH
Q 039342           85 KSSG---------I---LPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTG--QMIKGEFDDESNWQMVEY  150 (248)
Q Consensus        85 ~~~~---------~---~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~--~~l~~~~~~~~~~~~a~~  150 (248)
                      .+.-         .   ......|-..+....+.+.++.|..+|++. ... ..+..++.  +.+.  +...++.+.|..
T Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A-~~~-~~~~~v~i~~A~lE--~~~~~d~~~ar~  341 (493)
T 2uy1_A          266 KRKYSMGEAESAEKVFSKELDLLRINHLNYVLKKRGLELFRKLFIEL-GNE-GVGPHVFIYCAFIE--YYATGSRATPYN  341 (493)
T ss_dssp             HHHTC----------CHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH-TTS-CCCHHHHHHHHHHH--HHHHCCSHHHHH
T ss_pred             HHHHHhhccchhhhhcccccHHHHHHHHHHHHHcCCHHHHHHHHHHh-hCC-CCChHHHHHHHHHH--HHHCCChHHHHH
Confidence            3210         0   112355777777777888999999999998 321 12223332  2222  223346899999


Q ss_pred             HHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHH
Q 039342          151 VFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKM  230 (248)
Q Consensus       151 ~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m  230 (248)
                      +|+...+.-. -+...+...++...+.|+.+.|..+|+...+          ...+|...+.--.+.|+.+.+..++++.
T Consensus       342 ife~al~~~~-~~~~~~~~yid~e~~~~~~~~aR~l~er~~k----------~~~lw~~~~~fE~~~G~~~~~r~v~~~~  410 (493)
T 2uy1_A          342 IFSSGLLKHP-DSTLLKEEFFLFLLRIGDEENARALFKRLEK----------TSRMWDSMIEYEFMVGSMELFRELVDQK  410 (493)
T ss_dssp             HHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHSCC----------BHHHHHHHHHHHHHHSCHHHHHHHHHHH
T ss_pred             HHHHHHHHCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH----------HHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            9998877532 1344556677777889999999999998621          2344444445455678888888888888


Q ss_pred             HHHH
Q 039342          231 YEMF  234 (248)
Q Consensus       231 ~~~~  234 (248)
                      .+.-
T Consensus       411 ~~~~  414 (493)
T 2uy1_A          411 MDAI  414 (493)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            7643

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=97.79  E-value=0.0017  Score=50.83  Aligned_cols=186  Identities=8%  Similarity=-0.056  Sum_probs=128.4

Q ss_pred             chHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhc-C-CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChh-----
Q 039342            3 LYKECQAILSRMSESGVARNSDSFNAVIEAFRQG-G-RFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVD-----   75 (248)
Q Consensus         3 ~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~-~-~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~-----   75 (248)
                      +++++++.++.+..... .+..+|+.--..+.+. + ++++++++++.+.+.. +-|...|+.---...+.|.++     
T Consensus       104 ~l~eEL~~~~~~L~~nP-Kny~aW~hR~wlL~~l~~~~~~~EL~~~~k~L~~d-pkNy~AW~~R~wvl~~l~~~~~~~~~  181 (349)
T 3q7a_A          104 SLEDELRLMNEFAVQNL-KSYQVWHHRLLLLDRISPQDPVSEIEYIHGSLLPD-PKNYHTWAYLHWLYSHFSTLGRISEA  181 (349)
T ss_dssp             CHHHHHHHHHHHHHTTC-CCHHHHHHHHHHHHHHCCSCCHHHHHHHHHHTSSC-TTCHHHHHHHHHHHHHHHHTTCCCHH
T ss_pred             hHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccccccchh
Confidence            58899999999987553 4778888877777776 6 8999999999998664 457778876666665556666     


Q ss_pred             ---HHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCC-------HHHHHHHHHHHHHCCCCchHHhHHHHhcccccccch-
Q 039342           76 ---ESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNR-------WDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESN-  144 (248)
Q Consensus        76 ---~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~-------~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~-  144 (248)
                         ++.+.++++.+.... |-..|+-.-..+.+.++       ++++++.+++.....  |........+.+.+...+. 
T Consensus       182 ~~~eELe~~~k~I~~dp~-N~SAW~~R~~lL~~l~~~~~~~~~~~eELe~~~~aI~~~--P~n~SaW~Ylr~Ll~~~~~~  258 (349)
T 3q7a_A          182 QWGSELDWCNEMLRVDGR-NNSAWGWRWYLRVSRPGAETSSRSLQDELIYILKSIHLI--PHNVSAWNYLRGFLKHFSLP  258 (349)
T ss_dssp             HHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHTTSTTCCCCHHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCC
T ss_pred             hHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHhcCCC
Confidence               899999999876433 77788888777777775       688888888887654  5554444333332322221 


Q ss_pred             -------------------HHHHHHHHHHHHhcC-----CCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHC
Q 039342          145 -------------------WQMVEYVFDKLNCEG-----YGLGMRFYNALLEALWCLGLRERAARVLDEATKR  193 (248)
Q Consensus       145 -------------------~~~a~~~~~~m~~~~-----~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  193 (248)
                                         ..........+...+     -.++......+.+.|...|+.++|.++++.+.+.
T Consensus       259 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~l~d~~~~~~~~~~a~~~~~~l~~~  331 (349)
T 3q7a_A          259 LVPILPAILPYTASKLNPDIETVEAFGFPMPSDPLPEDTPLPVPLALEYLADSFIEQNRVDDAAKVFEKLSSE  331 (349)
T ss_dssp             SGGGHHHHGGGTC--------------CCCCC-CCCSSCCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             cccccccccccccccccccchhHHHHHHHHHhcccccccCCCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhh
Confidence                               122333333332221     1367888899999999999999999999998653

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=97.79  E-value=0.00037  Score=55.25  Aligned_cols=99  Identities=10%  Similarity=0.035  Sum_probs=73.6

Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHHc---------------CCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCC
Q 039342           24 DSFNAVIEAFRQGGRFEEAIKAYVEMEKV---------------RCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSG   88 (248)
Q Consensus        24 ~~y~~li~~~~~~~~~~~a~~~~~~m~~~---------------~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~   88 (248)
                      ..|..+-..+.+.|++++|.+.|++..+.               --+.+...|..+-.+|.+.|++++|.+.+++..+..
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            45777778888899999999999887651               112234677777788888888888888888887653


Q ss_pred             CCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           89 ILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        89 ~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                       +.+...|..+-.+|...|++++|+..|++..+..
T Consensus       304 -p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~  337 (370)
T 1ihg_A          304 -PSNTKALYRRAQGWQGLKEYDQALADLKKAQEIA  337 (370)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             -chhHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC
Confidence             1256677788888888888888888888876553

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=97.77  E-value=9.4e-05  Score=60.79  Aligned_cols=120  Identities=8%  Similarity=-0.014  Sum_probs=88.9

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCH
Q 039342           30 IEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRW  109 (248)
Q Consensus        30 i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~  109 (248)
                      -..+.+.|++++|.+.|++..+.. +-+...|..+-.+|.+.|++++|.+.+++..+.. +.+...|..+-.+|.+.|++
T Consensus        13 g~~~~~~g~~~~A~~~~~~Al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~   90 (477)
T 1wao_1           13 ANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKF   90 (477)
T ss_dssp             SSSTTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHHTCH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCH
Confidence            344567899999999999987763 3458899999999999999999999999998863 22678899999999999999


Q ss_pred             HHHHHHHHHHHHCCCCchHHhHHHHhccc--ccccchHHHHHHHHH
Q 039342          110 DDAYGLLDEMHTNRISNIHQVTGQMIKGE--FDDESNWQMVEYVFD  153 (248)
Q Consensus       110 ~~a~~~~~~m~~~~~~~~~~~~~~~l~~~--~~~~~~~~~a~~~~~  153 (248)
                      ++|+..|++..+..  |+.......+...  +...+++++|...++
T Consensus        91 ~eA~~~~~~al~~~--p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           91 RAALRDYETVVKVK--PHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHHHHHHHHHHS--TTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            99999999987754  3332222222221  445677888888777

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=97.74  E-value=0.0027  Score=42.52  Aligned_cols=111  Identities=5%  Similarity=-0.132  Sum_probs=76.3

Q ss_pred             chHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----cCChhHHH
Q 039342            3 LYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCF----AGLVDESK   78 (248)
Q Consensus         3 ~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~----~g~~~~a~   78 (248)
                      +.++|.+.|++..+.|. |+..    +-..|...+.++.|.+.|++..+.|   +...+..+-..|..    .+++++|.
T Consensus        10 d~~~A~~~~~~aa~~g~-~~a~----lg~~y~~g~~~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~   81 (138)
T 1klx_A           10 DLKKAIQYYVKACELNE-MFGC----LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKAA   81 (138)
T ss_dssp             HHHHHHHHHHHHHHTTC-TTHH----HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHH
T ss_pred             CHHHHHHHHHHHHcCCC-Hhhh----HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccHHHHH
Confidence            56778888888777663 3333    4455555567777888888776654   45566666666766    67888888


Q ss_pred             HHHHHHHHCCCCcCHhhHHHHHHHHHh----cCCHHHHHHHHHHHHHCCC
Q 039342           79 EQFQEIKSSGILPSVMCYCMLLAVYAK----SNRWDDAYGLLDEMHTNRI  124 (248)
Q Consensus        79 ~~~~~m~~~~~~p~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~  124 (248)
                      +.|++..+.|   +...+..|-..|..    .++.++|...|++-.+.|.
T Consensus        82 ~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  128 (138)
T 1klx_A           82 QYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  128 (138)
T ss_dssp             HHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCCC
Confidence            8888877764   45566666666666    6777888888877766653

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=97.72  E-value=0.0007  Score=55.26  Aligned_cols=117  Identities=11%  Similarity=0.133  Sum_probs=92.8

Q ss_pred             CCchHHHHHHHHHHHHcCCCCC--------------HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARN--------------SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLS   66 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~--------------~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~   66 (248)
                      .|++++|...|.+..+......              ...|..+-.+|.+.|++++|+..+++..+.. +.+...|..+-.
T Consensus       281 ~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~~g~  359 (457)
T 1kt0_A          281 GGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGE  359 (457)
T ss_dssp             TTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHH
Confidence            3789999999998876432111              5889999999999999999999999998764 457888999999


Q ss_pred             HHHhcCChhHHHHHHHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHH-HHHHHH
Q 039342           67 VYCFAGLVDESKEQFQEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYG-LLDEMH  120 (248)
Q Consensus        67 ~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~-~~~~m~  120 (248)
                      +|.+.|++++|...|++..+.  .| +...+..+-..+.+.++.+++.+ .+..|.
T Consensus       360 a~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~f  413 (457)
T 1kt0_A          360 AQLLMNEFESAKGDFEKVLEV--NPQNKAARLQISMCQKKAKEHNERDRRIYANMF  413 (457)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTT--C----CHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999875  34 55788888888888888877663 445443

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=97.70  E-value=0.01  Score=46.08  Aligned_cols=222  Identities=9%  Similarity=-0.057  Sum_probs=142.8

Q ss_pred             HHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCC----------HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC--
Q 039342            5 KECQAILSRMSESGVARNSDSFNAVIEAFRQGGR----------FEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAG--   72 (248)
Q Consensus         5 ~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~----------~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g--   72 (248)
                      ++|+++++.+..... -+...||.==..+...+.          +++++.+++.+.... +-+..+|+.--..+.+.+  
T Consensus        47 ~eaL~~t~~~L~~nP-~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~-PKny~aW~hR~wlL~~l~~~  124 (331)
T 3dss_A           47 ESVLELTSQILGANP-DFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWHHRCWLLSRLPEP  124 (331)
T ss_dssp             HHHHHHHHHHHTTCT-TCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHCSSC
T ss_pred             HHHHHHHHHHHHHCc-hhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHhccCcc
Confidence            478888888876432 234555553233322222          678888898887654 457788887777777777  


Q ss_pred             ChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCC-HHHHHHHHHHHHHCCCCchHHh-HHH-Hhccccc---------
Q 039342           73 LVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNR-WDDAYGLLDEMHTNRISNIHQV-TGQ-MIKGEFD---------  140 (248)
Q Consensus        73 ~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~-~~~a~~~~~~m~~~~~~~~~~~-~~~-~l~~~~~---------  140 (248)
                      .++++..+++.+.+... -|-.+|+---..+...|. ++++++.++++.+........- +.. ++.....         
T Consensus       125 ~~~~EL~~~~k~l~~dp-rNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~p~N~SAW~~R~~ll~~l~~~~~~~~~~~  203 (331)
T 3dss_A          125 NWARELELCARFLEADE-RNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDSGPQGR  203 (331)
T ss_dssp             CHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHHSCCC------C
T ss_pred             cHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHhhhccccccccc
Confidence            48999999999987642 267788877777778887 6899999999988764332221 112 2222111         


Q ss_pred             -ccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhc-----------CchHHHHHHHHHHHHCCCCCCcchhhhHHhh
Q 039342          141 -DESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCL-----------GLRERAARVLDEATKRGLFPELFRHNKLVWS  208 (248)
Q Consensus       141 -~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~-----------g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~  208 (248)
                       ..+.++.+.+.+......... |...|+-+--.+.+.           +.++++.+.++++.+.  .||. .+..+...
T Consensus       204 ~~~~~~~eEle~~~~ai~~~P~-d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l~~el~~~~elle~--~pd~-~w~l~~~~  279 (331)
T 3dss_A          204 LPENVLLKELELVQNAFFTDPN-DQSAWFYHRWLLGAGSGRCELSVEKSTVLQSELESCKELQEL--EPEN-KWCLLTII  279 (331)
T ss_dssp             CCHHHHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHSSSCGGGCCHHHHHHHHHHHHHHHHHHHH--CTTC-HHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhccCccccchHHHHHHHHHHHHHHHHHhh--Cccc-chHHHHHH
Confidence             115577788888877766543 666676444444443           4678899999998874  6764 34433333


Q ss_pred             hhhhccccchHHHHHHHHHHHHHHH
Q 039342          209 VDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       209 ~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      ++..+....|..+++..+++++++.
T Consensus       280 ~~~~~~~~~~~~~~~~~~l~~l~~~  304 (331)
T 3dss_A          280 LLMRALDPLLYEKETLQYFSTLKAV  304 (331)
T ss_dssp             HHHHHHCTTTTHHHHHHHHHHHHHH
T ss_pred             HHHHhhcccccHHHHHHHHHHHHHh
Confidence            3334444566777788888888754

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=97.68  E-value=0.00026  Score=55.36  Aligned_cols=130  Identities=8%  Similarity=-0.003  Sum_probs=71.4

Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHH------------------HHHHHHHHHHhcCChhHHHHHHHHH
Q 039342           23 SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNER------------------TLEAVLSVYCFAGLVDESKEQFQEI   84 (248)
Q Consensus        23 ~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~------------------t~~~ll~~~~~~g~~~~a~~~~~~m   84 (248)
                      ...|..+-..+.+.|++++|...|++..+.  .|+..                  .|..+-.+|.+.|++++|...+++.
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~~~~a  256 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNIV  256 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            345666677777888999999988887654  34433                  6777777888888888888888887


Q ss_pred             HHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhccc-ccccchHHHHHHHHHHHHh
Q 039342           85 KSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGE-FDDESNWQMVEYVFDKLNC  157 (248)
Q Consensus        85 ~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~-~~~~~~~~~a~~~~~~m~~  157 (248)
                      .+.. +.+...|..+-.+|...|++++|+..|++..+.  .|+.......+... ....+..+.+..+|..|..
T Consensus       257 l~~~-p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l--~p~~~~a~~~L~~l~~~~~~~~~~a~~~~~~~l~  327 (338)
T 2if4_A          257 LTEE-EKNPKALFRRGKAKAELGQMDSARDDFRKAQKY--APDDKAIRRELRALAEQEKALYQKQKEMYKGIFK  327 (338)
T ss_dssp             HHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC-------------------------------------
T ss_pred             HHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            7642 225677888888888888888888888876543  24443333322221 2233344555555555543

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=97.55  E-value=0.0015  Score=44.89  Aligned_cols=90  Identities=19%  Similarity=0.177  Sum_probs=73.6

Q ss_pred             CCchHHHHHHHHHHHHc--------C---------CCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHH
Q 039342            1 GGLYKECQAILSRMSES--------G---------VARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEA   63 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~--------g---------~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~   63 (248)
                      .|++++|.+.|.+..+.        .         -+.+...|..+-.+|.+.|++++|...++...+.. +.+...|..
T Consensus        24 ~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~  102 (162)
T 3rkv_A           24 QKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVLKRE-ETNEKALFR  102 (162)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhcC-CcchHHHHH
Confidence            37899999999987653        0         01234688889999999999999999999998764 456788999


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHCCCCcCH
Q 039342           64 VLSVYCFAGLVDESKEQFQEIKSSGILPSV   93 (248)
Q Consensus        64 ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~   93 (248)
                      +-.+|...|++++|...|++..+.  .|+.
T Consensus       103 ~g~~~~~~g~~~~A~~~~~~al~l--~p~~  130 (162)
T 3rkv_A          103 RAKARIAAWKLDEAEEDLKLLLRN--HPAA  130 (162)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--CGGG
T ss_pred             HHHHHHHHhcHHHHHHHHHHHHhc--CCCC
Confidence            999999999999999999998875  4544

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.54  E-value=0.00074  Score=42.82  Aligned_cols=90  Identities=9%  Similarity=-0.016  Sum_probs=63.8

Q ss_pred             CCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcC-------H
Q 039342           21 RNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPS-------V   93 (248)
Q Consensus        21 ~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~-------~   93 (248)
                      ++...|..+-..+.+.|++++|.+.|++..+.. +.+...|..+-.++.+.|++++|.+.+++..+.  .|+       .
T Consensus         2 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~   78 (111)
T 2l6j_A            2 SQFEKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRY--TSTAEHVAIRS   78 (111)
T ss_dssp             THHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS--CSSTTSHHHHH
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCccHHHHHH
Confidence            356677788888889999999999998887653 346778888888899999999999999888765  344       3


Q ss_pred             hhHHHHHHHHHhcCCHHHHH
Q 039342           94 MCYCMLLAVYAKSNRWDDAY  113 (248)
Q Consensus        94 ~~~~~li~~~~~~~~~~~a~  113 (248)
                      ..+..+-.++...|+.+.|.
T Consensus        79 ~~~~~~~~~~~~~~~~~~a~   98 (111)
T 2l6j_A           79 KLQYRLELAQGAVGSVQIPV   98 (111)
T ss_dssp             HHHHHHHHHHHHHHCCCCCS
T ss_pred             HHHHHHHHHHHHHHhHhhhH
Confidence            33444444444444444433

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=97.52  E-value=0.00047  Score=53.90  Aligned_cols=117  Identities=11%  Similarity=0.078  Sum_probs=70.3

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHH------------------hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSD------------------SFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLE   62 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~------------------~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~   62 (248)
                      .|++++|...|.+..+.  .|+..                  .|..+-.+|.+.|++++|...+++..+.. +-+...|.
T Consensus       192 ~g~~~~A~~~y~~Al~~--~p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~  268 (338)
T 2if4_A          192 EEKLEEAMQQYEMAIAY--MGDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNIVLTEE-EKNPKALF  268 (338)
T ss_dssp             SSCCHHHHHHHHHHHHH--SCHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             cCCHHHHHHHHHHHHHH--hccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHH
Confidence            37899999999987653  24432                  78889999999999999999999987754 34678899


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHCCCCc-CHhhHHHHHHH-HHhcCCHHHHHHHHHHHHHC
Q 039342           63 AVLSVYCFAGLVDESKEQFQEIKSSGILP-SVMCYCMLLAV-YAKSNRWDDAYGLLDEMHTN  122 (248)
Q Consensus        63 ~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~-~~~~~~~~~a~~~~~~m~~~  122 (248)
                      .+-.+|...|++++|...|++..+.  .| +...+..+... ....+..+.+...|..|...
T Consensus       269 ~lg~a~~~~g~~~~A~~~l~~al~l--~p~~~~a~~~L~~l~~~~~~~~~~a~~~~~~~l~~  328 (338)
T 2if4_A          269 RRGKAKAELGQMDSARDDFRKAQKY--APDDKAIRRELRALAEQEKALYQKQKEMYKGIFKG  328 (338)
T ss_dssp             HHHHHHHTTTCHHHHHHHHHHTTC--------------------------------------
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence            9999999999999999999998754  34 34445554444 23445677788888877644

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.50  E-value=0.0015  Score=42.03  Aligned_cols=79  Identities=9%  Similarity=0.005  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHH
Q 039342            6 ECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIK   85 (248)
Q Consensus         6 ~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~   85 (248)
                      .|.+.|++..+... .+...|..+-..+...|++++|...|++..+.. +.+...|..+-.+|.+.|++++|...|++..
T Consensus         3 ~a~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al   80 (115)
T 2kat_A            3 AITERLEAMLAQGT-DNMLLRFTLGKTYAEHEQFDAALPHLRAALDFD-PTYSVAWKWLGKTLQGQGDRAGARQAWESGL   80 (115)
T ss_dssp             CHHHHHHHHHTTTC-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCC-CcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            34455555544321 245555555566666666666666666655432 2334455555555666666666666655554


Q ss_pred             H
Q 039342           86 S   86 (248)
Q Consensus        86 ~   86 (248)
                      +
T Consensus        81 ~   81 (115)
T 2kat_A           81 A   81 (115)
T ss_dssp             H
T ss_pred             H
Confidence            3

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=97.47  E-value=0.023  Score=44.11  Aligned_cols=181  Identities=8%  Similarity=-0.043  Sum_probs=123.3

Q ss_pred             hHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcC--CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCC-hhHHHHH
Q 039342            4 YKECQAILSRMSESGVARNSDSFNAVIEAFRQGG--RFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGL-VDESKEQ   80 (248)
Q Consensus         4 ~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~--~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~-~~~a~~~   80 (248)
                      +++++..++.+..... .+..+|+.=-..+.+.+  ++++++++++.+.+.. +-|...|+.---.+.+.|. ++++.+.
T Consensus        90 l~~EL~~~~~~L~~~P-Kny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~d-prNy~AW~~R~~vl~~l~~~~~eel~~  167 (331)
T 3dss_A           90 VKAELGFLESCLRVNP-KSYGTWHHRCWLLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAF  167 (331)
T ss_dssp             HHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCC-CCHHHHHHHHHHHhccCcccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhCcCHHHHHHH
Confidence            5778888888876543 47888888777777777  4899999999998776 4677888877777778888 5899999


Q ss_pred             HHHHHHCCCCcCHhhHHHHHHHHHhc--------------CCHHHHHHHHHHHHHCCCCchHHhHHHHhccccccc----
Q 039342           81 FQEIKSSGILPSVMCYCMLLAVYAKS--------------NRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDE----  142 (248)
Q Consensus        81 ~~~m~~~~~~p~~~~~~~li~~~~~~--------------~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~----  142 (248)
                      ++.+.+..+. |...|+..-..+.+.              +.++++++.+.+.....  |+.........+.+...    
T Consensus       168 ~~~~I~~~p~-N~SAW~~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~--P~d~SaW~Y~r~ll~~~~~~~  244 (331)
T 3dss_A          168 TDSLITRNFS-NYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTD--PNDQSAWFYHRWLLGAGSGRC  244 (331)
T ss_dssp             HHHHHHHCSC-CHHHHHHHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHSSSCGG
T ss_pred             HHHHHHHCCC-CHHHHHHHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHhccCcc
Confidence            9999876533 666777665555544              45788899988887654  55544433222222222    


Q ss_pred             -------chHHHHHHHHHHHHhcCCCCCHHHHH--HH---HHHHHhcCchHHHHHHHHHHHH
Q 039342          143 -------SNWQMVEYVFDKLNCEGYGLGMRFYN--AL---LEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       143 -------~~~~~a~~~~~~m~~~~~~p~~~~~~--~l---i~~~~~~g~~~~a~~~~~~m~~  192 (248)
                             +.++.+.+.++++.+..  ||. .|+  .+   +......|..+++...+.++.+
T Consensus       245 ~~~~~~~~~l~~el~~~~elle~~--pd~-~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~  303 (331)
T 3dss_A          245 ELSVEKSTVLQSELESCKELQELE--PEN-KWCLLTIILLMRALDPLLYEKETLQYFSTLKA  303 (331)
T ss_dssp             GCCHHHHHHHHHHHHHHHHHHHHC--TTC-HHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHHHHHHhhC--ccc-chHHHHHHHHHHhhcccccHHHHHHHHHHHHH
Confidence                   45677788888887754  432 233  22   2222245667778888887765

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=97.46  E-value=0.0017  Score=51.46  Aligned_cols=63  Identities=13%  Similarity=0.180  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHC--------------CCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 039342           59 RTLEAVLSVYCFAGLVDESKEQFQEIKSS--------------GILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHT  121 (248)
Q Consensus        59 ~t~~~ll~~~~~~g~~~~a~~~~~~m~~~--------------~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  121 (248)
                      ..+..+-..+.+.|++++|.+.|++..+.              ...| +..+|..+-.+|.+.|++++|+..+++..+
T Consensus       224 ~~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~  301 (370)
T 1ihg_A          224 EDLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALE  301 (370)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHH
Confidence            34666777888899999999988887651              0122 345566666666666666666666666554

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=97.46  E-value=0.0051  Score=42.25  Aligned_cols=99  Identities=7%  Similarity=-0.056  Sum_probs=76.7

Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC------CH-----HHHHHHHHHHHhcCChhHHHHHHHHHHHC----
Q 039342           23 SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDP------NE-----RTLEAVLSVYCFAGLVDESKEQFQEIKSS----   87 (248)
Q Consensus        23 ~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p------~~-----~t~~~ll~~~~~~g~~~~a~~~~~~m~~~----   87 (248)
                      ...+...-..+.+.|++++|.+.|++..+..-..      +.     ..|+.+-.++.+.|++++|...+++..+.    
T Consensus        11 a~~~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~   90 (159)
T 2hr2_A           11 AYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRR   90 (159)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhcc
Confidence            3455666677888999999999999986643210      23     38888999999999999999999988764    


Q ss_pred             -CCCcC-HhhH----HHHHHHHHhcCCHHHHHHHHHHHHH
Q 039342           88 -GILPS-VMCY----CMLLAVYAKSNRWDDAYGLLDEMHT  121 (248)
Q Consensus        88 -~~~p~-~~~~----~~li~~~~~~~~~~~a~~~~~~m~~  121 (248)
                       .+.|+ ...|    ...-.++...|++++|+..|++..+
T Consensus        91 ~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAle  130 (159)
T 2hr2_A           91 GELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  130 (159)
T ss_dssp             CCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHh
Confidence             12464 4567    8888899999999999999998754

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.40  E-value=0.0041  Score=37.61  Aligned_cols=81  Identities=17%  Similarity=0.188  Sum_probs=53.2

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHH
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLA  101 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~  101 (248)
                      +...|..+-..+.+.|++++|...+++..+.. +.+...+..+-.++.+.|++++|...|++..+.. +.+...+..+-.
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~l~~   85 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAKQNLGN   85 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCHHHHHHHHH
Confidence            34566677777777888888888887776543 3356677777777788888888888887776542 113444544444


Q ss_pred             HHH
Q 039342          102 VYA  104 (248)
Q Consensus       102 ~~~  104 (248)
                      .+.
T Consensus        86 ~~~   88 (91)
T 1na3_A           86 AKQ   88 (91)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.39  E-value=0.002  Score=41.31  Aligned_cols=80  Identities=8%  Similarity=-0.085  Sum_probs=63.9

Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 039342           41 EAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMH  120 (248)
Q Consensus        41 ~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~  120 (248)
                      .+.+.|++..+.. +.+...+..+-..|.+.|++++|...|++..+.. +.+...|..+-.+|...|++++|...|++..
T Consensus         3 ~a~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al   80 (115)
T 2kat_A            3 AITERLEAMLAQG-TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFD-PTYSVAWKWLGKTLQGQGDRAGARQAWESGL   80 (115)
T ss_dssp             CHHHHHHHHHTTT-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4566777766543 3567888889999999999999999999988753 2256788889999999999999999999876


Q ss_pred             HC
Q 039342          121 TN  122 (248)
Q Consensus       121 ~~  122 (248)
                      +.
T Consensus        81 ~~   82 (115)
T 2kat_A           81 AA   82 (115)
T ss_dssp             HH
T ss_pred             Hh
Confidence            53

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=97.30  E-value=0.016  Score=38.72  Aligned_cols=78  Identities=12%  Similarity=-0.028  Sum_probs=42.8

Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHh----cCCHHHHH
Q 039342           38 RFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAK----SNRWDDAY  113 (248)
Q Consensus        38 ~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~----~~~~~~a~  113 (248)
                      ++++|.+.|++..+.| .|+..    +-..|...+.+++|.+.|++..+.|   +...+..|-..|..    .++.++|+
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 DLKKAIQYYVKACELN-EMFGC----LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKAA   81 (138)
T ss_dssp             HHHHHHHHHHHHHHTT-CTTHH----HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHH
T ss_pred             CHHHHHHHHHHHHcCC-CHhhh----HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccHHHHH
Confidence            4566666666666655 23333    4444445555666666666665553   34455555555554    45555666


Q ss_pred             HHHHHHHHCC
Q 039342          114 GLLDEMHTNR  123 (248)
Q Consensus       114 ~~~~~m~~~~  123 (248)
                      ..|++-.+.|
T Consensus        82 ~~~~~Aa~~g   91 (138)
T 1klx_A           82 QYYSKACGLN   91 (138)
T ss_dssp             HHHHHHHHTT
T ss_pred             HHHHHHHcCC
Confidence            6555554443

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=97.27  E-value=0.0048  Score=42.38  Aligned_cols=85  Identities=18%  Similarity=0.144  Sum_probs=68.6

Q ss_pred             CchHHHHHHHHHHHHcCCCC------C-----HHhHHHHHHHHHhcCCHHHHHHHHHHHHHc-----CCCCCH-HHH---
Q 039342            2 GLYKECQAILSRMSESGVAR------N-----SDSFNAVIEAFRQGGRFEEAIKAYVEMEKV-----RCDPNE-RTL---   61 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~------~-----~~~y~~li~~~~~~~~~~~a~~~~~~m~~~-----~~~p~~-~t~---   61 (248)
                      |++++|.+.|++..+.....      +     ...|+.+-.++.+.|++++|+..+++..+.     .+.|+. ..|   
T Consensus        25 g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~~pd~~~A~~~~  104 (159)
T 2hr2_A           25 GEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGKLWISA  104 (159)
T ss_dssp             TCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccCCCchHHHHHHH
Confidence            89999999999887643220      2     238999999999999999999999998764     125643 567   


Q ss_pred             -HHHHHHHHhcCChhHHHHHHHHHHH
Q 039342           62 -EAVLSVYCFAGLVDESKEQFQEIKS   86 (248)
Q Consensus        62 -~~ll~~~~~~g~~~~a~~~~~~m~~   86 (248)
                       ...-.++...|++++|...|++..+
T Consensus       105 ~~~rG~aL~~lgr~eEAl~~y~kAle  130 (159)
T 2hr2_A          105 VYSRALALDGLGRGAEAMPEFKKVVE  130 (159)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHhHHHHHHHCCCHHHHHHHHHHHHh
Confidence             7888899999999999999999865

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.14  E-value=0.0048  Score=38.58  Aligned_cols=62  Identities=10%  Similarity=0.038  Sum_probs=30.6

Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHH
Q 039342           23 SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIK   85 (248)
Q Consensus        23 ~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~   85 (248)
                      ...|..+-..|.+.|++++|...|++..+.. +-+...|..+-.+|.+.|++++|.+.|++..
T Consensus         7 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al   68 (100)
T 3ma5_A            7 PFTRYALAQEHLKHDNASRALALFEELVETD-PDYVGTYYHLGKLYERLDRTDDAIDTYAQGI   68 (100)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4445555555555555555555555554432 1223344455555555555555555555443

>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=97.14  E-value=0.0055  Score=49.57  Aligned_cols=87  Identities=8%  Similarity=-0.046  Sum_probs=66.6

Q ss_pred             hcCCHHHHHHHHHHHHH---cCCCCC----HHHHHHHHHHHHhcCChhHHHHHHHHHHHC-----C-CCcC-HhhHHHHH
Q 039342           35 QGGRFEEAIKAYVEMEK---VRCDPN----ERTLEAVLSVYCFAGLVDESKEQFQEIKSS-----G-ILPS-VMCYCMLL  100 (248)
Q Consensus        35 ~~~~~~~a~~~~~~m~~---~~~~p~----~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~-----~-~~p~-~~~~~~li  100 (248)
                      ..|++++|+.++++..+   .-+.|+    ..+++.+..+|...|++++|..++++..+.     | -.|+ ..+++.|-
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            35788999999988744   223333    377889999999999999999999887642     2 2343 46799999


Q ss_pred             HHHHhcCCHHHHHHHHHHHHH
Q 039342          101 AVYAKSNRWDDAYGLLDEMHT  121 (248)
Q Consensus       101 ~~~~~~~~~~~a~~~~~~m~~  121 (248)
                      ..|...|++++|+.++++..+
T Consensus       390 ~~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          390 RLYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhccCHHHHHHHHHHHHH
Confidence            999999999999999987643

>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=97.14  E-value=0.0017  Score=52.56  Aligned_cols=85  Identities=11%  Similarity=-0.061  Sum_probs=67.0

Q ss_pred             CchHHHHHHHHHHHHc---CCC---C-CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHc-----C-CCCC-HHHHHHHHHH
Q 039342            2 GLYKECQAILSRMSES---GVA---R-NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKV-----R-CDPN-ERTLEAVLSV   67 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~---g~~---~-~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~-----~-~~p~-~~t~~~ll~~   67 (248)
                      |++++|+.++++..+.   -..   | ...+++.|..+|...|++++|..++++..+-     | -.|+ ..+|+.|-..
T Consensus       312 g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~  391 (433)
T 3qww_A          312 KSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRL  391 (433)
T ss_dssp             SCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHH
Confidence            7889999999876542   112   2 3568999999999999999999999987432     2 1233 3778999999


Q ss_pred             HHhcCChhHHHHHHHHHHH
Q 039342           68 YCFAGLVDESKEQFQEIKS   86 (248)
Q Consensus        68 ~~~~g~~~~a~~~~~~m~~   86 (248)
                      |...|++++|..++++..+
T Consensus       392 ~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          392 YMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHhccCHHHHHHHHHHHHH
Confidence            9999999999999988754

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=97.13  E-value=0.033  Score=45.84  Aligned_cols=172  Identities=10%  Similarity=0.066  Sum_probs=106.4

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcC---------CCC---CHHHHHHHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVR---------CDP---NERTLEAVLSVY   68 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~---------~~p---~~~t~~~ll~~~   68 (248)
                      .|++++|.++|++....  +.+...|.    .|+...+.++.   ++.+.+.-         ..+   ....|...+...
T Consensus       226 ~~~~~~ar~i~erAi~~--P~~~~l~~----~y~~~~e~~~~---~~~l~~~~~~~~~~~~~~~~~~~~~~lw~~y~~~~  296 (493)
T 2uy1_A          226 IGQKEKAKKVVERGIEM--SDGMFLSL----YYGLVMDEEAV---YGDLKRKYSMGEAESAEKVFSKELDLLRINHLNYV  296 (493)
T ss_dssp             TTCHHHHHHHHHHHHHH--CCSSHHHH----HHHHHTTCTHH---HHHHHHHTC----------CHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhC--CCcHHHHH----HHHhhcchhHH---HHHHHHHHHhhccchhhhhcccccHHHHHHHHHHH
Confidence            37899999999999876  33433333    22222122222   22222110         011   124566677777


Q ss_pred             HhcCChhHHHHHHHHHHHCCCCcCHhhHH--HHHHHHHhcCCHHHHHHHHHHHHHCCCCchHH-hHHHHhcccccccchH
Q 039342           69 CFAGLVDESKEQFQEIKSSGILPSVMCYC--MLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQ-VTGQMIKGEFDDESNW  145 (248)
Q Consensus        69 ~~~g~~~~a~~~~~~m~~~~~~p~~~~~~--~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~-~~~~~l~~~~~~~~~~  145 (248)
                      .+.+.++.|..+|+.. +.. .++...|-  +.+.... .++.+.|..+|+...+..  |+.. .+...+. .....|+.
T Consensus       297 ~r~~~~~~AR~i~~~A-~~~-~~~~~v~i~~A~lE~~~-~~d~~~ar~ife~al~~~--~~~~~~~~~yid-~e~~~~~~  370 (493)
T 2uy1_A          297 LKKRGLELFRKLFIEL-GNE-GVGPHVFIYCAFIEYYA-TGSRATPYNIFSSGLLKH--PDSTLLKEEFFL-FLLRIGDE  370 (493)
T ss_dssp             HHHHCHHHHHHHHHHH-TTS-CCCHHHHHHHHHHHHHH-HCCSHHHHHHHHHHHHHC--TTCHHHHHHHHH-HHHHHTCH
T ss_pred             HHcCCHHHHHHHHHHh-hCC-CCChHHHHHHHHHHHHH-CCChHHHHHHHHHHHHHC--CCCHHHHHHHHH-HHHHcCCH
Confidence            7888999999999998 321 12333443  3333222 336999999999987753  3322 2222332 23456778


Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          146 QMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       146 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                      +.+..+|+...     -....|...++.-...|+.+.+.+++++..+
T Consensus       371 ~~aR~l~er~~-----k~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          371 ENARALFKRLE-----KTSRMWDSMIEYEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             HHHHHHHHHSC-----CBHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHH-----HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            88999999862     2577788888888888999999999888763

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.08  E-value=0.0059  Score=38.17  Aligned_cols=66  Identities=18%  Similarity=0.084  Sum_probs=55.8

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 039342           56 PNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTN  122 (248)
Q Consensus        56 p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  122 (248)
                      -+...+..+-.+|.+.|++++|...|++..+... .+...|..+-.+|...|++++|...|++..+.
T Consensus         5 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l   70 (100)
T 3ma5_A            5 EDPFTRYALAQEHLKHDNASRALALFEELVETDP-DYVGTYYHLGKLYERLDRTDDAIDTYAQGIEV   70 (100)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            4567888899999999999999999999887532 25678999999999999999999999987643

>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=97.06  E-value=0.0058  Score=49.39  Aligned_cols=92  Identities=12%  Similarity=0.064  Sum_probs=66.3

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHc---CCCCC----HHHHHHHHHHHHhcCChhHHHHHHHHHHHC-----C-CCc-CHh
Q 039342           29 VIEAFRQGGRFEEAIKAYVEMEKV---RCDPN----ERTLEAVLSVYCFAGLVDESKEQFQEIKSS-----G-ILP-SVM   94 (248)
Q Consensus        29 li~~~~~~~~~~~a~~~~~~m~~~---~~~p~----~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~-----~-~~p-~~~   94 (248)
                      .+..+.+.|++++|.+++++..+.   -+.|+    ..+++.+..+|...|++++|..++++..+.     | -.| ...
T Consensus       293 ~ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~  372 (429)
T 3qwp_A          293 KIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGV  372 (429)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHH
T ss_pred             HHHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHH
Confidence            355566778888888888887543   12232    367788888888888888888888877532     2 223 346


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHH
Q 039342           95 CYCMLLAVYAKSNRWDDAYGLLDEMH  120 (248)
Q Consensus        95 ~~~~li~~~~~~~~~~~a~~~~~~m~  120 (248)
                      +++.|-..|...|++++|+.++++..
T Consensus       373 ~l~nLa~~~~~~g~~~eA~~~~~~Al  398 (429)
T 3qwp_A          373 QVMKVGKLQLHQGMFPQAMKNLRLAF  398 (429)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            78888888888888888888888754

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=96.88  E-value=0.015  Score=46.99  Aligned_cols=97  Identities=9%  Similarity=-0.119  Sum_probs=60.0

Q ss_pred             HHHHHhcCChhHHHHHHHHHHHC--C-CCc----CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcc
Q 039342           65 LSVYCFAGLVDESKEQFQEIKSS--G-ILP----SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKG  137 (248)
Q Consensus        65 l~~~~~~g~~~~a~~~~~~m~~~--~-~~p----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~  137 (248)
                      +..+.+.|++++|..++++..+.  . +.|    ...+++.+..+|...|++++|+.++++..+.               
T Consensus       294 ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i---------------  358 (429)
T 3qwp_A          294 IEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEP---------------  358 (429)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---------------
T ss_pred             HHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHh---------------
Confidence            44455667777777777766532  1 111    2346677777777777777777776654321               


Q ss_pred             cccccchHHHHHHHHHHHHhcCCCC-CHHHHHHHHHHHHhcCchHHHHHHHHHHH
Q 039342          138 EFDDESNWQMVEYVFDKLNCEGYGL-GMRFYNALLEALWCLGLRERAARVLDEAT  191 (248)
Q Consensus       138 ~~~~~~~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~  191 (248)
                                    ++...-. -.| ...+++.|-..|...|++++|..++++..
T Consensus       359 --------------~~~~lg~-~Hp~~a~~l~nLa~~~~~~g~~~eA~~~~~~Al  398 (429)
T 3qwp_A          359 --------------YRIFFPG-SHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAF  398 (429)
T ss_dssp             --------------HHHHSCS-SCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             --------------HHHHcCC-CChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence                          1111001 122 34568888899999999999999998765

>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=96.80  E-value=0.008  Score=41.21  Aligned_cols=82  Identities=15%  Similarity=0.172  Sum_probs=42.5

Q ss_pred             chHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCH----------HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC
Q 039342            3 LYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRF----------EEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAG   72 (248)
Q Consensus         3 ~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~----------~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g   72 (248)
                      .+++|.+.++...+... .+...|+.+-.++...+++          ++|+..|++..+.+ +-+...|..+-.+|...|
T Consensus        17 ~feeA~~~~~~Ai~l~P-~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ld-P~~~~A~~~LG~ay~~lg   94 (158)
T 1zu2_A           17 LFEQIRQDAENTYKSNP-LDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLID-PKKDEAVWCIGNAYTSFA   94 (158)
T ss_dssp             HHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHhc
Confidence            35566666666554332 2455666555555555543          35555555554432 123445555555555443


Q ss_pred             -----------ChhHHHHHHHHHHH
Q 039342           73 -----------LVDESKEQFQEIKS   86 (248)
Q Consensus        73 -----------~~~~a~~~~~~m~~   86 (248)
                                 ++++|.+.|++..+
T Consensus        95 ~l~P~~~~a~g~~~eA~~~~~kAl~  119 (158)
T 1zu2_A           95 FLTPDETEAKHNFDLATQFFQQAVD  119 (158)
T ss_dssp             HHCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCcchhhhhccHHHHHHHHHHHHH
Confidence                       45555555555544

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.79  E-value=0.0058  Score=53.22  Aligned_cols=133  Identities=13%  Similarity=0.143  Sum_probs=87.7

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHH
Q 039342           25 SFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYA  104 (248)
Q Consensus        25 ~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  104 (248)
                      ....++..+.+.|.++.|+++.+.       |.     .-.......|+++.|.++.+.+      .+...|..+-..+.
T Consensus       631 ~~~~~~~~l~~~~~~~~a~~~~~~-------~~-----~~f~~~l~~~~~~~A~~~~~~~------~~~~~W~~la~~al  692 (814)
T 3mkq_A          631 SLTKIARFLEGQEYYEEALNISPD-------QD-----QKFELALKVGQLTLARDLLTDE------SAEMKWRALGDASL  692 (814)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHCCC-------HH-----HHHHHHHHHTCHHHHHHHHTTC------CCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCChHHheecCCC-------cc-----hheehhhhcCCHHHHHHHHHhh------CcHhHHHHHHHHHH
Confidence            337777778888888888776532       11     1134456779999998886443      36789999999999


Q ss_pred             hcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHH
Q 039342          105 KSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAA  184 (248)
Q Consensus       105 ~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~  184 (248)
                      +.++++.|.+.|.++.+..         .+..- +...++.+....+-+.....|.      ++....+|.+.|++++|.
T Consensus       693 ~~~~~~~A~~~y~~~~d~~---------~l~~l-~~~~~~~~~~~~~~~~a~~~~~------~~~A~~~~~~~g~~~~a~  756 (814)
T 3mkq_A          693 QRFNFKLAIEAFTNAHDLE---------SLFLL-HSSFNNKEGLVTLAKDAETTGK------FNLAFNAYWIAGDIQGAK  756 (814)
T ss_dssp             HTTCHHHHHHHHHHHTCHH---------HHHHH-HHHTTCHHHHHHHHHHHHHTTC------HHHHHHHHHHHTCHHHHH
T ss_pred             HcCCHHHHHHHHHHccChh---------hhHHH-HHHcCCHHHHHHHHHHHHHcCc------hHHHHHHHHHcCCHHHHH
Confidence            9999999999999874321         11111 1223444555555554444432      455666677788888888


Q ss_pred             HHHHHHH
Q 039342          185 RVLDEAT  191 (248)
Q Consensus       185 ~~~~~m~  191 (248)
                      +++.++.
T Consensus       757 ~~~~~~~  763 (814)
T 3mkq_A          757 DLLIKSQ  763 (814)
T ss_dssp             HHHHHTT
T ss_pred             HHHHHcC
Confidence            8877654

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=96.75  E-value=0.011  Score=35.63  Aligned_cols=65  Identities=17%  Similarity=0.152  Sum_probs=53.3

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           58 ERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        58 ~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      ...+..+-..+.+.|++++|...|++..+.. +.+...+..+-..+.+.|++++|...|++..+..
T Consensus         9 ~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~   73 (91)
T 1na3_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD   73 (91)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC
Confidence            4567778888899999999999999987653 2256788888889999999999999999887654

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=96.69  E-value=0.014  Score=36.58  Aligned_cols=67  Identities=9%  Similarity=0.046  Sum_probs=53.4

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           56 PNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        56 p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      ++...+..+-..+.+.|++++|.+.|++..+.. +.+...+..+-.++.+.|++++|+..+++..+..
T Consensus         2 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~   68 (111)
T 2l6j_A            2 SQFEKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYT   68 (111)
T ss_dssp             THHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSC
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC
Confidence            345667778888889999999999998887653 2266778888888999999999999998887654

>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=96.51  E-value=0.21  Score=41.84  Aligned_cols=170  Identities=8%  Similarity=-0.086  Sum_probs=96.7

Q ss_pred             HHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCC----------HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC--
Q 039342            5 KECQAILSRMSESGVARNSDSFNAVIEAFRQGGR----------FEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAG--   72 (248)
Q Consensus         5 ~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~----------~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g--   72 (248)
                      ++|++.++.+.+... -+...|+.-=..+.+.|+          ++++++.++.+.+.. +-+..+|+.--..+.+.+  
T Consensus        46 eeal~~~~~~l~~nP-~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~-pK~y~aW~hR~w~l~~l~~~  123 (567)
T 1dce_A           46 ESVLELTSQILGANP-DFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWHHRCWLLSRLPEP  123 (567)
T ss_dssp             HHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCSSC
T ss_pred             HHHHHHHHHHHHHCc-hhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcccc
Confidence            456666666655332 234555554444444444          777777777776654 345667777666677777  


Q ss_pred             ChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcC-CHHHHHHHHHHHHHCCCCchHHhHHH--Hh-ccccc--------
Q 039342           73 LVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSN-RWDDAYGLLDEMHTNRISNIHQVTGQ--MI-KGEFD--------  140 (248)
Q Consensus        73 ~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~-~~~~a~~~~~~m~~~~~~~~~~~~~~--~l-~~~~~--------  140 (248)
                      +++++.+.++++.+.... +-.+|+---..+.+.| ..+++++.++++.+.... +...|+.  .+ .....        
T Consensus       124 ~~~~el~~~~k~l~~d~~-N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~-n~saW~~r~~ll~~l~~~~~~~~~~  201 (567)
T 1dce_A          124 NWARELELCARFLEADER-NFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFS-NYSSWHYRSCLLPQLHPQPDSGPQG  201 (567)
T ss_dssp             CHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCC-CHHHHHHHHHHHHHHSCCCCSSSCC
T ss_pred             cHHHHHHHHHHHHhhccc-cccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCC-CccHHHHHHHHHHhhcccccccccc
Confidence            557788888777765322 5666776666666667 677777777777655422 1222221  11 11000        


Q ss_pred             --ccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCc
Q 039342          141 --DESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGL  179 (248)
Q Consensus       141 --~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~  179 (248)
                        ..+.++++.+.++........ |...|+..--.+.+.++
T Consensus       202 ~~~~~~~~eel~~~~~ai~~~P~-~~saW~y~~~ll~~~~~  241 (567)
T 1dce_A          202 RLPENVLLKELELVQNAFFTDPN-DQSAWFYHRWLLGRAEP  241 (567)
T ss_dssp             SSCHHHHHHHHHHHHHHHHHCSS-CSHHHHHHHHHHSCCCC
T ss_pred             cccHHHHHHHHHHHHHHHhhCCC-CccHHHHHHHHHhcCCC
Confidence              124566666666665554332 45556555555544444

>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=96.45  E-value=0.014  Score=39.97  Aligned_cols=98  Identities=12%  Similarity=0.007  Sum_probs=70.6

Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCh----------hHHHHHHHHHHHCCCCc-CHhhHHHHHHH
Q 039342           34 RQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLV----------DESKEQFQEIKSSGILP-SVMCYCMLLAV  102 (248)
Q Consensus        34 ~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~----------~~a~~~~~~m~~~~~~p-~~~~~~~li~~  102 (248)
                      .+.+.+++|.+.++...+.. +-+...|..+-.++.+.+++          ++|...|++..+.  .| +...|..+-.+
T Consensus        13 ~r~~~feeA~~~~~~Ai~l~-P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~l--dP~~~~A~~~LG~a   89 (158)
T 1zu2_A           13 DRILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLI--DPKKDEAVWCIGNA   89 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHh--CcCcHHHHHHHHHH
Confidence            45567888888888887664 45778888777787777664          5888888888775  34 56678888888


Q ss_pred             HHhcC-----------CHHHHHHHHHHHHHCCCCchHHhHHHHhc
Q 039342          103 YAKSN-----------RWDDAYGLLDEMHTNRISNIHQVTGQMIK  136 (248)
Q Consensus       103 ~~~~~-----------~~~~a~~~~~~m~~~~~~~~~~~~~~~l~  136 (248)
                      |...|           ++++|+..|++..+..  |+...|...+.
T Consensus        90 y~~lg~l~P~~~~a~g~~~eA~~~~~kAl~l~--P~~~~y~~al~  132 (158)
T 1zu2_A           90 YTSFAFLTPDETEAKHNFDLATQFFQQAVDEQ--PDNTHYLKSLE  132 (158)
T ss_dssp             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHC--TTCHHHHHHHH
T ss_pred             HHHhcccCcchhhhhccHHHHHHHHHHHHHhC--CCCHHHHHHHH
Confidence            88764           6778888887776553  66665555444

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=96.42  E-value=0.13  Score=35.81  Aligned_cols=95  Identities=12%  Similarity=0.122  Sum_probs=46.6

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |+++.|.++.+++      -+...|..|-......|+++-|.+.|....+         +..+.-.|.-.|+.++..++-
T Consensus        19 g~l~~A~e~a~~l------~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D---------~~~L~~Ly~~tg~~e~L~kla   83 (177)
T 3mkq_B           19 GNLDAALDEAKKL------NDSITWERLIQEALAQGNASLAEMIYQTQHS---------FDKLSFLYLVTGDVNKLSKMQ   83 (177)
T ss_dssp             TCHHHHHHHHHHH------CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC---------HHHHHHHHHHHTCHHHHHHHH
T ss_pred             CCHHHHHHHHHHh------CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC---------HHHHHHHHHHhCCHHHHHHHH
Confidence            5555555555444      2455555555555556666555555555432         333444444445554444443


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHH
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLD  117 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~  117 (248)
                      +.-...|      -++.-...+.-.|+++++.++|.
T Consensus        84 ~iA~~~g------~~n~af~~~l~lGdv~~~i~lL~  113 (177)
T 3mkq_B           84 NIAQTRE------DFGSMLLNTFYNNSTKERSSIFA  113 (177)
T ss_dssp             HHHHHTT------CHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHCc------cHHHHHHHHHHcCCHHHHHHHHH
Confidence            3333322      23333444445555555555554

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=96.34  E-value=0.19  Score=39.53  Aligned_cols=143  Identities=8%  Similarity=0.002  Sum_probs=82.9

Q ss_pred             CCCCHHhHHHHHHHHHh--cC---CHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHh---cC--C---hhHHHHHHHHH
Q 039342           19 VARNSDSFNAVIEAFRQ--GG---RFEEAIKAYVEMEKVRCDPN-ERTLEAVLSVYCF---AG--L---VDESKEQFQEI   84 (248)
Q Consensus        19 ~~~~~~~y~~li~~~~~--~~---~~~~a~~~~~~m~~~~~~p~-~~t~~~ll~~~~~---~g--~---~~~a~~~~~~m   84 (248)
                      .+.+...|...+++...  .+   +..+|..+|++..+.  .|+ ...|..+.-+|..   .+  .   .......++..
T Consensus       190 ~p~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~l--DP~~a~A~A~la~a~~~~~~~~~~~~~~~~~l~~a~~a~  267 (372)
T 3ly7_A          190 LPHRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQS--SPEFTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNI  267 (372)
T ss_dssp             SCSSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHH
Confidence            45678888888876553  23   347788888887765  454 2344333333321   11  1   11111122221


Q ss_pred             HHC-CCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCC
Q 039342           85 KSS-GILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLG  163 (248)
Q Consensus        85 ~~~-~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~  163 (248)
                      ... .-..+..+|..+-..+...|++++|...+++....+  |+...+ .++...+...|+++.|.+.+++....  .|.
T Consensus       268 ~a~~~~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~-~llG~~~~~~G~~~eA~e~~~~AlrL--~P~  342 (372)
T 3ly7_A          268 VTLPELNNLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNY-VLLGKVYEMKGMNREAADAYLTAFNL--RPG  342 (372)
T ss_dssp             HTCGGGTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHH-HHHHHHHHHTTCHHHHHHHHHHHHHH--SCS
T ss_pred             HhcccCCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHH-HHHHHHHHHCCCHHHHHHHHHHHHhc--CCC
Confidence            111 123467778777777777788999998888888776  543332 33333355678888888888776665  355


Q ss_pred             HHHHH
Q 039342          164 MRFYN  168 (248)
Q Consensus       164 ~~~~~  168 (248)
                      ..||.
T Consensus       343 ~~t~~  347 (372)
T 3ly7_A          343 ANTLY  347 (372)
T ss_dssp             HHHHH
T ss_pred             cChHH
Confidence            55654

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=96.27  E-value=0.042  Score=33.71  Aligned_cols=56  Identities=14%  Similarity=0.148  Sum_probs=36.4

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCCCHH-HHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 039342           31 EAFRQGGRFEEAIKAYVEMEKVRCDPNER-TLEAVLSVYCFAGLVDESKEQFQEIKSS   87 (248)
Q Consensus        31 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~-t~~~ll~~~~~~g~~~~a~~~~~~m~~~   87 (248)
                      ..+.+.|++++|.+.+++..+.. +.+.. .+..+-.+|.+.|++++|.+.|++..+.
T Consensus         8 ~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~   64 (99)
T 2kc7_A            8 KELINQGDIENALQALEEFLQTE-PVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIEL   64 (99)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHC-SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            34556677777777777765543 23445 6666666777777777777777776654

>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=96.27  E-value=0.39  Score=40.27  Aligned_cols=151  Identities=9%  Similarity=-0.067  Sum_probs=103.1

Q ss_pred             CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCC----------hhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhc
Q 039342           37 GRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGL----------VDESKEQFQEIKSSGILPSVMCYCMLLAVYAKS  106 (248)
Q Consensus        37 ~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~----------~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~  106 (248)
                      ..-++|++.++++.+.+ +-+...|+.-=.++.+.|+          ++++.+.++.+.+.... +..+|+.--..+.+.
T Consensus        43 ~~~eeal~~~~~~l~~n-P~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~pK-~y~aW~hR~w~l~~l  120 (567)
T 1dce_A           43 ELDESVLELTSQILGAN-PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPK-SYGTWHHRCWLLSRL  120 (567)
T ss_dssp             CCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHHHHHC-chhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHc
Confidence            34578899999997764 2344566655455555555          89999999999875422 667888888888888


Q ss_pred             C--CHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccc-hHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhc------
Q 039342          107 N--RWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDES-NWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCL------  177 (248)
Q Consensus       107 ~--~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~------  177 (248)
                      +  +++++++.++++.+....-.. .|+.--.. ....+ .++++.+.++.+.+..+. +...|+..-..+.+.      
T Consensus       121 ~~~~~~~el~~~~k~l~~d~~N~~-aW~~R~~~-l~~l~~~~~~el~~~~~~I~~~p~-n~saW~~r~~ll~~l~~~~~~  197 (567)
T 1dce_A          121 PEPNWARELELCARFLEADERNFH-CWDYRRFV-AAQAAVAPAEELAFTDSLITRNFS-NYSSWHYRSCLLPQLHPQPDS  197 (567)
T ss_dssp             SSCCHHHHHHHHHHHHHHCTTCHH-HHHHHHHH-HHHTCCCHHHHHHHHHTTTTTTCC-CHHHHHHHHHHHHHHSCCCCS
T ss_pred             ccccHHHHHHHHHHHHhhcccccc-HHHHHHHH-HHHcCCChHHHHHHHHHHHHHCCC-CccHHHHHHHHHHhhcccccc
Confidence            8  779999999999887643222 22221111 22233 678888888888776655 677787766666653      


Q ss_pred             --------CchHHHHHHHHHHHH
Q 039342          178 --------GLRERAARVLDEATK  192 (248)
Q Consensus       178 --------g~~~~a~~~~~~m~~  192 (248)
                              +.++++.+.+++...
T Consensus       198 ~~~~~~~~~~~~eel~~~~~ai~  220 (567)
T 1dce_A          198 GPQGRLPENVLLKELELVQNAFF  220 (567)
T ss_dssp             SSCCSSCHHHHHHHHHHHHHHHH
T ss_pred             cccccccHHHHHHHHHHHHHHHh
Confidence                    567888888887765

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=96.11  E-value=0.085  Score=35.77  Aligned_cols=80  Identities=4%  Similarity=-0.078  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcC---CHHHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHhcCChhHHHH
Q 039342            5 KECQAILSRMSESGVARNSDSFNAVIEAFRQGG---RFEEAIKAYVEMEKVRCDP--NERTLEAVLSVYCFAGLVDESKE   79 (248)
Q Consensus         5 ~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~---~~~~a~~~~~~m~~~~~~p--~~~t~~~ll~~~~~~g~~~~a~~   79 (248)
                      ..+++-|.+..+.|. ++..+.-.+-.++++.+   +.+++..+|++..+.+ .|  +...+=.+--+|.+.|++++|.+
T Consensus        15 ~~~~~~y~~e~~~~~-~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY~LAv~~~kl~~Y~~A~~   92 (152)
T 1pc2_A           15 LKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKALK   92 (152)
T ss_dssp             HHHHHHHHHHHHTTC-CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHTSCHHHHHH
T ss_pred             HHHHHHHHHHHccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHHHHHccCHHHHHH
Confidence            344444444444333 44555555555555555   4445555555554443 12  12222233334455555555555


Q ss_pred             HHHHHHH
Q 039342           80 QFQEIKS   86 (248)
Q Consensus        80 ~~~~m~~   86 (248)
                      .++.+.+
T Consensus        93 y~~~lL~   99 (152)
T 1pc2_A           93 YVRGLLQ   99 (152)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            5555554

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.09  E-value=0.064  Score=46.66  Aligned_cols=104  Identities=13%  Similarity=-0.015  Sum_probs=64.6

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHH
Q 039342           31 EAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWD  110 (248)
Q Consensus        31 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~  110 (248)
                      ......|+++.|+++.+.+      .+...|..+-..+.+.++++.|.+.|..+.+         |..+...|...++.+
T Consensus       660 ~~~l~~~~~~~A~~~~~~~------~~~~~W~~la~~al~~~~~~~A~~~y~~~~d---------~~~l~~l~~~~~~~~  724 (814)
T 3mkq_A          660 ELALKVGQLTLARDLLTDE------SAEMKWRALGDASLQRFNFKLAIEAFTNAHD---------LESLFLLHSSFNNKE  724 (814)
T ss_dssp             HHHHHHTCHHHHHHHHTTC------CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTC---------HHHHHHHHHHTTCHH
T ss_pred             ehhhhcCCHHHHHHHHHhh------CcHhHHHHHHHHHHHcCCHHHHHHHHHHccC---------hhhhHHHHHHcCCHH
Confidence            3456678888888876543      4667888888888888888888888887653         334455555566666


Q ss_pred             HHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHH
Q 039342          111 DAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLN  156 (248)
Q Consensus       111 ~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~  156 (248)
                      ...++-+.....|..  ...+..     +...|++++|.+++.++.
T Consensus       725 ~~~~~~~~a~~~~~~--~~A~~~-----~~~~g~~~~a~~~~~~~~  763 (814)
T 3mkq_A          725 GLVTLAKDAETTGKF--NLAFNA-----YWIAGDIQGAKDLLIKSQ  763 (814)
T ss_dssp             HHHHHHHHHHHTTCH--HHHHHH-----HHHHTCHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCch--HHHHHH-----HHHcCCHHHHHHHHHHcC
Confidence            665555555554421  111111     223456666666665544

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=95.93  E-value=0.2  Score=33.28  Aligned_cols=66  Identities=18%  Similarity=0.100  Sum_probs=36.8

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC
Q 039342           59 RTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRIS  125 (248)
Q Consensus        59 ~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~  125 (248)
                      ..+...++.....|+-|.-.+++..+.. +.+|++...-.+-.+|.+-|+..+|.+++.+.-+.|++
T Consensus        92 e~vd~ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~k  157 (172)
T 1wy6_A           92 EHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  157 (172)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhhH
Confidence            3445555566666666666666655432 22445555555666666666666666666666555543

>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=95.67  E-value=0.19  Score=31.24  Aligned_cols=64  Identities=13%  Similarity=0.058  Sum_probs=47.0

Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHH
Q 039342           38 RFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAV  102 (248)
Q Consensus        38 ~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~  102 (248)
                      |.-++.+-++.+....+.|++.+..+.+++|.|.+++..|.++|+-.+.+ +.+...+|..+++-
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K-~~~~~~iY~~~lqE   88 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVIQE   88 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-hcCchhhHHHHHHH
Confidence            55567777777777888888888888888888888888888888888743 12234457666543

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=95.64  E-value=0.18  Score=30.69  Aligned_cols=59  Identities=12%  Similarity=0.189  Sum_probs=47.4

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHCCCCcCHh-hHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           64 VLSVYCFAGLVDESKEQFQEIKSSGILPSVM-CYCMLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        64 ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      ....+.+.|++++|.+.|++..+.. +.+.. .+..+-.+|...|++++|...|++..+..
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~   65 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTE-PVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIELN   65 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC-SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            3456778899999999999988753 22456 78888889999999999999999987664

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=95.40  E-value=0.23  Score=37.66  Aligned_cols=67  Identities=10%  Similarity=0.034  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHhc-----CChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhc-CCHHHHHHHHHHHHHCCCC
Q 039342           59 RTLEAVLSVYCFA-----GLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKS-NRWDDAYGLLDEMHTNRIS  125 (248)
Q Consensus        59 ~t~~~ll~~~~~~-----g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~-~~~~~a~~~~~~m~~~~~~  125 (248)
                      ..|..+...|.+.     |+.++|.+.|++..+.+-.-+..++...-..+++. |+.+++.+.+++-......
T Consensus       200 sA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~~a~~~L~kAL~a~p~  272 (301)
T 3u64_A          200 AVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGFDEALDRALAIDPE  272 (301)
T ss_dssp             HHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHHHHHHHHHHHHHCCGG
T ss_pred             HHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCCC
Confidence            3444444445442     55555555555554432110234444444444442 5555555555555544433

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=95.28  E-value=0.23  Score=31.04  Aligned_cols=64  Identities=9%  Similarity=-0.050  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHHC------CCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 039342           58 ERTLEAVLSVYCFAGLVDESKEQFQEIKSS------GILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHT  121 (248)
Q Consensus        58 ~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~------~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  121 (248)
                      ..-+-.+-..+.+.|+++.|...|+...+.      .-.+....+..+-.++.+.|+++.|...+++..+
T Consensus         5 a~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~   74 (104)
T 2v5f_A            5 AEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLE   74 (104)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHh
Confidence            333444444555555555555555444321      0112344555555555555555555555555543

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=95.27  E-value=0.23  Score=31.02  Aligned_cols=71  Identities=6%  Similarity=-0.089  Sum_probs=57.5

Q ss_pred             CCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcC------CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCH
Q 039342           21 RNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVR------CDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSV   93 (248)
Q Consensus        21 ~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~------~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~   93 (248)
                      .+...+-.|-..+.+.+++..|...|+...+.-      -.+....+..+-.+|.+.|+++.|...+++..+.  .|+.
T Consensus         3 Lsa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l--~P~~   79 (104)
T 2v5f_A            3 LTAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL--DPEH   79 (104)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTC
T ss_pred             CCHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhc--CCCC
Confidence            466677788899999999999999998875431      2355678899999999999999999999998864  4543

>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=95.21  E-value=0.15  Score=40.49  Aligned_cols=70  Identities=16%  Similarity=0.103  Sum_probs=48.3

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHH-----CCCCchHHh
Q 039342           60 TLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHT-----NRISNIHQV  130 (248)
Q Consensus        60 t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~~~~~~~~  130 (248)
                      ....++.++...|+++++...+..+.... +.+...|..+|.++.+.|+..+|++.|++..+     -|+.|...+
T Consensus       173 a~~~~~~~~l~~g~~~~a~~~l~~~~~~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l  247 (388)
T 2ff4_A          173 AHTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  247 (388)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHH
Confidence            34556677777788888877777766432 23666788888888888888888888777643     377775554

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=95.04  E-value=0.31  Score=29.86  Aligned_cols=66  Identities=11%  Similarity=0.021  Sum_probs=38.3

Q ss_pred             CCHHhHHHHHHHHHhcCC---HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 039342           21 RNSDSFNAVIEAFRQGGR---FEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSS   87 (248)
Q Consensus        21 ~~~~~y~~li~~~~~~~~---~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~   87 (248)
                      .++..+..+-.++...++   .++|..++++..+.. +-+......+-..+.+.|++++|...|+.+.+.
T Consensus         4 ~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~d-p~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~   72 (93)
T 3bee_A            4 VTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLE-PYNEAALSLIANDHFISFRFQEAIDTWVLLLDS   72 (93)
T ss_dssp             CCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTC
T ss_pred             CCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            345555555555543333   566666666665543 234455555566666667777777777666654

>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=94.88  E-value=0.25  Score=38.86  Aligned_cols=77  Identities=14%  Similarity=-0.024  Sum_probs=63.2

Q ss_pred             CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHH
Q 039342           54 CDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQ  133 (248)
Q Consensus        54 ~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~  133 (248)
                      -+.+..+|..+-..+...|++++|...+++..+.+  |+...|..+-..+.-.|++++|.+.|++....+  |...++..
T Consensus       273 ~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL~--P~~~t~~~  348 (372)
T 3ly7_A          273 LNNLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNLR--PGANTLYW  348 (372)
T ss_dssp             GTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CSHHHHHH
T ss_pred             CCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CCcChHHH
Confidence            46788899888777777899999999999998875  788888888888899999999999999877654  55555544


Q ss_pred             H
Q 039342          134 M  134 (248)
Q Consensus       134 ~  134 (248)
                      .
T Consensus       349 ~  349 (372)
T 3ly7_A          349 I  349 (372)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=94.84  E-value=0.47  Score=31.25  Aligned_cols=46  Identities=13%  Similarity=0.212  Sum_probs=23.3

Q ss_pred             HHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 039342           76 ESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHT  121 (248)
Q Consensus        76 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  121 (248)
                      +..+-++.+....+.|++.+..+-+++|-+.+++..|.++|+-.+.
T Consensus        71 ElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~  116 (152)
T 2y69_E           71 ELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKD  116 (152)
T ss_dssp             HHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            3344444444445555555555555555555555555555554443

>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=94.70  E-value=0.61  Score=31.52  Aligned_cols=104  Identities=10%  Similarity=0.090  Sum_probs=69.5

Q ss_pred             CCHHhHHHHHHHHHhcCCH------HHHHHHHHHHHHcCCCCCH-HHHHHHHHH------HHhcCChhHHHHHHHHHHHC
Q 039342           21 RNSDSFNAVIEAFRQGGRF------EEAIKAYVEMEKVRCDPNE-RTLEAVLSV------YCFAGLVDESKEQFQEIKSS   87 (248)
Q Consensus        21 ~~~~~y~~li~~~~~~~~~------~~a~~~~~~m~~~~~~p~~-~t~~~ll~~------~~~~g~~~~a~~~~~~m~~~   87 (248)
                      -|..+|-..+...-+.|++      +...++|++... .++|+. ..|...|..      +-..++.++|.++|+.+.+.
T Consensus        11 ~~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia-~~Pp~k~~~wrrYI~LWIrYA~~~ei~D~d~aR~vy~~a~~~   89 (161)
T 4h7y_A           11 NNPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIE-ALPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARAN   89 (161)
T ss_dssp             CSHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHH-HSCGGGGTTCHHHHHHHHHHHHHHHHHCGGGCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHH-cCCccccccHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence            4677888888888888888      777788887755 355542 111121211      12347888999999888654


Q ss_pred             CCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCc
Q 039342           88 GILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISN  126 (248)
Q Consensus        88 ~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~  126 (248)
                      .-.- ...|-.--..=.+.|+++.|.+++.+-...+.+|
T Consensus        90 hKkF-AKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k~  127 (161)
T 4h7y_A           90 CKKF-AFVHISFAQFELSQGNVKKSKQLLQKAVERGAVP  127 (161)
T ss_dssp             CTTB-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBC
T ss_pred             hHHH-HHHHHHHHHHHHHcccHHHHHHHHHHHhccCCCc
Confidence            2222 6666666666678899999999998887766444

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=94.57  E-value=0.43  Score=29.22  Aligned_cols=67  Identities=12%  Similarity=0.063  Sum_probs=52.2

Q ss_pred             CCCHHHHHHHHHHHHhcCC---hhHHHHHHHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           55 DPNERTLEAVLSVYCFAGL---VDESKEQFQEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        55 ~p~~~t~~~ll~~~~~~g~---~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      +.|...+..+-.++...++   .++|..++++..+.  .| +......+-..+.+.|++++|+..|+++.+..
T Consensus         3 p~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~--dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~   73 (93)
T 3bee_A            3 AVTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQL--EPYNEAALSLIANDHFISFRFQEAIDTWVLLLDSN   73 (93)
T ss_dssp             CCCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCC
T ss_pred             CCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHH--CcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            4566777777777765544   78999999998875  34 56677777888889999999999999998765

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=94.53  E-value=0.63  Score=30.94  Aligned_cols=137  Identities=8%  Similarity=-0.051  Sum_probs=83.4

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |.+++..++..+...+   .+..-||=+|......-+-+...++++..-+   -.|.          ..+|++....+.+
T Consensus        21 G~v~qGveii~k~~~s---sni~E~NW~ICNiiD~a~C~y~v~vLd~IGk---iFDi----------s~C~NlKrVi~C~   84 (172)
T 1wy6_A           21 GYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGS---YFDL----------DKCQNLKSVVECG   84 (172)
T ss_dssp             TCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGG---GSCG----------GGCSCTHHHHHHH
T ss_pred             hhHHHHHHHHHHHcCC---CCccccceeeeecchhhchhHHHHHHHHHhh---hcCc----------HhhhcHHHHHHHH
Confidence            4555555555555431   2444555555555555555555555444421   1111          1234444443333


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCC
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYG  161 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~  161 (248)
                      -.+-     .+....+.-++.....|+-|+-.+++.++.. +.+|.......+-.+ |.+-|+..++.+++.+..+.|++
T Consensus        85 ~~~n-----~~se~vd~ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~A-y~Klg~~r~a~eLl~~AC~kG~k  157 (172)
T 1wy6_A           85 VINN-----TLNEHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANA-LRRVGDERDATTLLIEACKKGEK  157 (172)
T ss_dssp             HHTT-----CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHH-HHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHhc-----chHHHHHHHHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHH-HHHhcchhhHHHHHHHHHHhhhH
Confidence            2221     2456677888899999999999999998643 334555555555555 89999999999999999999875

>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=94.50  E-value=1.1  Score=33.87  Aligned_cols=93  Identities=12%  Similarity=0.058  Sum_probs=62.6

Q ss_pred             HHHHHHHHHHHCCCCcC---HhhHHHHHHHHHhc-----CCHHHHHHHHHHHHHCCCC--chHHhHHHHhcccccccchH
Q 039342           76 ESKEQFQEIKSSGILPS---VMCYCMLLAVYAKS-----NRWDDAYGLLDEMHTNRIS--NIHQVTGQMIKGEFDDESNW  145 (248)
Q Consensus        76 ~a~~~~~~m~~~~~~p~---~~~~~~li~~~~~~-----~~~~~a~~~~~~m~~~~~~--~~~~~~~~~l~~~~~~~~~~  145 (248)
                      .|...+++..+.  .|+   ...|..+-..|.+.     |+.++|.+.|++-.+.+-.  ++...+  .-...+...++.
T Consensus       181 ~A~a~lerAleL--DP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~--YA~~l~~~~gd~  256 (301)
T 3u64_A          181 AAVMMLERACDL--WPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHIT--YADALCIPLNNR  256 (301)
T ss_dssp             HHHHHHHHHHHH--CTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHH--HHHHTTTTTTCH
T ss_pred             HHHHHHHHHHHh--CCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHH--HHHHHHHhcCCH
Confidence            456666666653  354   56788888888884     8999999999998776521  333322  222324445888


Q ss_pred             HHHHHHHHHHHhcCCC--CCHHHHHHHHH
Q 039342          146 QMVEYVFDKLNCEGYG--LGMRFYNALLE  172 (248)
Q Consensus       146 ~~a~~~~~~m~~~~~~--p~~~~~~~li~  172 (248)
                      +.+.+.+++.......  |+....|.+-+
T Consensus       257 ~~a~~~L~kAL~a~p~~~P~~~lan~~~q  285 (301)
T 3u64_A          257 AGFDEALDRALAIDPESVPHNKLLVILSQ  285 (301)
T ss_dssp             HHHHHHHHHHHHCCGGGCSSCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCCCChhHHHHHHH
Confidence            9999999998888776  77665555544

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=94.46  E-value=0.71  Score=31.26  Aligned_cols=83  Identities=7%  Similarity=-0.010  Sum_probs=59.0

Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC---ChhHHHHHHHHHHHCCCCc--CHhhHHHHHHHHHhcCCHHHHH
Q 039342           39 FEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAG---LVDESKEQFQEIKSSGILP--SVMCYCMLLAVYAKSNRWDDAY  113 (248)
Q Consensus        39 ~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g---~~~~a~~~~~~m~~~~~~p--~~~~~~~li~~~~~~~~~~~a~  113 (248)
                      ...+.+-|.+..+.|. ++..+--.+-.++++.+   +++++..++++..+.. .|  ....+-.+--+|.+.+++++|.
T Consensus        14 l~~~~~~y~~e~~~~~-~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY~LAv~~~kl~~Y~~A~   91 (152)
T 1pc2_A           14 LLKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKAL   91 (152)
T ss_dssp             HHHHHHHHHHHHHTTC-CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHTSCHHHHH
T ss_pred             HHHHHHHHHHHHccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHHHHHccCHHHHH
Confidence            4455566666555554 77778778888888888   6678899998887654 24  2344445556678899999999


Q ss_pred             HHHHHHHHCC
Q 039342          114 GLLDEMHTNR  123 (248)
Q Consensus       114 ~~~~~m~~~~  123 (248)
                      +.++.+.+..
T Consensus        92 ~y~~~lL~ie  101 (152)
T 1pc2_A           92 KYVRGLLQTE  101 (152)
T ss_dssp             HHHHHHHHHC
T ss_pred             HHHHHHHhcC
Confidence            9999887653

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=94.43  E-value=0.7  Score=32.16  Aligned_cols=102  Identities=7%  Similarity=0.062  Sum_probs=61.7

Q ss_pred             HHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchH
Q 039342           66 SVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNW  145 (248)
Q Consensus        66 ~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~  145 (248)
                      ......|+++.|.++.+++      -+...|..|-....+.|+++-|.+.|.+..+-+    ..   .++   +...|+.
T Consensus        13 ~LAL~lg~l~~A~e~a~~l------~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D~~----~L---~~L---y~~tg~~   76 (177)
T 3mkq_B           13 DLALEYGNLDAALDEAKKL------NDSITWERLIQEALAQGNASLAEMIYQTQHSFD----KL---SFL---YLVTGDV   76 (177)
T ss_dssp             HHHHHTTCHHHHHHHHHHH------CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTCHH----HH---HHH---HHHHTCH
T ss_pred             HHHHhcCCHHHHHHHHHHh------CCHHHHHHHHHHHHHcCChHHHHHHHHHhCCHH----HH---HHH---HHHhCCH
Confidence            4455677788877776665      256678888888888888888888877653221    11   111   2223333


Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHH
Q 039342          146 QMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDE  189 (248)
Q Consensus       146 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  189 (248)
                      +....+-+.-...|      -++.....+.-.|+++++.++|.+
T Consensus        77 e~L~kla~iA~~~g------~~n~af~~~l~lGdv~~~i~lL~~  114 (177)
T 3mkq_B           77 NKLSKMQNIAQTRE------DFGSMLLNTFYNNSTKERSSIFAE  114 (177)
T ss_dssp             HHHHHHHHHHHHTT------CHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCc------cHHHHHHHHHHcCCHHHHHHHHHH
Confidence            44444433333332      256677777778888888888765

>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=93.62  E-value=0.76  Score=28.60  Aligned_cols=69  Identities=14%  Similarity=0.036  Sum_probs=52.4

Q ss_pred             ccccccc-hHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHH
Q 039342          137 GEFDDES-NWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLV  206 (248)
Q Consensus       137 ~~~~~~~-~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li  206 (248)
                      .++.+.. +.-.+.+-++.+......|++....+.+++|-+.+++..|..+|+-.+.+- .+....|..++
T Consensus        17 ~~F~~~~iD~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~-~~~~~iY~~~l   86 (109)
T 1v54_E           17 TYFNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVI   86 (109)
T ss_dssp             HHHTCTTCCHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHH
T ss_pred             HHcCCcCccHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh-cCchhhHHHHH
Confidence            3355554 555666777777788999999999999999999999999999999887542 33344566666

>2y69_E Cytochrome C oxidase subunit 5A; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}

Probab=93.05  E-value=1.2  Score=29.33  Aligned_cols=67  Identities=15%  Similarity=0.047  Sum_probs=51.8

Q ss_pred             ccccc-hHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHH
Q 039342          139 FDDES-NWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLV  206 (248)
Q Consensus       139 ~~~~~-~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li  206 (248)
                      +.+.. +.-+..+-++.+...++.|++......+++|-+.+++..|..+|+-.+.+ +.+....|..++
T Consensus        62 F~~~~iD~wElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K-~~~~~~iY~y~l  129 (152)
T 2y69_E           62 FNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVI  129 (152)
T ss_dssp             HTCTTCCHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHH
T ss_pred             cCCcCccHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHh-cCCchhhHHHHH
Confidence            44444 44556666777777899999999999999999999999999999988764 334445576666

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=92.01  E-value=1.1  Score=35.63  Aligned_cols=73  Identities=8%  Similarity=0.015  Sum_probs=54.9

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHH-hHHHHhcccccccchHHHHHHHHHHHHh-----cCCCCCHHHHH
Q 039342           95 CYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQ-VTGQMIKGEFDDESNWQMVEYVFDKLNC-----EGYGLGMRFYN  168 (248)
Q Consensus        95 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~m~~-----~~~~p~~~~~~  168 (248)
                      +...++.++...|+.++|...+..+....  |... .+..++.+ +...|+...|.+.|+.+.+     .|+.|+..+-.
T Consensus       173 a~~~~~~~~l~~g~~~~a~~~l~~~~~~~--P~~E~~~~~lm~a-l~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~  249 (388)
T 2ff4_A          173 AHTAKAEAEIACGRASAVIAELEALTFEH--PYREPLWTQLITA-YYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRA  249 (388)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHH-HHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHH-HHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            45667888899999999999999887554  5444 55566666 6777888999998887644     49999888744


Q ss_pred             HH
Q 039342          169 AL  170 (248)
Q Consensus       169 ~l  170 (248)
                      ..
T Consensus       250 l~  251 (388)
T 2ff4_A          250 LN  251 (388)
T ss_dssp             HH
T ss_pred             HH
Confidence            33

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=91.78  E-value=1.3  Score=29.90  Aligned_cols=54  Identities=13%  Similarity=0.119  Sum_probs=35.9

Q ss_pred             chHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCC
Q 039342          143 SNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFP  197 (248)
Q Consensus       143 ~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  197 (248)
                      ++.+.|.++|+.+.+..-.- ...|-..-+--.++|+++.|.+++......+-+|
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            45666777777765542222 5555555556677888888888888877766555

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=91.19  E-value=5.1  Score=32.39  Aligned_cols=187  Identities=10%  Similarity=0.079  Sum_probs=112.9

Q ss_pred             CchHHHHHHHHHHHHc-----CCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHH-HcCCCCCHHHHHHHHHHH----Hhc
Q 039342            2 GLYKECQAILSRMSES-----GVARNSDSFNAVIEAFRQGGRFEEAIKAYVEME-KVRCDPNERTLEAVLSVY----CFA   71 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~-----g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~-~~~~~p~~~t~~~ll~~~----~~~   71 (248)
                      |+++.|.+.+..+.+.     ...-+......++..|.+.++|+...+.+..+. ++|..+...  ..++..+    ...
T Consensus        30 ~~~~~a~e~ll~lEK~~r~~~d~~s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lskkr~qlk~ai--~~~V~~~~~~l~~~  107 (445)
T 4b4t_P           30 NDCNSALDQLLVLEKKTRQASDLASSKEVLAKIVDLLASRNKWDDLNEQLTLLSKKHGQLKLSI--QYMIQKVMEYLKSS  107 (445)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSCSTTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHTTTTTSHHHH--HHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhhhhHHHH--HHHHHHHHHHHhcC
Confidence            4677788877766542     234456778889999999999999988887764 344433332  2333332    233


Q ss_pred             CChhHHH--HHHHHHHH---CCCCc---CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHC--CCCchH---HhHHHHhccc
Q 039342           72 GLVDESK--EQFQEIKS---SGILP---SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTN--RISNIH---QVTGQMIKGE  138 (248)
Q Consensus        72 g~~~~a~--~~~~~m~~---~~~~p---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~--~~~~~~---~~~~~~l~~~  138 (248)
                      ...+...  .+.+.+..   ..+..   .......|...|-..|++.+|.+++.++...  +.....   ..+...++ .
T Consensus       108 ~~~d~~~~~~~i~~l~~vte~kiflE~erarl~~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~r-l  186 (445)
T 4b4t_P          108 KSLDLNTRISVIETIRVVTENKIFVEVERARVTKDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQME-L  186 (445)
T ss_dssp             CTTHHHHHHHHHHCCSSSSSCCCCCCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHH-H
T ss_pred             CchhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHH-H
Confidence            3333211  12211111   11111   1234467788888999999999999998643  222222   12222233 3


Q ss_pred             ccccchHHHHHHHHHHHHh----cCCCCC--HHHHHHHHHHHHhcCchHHHHHHHHHHH
Q 039342          139 FDDESNWQMVEYVFDKLNC----EGYGLG--MRFYNALLEALWCLGLRERAARVLDEAT  191 (248)
Q Consensus       139 ~~~~~~~~~a~~~~~~m~~----~~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~m~  191 (248)
                      |...+++..|..++.....    ....|+  ...|...+..+...+++.+|...|.+.-
T Consensus       187 ~l~~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~~~~~~~~~~~~e~~y~~a~~~y~e~~  245 (445)
T 4b4t_P          187 SILKGDYSQATVLSRKILKKTFKNPKYESLKLEYYNLLVKISLHKREYLEVAQYLQEIY  245 (445)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHhhcccCCcHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            6667888999988887643    223333  3456778888888899988888877764

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=90.54  E-value=5.9  Score=32.02  Aligned_cols=190  Identities=13%  Similarity=0.139  Sum_probs=113.4

Q ss_pred             CCHHHHHHHHHHHHH-----cCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHH-CCCCcCHhhHHHHHHHH----Hhc
Q 039342           37 GRFEEAIKAYVEMEK-----VRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKS-SGILPSVMCYCMLLAVY----AKS  106 (248)
Q Consensus        37 ~~~~~a~~~~~~m~~-----~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~-~~~~p~~~~~~~li~~~----~~~  106 (248)
                      |+++.|++.+..+.+     .+...+......++..|...|+++...+.+..+.+ +|..+..  ...+++.+    ...
T Consensus        30 ~~~~~a~e~ll~lEK~~r~~~d~~s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lskkr~qlk~a--i~~~V~~~~~~l~~~  107 (445)
T 4b4t_P           30 NDCNSALDQLLVLEKKTRQASDLASSKEVLAKIVDLLASRNKWDDLNEQLTLLSKKHGQLKLS--IQYMIQKVMEYLKSS  107 (445)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSCSTTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHTTTTTSHHH--HHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhhhhHHH--HHHHHHHHHHHHhcC
Confidence            678888888776653     34566788899999999999999999888877764 3443332  23444333    233


Q ss_pred             CCHHH--HHHHHHHHH--HCCC---CchHHhHHHHhcccccccchHHHHHHHHHHHHhc--CCCCC---HHHHHHHHHHH
Q 039342          107 NRWDD--AYGLLDEMH--TNRI---SNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCE--GYGLG---MRFYNALLEAL  174 (248)
Q Consensus       107 ~~~~~--a~~~~~~m~--~~~~---~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~--~~~p~---~~~~~~li~~~  174 (248)
                      ...+.  -..+.+.+.  ..|.   .....-....+...+...|++..|..++..+...  |..+.   ...|...++.|
T Consensus       108 ~~~d~~~~~~~i~~l~~vte~kiflE~erarl~~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~rl~  187 (445)
T 4b4t_P          108 KSLDLNTRISVIETIRVVTENKIFVEVERARVTKDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMELS  187 (445)
T ss_dssp             CTTHHHHHHHHHHCCSSSSSCCCCCCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHH
T ss_pred             CchhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHH
Confidence            33222  222222111  0111   1112233344445577789999999999998754  32222   34677888999


Q ss_pred             HhcCchHHHHHHHHHHHH----CCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHH
Q 039342          175 WCLGLRERAARVLDEATK----RGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMY  231 (248)
Q Consensus       175 ~~~g~~~~a~~~~~~m~~----~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~  231 (248)
                      ...+++.+|..++.+...    ....|+   ...-++.+...-+...+++.+|.+.|.+..
T Consensus       188 l~~~d~~~a~~~~~ki~~~~~~~~~~~~---lk~~~~~~~~~~~~~e~~y~~a~~~y~e~~  245 (445)
T 4b4t_P          188 ILKGDYSQATVLSRKILKKTFKNPKYES---LKLEYYNLLVKISLHKREYLEVAQYLQEIY  245 (445)
T ss_dssp             HHHTCHHHHHHHHHHHHHHHHHSSCCHH---HHHHHHHHHHHHHHHHCCHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHhhcccCCcHH---HHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            999999999999998642    222222   222233333344555666666666554443

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=90.04  E-value=2.1  Score=27.92  Aligned_cols=23  Identities=17%  Similarity=0.109  Sum_probs=13.7

Q ss_pred             HHHHHHhcCchHHHHHHHHHHHH
Q 039342          170 LLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       170 li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                      +--++.+.|++++|.+.++.+.+
T Consensus        80 LAvg~yklg~Y~~A~~~~~~lL~  102 (126)
T 1nzn_A           80 LAVGNYRLKEYEKALKYVRGLLQ  102 (126)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhHHHHHHHHHHHHH
Confidence            33455666666666666666655

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=88.87  E-value=3  Score=36.26  Aligned_cols=114  Identities=11%  Similarity=-0.003  Sum_probs=71.9

Q ss_pred             hHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCC-HHHHHHHHHHHHHc------CCCCC-H----------HHHHHHH
Q 039342            4 YKECQAILSRMSESGVARNSDSFNAVIEAFRQGGR-FEEAIKAYVEMEKV------RCDPN-E----------RTLEAVL   65 (248)
Q Consensus         4 ~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~-~~~a~~~~~~m~~~------~~~p~-~----------~t~~~ll   65 (248)
                      .+.|..+|+++.+.....+......+|..+.+.++ --+|.+++.+..+.      ...+. .          ...+.=.
T Consensus       265 ~~~a~~~le~L~~~~p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~LL~~Qa  344 (754)
T 4gns_B          265 VDFTIDYLKGLTKKDPIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPRDADSARLMNCMSDLLNIQT  344 (754)
T ss_dssp             HHHHHHHHHHHHHHCGGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhcccccccccccCcchHHHHHHH
Confidence            57799999998875432222222334444333332 23344444443221      12221 1          1122223


Q ss_pred             HHHHhcCChhHHHHHHHHHHHCCCCcC-HhhHHHHHHHHHhcCCHHHHHHHHHHH
Q 039342           66 SVYCFAGLVDESKEQFQEIKSSGILPS-VMCYCMLLAVYAKSNRWDDAYGLLDEM  119 (248)
Q Consensus        66 ~~~~~~g~~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~m  119 (248)
                      ..|...|+++.|.++-++....  .|+ -.+|-.|...|.+.|+++.|+-.++.+
T Consensus       345 ~FLl~K~~~elAL~~Ak~AV~~--aPseF~tW~~La~vYi~l~d~e~ALLtLNSc  397 (754)
T 4gns_B          345 NFLLNRGDYELALGVSNTSTEL--ALDSFESWYNLARCHIKKEEYEKALFAINSM  397 (754)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH--CSSCHHHHHHHHHHHHHTTCHHHHHHHHHHS
T ss_pred             HHHhccCcHHHHHHHHHHHHhc--CchhhHHHHHHHHHHHHhccHHHHHHHHhcC
Confidence            4567889999999999988764  565 579999999999999999999999877

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=88.54  E-value=3.8  Score=35.56  Aligned_cols=127  Identities=9%  Similarity=0.042  Sum_probs=76.1

Q ss_pred             HHHHHHHHhcCC-hhHHHHHHHHHHHCCCCcCHhh--HHHHHHHHHhcCC-HHHHHHHHHHHHHC------CCCchH---
Q 039342           62 EAVLSVYCFAGL-VDESKEQFQEIKSSGILPSVMC--YCMLLAVYAKSNR-WDDAYGLLDEMHTN------RISNIH---  128 (248)
Q Consensus        62 ~~ll~~~~~~g~-~~~a~~~~~~m~~~~~~p~~~~--~~~li~~~~~~~~-~~~a~~~~~~m~~~------~~~~~~---  128 (248)
                      ..+++.+.-.++ .+.|.++|+++.+..  |...+  ...+|..+.+.++ --+|.+++.+..+.      ...+..   
T Consensus       252 ~~Ll~~~~~t~~~~~~a~~~le~L~~~~--p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~~~~~  329 (754)
T 4gns_B          252 YSLKSFIAITPSLVDFTIDYLKGLTKKD--PIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPRDADS  329 (754)
T ss_dssp             HHHHHHHHTCGGGHHHHHHHHHHHHHHC--GGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSCCHHH
T ss_pred             HHHHHHHcccccHHHHHHHHHHHHHhhC--CchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhccccccc
Confidence            445555555666 588999999998763  43322  2333433333332 22345555443321      111110   


Q ss_pred             H-hH---HHHhc---ccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHH
Q 039342          129 Q-VT---GQMIK---GEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEAT  191 (248)
Q Consensus       129 ~-~~---~~~l~---~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  191 (248)
                      . ..   ..++.   .++...++++.|..+-++....- +-+..+|..|..+|...|+++.|+-.++.+.
T Consensus       330 ~~~~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~~a-PseF~tW~~La~vYi~l~d~e~ALLtLNScP  398 (754)
T 4gns_B          330 ARLMNCMSDLLNIQTNFLLNRGDYELALGVSNTSTELA-LDSFESWYNLARCHIKKEEYEKALFAINSMP  398 (754)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHSC
T ss_pred             ccccCcchHHHHHHHHHHhccCcHHHHHHHHHHHHhcC-chhhHHHHHHHHHHHHhccHHHHHHHHhcCC
Confidence            0 00   11211   22445788999999988876642 2258899999999999999999999999873

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=86.60  E-value=4.9  Score=26.14  Aligned_cols=81  Identities=9%  Similarity=0.000  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhH---HHHHHHHHHHCCCCc--CHhhHHHHHHHHHhcCCHHHHHH
Q 039342           40 EEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDE---SKEQFQEIKSSGILP--SVMCYCMLLAVYAKSNRWDDAYG  114 (248)
Q Consensus        40 ~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~---a~~~~~~m~~~~~~p--~~~~~~~li~~~~~~~~~~~a~~  114 (248)
                      ..+.+-|......|. |+..+--.+-.++.+......   +..+++.+.+.+ .|  .....-.|--++.+.|++++|.+
T Consensus        18 ~~~~~~y~~e~~~~~-~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~-~p~~~Rd~lY~LAvg~yklg~Y~~A~~   95 (126)
T 1nzn_A           18 LKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKALK   95 (126)
T ss_dssp             HHHHHHHHHHHHHSC-CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTS-CHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHhccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHHhhhHHHHHH
Confidence            334444444444343 555555555566666665444   666666665542 12  22233344456666777777777


Q ss_pred             HHHHHHHC
Q 039342          115 LLDEMHTN  122 (248)
Q Consensus       115 ~~~~m~~~  122 (248)
                      .++.+.+.
T Consensus        96 ~~~~lL~~  103 (126)
T 1nzn_A           96 YVRGLLQT  103 (126)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHh
Confidence            77766544

>3t8k_A Uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center F or structural genomics, MCSG; 1.77A {Leptotrichia buccalis}

Probab=86.11  E-value=6.7  Score=27.21  Aligned_cols=93  Identities=9%  Similarity=0.009  Sum_probs=52.4

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHh---hHHHHHHHHHh-
Q 039342           31 EAFRQGGRFEEAIKAYVEMEKVRCDPNE-RTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVM---CYCMLLAVYAK-  105 (248)
Q Consensus        31 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~---~~~~li~~~~~-  105 (248)
                      ...++.|+.+....++..    ++.... ..-.+.+...+..|+.+.-.++.+.+.+.|..++..   -++.|..++.. 
T Consensus        11 ~~Aa~~g~~~~~~~l~~~----~~~~~~~~~g~T~Lh~A~~~~~~~~~~~iv~~Ll~~Gadvn~~d~~g~TpLh~a~~~~   86 (186)
T 3t8k_A           11 SAAAMLGTYEDFLELFEK----GYEDKESVLKSNILYDVLRNNNDEARYKISMFLINKGADIKSRTKEGTTLFFPLFQGG   86 (186)
T ss_dssp             HHHHHHSCHHHHHHHHHH----SSSCHHHHHTTTHHHHHTTCSCHHHHHHHHHHHHHTTCCSSCCCTTCCCTHHHHHHHC
T ss_pred             HHHHHcCCHHHHHHHHhc----CcccccccCCCCHHHHHHHcCCcchHHHHHHHHHHCCCCCCCCCCCCCcHHHHHHHcC
Confidence            344567888876555543    322111 112345566666777776677888888888776543   23344433332 


Q ss_pred             cCCHHHHHHHHHHHHHCCCCch
Q 039342          106 SNRWDDAYGLLDEMHTNRISNI  127 (248)
Q Consensus       106 ~~~~~~a~~~~~~m~~~~~~~~  127 (248)
                      ..+.....++.+.+.+.|..++
T Consensus        87 ~~~~~~~~~iv~~Ll~~Gadin  108 (186)
T 3t8k_A           87 GNDITGTTELCKIFLEKGADIT  108 (186)
T ss_dssp             TTCHHHHHHHHHHHHHTTCCSS
T ss_pred             CcchhhHHHHHHHHHHCCCCCC
Confidence            2345555667777777776543

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=85.97  E-value=9.1  Score=30.74  Aligned_cols=95  Identities=7%  Similarity=-0.090  Sum_probs=63.6

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHC--CCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHH---CCCCchHH----h
Q 039342           60 TLEAVLSVYCFAGLVDESKEQFQEIKSS--GILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHT---NRISNIHQ----V  130 (248)
Q Consensus        60 t~~~ll~~~~~~g~~~~a~~~~~~m~~~--~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~----~  130 (248)
                      ++..+-..|.+.|+++.|.+.+.++.+.  +..--...+-.+|+.+...+++..+...+.+...   .+..|...    .
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            4566788899999999999999999864  2223356788888999999999999998888643   33233322    1


Q ss_pred             HHHHhcccccccchHHHHHHHHHHHHh
Q 039342          131 TGQMIKGEFDDESNWQMVEYVFDKLNC  157 (248)
Q Consensus       131 ~~~~l~~~~~~~~~~~~a~~~~~~m~~  157 (248)
                      +..++   +...+++..|...|-+...
T Consensus       213 ~~gl~---~l~~r~f~~Aa~~f~e~~~  236 (429)
T 4b4t_R          213 YYGIH---CLAVRNFKEAAKLLVDSLA  236 (429)
T ss_dssp             HHHHG---GGGTSCHHHHHHHHHHHHH
T ss_pred             HHHHH---HHHhChHHHHHHHHHHHhc
Confidence            22222   2345666776666655443

>3kea_A K1L; tropism, ANK repeat, viral protein; 2.30A {Vaccinia virus}

Probab=85.38  E-value=2.6  Score=31.53  Aligned_cols=17  Identities=6%  Similarity=-0.148  Sum_probs=10.0

Q ss_pred             HHHHHHHHHHcCCCCCc
Q 039342          226 WLNKMYEMFMMGEDLPQ  242 (248)
Q Consensus       226 ~~~~m~~~~~~~~~~~~  242 (248)
                      +++.+.+.|.+.+...+
T Consensus       236 iv~~Ll~~g~~~~~~~~  252 (285)
T 3kea_A          236 IAKMIIEKHVEYKSDSY  252 (285)
T ss_dssp             HHHHHHHHHHHHTTCTT
T ss_pred             HHHHHHHcCCCCCCccc
Confidence            55666666766554443

>1wdy_A 2-5A-dependent ribonuclease; hydrolase, RNA-binding; HET: 25A; 1.80A {Homo sapiens} SCOP: d.211.1.1

Probab=84.77  E-value=0.85  Score=33.72  Aligned_cols=16  Identities=0%  Similarity=-0.338  Sum_probs=10.3

Q ss_pred             HHHHHHHHHHcCCCCC
Q 039342          226 WLNKMYEMFMMGEDLP  241 (248)
Q Consensus       226 ~~~~m~~~~~~~~~~~  241 (248)
                      +++.+.+.|..++...
T Consensus       268 i~~~Ll~~Ga~~~~~d  283 (285)
T 1wdy_A          268 IAELLCKRGASTDCGD  283 (285)
T ss_dssp             HHHHHHHHSSCSCCSS
T ss_pred             HHHHHHHcCCCCCccc
Confidence            5666777777766543

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=84.75  E-value=8.7  Score=30.84  Aligned_cols=97  Identities=14%  Similarity=0.050  Sum_probs=69.7

Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHC---CCCcCHh----
Q 039342           24 DSFNAVIEAFRQGGRFEEAIKAYVEMEKVR--CDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSS---GILPSVM----   94 (248)
Q Consensus        24 ~~y~~li~~~~~~~~~~~a~~~~~~m~~~~--~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~---~~~p~~~----   94 (248)
                      .++..+-..|.+.|+.+.|.+.|.++...-  ..--...+-.+|..+...+++..+...+++....   +-.|+..    
T Consensus       132 ~~~~~la~~~~~~Gd~~~A~~~~~~~~~~~~~~~~kid~~l~~irl~l~~~d~~~~~~~~~ka~~~~~~~~d~~~~~~lk  211 (429)
T 4b4t_R          132 QAWINLGEYYAQIGDKDNAEKTLGKSLSKAISTGAKIDVMLTIARLGFFYNDQLYVKEKLEAVNSMIEKGGDWERRNRYK  211 (429)
T ss_dssp             SCCHHHHHHHHHHCCCTTHHHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTCCCTHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhhhcCCCHHHHHHHH
Confidence            467788899999999999999999997653  3334567778899999999999999999988642   3223222    


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 039342           95 CYCMLLAVYAKSNRWDDAYGLLDEMHTN  122 (248)
Q Consensus        95 ~~~~li~~~~~~~~~~~a~~~~~~m~~~  122 (248)
                      .|..+  .+...+++..|-..|-+....
T Consensus       212 ~~~gl--~~l~~r~f~~Aa~~f~e~~~t  237 (429)
T 4b4t_R          212 TYYGI--HCLAVRNFKEAAKLLVDSLAT  237 (429)
T ss_dssp             HHHHH--GGGGTSCHHHHHHHHHHHHHH
T ss_pred             HHHHH--HHHHhChHHHHHHHHHHHhcc
Confidence            12211  223567888888888776443

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=84.69  E-value=24  Score=32.39  Aligned_cols=108  Identities=9%  Similarity=0.088  Sum_probs=67.8

Q ss_pred             CCchHHHHHHHHHHHHcCCCC-----------------------CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC
Q 039342            1 GGLYKECQAILSRMSESGVAR-----------------------NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN   57 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~-----------------------~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~   57 (248)
                      +|++++|.+.|.+... |+..                       -..=|..++..|-+.+.++.+.++-....+..-+-+
T Consensus       855 ~ge~~~A~~~F~kaa~-~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~YY~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~  933 (1139)
T 4fhn_B          855 SKEAVKAVRCFKTTSL-VLYSHTSQFAVLREFQEIAEKYHHQNLLSCYYLHLSKKLFEESAYIDALEFSLLADASKETDD  933 (1139)
T ss_dssp             TTCHHHHHHHHHTCCC-SCTTCCCSCSSHHHHHHHHHTTTSCCSSHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCC
T ss_pred             cCCHHHHHHHHHHHhh-hhcccchhhhhhcccccccccccccccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccCCC
Confidence            5889999999977532 1111                       112256677777777887777776665544321111


Q ss_pred             ----HHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHH
Q 039342           58 ----ERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDD  111 (248)
Q Consensus        58 ----~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~  111 (248)
                          ...|..+.+++...|++++|...+-.+.....+  ......+|..++..+..+.
T Consensus       934 ~~~~~~l~~~iFk~~L~l~~ye~Ay~aL~~~pd~~~r--~~cLr~LV~~lce~~~~~~  989 (1139)
T 4fhn_B          934 EDLSIAITHETLKTACAAGKFDAAHVALMVLSTTPLK--KSCLLDFVNQLTKQGKINQ  989 (1139)
T ss_dssp             HHHHHHHHHHHHHHHHHHCCSGGGGHHHHHHHHSSSC--HHHHHHHHHHHHHHCCHHH
T ss_pred             hhhHHHHHHHHHHHHHhhCCHHHHHHHHHhCCCHHHH--HHHHHHHHHHHHhCCChhh
Confidence                125677788888888888888887777655433  4456666666666665443

>1k1a_A B-cell lymphoma 3-encoded protein; BCL-3, NF-kappab transcription factors, ikappab proteins; 1.86A {Homo sapiens} SCOP: d.211.1.1 PDB: 1k1b_A

Probab=84.01  E-value=1.9  Score=30.94  Aligned_cols=86  Identities=9%  Similarity=0.007  Sum_probs=45.8

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHH--HHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhh--HHHHHHHHH
Q 039342           29 VIEAFRQGGRFEEAIKAYVEMEKVRCDPNERT--LEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMC--YCMLLAVYA  104 (248)
Q Consensus        29 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t--~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~--~~~li~~~~  104 (248)
                      .+...++.|+.+.+..+++.+.+.|..++...  -.+.+...+..|+.+    +++.+.+.|..|+...  -.+.+...+
T Consensus        12 ~L~~A~~~g~~~~v~~Ll~~~~~~~~~~~~~~~~g~t~L~~A~~~~~~~----~v~~Ll~~g~~~~~~~~~g~t~l~~A~   87 (241)
T 1k1a_A           12 PLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPS----VVRLLVTAGASPMALDRHGQTAAHLAC   87 (241)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTTCCSCCCCTTSCCHHHHHHHTTCHH----HHHHHHHTTCCTTCCCTTSCCHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCcccccCCCHHHHHHHcCCHH----HHHHHHHcCCCccccCCCCCCHHHHHH
Confidence            34556677888887777777766665544321  123344455566654    4444445555543221  123334445


Q ss_pred             hcCCHHHHHHHHHH
Q 039342          105 KSNRWDDAYGLLDE  118 (248)
Q Consensus       105 ~~~~~~~a~~~~~~  118 (248)
                      ..|+.+-+..+++.
T Consensus        88 ~~~~~~~~~~Ll~~  101 (241)
T 1k1a_A           88 EHRSPTCLRALLDS  101 (241)
T ss_dssp             HTTCHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHc
Confidence            56676655555554

>3jxi_A Vanilloid receptor-related osmotically activated protein; ankyrin repeats, ANK repeat, ION transport, ionic channel, R transmembrane, transport; 2.30A {Gallus gallus} PDB: 3jxj_A 4dx1_A 4dx2_A*

Probab=83.07  E-value=1.9  Score=31.59  Aligned_cols=49  Identities=14%  Similarity=0.063  Sum_probs=31.2

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHH-------hHHHHHHHHH--hcCCHHHHHHHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSD-------SFNAVIEAFR--QGGRFEEAIKAYVEME   50 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~-------~y~~li~~~~--~~~~~~~a~~~~~~m~   50 (248)
                      |+.+....+++.+.+.|..++..       -++.|..+..  +.|+.+-+..+++.-.
T Consensus        16 g~~~~v~~ll~~l~~~~~~~~~~~~~~~~~g~t~L~~A~~~~~~g~~~~v~~Ll~~g~   73 (260)
T 3jxi_A           16 GSPDGLEGLLSFLLTHKKRLTDEEFREPSTGKTCLPKALLNLSAGRNDTIPILLDIAE   73 (260)
T ss_dssp             TCGGGGTTHHHHHHHHTCCTTSGGGSCTTTCCCHHHHHHTSCBTTBCTHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhcCCCcchhhhhccCCCCcHHHHHHHHhhcCCHHHHHHHHHhcc
Confidence            66677777788777777666543       3344544442  5688887777776643

>1k1a_A B-cell lymphoma 3-encoded protein; BCL-3, NF-kappab transcription factors, ikappab proteins; 1.86A {Homo sapiens} SCOP: d.211.1.1 PDB: 1k1b_A

Probab=82.95  E-value=1.8  Score=31.16  Aligned_cols=180  Identities=8%  Similarity=-0.000  Sum_probs=86.8

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHh--HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHH--HHHHHHHHhcCChhH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDS--FNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTL--EAVLSVYCFAGLVDE   76 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~--y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~--~~ll~~~~~~g~~~~   76 (248)
                      .|+.+.+..+++.+.+.|..++...  -.+.+...+..|+.+-    ++.+.+.|..|+....  .+.+...++.|+.+-
T Consensus        19 ~g~~~~v~~Ll~~~~~~~~~~~~~~~~g~t~L~~A~~~~~~~~----v~~Ll~~g~~~~~~~~~g~t~l~~A~~~~~~~~   94 (241)
T 1k1a_A           19 QGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSV----VRLLVTAGASPMALDRHGQTAAHLACEHRSPTC   94 (241)
T ss_dssp             TTCHHHHHHHHHHHHHTTCCSCCCCTTSCCHHHHHHHTTCHHH----HHHHHHTTCCTTCCCTTSCCHHHHHHHTTCHHH
T ss_pred             cCCHHHHHHHHHHHHhcCCCCCcccccCCCHHHHHHHcCCHHH----HHHHHHcCCCccccCCCCCCHHHHHHHcCCHHH
Confidence            3677777777777766666554321  2234555666777654    4455556665543221  234555567788776


Q ss_pred             HHHHHHHHHHCCCCc---CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHh----HHHHhcccccccchHHHHH
Q 039342           77 SKEQFQEIKSSGILP---SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQV----TGQMIKGEFDDESNWQMVE  149 (248)
Q Consensus        77 a~~~~~~m~~~~~~p---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~----~~~~l~~~~~~~~~~~~a~  149 (248)
                      +..+++.....++.+   +....+. +...+..|+.+-+    +.+.+.|..++...    .+.+..  ....++.+   
T Consensus        95 ~~~Ll~~~~~~~~~~~~~~~~g~t~-L~~A~~~~~~~~~----~~Ll~~g~~~~~~~~~~g~t~L~~--A~~~~~~~---  164 (241)
T 1k1a_A           95 LRALLDSAAPGTLDLEARNYDGLTA-LHVAVNTECQETV----QLLLERGADIDAVDIKSGRSPLIH--AVENNSLS---  164 (241)
T ss_dssp             HHHHHHHSCTTSCCTTCCCTTSCCH-HHHHHHHTCHHHH----HHHHHTTCCTTCCCTTTCCCHHHH--HHHTTCHH---
T ss_pred             HHHHHHcCCCccccccccCcCCCcH-HHHHHHcCCHHHH----HHHHHcCCCcccccccCCCcHHHH--HHHcCCHH---
Confidence            666665543221222   2222233 3333455665444    44444454332111    111111  11233433   


Q ss_pred             HHHHHHHhcCCCCCHHH--HHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCc
Q 039342          150 YVFDKLNCEGYGLGMRF--YNALLEALWCLGLRERAARVLDEATKRGLFPEL  199 (248)
Q Consensus       150 ~~~~~m~~~~~~p~~~~--~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  199 (248)
                       +++.+.+.|..++...  -.+.+...+..|+.+    +.+.+.+.|..|+.
T Consensus       165 -~v~~Ll~~g~~~~~~~~~g~t~L~~A~~~~~~~----~v~~Ll~~ga~~~~  211 (241)
T 1k1a_A          165 -MVQLLLQHGANVNAQMYSGSSALHSASGRGLLP----LVRTLVRSGADSSL  211 (241)
T ss_dssp             -HHHHHHHTTCCTTCBCTTSCBHHHHHHHHTCHH----HHHHHHHTTCCTTC
T ss_pred             -HHHHHHHcCCCCCCcCCCCCCHHHHHHHcCCHH----HHHHHHhcCCCCCC
Confidence             4444445565554321  123444555666655    34444456766654

>3esl_A Checkpoint serine/threonine-protein kinase BUB1; mitotic spindle checkpoint, TPR motif, all-alpha domain, MAD3-like domain; HET: NHE; 1.74A {Saccharomyces cerevisiae}

Probab=82.91  E-value=7  Score=27.73  Aligned_cols=88  Identities=14%  Similarity=0.098  Sum_probs=60.1

Q ss_pred             hHHHHHHHHHHHHcCCCCCHH---hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCChhHHHH
Q 039342            4 YKECQAILSRMSESGVARNSD---SFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPN-ERTLEAVLSVYCFAGLVDESKE   79 (248)
Q Consensus         4 ~~~a~~~~~~m~~~g~~~~~~---~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~ll~~~~~~g~~~~a~~   79 (248)
                      ++++.+.|.....  .+-|+.   .|-..+..| ..+...++.++|..|..+||--. +..|...-..+-..|++.+|.+
T Consensus        60 LErc~~~F~~~~r--YkND~RYLklWl~Ya~~~-~~~~~~~p~~if~~L~~~~IG~~~AlfYe~wA~~lE~~g~~~~A~~  136 (202)
T 3esl_A           60 MERCLIYIQDMET--YRNDPRFLKIWIWYINLF-LSNNFHESENTFKYMFNKGIGTKLSLFYEEFSKLLENAQFFLEAKV  136 (202)
T ss_dssp             HHHHHHHHTTCGG--GTTCHHHHHHHHHHHHHH-STTCHHHHHHHHHHHHHHTSSTTBHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHhccccc--ccCCHHHHHHHHHHHHhh-cccccCCHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            3455555555443  333443   444444443 24457789999999988876543 4667788888888999999999


Q ss_pred             HHHHHHHCCCCcCHh
Q 039342           80 QFQEIKSSGILPSVM   94 (248)
Q Consensus        80 ~~~~m~~~~~~p~~~   94 (248)
                      +|+.=.+.+-.|-..
T Consensus       137 Vy~~GI~~~A~P~~r  151 (202)
T 3esl_A          137 LLELGAENNCRPYNR  151 (202)
T ss_dssp             HHHHHHHTTCBSHHH
T ss_pred             HHHHHHHcCCccHHH
Confidence            999988888787543

>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=81.91  E-value=10  Score=30.12  Aligned_cols=132  Identities=11%  Similarity=0.011  Sum_probs=58.9

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHC-CCCc---CHhhHHHHHHHHHhcCC-HHHHHHHHHHHHH----CCCCchHHh
Q 039342           60 TLEAVLSVYCFAGLVDESKEQFQEIKSS-GILP---SVMCYCMLLAVYAKSNR-WDDAYGLLDEMHT----NRISNIHQV  130 (248)
Q Consensus        60 t~~~ll~~~~~~g~~~~a~~~~~~m~~~-~~~p---~~~~~~~li~~~~~~~~-~~~a~~~~~~m~~----~~~~~~~~~  130 (248)
                      ....|...|.+.|+.++..+++...+.. +..|   .......+|+.+....+ .+.-.++..+..+    ....--...
T Consensus        21 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~kak~~k~v~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~~~r~flr~~  100 (394)
T 3txn_A           21 GILQQGELYKQEGKAKELADLIKVTRPFLSSISKAKAAKLVRSLVDMFLDMDAGTGIEVQLCKDCIEWAKQEKRTFLRQS  100 (394)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHTTTGGGGSCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555667777777777777777665432 1112   23345555665554322 3333333333322    111000111


Q ss_pred             HHHHhcccccccchHHHHHHHHHHHHhcCCCCC-----HHHHHHHHHHHHhcCchHHHHHHHHHHH
Q 039342          131 TGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLG-----MRFYNALLEALWCLGLRERAARVLDEAT  191 (248)
Q Consensus       131 ~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~-----~~~~~~li~~~~~~g~~~~a~~~~~~m~  191 (248)
                      ...=+...+-..|++..|..++..+.+.--..|     ...|..-++.|...+++.++...+....
T Consensus       101 l~~kL~~l~~~~~~y~~a~~~i~~l~~~~~~~dd~~~llev~lle~~~~~~~~n~~k~k~~l~~a~  166 (394)
T 3txn_A          101 LEARLIALYFDTALYTEALALGAQLLRELKKLDDKNLLVEVQLLESKTYHALSNLPKARAALTSAR  166 (394)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSSCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            111222234445555555555555444311111     1223344445555555555555555543

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=81.73  E-value=10  Score=25.96  Aligned_cols=103  Identities=12%  Similarity=0.100  Sum_probs=60.2

Q ss_pred             cCCCCCHHh--HHHHHHHHHhcCCHHHHHHHHHHHHHc-CCCCCH-------HHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 039342           17 SGVARNSDS--FNAVIEAFRQGGRFEEAIKAYVEMEKV-RCDPNE-------RTLEAVLSVYCFAGLVDESKEQFQEIKS   86 (248)
Q Consensus        17 ~g~~~~~~~--y~~li~~~~~~~~~~~a~~~~~~m~~~-~~~p~~-------~t~~~ll~~~~~~g~~~~a~~~~~~m~~   86 (248)
                      .|..|.-..  +-.-+..+...+.++.|.-+.+.+... +-.|+.       .++..+-+++...|++..|...|++..+
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            455554443  444577888899999998888776432 223441       3556677888999999999999988532


Q ss_pred             C-CCCc-----------------------CHhhHHHHHHHHHhcCCHHHHHHHHHHH
Q 039342           87 S-GILP-----------------------SVMCYCMLLAVYAKSNRWDDAYGLLDEM  119 (248)
Q Consensus        87 ~-~~~p-----------------------~~~~~~~li~~~~~~~~~~~a~~~~~~m  119 (248)
                      . ..-+                       +...---+-.+|.+.+++++|+.+++.+
T Consensus        92 ~~k~l~k~~s~~~~~~~~ss~p~s~~~~~e~Elkykia~C~~~l~~~~~Ai~~Le~I  148 (167)
T 3ffl_A           92 QKKALSKTSKVRPSTGNSASTPQSQCLPSEIEVKYKLAECYTVLKQDKDAIAILDGI  148 (167)
T ss_dssp             HHHCC--------------------CCCCHHHHHHHHHHHHHHTTCHHHHHHHHHTS
T ss_pred             HHHHHhcCCCccccccccCCCcccccccchHHHHHHHHHHHHHHCCHHHHHHHHhcC
Confidence            1 1101                       1122223555666777777777777744

>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=81.58  E-value=2.7  Score=26.08  Aligned_cols=72  Identities=18%  Similarity=0.151  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHH
Q 039342          146 QMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISV  225 (248)
Q Consensus       146 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~  225 (248)
                      ++|.-|-+.+...+.  ...+--+-+..+.++|++++|..+.+.+    ..||...+-.|-       -++.|..++++.
T Consensus        24 qEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~----c~pdlepw~ALc-------e~rlGl~s~le~   90 (116)
T 2p58_C           24 EEANCIAEWLHLKGE--EEAVQLIRLSSLMNRGDYASALQQGNKL----AYPDLEPWLALC-------EYRLGLGSALES   90 (116)
T ss_dssp             HHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHHHHTTS----CCGGGHHHHHHH-------HHHHTCHHHHHH
T ss_pred             HHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCC----CCchHHHHHHHH-------HHhcccHHHHHH
Confidence            455555555554433  2222223334556666666666665433    255554444433       234555555555


Q ss_pred             HHHHH
Q 039342          226 WLNKM  230 (248)
Q Consensus       226 ~~~~m  230 (248)
                      .+..+
T Consensus        91 rL~~l   95 (116)
T 2p58_C           91 RLNRL   95 (116)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            44333

---

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	248
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.41
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.39
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.38
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.31
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.19
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.07
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.93
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	98.79
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.77
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.6
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.59
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.58
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.37
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.34
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.32
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.32
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.27
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.24
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.2
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	98.18
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.15
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.15
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	98.11
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.07
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.01
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.0
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.97
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.77
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	97.73
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	97.71
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.69
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.66
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	97.66
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.65
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.6
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.55
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.46
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.45
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.41
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.31
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.27
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.15
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	96.99
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	96.85
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	96.72
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	96.59
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	96.31
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	96.04
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	95.75
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	95.67
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	95.45
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	94.97
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	94.86
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	94.07
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	94.02
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	94.01
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	93.94
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	93.43
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	93.13
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	93.05
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	87.16
d1ug3a1	193	Eukaryotic initiation factor eIF4G {Human (Homo sa	80.23

>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=99.41  E-value=5.1e-11  Score=90.90  Aligned_cols=220  Identities=12%  Similarity=0.018  Sum_probs=160.3

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|.+.|++..+... -+..+|..+-..+...|++++|...|++..+.. +-+...|..+..+|...|++++|.+.
T Consensus        32 ~g~~~~A~~~~~~al~~~P-~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~A~~~  109 (323)
T d1fcha_          32 EGDLPNAVLLFEAAVQQDP-KHMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSFTNESLQRQACEI  109 (323)
T ss_dssp             TTCHHHHHHHHHHHHHSCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCChHHHHHHHHhhhccc-cccccccccccccccccccccccccc
Confidence            3899999999999987542 358899999999999999999999999987654 34567888889999999999999999


Q ss_pred             HHHHHHCCCCcCH----------------hhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC-chHHhHHHHhcccccccc
Q 039342           81 FQEIKSSGILPSV----------------MCYCMLLAVYAKSNRWDDAYGLLDEMHTNRIS-NIHQVTGQMIKGEFDDES  143 (248)
Q Consensus        81 ~~~m~~~~~~p~~----------------~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-~~~~~~~~~l~~~~~~~~  143 (248)
                      ++......  |+.                ......+..+...+..++|...|.+..+.... ++...+..+-. .+...|
T Consensus       110 ~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~-~~~~~~  186 (323)
T d1fcha_         110 LRDWLRYT--PAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGV-LFNLSG  186 (323)
T ss_dssp             HHHHHHTS--TTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHH-HHHHTT
T ss_pred             hhhHHHhc--cchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHH-HHHHHH
Confidence            99987642  211                11112223344556677888888877654322 22333333332 366778


Q ss_pred             hHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCc-chhhhHHhhhhhhccccchHHHH
Q 039342          144 NWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPEL-FRHNKLVWSVDVHRMWEGGAYTA  222 (248)
Q Consensus       144 ~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~-~t~~~li~~~~~~~~~~~g~~~~  222 (248)
                      +++.|...++........ +...|..+-..+.+.|++++|.+.|++..+.  .|+. ..+..+-     ..|.+.|++++
T Consensus       187 ~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg-----~~~~~~g~~~~  258 (323)
T d1fcha_         187 EYDKAVDCFTAALSVRPN-DYLLWNKLGATLANGNQSEEAVAAYRRALEL--QPGYIRSRYNLG-----ISCINLGAHRE  258 (323)
T ss_dssp             CHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHH-----HHHHHHTCHHH
T ss_pred             HHhhhhcccccccccccc-cccchhhhhhcccccccchhHHHHHHHHHHH--hhccHHHHHHHH-----HHHHHCCCHHH
Confidence            899999999988776433 5778888999999999999999999988764  4542 2333333     67788899999


Q ss_pred             HHHHHHHHHHH
Q 039342          223 ISVWLNKMYEM  233 (248)
Q Consensus       223 ~~~~~~~m~~~  233 (248)
                      |...+++-.+.
T Consensus       259 A~~~~~~al~l  269 (323)
T d1fcha_         259 AVEHFLEALNM  269 (323)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHh
Confidence            99988876664

>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=99.39  E-value=2.5e-10  Score=88.38  Aligned_cols=83  Identities=12%  Similarity=0.093  Sum_probs=68.0

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|.+.|+++.+.. +-++..+..+-..|.+.|++++|...+++..+.. +-+..+|..+..+|.+.|++++|.+.+
T Consensus        13 G~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~l~~~~~~~g~~~~A~~~~   90 (388)
T d1w3ba_          13 GDFEAAERHCMQLWRQE-PDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQLQEAIEHY   90 (388)
T ss_dssp             TCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHhhhhcccccccccc
Confidence            88999999999987653 2357888888899999999999999999987654 345678888888999999999998888


Q ss_pred             HHHHH
Q 039342           82 QEIKS   86 (248)
Q Consensus        82 ~~m~~   86 (248)
                      ....+
T Consensus        91 ~~~~~   95 (388)
T d1w3ba_          91 RHALR   95 (388)
T ss_dssp             HHHHH
T ss_pred             ccccc
Confidence            77654

>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=99.38  E-value=1.2e-10  Score=90.16  Aligned_cols=200  Identities=14%  Similarity=0.060  Sum_probs=103.6

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHH
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLA  101 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~  101 (248)
                      +...+..+...+...|+++.|...+++..+.. +-+...|..+...+...|++++|...++...+.. ..+...+..+-.
T Consensus       168 ~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~  245 (388)
T d1w3ba_         168 FAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLS-PNHAVVHGNLAC  245 (388)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hhHHHHhhcccccccCcHHHHHHHHHHHHHhC-cccHHHHHHHhhhhhccccHHHHHHHHHHhHHHh-hhHHHHHHHHHH
Confidence            34455555555666666666666666554432 2234455555666666666666666666655432 123445555556


Q ss_pred             HHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchH
Q 039342          102 VYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRE  181 (248)
Q Consensus       102 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~  181 (248)
                      .+.+.|++++|+..|++..+..  |+.......+...+...++++.|...++...... +.+...+..+...+.+.|+++
T Consensus       246 ~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~  322 (388)
T d1w3ba_         246 VYYEQGLIDLAIDTYRRAIELQ--PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLANIKREQGNIE  322 (388)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTC--SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccC-CccchhhhHHHHHHHHCCCHH
Confidence            6666666666666666655433  3222222222222444555666666665554442 234455555556666666666


Q ss_pred             HHHHHHHHHHHCCCCCCc-chhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          182 RAARVLDEATKRGLFPEL-FRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       182 ~a~~~~~~m~~~g~~p~~-~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      +|.+.|++..+.  .|+. ..+..+     ...+.+.|++++|...+++..+.
T Consensus       323 ~A~~~~~~al~~--~p~~~~~~~~l-----a~~~~~~g~~~~A~~~~~~al~l  368 (388)
T d1w3ba_         323 EAVRLYRKALEV--FPEFAAAHSNL-----ASVLQQQGKLQEALMHYKEAIRI  368 (388)
T ss_dssp             HHHHHHHHHTTS--CTTCHHHHHHH-----HHHHHTTTCCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHh--CCCCHHHHHHH-----HHHHHHcCCHHHHHHHHHHHHHh
Confidence            666666655432  3432 112222     24455566666666666555444

>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=99.31  E-value=1.2e-09  Score=82.95  Aligned_cols=224  Identities=9%  Similarity=0.013  Sum_probs=162.9

Q ss_pred             hHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhc--------------CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 039342            4 YKECQAILSRMSESGVARNSDSFNAVIEAFRQG--------------GRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYC   69 (248)
Q Consensus         4 ~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~--------------~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~   69 (248)
                      .+++..+|++....- +-++..|-..+..+-..              +..++|..+|++..+...+-+...|...+....
T Consensus        32 ~~Rv~~vyerAl~~~-~~~~~lW~~y~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~  110 (308)
T d2onda1          32 TKRVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEE  110 (308)
T ss_dssp             HHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCchHHHHHHHhhcccchHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            355677787776532 23556666655544322              335788889998887656667778888899999


Q ss_pred             hcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHH
Q 039342           70 FAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVE  149 (248)
Q Consensus        70 ~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  149 (248)
                      +.|+++.|..+|+.+.+........+|...+..+.+.|+.+.|.++|++..+................ ....++.+.|.
T Consensus       111 ~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al~~~~~~~~~~~~~a~~e-~~~~~~~~~a~  189 (308)
T d2onda1         111 SRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYVTAALME-YYCSKDKSVAF  189 (308)
T ss_dssp             HTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTTCCTHHHHHHHHHH-HHTSCCHHHHH
T ss_pred             hcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCcHHHHHHHHHHH-HHhccCHHHHH
Confidence            99999999999999987543334567999999999999999999999999876643332222222211 34557789999


Q ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHC-CCCCCcchhhhHHhhhhhhccccchHHHHHHHHHH
Q 039342          150 YVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKR-GLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLN  228 (248)
Q Consensus       150 ~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~  228 (248)
                      .+|+...+.. ..+...+...++.+.+.|+.+.|..+|++..+. +..|+..   ..+|...+.-....|+.+.+..+.+
T Consensus       190 ~i~e~~l~~~-p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~~~~---~~iw~~~~~fE~~~G~~~~~~~~~~  265 (308)
T d2onda1         190 KIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKS---GEIWARFLAFESNIGDLASILKVEK  265 (308)
T ss_dssp             HHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGC---HHHHHHHHHHHHHHSCHHHHHHHHH
T ss_pred             HHHHHHHHhh-hhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHH---HHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            9999988863 336788999999999999999999999997764 3455422   2344444455567899999999888


Q ss_pred             HHHHH
Q 039342          229 KMYEM  233 (248)
Q Consensus       229 ~m~~~  233 (248)
                      ++.+.
T Consensus       266 r~~~~  270 (308)
T d2onda1         266 RRFTA  270 (308)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            88766

>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=99.19  E-value=5e-09  Score=79.39  Aligned_cols=186  Identities=10%  Similarity=0.034  Sum_probs=143.1

Q ss_pred             chHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHH
Q 039342            3 LYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQ   82 (248)
Q Consensus         3 ~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~   82 (248)
                      ..++|..+|++..+...+.+...|........+.|+++.|..+|+.+.+.........|...+..+.+.|+.+.|.++|+
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            35788899998876555556778899999999999999999999999876443445678999999999999999999999


Q ss_pred             HHHHCCCCcCHhhHHHHHHH-HHhcCCHHHHHHHHHHHHHCCCCchH-HhHHHHhcccccccchHHHHHHHHHHHHhcC-
Q 039342           83 EIKSSGILPSVMCYCMLLAV-YAKSNRWDDAYGLLDEMHTNRISNIH-QVTGQMIKGEFDDESNWQMVEYVFDKLNCEG-  159 (248)
Q Consensus        83 ~m~~~~~~p~~~~~~~li~~-~~~~~~~~~a~~~~~~m~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~-  159 (248)
                      ...+.+.. +...|...... +...|+.+.|..+|+...+..  |+. ..+...+.- ....|+.+.|..+|++..... 
T Consensus       159 ~al~~~~~-~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~--p~~~~~w~~y~~~-~~~~g~~~~aR~~fe~ai~~~~  234 (308)
T d2onda1         159 KAREDART-RHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY--GDIPEYVLAYIDY-LSHLNEDNNTRVLFERVLTSGS  234 (308)
T ss_dssp             HHHTSTTC-CTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH--TTCHHHHHHHHHH-HHTTCCHHHHHHHHHHHHHSSS
T ss_pred             HHHHhCCC-cHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhh--hhhHHHHHHHHHH-HHHcCChHHHHHHHHHHHHhCC
Confidence            98876422 33444433332 345689999999999998753  443 334444433 567788999999999987763 


Q ss_pred             CCCC--HHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          160 YGLG--MRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       160 ~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                      ..|+  ...|...+..-...|+.+.+.++++++.+
T Consensus       235 ~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~  269 (308)
T d2onda1         235 LPPEKSGEIWARFLAFESNIGDLASILKVEKRRFT  269 (308)
T ss_dssp             SCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            4553  45788888888889999999999998865

>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=99.07  E-value=1.4e-08  Score=77.00  Aligned_cols=187  Identities=14%  Similarity=0.037  Sum_probs=140.3

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC--------------CCHHHHHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCD--------------PNERTLEAVLSV   67 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~--------------p~~~t~~~ll~~   67 (248)
                      |++++|...|.+..+... -+...|..+...|...|++++|.+.++......-.              .+.......+..
T Consensus        67 ~~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  145 (323)
T d1fcha_          67 EQELLAISALRRCLELKP-DNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGS  145 (323)
T ss_dssp             TCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHH
T ss_pred             CChHHHHHHHHhhhcccc-ccccccccccccccccccccccccchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHH
Confidence            789999999999877542 35788999999999999999999999998654210              011111222334


Q ss_pred             HHhcCChhHHHHHHHHHHHCC-CCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHH
Q 039342           68 YCFAGLVDESKEQFQEIKSSG-ILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQ  146 (248)
Q Consensus        68 ~~~~g~~~~a~~~~~~m~~~~-~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~  146 (248)
                      +.+.+.++++.+.|.+..+.. -.++..++..+-..+...|++++|+..|++.....  |+.......+...+...|+++
T Consensus       146 ~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~  223 (323)
T d1fcha_         146 LLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR--PNDYLLWNKLGATLANGNQSE  223 (323)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHHHHHhhhhcccccccccc--cccccchhhhhhcccccccch
Confidence            455667888888888876532 23456788888899999999999999999987654  554444444444477889999


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHH
Q 039342          147 MVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATK  192 (248)
Q Consensus       147 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  192 (248)
                      .|...++...+.... +...+..+..+|.+.|++++|.+.|++..+
T Consensus       224 ~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~g~~~~A~~~~~~al~  268 (323)
T d1fcha_         224 EAVAAYRRALELQPG-YIRSRYNLGISCINLGAHREAVEHFLEALN  268 (323)
T ss_dssp             HHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhhc-cHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            999999998876432 567788999999999999999999998764

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=98.93  E-value=9.6e-08  Score=69.86  Aligned_cols=118  Identities=11%  Similarity=-0.049  Sum_probs=70.4

Q ss_pred             hHHHHHHHHHHHHcCC-CC--CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            4 YKECQAILSRMSESGV-AR--NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         4 ~~~a~~~~~~m~~~g~-~~--~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .+.++.-+++...... .+  ...+|..+-..|.+.|++++|.+.|++..+.. +-+..+|+.+-.+|.+.|++++|.+.
T Consensus        15 ~e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~-p~~~~a~~~lg~~~~~~g~~~~A~~~   93 (259)
T d1xnfa_          15 QEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAYEA   93 (259)
T ss_dssp             HHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccC-CCCHHHHhhhchHHHHHHHHHHhhhh
Confidence            3455555555543321 11  23355555666667777777777777765543 33556666677777777777777777


Q ss_pred             HHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           81 FQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        81 ~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      |++..+... -+..++..+-..|...|++++|...|++..+..
T Consensus        94 ~~~al~~~p-~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~  135 (259)
T d1xnfa_          94 FDSVLELDP-TYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD  135 (259)
T ss_dssp             HHHHHHHCT-TCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             hhHHHHHHh-hhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhc
Confidence            777665421 134556666666777777777777776665443

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=98.79  E-value=1.1e-06  Score=66.39  Aligned_cols=229  Identities=12%  Similarity=0.032  Sum_probs=138.6

Q ss_pred             CCchHHHHHHHHHHHHcCCCCC----HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-CCC----HHHHHHHHHHHHhc
Q 039342            1 GGLYKECQAILSRMSESGVARN----SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRC-DPN----ERTLEAVLSVYCFA   71 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~----~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~----~~t~~~ll~~~~~~   71 (248)
                      .|++++|++++++..+.....+    ...++.+-..+...|++++|.+.+++..+..- .++    ..++..+...+...
T Consensus        25 ~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  104 (366)
T d1hz4a_          25 DGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFAQ  104 (366)
T ss_dssp             TTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHH
Confidence            4899999999998876432111    34677777889999999999999998754211 111    24455666777888


Q ss_pred             CChhHHHHHHHHHHH----CCCC--c-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC----chHHh----------
Q 039342           72 GLVDESKEQFQEIKS----SGIL--P-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRIS----NIHQV----------  130 (248)
Q Consensus        72 g~~~~a~~~~~~m~~----~~~~--p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~----~~~~~----------  130 (248)
                      |++..+...+....+    .+..  + ....+..+-..+...|+++.+...+.........    .....          
T Consensus       105 ~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  184 (366)
T d1hz4a_         105 GFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLA  184 (366)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHh
Confidence            888888888876543    1111  1 1234555666777888888888887766543211    00000          


Q ss_pred             ------------------------------HHHHhcccccccchHHHHHHHHHHHHhcCCC---CCHHHHHHHHHHHHhc
Q 039342          131 ------------------------------TGQMIKGEFDDESNWQMVEYVFDKLNCEGYG---LGMRFYNALLEALWCL  177 (248)
Q Consensus       131 ------------------------------~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~---p~~~~~~~li~~~~~~  177 (248)
                                                    ........+...++++.+...+.........   .....+..+..++...
T Consensus       185 ~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~  264 (366)
T d1hz4a_         185 RGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILL  264 (366)
T ss_dssp             HTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHT
T ss_pred             hhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHc
Confidence                                          0111111123345556666666554433221   2234455677788889


Q ss_pred             CchHHHHHHHHHHHH----CCCCCCcchhhhHHhhhhhhccccchHHHHHHHHHHHHHHH
Q 039342          178 GLRERAARVLDEATK----RGLFPELFRHNKLVWSVDVHRMWEGGAYTAISVWLNKMYEM  233 (248)
Q Consensus       178 g~~~~a~~~~~~m~~----~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~~~~~m~~~  233 (248)
                      |++++|...++....    .+..|+    ....+..+-..|...|+.++|.+.+++-.+.
T Consensus       265 g~~~~A~~~~~~al~~~~~~~~~~~----~~~~~~~la~~~~~~g~~~~A~~~l~~Al~l  320 (366)
T d1hz4a_         265 GEFEPAEIVLEELNENARSLRLMSD----LNRNLLLLNQLYWQAGRKSDAQRVLLDALKL  320 (366)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTTCHHH----HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHhhcccChH----HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            999999988887653    333343    2223333336677888888888888765544

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.77  E-value=3.6e-06  Score=63.51  Aligned_cols=186  Identities=10%  Similarity=0.012  Sum_probs=139.3

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcC-CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGG-RFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~-~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      ++.++|+++++.+.+... -+...|+..-.++...| ++++|+..++...+.. +-+..+|+.+-..+.+.|++++|.+.
T Consensus        57 e~~~~Al~~~~~ai~lnP-~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~-p~~~~a~~~~~~~~~~l~~~~eAl~~  134 (315)
T d2h6fa1          57 ERSERAFKLTRDAIELNA-ANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRRVLVEWLRDPSQELEF  134 (315)
T ss_dssp             CCCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHH
T ss_pred             CchHHHHHHHHHHHHHCC-CChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHH-HhhhhHHHHHhHHHHhhccHHHHHHH
Confidence            578999999999988542 25678888888888876 5999999999987664 45678999999999999999999999


Q ss_pred             HHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHH--Hh-c--ccccccchHHHHHHHHHHH
Q 039342           81 FQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQ--MI-K--GEFDDESNWQMVEYVFDKL  155 (248)
Q Consensus        81 ~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~--~l-~--~~~~~~~~~~~a~~~~~~m  155 (248)
                      ++...+.. +-+...|..+...+.+.|++++|+..+++..+....-.. .|+.  .+ .  ..+...+.++.+...+...
T Consensus       135 ~~kal~~d-p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p~n~~-a~~~r~~~l~~~~~~~~~~~~~~ai~~~~~a  212 (315)
T d2h6fa1         135 IADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNS-VWNQRYFVISNTTGYNDRAVLEREVQYTLEM  212 (315)
T ss_dssp             HHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHH-HHHHHHHHHHHTTCSCSHHHHHHHHHHHHHH
T ss_pred             Hhhhhhhh-hcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCCccHH-HHHHHHHHHHHccccchhhhhHHhHHHHHHH
Confidence            99998753 226889999999999999999999999999887632222 2221  11 1  1134455678888888877


Q ss_pred             HhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHC
Q 039342          156 NCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKR  193 (248)
Q Consensus       156 ~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  193 (248)
                      .+.... +...|+.+...+... ..+++.+.++...+.
T Consensus       213 l~~~P~-~~~~~~~l~~ll~~~-~~~~~~~~~~~~~~l  248 (315)
T d2h6fa1         213 IKLVPH-NESAWNYLKGILQDR-GLSKYPNLLNQLLDL  248 (315)
T ss_dssp             HHHSTT-CHHHHHHHHHHHTTT-CGGGCHHHHHHHHHH
T ss_pred             HHhCCC-chHHHHHHHHHHHhc-ChHHHHHHHHHHHHh
Confidence            776433 567777665555444 457777888777653

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=98.60  E-value=1.5e-05  Score=57.78  Aligned_cols=190  Identities=11%  Similarity=0.004  Sum_probs=130.2

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |++++|.+.|++..+... -++.+|+.+-.++.+.|++++|.+.|++..+.. +-+..++..+-.+|...|++++|.+.|
T Consensus        51 g~~~~A~~~~~~al~l~p-~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~  128 (259)
T d1xnfa_          51 GLRALARNDFSQALAIRP-DMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD-PTYNYAHLNRGIALYYGGRDKLAQDDL  128 (259)
T ss_dssp             TCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             CCHHHHHHHHHHhhccCC-CCHHHHhhhchHHHHHHHHHHhhhhhhHHHHHH-hhhhhhHHHHHHHHHHHhhHHHHHHHH
Confidence            899999999999887542 368899999999999999999999999998764 234567888889999999999999999


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCC
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYG  161 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~  161 (248)
                      +...+... .+......+..++.+.+..+.+..+..........+..........+.....+..+.+...+......  .
T Consensus       129 ~~al~~~p-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~  205 (259)
T d1xnfa_         129 LAFYQDDP-NDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSDKEQWGWNIVEFYLGNISEQTLMERLKADATDNTSL--A  205 (259)
T ss_dssp             HHHHHHCT-TCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSCCCSTHHHHHHHHTTSSCHHHHHHHHHHHCCSHHHH--H
T ss_pred             HHHHhhcc-ccHHHHHHHHHHHHHhhhHHHHHHHHHHhhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhc--C
Confidence            99887531 24444444445556666666666666666554433333222222222233333333333333222211  1


Q ss_pred             CC-HHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCC
Q 039342          162 LG-MRFYNALLEALWCLGLRERAARVLDEATKRGLFPE  198 (248)
Q Consensus       162 p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  198 (248)
                      |+ ..+|..+-..+...|++++|.+.|+.....  .|+
T Consensus       206 ~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~  241 (259)
T d1xnfa_         206 EHLSETNFYLGKYYLSLGDLDSATALFKLAVAN--NVH  241 (259)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CCT
T ss_pred             cccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHc--CCC
Confidence            22 346778889999999999999999998864  565

>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=98.59  E-value=2.6e-06  Score=59.46  Aligned_cols=81  Identities=17%  Similarity=0.248  Sum_probs=37.0

Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHH
Q 039342           34 RQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAY  113 (248)
Q Consensus        34 ~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~  113 (248)
                      ...|+++.|++.|.+.    .+|+..+|..+-.+|.+.|++++|.+.|++..+.. +-+...|..+-.+|.+.|++++|+
T Consensus        16 ~~~~d~~~Al~~~~~i----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld-p~~~~a~~~~g~~~~~~g~~~~A~   90 (192)
T d1hh8a_          16 ADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKYDLAI   90 (192)
T ss_dssp             HHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHCCCHHHHHHHHHhc----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh-hhhhhhHHHHHHHHHhhccHHHHH
Confidence            3444455554444432    13444444444445555555555555554444332 113344444444444555555555


Q ss_pred             HHHHHH
Q 039342          114 GLLDEM  119 (248)
Q Consensus       114 ~~~~~m  119 (248)
                      ..|++.
T Consensus        91 ~~~~kA   96 (192)
T d1hh8a_          91 KDLKEA   96 (192)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            444443

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.58  E-value=4.4e-06  Score=63.00  Aligned_cols=166  Identities=11%  Similarity=-0.011  Sum_probs=127.4

Q ss_pred             HHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC-ChhHHHHHHHHHHHCCCCcCHhhHHHHHH
Q 039342           23 SDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAG-LVDESKEQFQEIKSSGILPSVMCYCMLLA  101 (248)
Q Consensus        23 ~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g-~~~~a~~~~~~m~~~~~~p~~~~~~~li~  101 (248)
                      ...|+-+-..+.+.+..++|++++++..+.+ +-+...|+..-.++...| ++++|.+.++...+... -+..+|..+-.
T Consensus        43 ~~a~~~~~~~~~~~e~~~~Al~~~~~ai~ln-P~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p-~~~~a~~~~~~  120 (315)
T d2h6fa1          43 RDVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQP-KNYQVWHHRRV  120 (315)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHH-hhhhHHHHHhH
Confidence            4567777777888999999999999998864 345567788888888876 58999999999877532 26789999999


Q ss_pred             HHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCc--
Q 039342          102 VYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGL--  179 (248)
Q Consensus       102 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~--  179 (248)
                      .+.+.|++++|+..+++..+..  |.......-....+...++++.|...++...+.+.. +...|+.+-..+.+.+.  
T Consensus       121 ~~~~l~~~~eAl~~~~kal~~d--p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p~-n~~a~~~r~~~l~~~~~~~  197 (315)
T d2h6fa1         121 LVEWLRDPSQELEFIADILNQD--AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVR-NNSVWNQRYFVISNTTGYN  197 (315)
T ss_dssp             HHHHHTCCTTHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCSC
T ss_pred             HHHhhccHHHHHHHHhhhhhhh--hcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCCc-cHHHHHHHHHHHHHccccc
Confidence            9999999999999999998765  544333333333366778889999999999887654 56677776666666554  


Q ss_pred             ----hHHHHHHHHHHHHC
Q 039342          180 ----RERAARVLDEATKR  193 (248)
Q Consensus       180 ----~~~a~~~~~~m~~~  193 (248)
                          +++|.+.+....+.
T Consensus       198 ~~~~~~~ai~~~~~al~~  215 (315)
T d2h6fa1         198 DRAVLEREVQYTLEMIKL  215 (315)
T ss_dssp             SHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhHHhHHHHHHHHHh
Confidence                57888888877654

>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=98.37  E-value=1e-05  Score=51.47  Aligned_cols=99  Identities=15%  Similarity=0.057  Sum_probs=77.9

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCH
Q 039342           30 IEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRW  109 (248)
Q Consensus        30 i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~  109 (248)
                      -..+.+.|++++|...|++..+.. +-+...|..+-.+|.+.|++++|...++...+.+ +.+...|..+-.++...|++
T Consensus        10 g~~~~~~g~~~eAi~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~g~~~~~~~~~   87 (117)
T d1elwa_          10 GNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEFLNRF   87 (117)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhcC-CcchhhhhcccccccccccccccchhhhhHHHhc-cchhhHHHHHHHHHHHccCH
Confidence            345778889999999999987664 5667788888888999999999999998888754 33677888888899999999


Q ss_pred             HHHHHHHHHHHHCCCCchHHhHH
Q 039342          110 DDAYGLLDEMHTNRISNIHQVTG  132 (248)
Q Consensus       110 ~~a~~~~~~m~~~~~~~~~~~~~  132 (248)
                      ++|+..|++..+..  |+...+.
T Consensus        88 ~~A~~~~~~a~~~~--p~~~~~~  108 (117)
T d1elwa_          88 EEAKRTYEEGLKHE--ANNPQLK  108 (117)
T ss_dssp             HHHHHHHHHHHTTC--TTCHHHH
T ss_pred             HHHHHHHHHHHHhC--CCCHHHH
Confidence            99999999887543  5544443

>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=98.34  E-value=9.7e-06  Score=60.22  Aligned_cols=121  Identities=7%  Similarity=0.098  Sum_probs=63.9

Q ss_pred             CchHHHHHHHHHHHHc----CCCC-CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHc----C-CCCCHHHHHHHHHHHHh-
Q 039342            2 GLYKECQAILSRMSES----GVAR-NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKV----R-CDPNERTLEAVLSVYCF-   70 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~----g~~~-~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~----~-~~p~~~t~~~ll~~~~~-   70 (248)
                      |++++|.+.|.+..+.    +-++ -..+|+.+-.+|.+.|++++|.+.+++..+.    | ......++..+...|.. 
T Consensus        51 ~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~  130 (290)
T d1qqea_          51 KELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILEND  130 (290)
T ss_dssp             TCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             cCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHHHHHHhHhhH
Confidence            5566666666655432    1111 1345666666666677777766666654321    1 11112334444444433 


Q ss_pred             cCChhHHHHHHHHHHH----CCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHC
Q 039342           71 AGLVDESKEQFQEIKS----SGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTN  122 (248)
Q Consensus        71 ~g~~~~a~~~~~~m~~----~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  122 (248)
                      .|++++|.+.+++..+    .+-.+ ...+|..+...+...|++++|+..|++....
T Consensus       131 ~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~  187 (290)
T d1qqea_         131 LHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKS  187 (290)
T ss_dssp             TCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHh
Confidence            4667777766665532    12111 1234566666666777777777777665543

>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=98.32  E-value=2.4e-05  Score=54.34  Aligned_cols=118  Identities=14%  Similarity=0.024  Sum_probs=86.6

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|+++.|++.|.++.    +|++.+|..+-..|.+.|++++|++.|++..+.+ +-+...|..+-.+|.+.|++++|.+.
T Consensus        18 ~~d~~~Al~~~~~i~----~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld-p~~~~a~~~~g~~~~~~g~~~~A~~~   92 (192)
T d1hh8a_          18 KKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKYDLAIKD   92 (192)
T ss_dssp             TTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CCCHHHHHHHHHhcC----CCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh-hhhhhhHHHHHHHHHhhccHHHHHHH
Confidence            378999999998753    4788888889999999999999999999987765 45678888899999999999999999


Q ss_pred             HHHHHHCCCCcC---------------HhhHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           81 FQEIKSSGILPS---------------VMCYCMLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        81 ~~~m~~~~~~p~---------------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      |++..+..-...               ..++..+-.++.+.|++++|.+.|....+..
T Consensus        93 ~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~  150 (192)
T d1hh8a_          93 LKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMK  150 (192)
T ss_dssp             HHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC
Confidence            988765311100               1234445555666666666666666554443

>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=98.32  E-value=1.4e-05  Score=55.67  Aligned_cols=98  Identities=11%  Similarity=0.029  Sum_probs=85.3

Q ss_pred             CCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCc-CHhhHHHH
Q 039342           21 RNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILP-SVMCYCML   99 (248)
Q Consensus        21 ~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~l   99 (248)
                      |+...+-..-..|.+.|++++|+..|.+..+.. +-+...|..+-.+|.+.|++++|...|+...+.  .| +..+|..+
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l--~p~~~~a~~~l   78 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALEL--DGQSVKAHFFL   78 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--CTTCHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHh--CCCcHHHHHHH
Confidence            667777777788999999999999999987764 567888999999999999999999999998864  45 56789999


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHH
Q 039342          100 LAVYAKSNRWDDAYGLLDEMHT  121 (248)
Q Consensus       100 i~~~~~~~~~~~a~~~~~~m~~  121 (248)
                      -.+|.+.|++++|+..|++..+
T Consensus        79 g~~~~~l~~~~~A~~~~~~al~  100 (201)
T d2c2la1          79 GQCQLEMESYDEAIANLQRAYS  100 (201)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHH
Confidence            9999999999999999998764

>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=98.27  E-value=5.2e-05  Score=50.78  Aligned_cols=92  Identities=11%  Similarity=0.039  Sum_probs=77.6

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCH
Q 039342           30 IEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRW  109 (248)
Q Consensus        30 i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~  109 (248)
                      -..|.+.|++++|...|++..+.. +-+...|..+-.+|.+.|++++|.+.|+...+.. +-+...|..+..++...|++
T Consensus        17 gn~~~~~~~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~-p~~~~a~~~~g~~~~~~g~~   94 (159)
T d1a17a_          17 ANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKF   94 (159)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHcCCHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHHHHHHc-ccchHHHHHHHHHHHHcCCH
Confidence            446779999999999999988765 4577888889999999999999999999988753 22567899999999999999


Q ss_pred             HHHHHHHHHHHHCC
Q 039342          110 DDAYGLLDEMHTNR  123 (248)
Q Consensus       110 ~~a~~~~~~m~~~~  123 (248)
                      ++|...+++.....
T Consensus        95 ~eA~~~~~~a~~~~  108 (159)
T d1a17a_          95 RAALRDYETVVKVK  108 (159)
T ss_dssp             HHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHcC
Confidence            99999999987754

>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=98.24  E-value=2.8e-05  Score=49.33  Aligned_cols=89  Identities=11%  Similarity=0.109  Sum_probs=78.0

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|...|.+..+... -+...|..+-.++.+.|++++|+..+....+.+ +.+...|..+-.++...|++++|...
T Consensus        16 ~g~~~eAi~~~~~al~~~p-~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~g~~~~~~~~~~~A~~~   93 (117)
T d1elwa_          16 VGNIDDALQCYSEAIKLDP-HNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEFLNRFEEAKRT   93 (117)
T ss_dssp             TTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhcCC-cchhhhhcccccccccccccccchhhhhHHHhc-cchhhHHHHHHHHHHHccCHHHHHHH
Confidence            3899999999999987542 468889999999999999999999999998775 57888999999999999999999999


Q ss_pred             HHHHHHCCCCcCH
Q 039342           81 FQEIKSSGILPSV   93 (248)
Q Consensus        81 ~~~m~~~~~~p~~   93 (248)
                      |+...+.  .|+.
T Consensus        94 ~~~a~~~--~p~~  104 (117)
T d1elwa_          94 YEEGLKH--EANN  104 (117)
T ss_dssp             HHHHHTT--CTTC
T ss_pred             HHHHHHh--CCCC
Confidence            9999875  4544

>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=98.20  E-value=3.6e-05  Score=57.03  Aligned_cols=169  Identities=9%  Similarity=0.036  Sum_probs=118.3

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHhcCChhHHHHHHHHHHHC----CCC-cCHh
Q 039342           25 SFNAVIEAFRQGGRFEEAIKAYVEMEKV----RCDP-NERTLEAVLSVYCFAGLVDESKEQFQEIKSS----GIL-PSVM   94 (248)
Q Consensus        25 ~y~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p-~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~~-p~~~   94 (248)
                      .|.-.-..|...+++++|.+.|.+..+.    +-++ -..+|..+-.+|.+.|++++|.+.+++..+.    |-. ....
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            5777788888999999999999988542    2122 2367888999999999999999999876542    211 1245


Q ss_pred             hHHHHHHHHHh-cCCHHHHHHHHHHHHH----CCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCC-----CH
Q 039342           95 CYCMLLAVYAK-SNRWDDAYGLLDEMHT----NRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGL-----GM  164 (248)
Q Consensus        95 ~~~~li~~~~~-~~~~~~a~~~~~~m~~----~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p-----~~  164 (248)
                      ++..+...|-. .|++++|+..+++..+    .+..+.......-+...+...|+++.|...++.........     ..
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            56666666744 6999999999988643    33333333333333344788899999999999987653221     11


Q ss_pred             -HHHHHHHHHHHhcCchHHHHHHHHHHHHC
Q 039342          165 -RFYNALLEALWCLGLRERAARVLDEATKR  193 (248)
Q Consensus       165 -~~~~~li~~~~~~g~~~~a~~~~~~m~~~  193 (248)
                       ..+...+..+...|+++.|...+++..+.
T Consensus       199 ~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~  228 (290)
T d1qqea_         199 KDYFLKKGLCQLAATDAVAAARTLQEGQSE  228 (290)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHGGGCC
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence             22344555677889999999999987654

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=98.18  E-value=0.00055  Score=50.99  Aligned_cols=162  Identities=9%  Similarity=-0.051  Sum_probs=102.4

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCC----HHHHHHHHHHHHhcCChhHHHHHHHHHHHC----CCCc-CHhhHHHH
Q 039342           29 VIEAFRQGGRFEEAIKAYVEMEKVRCDPN----ERTLEAVLSVYCFAGLVDESKEQFQEIKSS----GILP-SVMCYCML   99 (248)
Q Consensus        29 li~~~~~~~~~~~a~~~~~~m~~~~~~p~----~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~----~~~p-~~~~~~~l   99 (248)
                      .-..+...|++++|.+++++..+..-..+    ...+..+-.+|...|++++|...|++..+.    +-.+ ....+..+
T Consensus        18 rA~~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~   97 (366)
T d1hz4a_          18 RAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQ   97 (366)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHHH
Confidence            34456789999999999999876431111    246677788999999999999999987642    2111 23466777


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHH----CC--CCchHHhHHHHhcccccccchHHHHHHHHHHHHhc----CCCCCHHHHHH
Q 039342          100 LAVYAKSNRWDDAYGLLDEMHT----NR--ISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCE----GYGLGMRFYNA  169 (248)
Q Consensus       100 i~~~~~~~~~~~a~~~~~~m~~----~~--~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~----~~~p~~~~~~~  169 (248)
                      ...+...|++..+...+.+...    ..  ..+........+...+...++++.+...+......    +.......+..
T Consensus        98 ~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  177 (366)
T d1hz4a_          98 SEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAM  177 (366)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHH
Confidence            7888899999999999887643    11  12222223333333355567777777777665543    22223344444


Q ss_pred             HHHHHHhcCchHHHHHHHHHH
Q 039342          170 LLEALWCLGLRERAARVLDEA  190 (248)
Q Consensus       170 li~~~~~~g~~~~a~~~~~~m  190 (248)
                      ....+...+....+...+.+.
T Consensus       178 ~~~~~~~~~~~~~a~~~~~~a  198 (366)
T d1hz4a_         178 LIQCSLARGDLDNARSQLNRL  198 (366)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHhhhhHHHHHHHHHHH
Confidence            555555666666666555543

>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=98.15  E-value=6e-05  Score=50.44  Aligned_cols=85  Identities=8%  Similarity=0.026  Sum_probs=75.5

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|+..|.+..+... -+...|..+-..|...|++++|.+.|+...+.. +-+...|..+..+|...|++++|...
T Consensus        23 ~~~y~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~-p~~~~a~~~~g~~~~~~g~~~eA~~~  100 (159)
T d1a17a_          23 AKDYENAIKFYSQAIELNP-SNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAALRD  100 (159)
T ss_dssp             TTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cCCHHHHHHHhhhccccch-hhhhhhhhhHHHHHhccccchHHHHHHHHHHHc-ccchHHHHHHHHHHHHcCCHHHHHHH
Confidence            4899999999999988653 478899999999999999999999999998765 45668999999999999999999999


Q ss_pred             HHHHHHC
Q 039342           81 FQEIKSS   87 (248)
Q Consensus        81 ~~~m~~~   87 (248)
                      +++..+.
T Consensus       101 ~~~a~~~  107 (159)
T d1a17a_         101 YETVVKV  107 (159)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHc
Confidence            9999875

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.15  E-value=1.8e-05  Score=50.70  Aligned_cols=102  Identities=8%  Similarity=0.015  Sum_probs=75.2

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCC---hhHHHHHHHHHHHCCCCcC-HhhHHHHHHH
Q 039342           27 NAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGL---VDESKEQFQEIKSSGILPS-VMCYCMLLAV  102 (248)
Q Consensus        27 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~---~~~a~~~~~~m~~~~~~p~-~~~~~~li~~  102 (248)
                      ..++..+...+++++|.+.|+...+.+ +.+..++..+-.++.+.++   +++|.++|++..+....|+ ..++..+-.+
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~   81 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVG   81 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHH
Confidence            457778888888999999998887765 4677788888888877554   4568888888776543333 2367778888


Q ss_pred             HHhcCCHHHHHHHHHHHHHCCCCchHHhH
Q 039342          103 YAKSNRWDDAYGLLDEMHTNRISNIHQVT  131 (248)
Q Consensus       103 ~~~~~~~~~a~~~~~~m~~~~~~~~~~~~  131 (248)
                      |.+.|++++|++.|++..+..  |+..-.
T Consensus        82 y~~~g~~~~A~~~~~~aL~~~--P~~~~A  108 (122)
T d1nzna_          82 NYRLKEYEKALKYVRGLLQTE--PQNNQA  108 (122)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC--TTCHHH
T ss_pred             HHHHhhhHHHHHHHHHHHHhC--cCCHHH
Confidence            888999999999999887754  655443

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=98.11  E-value=4.9e-06  Score=63.08  Aligned_cols=112  Identities=6%  Similarity=-0.026  Sum_probs=81.9

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcC--CHHHHHHHHHHHHHcCCCCCHHHHH-HHHHHHHhcCChhHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGG--RFEEAIKAYVEMEKVRCDPNERTLE-AVLSVYCFAGLVDESK   78 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~--~~~~a~~~~~~m~~~~~~p~~~t~~-~ll~~~~~~g~~~~a~   78 (248)
                      |++++|+..++...+.. +.+...|..+..++...+  ++++|...+....+.. +++...+. ..-..+...+.++.|.
T Consensus        87 ~~~~~al~~~~~~l~~~-pk~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~~Al  164 (334)
T d1dcea1          87 ALVKAELGFLESCLRVN-PKSYGTWHHRCWLLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEEL  164 (334)
T ss_dssp             HHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHHHH
T ss_pred             HHHHHHHHHHHHHHHhC-CCcHHHHHHhhHHHHHhccccHHHHHHHHHHHHhhC-chhhhhhhhHHHHHHHhccccHHHH
Confidence            35678899999887644 236777877777777665  5889999999987764 34555554 4446777889999999


Q ss_pred             HHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHH
Q 039342           79 EQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLL  116 (248)
Q Consensus        79 ~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~  116 (248)
                      ..++...+... -+...|+.+-..+.+.|+.++|...+
T Consensus       165 ~~~~~~i~~~p-~~~~a~~~l~~~~~~~~~~~~A~~~~  201 (334)
T d1dcea1         165 AFTDSLITRNF-SNYSSWHYRSCLLPQLHPQPDSGPQG  201 (334)
T ss_dssp             HHHHTTTTTTC-CCHHHHHHHHHHHHHHSCCCCSSSCC
T ss_pred             HHHHHHHHcCC-CCHHHHHHHHHHHHHhcCHHHHHHHH
Confidence            99998877642 26778888888888888876654433

>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=98.07  E-value=3e-05  Score=48.72  Aligned_cols=89  Identities=8%  Similarity=-0.055  Sum_probs=73.8

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCC
Q 039342           29 VIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNR  108 (248)
Q Consensus        29 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~  108 (248)
                      +-..+.+.|++++|...|++..+.. +-+...|..+-.++.+.|++++|...|++..+.. +.+...|..+-..|...|+
T Consensus        22 ~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~la~~y~~~g~   99 (112)
T d1hxia_          22 EGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHN   99 (112)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHhhhcccc-cccchhhhhhhhhhhhhhhHHHhhcccccccccc-cccccchHHHHHHHHHCCC
Confidence            4556778899999999999987764 3367888899999999999999999999987753 2257888889999999999


Q ss_pred             HHHHHHHHHHH
Q 039342          109 WDDAYGLLDEM  119 (248)
Q Consensus       109 ~~~a~~~~~~m  119 (248)
                      +++|++.+++.
T Consensus       100 ~~~A~~~l~~~  110 (112)
T d1hxia_         100 ANAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999998875

>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=98.01  E-value=3.8e-05  Score=48.26  Aligned_cols=82  Identities=6%  Similarity=-0.042  Sum_probs=72.2

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      .|++++|...|++..+... -++..|..+-.++.+.|++++|...|++..+.. +-+...|..+-..|...|++++|.+.
T Consensus        29 ~g~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~la~~y~~~g~~~~A~~~  106 (112)
T d1hxia_          29 LANLAEAALAFEAVCQKEP-EREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHNANAALAS  106 (112)
T ss_dssp             TTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhhHHHHHHHhhhccccc-ccchhhhhhhhhhhhhhhHHHhhcccccccccc-cccccchHHHHHHHHHCCCHHHHHHH
Confidence            4899999999999887542 268899999999999999999999999987764 45688899999999999999999999


Q ss_pred             HHHH
Q 039342           81 FQEI   84 (248)
Q Consensus        81 ~~~m   84 (248)
                      +++.
T Consensus       107 l~~~  110 (112)
T d1hxia_         107 LRAW  110 (112)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            9875

>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=98.00  E-value=4.8e-05  Score=52.75  Aligned_cols=99  Identities=7%  Similarity=-0.027  Sum_probs=78.1

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHh
Q 039342           56 PNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMI  135 (248)
Q Consensus        56 p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l  135 (248)
                      |+...+...-..|.+.|++++|...|++..+.. +-+...|..+-.+|.+.|++++|+..|++..+.  .|+.......+
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l--~p~~~~a~~~l   78 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALEL--DGQSVKAHFFL   78 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--CTTCHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHh--CCCcHHHHHHH
Confidence            777788888889999999999999999987753 236788999999999999999999999998754  36544333334


Q ss_pred             cccccccchHHHHHHHHHHHHh
Q 039342          136 KGEFDDESNWQMVEYVFDKLNC  157 (248)
Q Consensus       136 ~~~~~~~~~~~~a~~~~~~m~~  157 (248)
                      ..++...|+++.|...|+...+
T Consensus        79 g~~~~~l~~~~~A~~~~~~al~  100 (201)
T d2c2la1          79 GQCQLEMESYDEAIANLQRAYS  100 (201)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHH
Confidence            4447777888999888887654

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.97  E-value=9.2e-05  Score=50.66  Aligned_cols=71  Identities=14%  Similarity=0.080  Sum_probs=48.2

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHH-----HCCCCchHHh
Q 039342           59 RTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMH-----TNRISNIHQV  130 (248)
Q Consensus        59 ~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~-----~~~~~~~~~~  130 (248)
                      ..+..+..++.+.|++++|...+++..+.. +-+...|..++.+|.+.|+..+|++.|+++.     +-|+.|...+
T Consensus        68 ~a~~~la~~~~~~g~~~~Al~~~~~al~~~-P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          68 LAHTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHHHHHCCCchHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            355667777777777777777777776542 1256677777777777777777777777763     3466665543

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.77  E-value=0.00012  Score=46.70  Aligned_cols=90  Identities=4%  Similarity=-0.083  Sum_probs=70.9

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCC---HHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHhcCChhHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGR---FEEAIKAYVEMEKVRCDPNE-RTLEAVLSVYCFAGLVDES   77 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~---~~~a~~~~~~m~~~~~~p~~-~t~~~ll~~~~~~g~~~~a   77 (248)
                      +++++|++.|+...+.+. .++.++..+-.++.+.++   +++|.++|++..+.+..|+. .+|..+-.+|.+.|++++|
T Consensus        13 ~~l~~Ae~~Y~~aL~~~p-~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~y~~~g~~~~A   91 (122)
T d1nzna_          13 EDLLKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKA   91 (122)
T ss_dssp             HHHHHHHHHHHHHHHHSC-CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHHhhCC-CCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHHHHHhhhHHH
Confidence            468999999999887653 477888888888887654   45699999998766543432 4677888999999999999


Q ss_pred             HHHHHHHHHCCCCcCHh
Q 039342           78 KEQFQEIKSSGILPSVM   94 (248)
Q Consensus        78 ~~~~~~m~~~~~~p~~~   94 (248)
                      .+.|++..+.  .|+..
T Consensus        92 ~~~~~~aL~~--~P~~~  106 (122)
T d1nzna_          92 LKYVRGLLQT--EPQNN  106 (122)
T ss_dssp             HHHHHHHHHH--CTTCH
T ss_pred             HHHHHHHHHh--CcCCH
Confidence            9999999885  46544

>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=97.73  E-value=0.0011  Score=44.63  Aligned_cols=104  Identities=6%  Similarity=-0.057  Sum_probs=74.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcC-----CCC---------CHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCc
Q 039342           26 FNAVIEAFRQGGRFEEAIKAYVEMEKVR-----CDP---------NERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILP   91 (248)
Q Consensus        26 y~~li~~~~~~~~~~~a~~~~~~m~~~~-----~~p---------~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p   91 (248)
                      +...-..+.+.|++++|...|.+..+.-     ...         -..+|+.+-.+|.+.|++++|...++...+.. +.
T Consensus        16 l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~-p~   94 (170)
T d1p5qa1          16 VKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD-SN   94 (170)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TT
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhcc-cc
Confidence            3344456778888888888888775431     000         12456667778889999999999998888753 22


Q ss_pred             CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHH
Q 039342           92 SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTG  132 (248)
Q Consensus        92 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~  132 (248)
                      ++..|..+-.+|...|++++|+..|++..+..  |+.....
T Consensus        95 ~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~--P~n~~~~  133 (170)
T d1p5qa1          95 NEKGLSRRGEAHLAVNDFELARADFQKVLQLY--PNNKAAK  133 (170)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--SSCHHHH
T ss_pred             chhhhHHHHHHHHHhhhHHHHHHHHHHHHHhC--CCCHHHH
Confidence            67788888888999999999999999887654  5444333

>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=97.71  E-value=0.0012  Score=44.37  Aligned_cols=95  Identities=15%  Similarity=0.104  Sum_probs=74.4

Q ss_pred             CchHHHHHHHHHHHHcCC-CC-------------CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 039342            2 GLYKECQAILSRMSESGV-AR-------------NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSV   67 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~-~~-------------~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~   67 (248)
                      |++++|++.|.+..+.-. .+             ...+|+.+-.+|.+.|++++|+..++...+.+ +-+...|..+-.+
T Consensus        27 ~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~-p~~~~a~~~~g~~  105 (170)
T d1p5qa1          27 GKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD-SNNEKGLSRRGEA  105 (170)
T ss_dssp             TCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhcc-ccchhhhHHHHHH
Confidence            789999999988764311 11             12467778888999999999999999998764 4588899999999


Q ss_pred             HHhcCChhHHHHHHHHHHHCCCCc-CHhhHHHH
Q 039342           68 YCFAGLVDESKEQFQEIKSSGILP-SVMCYCML   99 (248)
Q Consensus        68 ~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~l   99 (248)
                      |...|+++.|...|+...+.  .| +......+
T Consensus       106 ~~~~g~~~~A~~~~~~al~l--~P~n~~~~~~l  136 (170)
T d1p5qa1         106 HLAVNDFELARADFQKVLQL--YPNNKAAKTQL  136 (170)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH--CSSCHHHHHHH
T ss_pred             HHHhhhHHHHHHHHHHHHHh--CCCCHHHHHHH
Confidence            99999999999999999875  45 34444443

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.69  E-value=0.00075  Score=45.93  Aligned_cols=71  Identities=10%  Similarity=0.061  Sum_probs=46.1

Q ss_pred             HhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHH-hHHHHhcccccccchHHHHHHHHHHHH-----hcCCCCCHHH
Q 039342           93 VMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQ-VTGQMIKGEFDDESNWQMVEYVFDKLN-----CEGYGLGMRF  166 (248)
Q Consensus        93 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~m~-----~~~~~p~~~~  166 (248)
                      ...+..+...+.+.|++++|+..+++..+..  |... .+..++.. +...|+...|.+.|+.+.     +.|+.|+..+
T Consensus        67 ~~a~~~la~~~~~~g~~~~Al~~~~~al~~~--P~~e~~~~~l~~a-l~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          67 VLAHTAKAEAEIACGRASAVIAELEALTFEH--PYREPLWTQLITA-YYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHH-HHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHHHHHHCCCchHHHHHHHHHHHhC--CccHHHHHHHHHH-HHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            3456667777777777777777777776544  4443 34444444 666777777777777653     3477777655

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.66  E-value=0.00058  Score=43.65  Aligned_cols=95  Identities=16%  Similarity=0.225  Sum_probs=70.4

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCC---CC--cC-HhhHHHHH
Q 039342           27 NAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSG---IL--PS-VMCYCMLL  100 (248)
Q Consensus        27 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~---~~--p~-~~~~~~li  100 (248)
                      -.+=..+.+.|++++|.+.|.+..+.+ +.+...|..+-.+|.+.|++++|...+++..+..   ..  +. ..+|..+-
T Consensus         8 k~~G~~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~lg   86 (128)
T d1elra_           8 KELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIG   86 (128)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHH
Confidence            345566888899999999999987764 3567888888999999999999999998876531   00  11 23566666


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHC
Q 039342          101 AVYAKSNRWDDAYGLLDEMHTN  122 (248)
Q Consensus       101 ~~~~~~~~~~~a~~~~~~m~~~  122 (248)
                      ..+...+++++|+..|.+-...
T Consensus        87 ~~~~~~~~~~~A~~~~~kal~~  108 (128)
T d1elra_          87 NSYFKEEKYKDAIHFYNKSLAE  108 (128)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCHHHHHHHHHHHHhc
Confidence            7777788888888888776544

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.66  E-value=2e-05  Score=59.63  Aligned_cols=185  Identities=11%  Similarity=-0.095  Sum_probs=123.4

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHH-HHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVI-EAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQ   80 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li-~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~   80 (248)
                      +++++|...+....+... ++...+...+ ..+...+.++.|+..++...+.+ +-+...|+.+-..+.+.|++++|...
T Consensus       123 ~~~~~a~~~~~~al~~~~-~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~-p~~~~a~~~l~~~~~~~~~~~~A~~~  200 (334)
T d1dcea1         123 PNWARELELCARFLEADE-RNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSSWHYRSCLLPQLHPQPDSGPQ  200 (334)
T ss_dssp             CCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT-CCCHHHHHHHHHHHHHHSCCCCSSSC
T ss_pred             ccHHHHHHHHHHHHhhCc-hhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhcCHHHHHHH
Confidence            457899999999877532 3566665544 56667899999999999887765 35678899999999999999888766


Q ss_pred             HHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCC
Q 039342           81 FQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGY  160 (248)
Q Consensus        81 ~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~  160 (248)
                      ++...+.  .|+   ...+...+...+..+++...+.......  |+.......+...+...++++.+...+........
T Consensus       201 ~~~~~~~--~~~---~~~~~~~~~~l~~~~~a~~~~~~~l~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~p  273 (334)
T d1dcea1         201 GRLPENV--LLK---ELELVQNAFFTDPNDQSAWFYHRWLLGR--AEPLFRCELSVEKSTVLQSELESCKELQELEPENK  273 (334)
T ss_dssp             CSSCHHH--HHH---HHHHHHHHHHHCSSCSHHHHHHHHHHSC--CCCSSSCCCCHHHHHHHHHHHHHHHHHHHHCTTCH
T ss_pred             HHHhHHh--HHH---HHHHHHHHHHhcchhHHHHHHHHHHHhC--cchhhHHHHHHHHHHHHhhHHHHHHHHHHHHhhCc
Confidence            6544432  121   1223344555677777877777766554  22111111111113344666777777666554432


Q ss_pred             CCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCC
Q 039342          161 GLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPE  198 (248)
Q Consensus       161 ~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  198 (248)
                      . +..++..+...+.+.|+.++|.+.+++..+.  .|+
T Consensus       274 ~-~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~l--dP~  308 (334)
T d1dcea1         274 W-CLLTIILLMRALDPLLYEKETLQYFSTLKAV--DPM  308 (334)
T ss_dssp             H-HHHHHHHHHHHHCTGGGHHHHHHHHHHHHHH--CGG
T ss_pred             h-HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--Ccc
Confidence            2 4567778888999999999999999998773  665

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=97.65  E-value=0.002  Score=42.41  Aligned_cols=103  Identities=11%  Similarity=-0.060  Sum_probs=75.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcC----CCCC-----------HHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCC
Q 039342           26 FNAVIEAFRQGGRFEEAIKAYVEMEKVR----CDPN-----------ERTLEAVLSVYCFAGLVDESKEQFQEIKSSGIL   90 (248)
Q Consensus        26 y~~li~~~~~~~~~~~a~~~~~~m~~~~----~~p~-----------~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~   90 (248)
                      +..--..+.+.|++.+|...|.+..+.-    -.++           ..+|+.+-.+|.+.|++++|.+.++...+.. +
T Consensus        20 ~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~-p   98 (153)
T d2fbna1          20 IKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID-K   98 (153)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-T
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhcccccc-c
Confidence            3344456778889999988888875421    1111           2466677888899999999999999887653 2


Q ss_pred             cCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhH
Q 039342           91 PSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVT  131 (248)
Q Consensus        91 p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~  131 (248)
                      .+..+|..+..++...|++++|+..|++..+..  |++...
T Consensus        99 ~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l~--P~n~~~  137 (153)
T d2fbna1          99 NNVKALYKLGVANMYFGFLEEAKENLYKAASLN--PNNLDI  137 (153)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS--TTCHHH
T ss_pred             hhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHH
Confidence            367889999999999999999999999887654  554443

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=97.60  E-value=0.0016  Score=42.90  Aligned_cols=90  Identities=13%  Similarity=0.133  Sum_probs=72.7

Q ss_pred             CCchHHHHHHHHHHHHcCC----CC-----------CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 039342            1 GGLYKECQAILSRMSESGV----AR-----------NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVL   65 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~----~~-----------~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll   65 (248)
                      .|++++|...|.+..+.-.    .+           ...+|+.+-.+|.+.|++++|++.++...+.+ +.+..+|..+.
T Consensus        30 ~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~-p~~~ka~~~~g  108 (153)
T d2fbna1          30 KNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLG  108 (153)
T ss_dssp             TTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhcccccc-chhhhhhHHhH
Confidence            3788999999988664211    11           12467778889999999999999999988765 56789999999


Q ss_pred             HHHHhcCChhHHHHHHHHHHHCCCCcCH
Q 039342           66 SVYCFAGLVDESKEQFQEIKSSGILPSV   93 (248)
Q Consensus        66 ~~~~~~g~~~~a~~~~~~m~~~~~~p~~   93 (248)
                      .++...|+++.|...|+...+.  .|+.
T Consensus       109 ~~~~~lg~~~~A~~~~~~al~l--~P~n  134 (153)
T d2fbna1         109 VANMYFGFLEEAKENLYKAASL--NPNN  134 (153)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHH--STTC
T ss_pred             HHHHHcCCHHHHHHHHHHHHHh--CCCC
Confidence            9999999999999999999875  4543

>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=97.55  E-value=0.00011  Score=53.57  Aligned_cols=120  Identities=13%  Similarity=0.098  Sum_probs=76.5

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHhcCChhHHHH
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNE-RTLEAVLSVYCFAGLVDESKE   79 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~t~~~ll~~~~~~g~~~~a~~   79 (248)
                      .|++++|+..+++..+... -|...+..+...++..|++++|.+.++...+.  .|+. ..+..+-..+...+..+++..
T Consensus         9 ~G~l~eAl~~l~~al~~~P-~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l--~P~~~~~~~~l~~ll~a~~~~~~a~~   85 (264)
T d1zbpa1           9 EGQLQQALELLIEAIKASP-KDASLRSSFIELLCIDGDFERADEQLMQSIKL--FPEYLPGASQLRHLVKAAQARKDFAQ   85 (264)
T ss_dssp             TTCHHHHHHHHHHHHHTCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CGGGHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHhccccHHHHH
Confidence            4889999999999887543 47899999999999999999999999998765  3443 333333333332222222111


Q ss_pred             HHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           80 QFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        80 ~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      -...-...+-.++...+......+.+.|+.++|.+.+++..+..
T Consensus        86 ~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~~  129 (264)
T d1zbpa1          86 GAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEELR  129 (264)
T ss_dssp             SCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC
Confidence            11000001112233444555666778899999999998886643

>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=97.46  E-value=0.00018  Score=52.43  Aligned_cols=123  Identities=6%  Similarity=-0.098  Sum_probs=69.4

Q ss_pred             HHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHH
Q 039342           68 YCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQM  147 (248)
Q Consensus        68 ~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~  147 (248)
                      ..+.|++++|...+++..+.. +-+...+..+...++..|++++|...|+...+..  |+.......+...+...+..+.
T Consensus         6 aL~~G~l~eAl~~l~~al~~~-P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l~--P~~~~~~~~l~~ll~a~~~~~~   82 (264)
T d1zbpa1           6 ALSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIKLF--PEYLPGASQLRHLVKAAQARKD   82 (264)
T ss_dssp             HTTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--GGGHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHhccccHH
Confidence            345677788888887777653 2256777778888888888888888887776553  4443333222221111111111


Q ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHC
Q 039342          148 VEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKR  193 (248)
Q Consensus       148 a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  193 (248)
                      +..-...-...+-.++...+......+...|+.++|.+.+++..+.
T Consensus        83 a~~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~  128 (264)
T d1zbpa1          83 FAQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEEL  128 (264)
T ss_dssp             HTTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhc
Confidence            1100000000011223344445566788899999999999987753

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.45  E-value=0.0014  Score=41.72  Aligned_cols=86  Identities=6%  Similarity=0.062  Sum_probs=69.5

Q ss_pred             CCchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCCC----HHHHHHHHHHHHhcCCh
Q 039342            1 GGLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVR--CDPN----ERTLEAVLSVYCFAGLV   74 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~--~~p~----~~t~~~ll~~~~~~g~~   74 (248)
                      .|++++|++.|.+..+... .+...|..+-.+|.+.|++++|.+.+++..+..  ....    ..+|..+-..+...+++
T Consensus        17 ~~~y~~Ai~~y~~al~~~p-~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~lg~~~~~~~~~   95 (128)
T d1elra_          17 KKDFDTALKHYDKAKELDP-TNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEKY   95 (128)
T ss_dssp             TTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             cCCHHHHHHHHHHHHHhCc-ccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHhCCH
Confidence            3899999999999987653 468899999999999999999999999986532  1111    24677777888899999


Q ss_pred             hHHHHHHHHHHHC
Q 039342           75 DESKEQFQEIKSS   87 (248)
Q Consensus        75 ~~a~~~~~~m~~~   87 (248)
                      ++|.+.|+.-...
T Consensus        96 ~~A~~~~~kal~~  108 (128)
T d1elra_          96 KDAIHFYNKSLAE  108 (128)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhc
Confidence            9999999887653

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.41  E-value=0.0021  Score=43.01  Aligned_cols=97  Identities=10%  Similarity=0.050  Sum_probs=70.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHc--------------CCC-CCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCC
Q 039342           26 FNAVIEAFRQGGRFEEAIKAYVEMEKV--------------RCD-PNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGIL   90 (248)
Q Consensus        26 y~~li~~~~~~~~~~~a~~~~~~m~~~--------------~~~-p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~   90 (248)
                      +...-..+.+.|++++|+..|.+..+.              .+. .+...|..+-.++.+.|++++|...+++..+.. +
T Consensus        30 ~~~~~~~~~~~~~y~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p  108 (169)
T d1ihga1          30 LKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID-P  108 (169)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-T
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhhhhhhhhhhhHHHHHhChhhHHHHHHHHHHHHhhcccchhhhhhhhhhhhh-h
Confidence            344555677889999998888776431              011 233456667778888889999988888887653 2


Q ss_pred             cCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCC
Q 039342           91 PSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        91 p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  123 (248)
                      .+...|..+-.+|.+.|++++|+..|++..+..
T Consensus       109 ~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~  141 (169)
T d1ihga1         109 SNTKALYRRAQGWQGLKEYDQALADLKKAQEIA  141 (169)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             hhhhHHHhHHHHHHHccCHHHHHHHHHHHHHhC
Confidence            366788888888888889999888888887653

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=97.31  E-value=0.0042  Score=41.46  Aligned_cols=109  Identities=9%  Similarity=0.022  Sum_probs=76.8

Q ss_pred             HhHHHHHHHHHhcCCHHHHHHHHHHHHHc---CCCC-----------CHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCC
Q 039342           24 DSFNAVIEAFRQGGRFEEAIKAYVEMEKV---RCDP-----------NERTLEAVLSVYCFAGLVDESKEQFQEIKSSGI   89 (248)
Q Consensus        24 ~~y~~li~~~~~~~~~~~a~~~~~~m~~~---~~~p-----------~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~   89 (248)
                      ..+.-.-..+.+.|++.+|...|++....   ...+           ...+|+.+-.+|.+.|++++|...++...+.. 
T Consensus        16 ~~~~e~G~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-   94 (168)
T d1kt1a1          16 AIVKEKGTVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD-   94 (168)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcc-
Confidence            34445556778889999999888776431   1111           12345556677888999999999998887653 


Q ss_pred             CcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHh
Q 039342           90 LPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMI  135 (248)
Q Consensus        90 ~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l  135 (248)
                      +.+..+|..+-.++...|++++|...|++..+..  |+.......+
T Consensus        95 p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~--P~n~~~~~~l  138 (168)
T d1kt1a1          95 SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVN--PQNKAARLQI  138 (168)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC--TTCHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHH
Confidence            3367788888889999999999999999887654  5555444333

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.27  E-value=0.0026  Score=42.49  Aligned_cols=98  Identities=9%  Similarity=0.045  Sum_probs=74.2

Q ss_pred             CchHHHHHHHHHHHHc--------------CCC-CCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 039342            2 GLYKECQAILSRMSES--------------GVA-RNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLS   66 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~--------------g~~-~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~   66 (248)
                      |++++|++.|.+..+.              .+. .....|..+-.++.+.|++++|+..++...+.. +-+...|..+-.
T Consensus        41 ~~y~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p~~~~a~~~~g~  119 (169)
T d1ihga1          41 QNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID-PSNTKALYRRAQ  119 (169)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhhhhhhhhhhhHHHHHhChhhHHHHHHHHHHHHhhcccchhhhhhhhhhhhh-hhhhhHHHhHHH
Confidence            6788888888765321              011 234567778888999999999999999998765 467789999999


Q ss_pred             HHHhcCChhHHHHHHHHHHHCCCCc-CHhhHHHHHHH
Q 039342           67 VYCFAGLVDESKEQFQEIKSSGILP-SVMCYCMLLAV  102 (248)
Q Consensus        67 ~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~  102 (248)
                      +|.+.|+++.|.+.|+...+.  .| +......+-..
T Consensus       120 ~~~~l~~~~~A~~~~~~al~l--~p~n~~~~~~l~~~  154 (169)
T d1ihga1         120 GWQGLKEYDQALADLKKAQEI--APEDKAIQAELLKV  154 (169)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHH
T ss_pred             HHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHH
Confidence            999999999999999999875  34 44444444433

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=97.15  E-value=0.007  Score=40.30  Aligned_cols=96  Identities=11%  Similarity=0.136  Sum_probs=73.0

Q ss_pred             CCchHHHHHHHHHHHHc---CCCC-----------CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 039342            1 GGLYKECQAILSRMSES---GVAR-----------NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLS   66 (248)
Q Consensus         1 ~g~~~~a~~~~~~m~~~---g~~~-----------~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~   66 (248)
                      .|++++|.+.|.+....   ...+           ....|+.+-.+|.+.|++++|+..++...+.. +.+...|..+..
T Consensus        28 ~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-p~~~~a~~~~~~  106 (168)
T d1kt1a1          28 GGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGE  106 (168)
T ss_dssp             TTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcc-cchHHHHHHHHH
Confidence            48899999999875531   1111           12346667778899999999999999997764 577889999999


Q ss_pred             HHHhcCChhHHHHHHHHHHHCCCCcC-HhhHHHH
Q 039342           67 VYCFAGLVDESKEQFQEIKSSGILPS-VMCYCML   99 (248)
Q Consensus        67 ~~~~~g~~~~a~~~~~~m~~~~~~p~-~~~~~~l   99 (248)
                      +|...|++++|...|+...+.  .|+ ......+
T Consensus       107 ~~~~l~~~~~A~~~~~~al~l--~P~n~~~~~~l  138 (168)
T d1kt1a1         107 AQLLMNEFESAKGDFEKVLEV--NPQNKAARLQI  138 (168)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHS--CTTCHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHH
Confidence            999999999999999999875  454 3444443

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=96.99  E-value=0.017  Score=37.75  Aligned_cols=99  Identities=9%  Similarity=0.044  Sum_probs=71.0

Q ss_pred             HHhHHHH--HHHHHhcCCHHHHHHHHHHHHHc--CCCC---------CHHHHHHHHHHHHhcCChhHHHHHHHHHHHC--
Q 039342           23 SDSFNAV--IEAFRQGGRFEEAIKAYVEMEKV--RCDP---------NERTLEAVLSVYCFAGLVDESKEQFQEIKSS--   87 (248)
Q Consensus        23 ~~~y~~l--i~~~~~~~~~~~a~~~~~~m~~~--~~~p---------~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~--   87 (248)
                      ..+|..+  ...+.+.|++++|++.|++..+.  ..+.         ....|+.+-.+|.+.|++++|.+.+++..+.  
T Consensus         7 a~a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~   86 (156)
T d2hr2a1           7 VGAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFN   86 (156)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhccc
Confidence            3466666  44566779999999999998642  2211         1467888899999999999999888887542  


Q ss_pred             ---CCCcC-----HhhHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 039342           88 ---GILPS-----VMCYCMLLAVYAKSNRWDDAYGLLDEMHT  121 (248)
Q Consensus        88 ---~~~p~-----~~~~~~li~~~~~~~~~~~a~~~~~~m~~  121 (248)
                         ...++     ...++.+-.+|...|++++|+..|++..+
T Consensus        87 ~~~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~  128 (156)
T d2hr2a1          87 RRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  128 (156)
T ss_dssp             HHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ccccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence               11221     22566777888999999999999988643

>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=96.85  E-value=0.0098  Score=38.56  Aligned_cols=68  Identities=12%  Similarity=0.121  Sum_probs=39.9

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCC----------HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGR----------FEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFA   71 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~----------~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~   71 (248)
                      +.+++|++.|+...+.. +.++..|..+-.++...++          +++|.+.|++..+.+ +-+..+|..+-.+|...
T Consensus        11 ~~fe~A~~~~e~al~~~-P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~-P~~~~a~~~lG~~y~~~   88 (145)
T d1zu2a1          11 LLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLID-PKKDEAVWCIGNAYTSF   88 (145)
T ss_dssp             HHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHhhC-CcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhc-chhhHHHhhHHHHHHHc
Confidence            35778888888877644 2356666666666654433          455666666655443 23445555555555443

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=96.72  E-value=0.017  Score=37.74  Aligned_cols=85  Identities=16%  Similarity=0.124  Sum_probs=64.7

Q ss_pred             CchHHHHHHHHHHHHcCC-CC----------CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHc-----CCCCC-----HHH
Q 039342            2 GLYKECQAILSRMSESGV-AR----------NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKV-----RCDPN-----ERT   60 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~-~~----------~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~-----~~~p~-----~~t   60 (248)
                      |++++|++.|.+..+... .|          ....|+.+-.+|.+.|++++|.+-+++..+.     ...++     ...
T Consensus        23 g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~a  102 (156)
T d2hr2a1          23 GEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGKLWISA  102 (156)
T ss_dssp             TCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhcccccccccccccchhHHH
Confidence            789999999998865211 12          1467889999999999999999999887542     22222     224


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHH
Q 039342           61 LEAVLSVYCFAGLVDESKEQFQEIKS   86 (248)
Q Consensus        61 ~~~ll~~~~~~g~~~~a~~~~~~m~~   86 (248)
                      |+.+-.+|...|++++|...|++..+
T Consensus       103 ~~~~g~~~~~lg~~eeA~~~~~~Al~  128 (156)
T d2hr2a1         103 VYSRALALDGLGRGAEAMPEFKKVVE  128 (156)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            66778899999999999999998754

>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=96.59  E-value=0.011  Score=38.37  Aligned_cols=72  Identities=15%  Similarity=0.056  Sum_probs=47.7

Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc----------CChhHHHHHHHHHHHCCCCc-CHhhHHHHHH
Q 039342           33 FRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFA----------GLVDESKEQFQEIKSSGILP-SVMCYCMLLA  101 (248)
Q Consensus        33 ~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~----------g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~  101 (248)
                      |-+.+.+++|...|+...+.. +-+...+..+-.+|...          +.+++|...|++..+.  .| +..+|..+-.
T Consensus         7 ~~r~~~fe~A~~~~e~al~~~-P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l--~P~~~~a~~~lG~   83 (145)
T d1zu2a1           7 FDRILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLI--DPKKDEAVWCIGN   83 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHH
T ss_pred             HHHHccHHHHHHHHHHHHhhC-CcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHh--cchhhHHHhhHHH
Confidence            345566888888888887664 45666777766666543          3456777788777764  34 5567777766


Q ss_pred             HHHhcC
Q 039342          102 VYAKSN  107 (248)
Q Consensus       102 ~~~~~~  107 (248)
                      +|...|
T Consensus        84 ~y~~~g   89 (145)
T d1zu2a1          84 AYTSFA   89 (145)
T ss_dssp             HHHHHH
T ss_pred             HHHHcc
Confidence            665543

>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=96.31  E-value=0.13  Score=38.24  Aligned_cols=135  Identities=10%  Similarity=0.049  Sum_probs=52.4

Q ss_pred             CCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHH
Q 039342           21 RNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLL  100 (248)
Q Consensus        21 ~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li  100 (248)
                      ||..--..+..-|.+.|.++.|..+|..+..         |.-++..+.+.++++.|.+++....      +..+|..+.
T Consensus        12 ~n~~d~~~i~~~c~~~~lye~A~~lY~~~~d---------~~rl~~~~v~l~~~~~avd~~~k~~------~~~~~k~~~   76 (336)
T d1b89a_          12 PNNAHIQQVGDRCYDEKMYDAAKLLYNNVSN---------FGRLASTLVHLGEYQAAVDGARKAN------STRTWKEVC   76 (336)
T ss_dssp             C----------------CTTTHHHHHHHTTC---------HHHHHHHHHTTTCHHHHHHHHHHHT------CHHHHHHHH
T ss_pred             CCcCCHHHHHHHHHHCCCHHHHHHHHHhCCC---------HHHHHHHHHhhccHHHHHHHHHHcC------CHHHHHHHH
Confidence            3333334444555556666666666554321         4455555555555555555443221      344555555


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhc
Q 039342          101 AVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCL  177 (248)
Q Consensus       101 ~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~  177 (248)
                      .++.+......|.-     ..............++.. +...|.++....+++..... -.++...++-++..|++.
T Consensus        77 ~~l~~~~e~~la~i-----~~~~~~~~~d~l~~~v~~-ye~~~~~e~Li~~Le~~~~~-~~~~~~~~~~L~~lyak~  146 (336)
T d1b89a_          77 FACVDGKEFRLAQM-----CGLHIVVHADELEELINY-YQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSKF  146 (336)
T ss_dssp             HHHHHTTCHHHHHH-----TTTTTTTCHHHHHHHHHH-HHHTTCHHHHHHHHHHHTTS-TTCCHHHHHHHHHHHHTT
T ss_pred             HHHHhCcHHHHHHH-----HHHHhhcCHHHHHHHHHH-HHHcCChHHHHHHHHHHHcC-CccchHHHHHHHHHHHHh
Confidence            55555444333211     111111222222233333 34444555555555543322 233444555555555554

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.04  E-value=0.048  Score=32.15  Aligned_cols=63  Identities=5%  Similarity=-0.112  Sum_probs=34.1

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHc-----CCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 039342           25 SFNAVIEAFRQGGRFEEAIKAYVEMEKV-----RCDPN-ERTLEAVLSVYCFAGLVDESKEQFQEIKSS   87 (248)
Q Consensus        25 ~y~~li~~~~~~~~~~~a~~~~~~m~~~-----~~~p~-~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~   87 (248)
                      .+--+-..+.+.|++++|...|++..+.     ...++ ..+++.+-.+|.+.|++++|.+.+++..+.
T Consensus         7 dc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l   75 (95)
T d1tjca_           7 DSFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (95)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHh
Confidence            3334455556666666666666555322     11112 345556666666666666666666665553

>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=95.75  E-value=0.19  Score=35.42  Aligned_cols=219  Identities=6%  Similarity=-0.075  Sum_probs=123.5

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHh----cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----cCC
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQ----GGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCF----AGL   73 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~----~g~   73 (248)
                      |++++|.+.|++..+.|   +...+..|=..|..    ..+...+...+..-.+.+.   ......+...+..    ..+
T Consensus        16 ~d~~~A~~~~~kAa~~g---~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~~---~~a~~~l~~~~~~~~~~~~~   89 (265)
T d1ouva_          16 KDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNY---SNGCHLLGNLYYSGQGVSQN   89 (265)
T ss_dssp             TCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC---HHHHHHHHHHHHHTSSSCCC
T ss_pred             CCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcchhHHHHHHhhcccccccc---cchhhccccccccccccchh
Confidence            67888888888887765   34444445555554    4577888877777766553   2233333333332    456


Q ss_pred             hhHHHHHHHHHHHCCCCcCHhhHHHHHHHHH----hcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHH
Q 039342           74 VDESKEQFQEIKSSGILPSVMCYCMLLAVYA----KSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVE  149 (248)
Q Consensus        74 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~----~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  149 (248)
                      .+.|...++...+.|..   .....+...+.    .......+...+......+.......+............+...+.
T Consensus        90 ~~~a~~~~~~a~~~g~~---~a~~~l~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~  166 (265)
T d1ouva_          90 TNKALQYYSKACDLKYA---EGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLNDGDGCTILGSLYDAGRGTPKDLKKAL  166 (265)
T ss_dssp             HHHHHHHHHHHHHTTCH---HHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHH
T ss_pred             hHHHHHHHhhhhhhhhh---hHHHhhcccccCCCcccchhHHHHHHhhhhhcccccchhhhhhhhhccCCCcccccccch
Confidence            77788888777766532   22222222222    234566677777766655432211111111211133455667777


Q ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHHHh----cCchHHHHHHHHHHHHCCCCCCcchhhhHHhhhhhhccccchHHHHHHH
Q 039342          150 YVFDKLNCEGYGLGMRFYNALLEALWC----LGLRERAARVLDEATKRGLFPELFRHNKLVWSVDVHRMWEGGAYTAISV  225 (248)
Q Consensus       150 ~~~~~m~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~g~~~~~~~  225 (248)
                      ..++...+.|   +......+-..|..    ..+.++|...|....+.|-.   ..+..|-..+ ..|.....+.++|.+
T Consensus       167 ~~~~~a~~~g---~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~~g~~---~a~~~LG~~y-~~G~g~~~n~~~A~~  239 (265)
T d1ouva_         167 ASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELENG---GGCFNLGAMQ-YNGEGVTRNEKQAIE  239 (265)
T ss_dssp             HHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTTCH---HHHHHHHHHH-HTTSSSSCCSTTHHH
T ss_pred             hhhhcccccc---ccccccchhhhcccCcccccchhhhhhhHhhhhcccCH---HHHHHHHHHH-HcCCCCccCHHHHHH
Confidence            7777766665   34444444444544    56888999999998887632   2222332222 244444557888888


Q ss_pred             HHHHHHHHHHc
Q 039342          226 WLNKMYEMFMM  236 (248)
Q Consensus       226 ~~~~m~~~~~~  236 (248)
                      ++++=.+.|.+
T Consensus       240 ~~~kAa~~g~~  250 (265)
T d1ouva_         240 NFKKGCKLGAK  250 (265)
T ss_dssp             HHHHHHHHTCH
T ss_pred             HHHHHHHCcCH
Confidence            88887776643

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=95.67  E-value=0.26  Score=36.49  Aligned_cols=84  Identities=12%  Similarity=0.139  Sum_probs=46.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHh
Q 039342           26 FNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAK  105 (248)
Q Consensus        26 y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~  105 (248)
                      |..++..+.+.++++.|.+++.+.      -+..+|..+..+|.+......+     .+........+.....++..|-.
T Consensus        43 ~~rl~~~~v~l~~~~~avd~~~k~------~~~~~~k~~~~~l~~~~e~~la-----~i~~~~~~~~~d~l~~~v~~ye~  111 (336)
T d1b89a_          43 FGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLA-----QMCGLHIVVHADELEELINYYQD  111 (336)
T ss_dssp             HHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHH-----HHTTTTTTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhccHHHHHHHHHHc------CCHHHHHHHHHHHHhCcHHHHH-----HHHHHHhhcCHHHHHHHHHHHHH
Confidence            445666667777777776665543      2345666666666655544332     12222223344444556666666


Q ss_pred             cCCHHHHHHHHHHHH
Q 039342          106 SNRWDDAYGLLDEMH  120 (248)
Q Consensus       106 ~~~~~~a~~~~~~m~  120 (248)
                      .|.+++...+++...
T Consensus       112 ~~~~e~Li~~Le~~~  126 (336)
T d1b89a_         112 RGYFEELITMLEAAL  126 (336)
T ss_dssp             TTCHHHHHHHHHHHT
T ss_pred             cCChHHHHHHHHHHH
Confidence            666666666666554

>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=95.45  E-value=0.11  Score=30.63  Aligned_cols=63  Identities=13%  Similarity=0.068  Sum_probs=45.9

Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHH
Q 039342           38 RFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLA  101 (248)
Q Consensus        38 ~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~  101 (248)
                      |.-++.+-++.+....+.|++.+..+.+++|.|.+++..|.++|+-.+.+ +.++...|.-+++
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K-~~~~k~~y~yilq   83 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVIQ   83 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-hcCcHHHHHHHHH
Confidence            55566667777777788888888888888888888888888888887743 2234556666554

>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=94.97  E-value=0.15  Score=29.77  Aligned_cols=71  Identities=11%  Similarity=-0.092  Sum_probs=54.8

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHHC-----CCCcC-HhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHH
Q 039342           57 NERTLEAVLSVYCFAGLVDESKEQFQEIKSS-----GILPS-VMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQ  129 (248)
Q Consensus        57 ~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~-----~~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~  129 (248)
                      +...+-.+-..+.+.|+++.|...|++..+.     ...++ ..+++.+-.++.+.|++++|+..+++..+..  |+..
T Consensus         4 saddc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~--P~~~   80 (95)
T d1tjca_           4 TAEDSFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELD--PEHQ   80 (95)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCH
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhC--cCCH
Confidence            4445556778889999999999999887642     11222 4678999999999999999999999988764  5543

>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=94.86  E-value=0.38  Score=33.71  Aligned_cols=164  Identities=9%  Similarity=-0.023  Sum_probs=96.4

Q ss_pred             CHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----cCChhHHHHHHHHHHHCCCCcCHhhHH
Q 039342           22 NSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCF----AGLVDESKEQFQEIKSSGILPSVMCYC   97 (248)
Q Consensus        22 ~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~----~g~~~~a~~~~~~m~~~~~~p~~~~~~   97 (248)
                      |+..+..|=..+-+.+++++|++.|++..+.|   |...+-.|-..|..    ..+...+...++.-.+.+   +.....
T Consensus         1 ~p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g---~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~---~~~a~~   74 (265)
T d1ouva_           1 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCH   74 (265)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccc---ccchhh
Confidence            34556666667778899999999999988776   34455555555654    568888888888877765   233333


Q ss_pred             HHHHHHHh----cCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Q 039342           98 MLLAVYAK----SNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYGLGMRFYNALLEA  173 (248)
Q Consensus        98 ~li~~~~~----~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~  173 (248)
                      .+...+..    ..+.+.|...+++..+.|.......+................+...+......+   +...+..+...
T Consensus        75 ~l~~~~~~~~~~~~~~~~a~~~~~~a~~~g~~~a~~~l~~~~~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~L~~~  151 (265)
T d1ouva_          75 LLGNLYYSGQGVSQNTNKALQYYSKACDLKYAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGCTILGSL  151 (265)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHH
T ss_pred             ccccccccccccchhhHHHHHHHhhhhhhhhhhHHHhhcccccCCCcccchhHHHHHHhhhhhccc---ccchhhhhhhh
Confidence            44333332    457888999999888777543333332222221333445566666655544432   33444555555


Q ss_pred             HHh----cCchHHHHHHHHHHHHCC
Q 039342          174 LWC----LGLRERAARVLDEATKRG  194 (248)
Q Consensus       174 ~~~----~g~~~~a~~~~~~m~~~g  194 (248)
                      +..    ..+...+...++...+.|
T Consensus       152 ~~~~~~~~~~~~~~~~~~~~a~~~g  176 (265)
T d1ouva_         152 YDAGRGTPKDLKKALASYDKACDLK  176 (265)
T ss_dssp             HHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             hccCCCcccccccchhhhhcccccc
Confidence            544    334445555555544443

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=94.07  E-value=0.35  Score=30.05  Aligned_cols=65  Identities=18%  Similarity=0.102  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCC
Q 039342           60 TLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRIS  125 (248)
Q Consensus        60 t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~  125 (248)
                      -+...++.....|+-|.-.++++.+.+. -+|++...-.+-.+|.+-|...++.+++.+.-+.|++
T Consensus        88 ~vdlALd~lv~~~kkd~Ld~i~~~l~kn-~~i~~~~llkia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          88 HVNKALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence            3444555555555555555555554432 2444555555555555555555555555555555543

>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=94.02  E-value=0.14  Score=40.27  Aligned_cols=73  Identities=5%  Similarity=0.037  Sum_probs=49.5

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCc-CHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHH
Q 039342           59 RTLEAVLSVYCFAGLVDESKEQFQEIKSSGILP-SVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQM  134 (248)
Q Consensus        59 ~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~  134 (248)
                      .++..+-..+...|++++|...|++..+.  .| +...|+.+-..+...|+..+|...|.+-..... |.......+
T Consensus       153 ~~~~~LG~l~~~~~~~~~A~~~y~~A~~l--~P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~~-~~~~a~~nL  226 (497)
T d1ya0a1         153 HCLVHLGDIARYRNQTSQAESYYRHAAQL--VPSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVKF-PFPAASTNL  226 (497)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSSB-CCHHHHHHH
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCC-CCHHHHHHH
Confidence            34555666777778888888888877764  34 456788888888888888888888877765542 333344333

>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=94.01  E-value=0.075  Score=41.81  Aligned_cols=81  Identities=10%  Similarity=-0.008  Sum_probs=54.9

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCHhhHHHHHHHHH
Q 039342           25 SFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSVMCYCMLLAVYA  104 (248)
Q Consensus        25 ~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  104 (248)
                      ++..+-..+...|++++|...|++..+.. +-+...|+.+-..+...|+..+|...|.+-.... .|-..++..|...+.
T Consensus       154 ~~~~LG~l~~~~~~~~~A~~~y~~A~~l~-P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~-~~~~~a~~nL~~~~~  231 (497)
T d1ya0a1         154 CLVHLGDIARYRNQTSQAESYYRHAAQLV-PSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVK-FPFPAASTNLQKALS  231 (497)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSS-BCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHH
Confidence            45556666777777888887777776542 2344677777777777888888877777776553 356667777776665


Q ss_pred             hcC
Q 039342          105 KSN  107 (248)
Q Consensus       105 ~~~  107 (248)
                      +..
T Consensus       232 ~~~  234 (497)
T d1ya0a1         232 KAL  234 (497)
T ss_dssp             HHT
T ss_pred             Hhh
Confidence            543

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=93.94  E-value=0.38  Score=29.92  Aligned_cols=137  Identities=9%  Similarity=-0.031  Sum_probs=84.4

Q ss_pred             CchHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 039342            2 GLYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAGLVDESKEQF   81 (248)
Q Consensus         2 g~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~   81 (248)
                      |.+++..++..+...+   .+..-||=+|......-+-+...++++..-+.   .|.          ..++++......+
T Consensus        16 G~ve~Gveii~k~~~s---s~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~---FDl----------s~C~Nlk~vv~C~   79 (161)
T d1wy6a1          16 GYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGSY---FDL----------DKCQNLKSVVECG   79 (161)
T ss_dssp             TCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGG---SCG----------GGCSCTHHHHHHH
T ss_pred             hhHHhHHHHHHHHccc---CCccccceeeeecccccchHHHHHHHHHHhhh---cCc----------hhhhcHHHHHHHH
Confidence            5566666666665542   34556666666666666666666555554221   111          1223333322222


Q ss_pred             HHHHHCCCCcCHhhHHHHHHHHHhcCCHHHHHHHHHHHHHCCCCchHHhHHHHhcccccccchHHHHHHHHHHHHhcCCC
Q 039342           82 QEIKSSGILPSVMCYCMLLAVYAKSNRWDDAYGLLDEMHTNRISNIHQVTGQMIKGEFDDESNWQMVEYVFDKLNCEGYG  161 (248)
Q Consensus        82 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~  161 (248)
                      -.+-     .+...++.-++....+|+-+.-.++++++.+.+ +|+....-.+-.+ +.+-|+..++..++.+..+.|++
T Consensus        80 ~~~n-----~~se~vdlALd~lv~~~kkd~Ld~i~~~l~kn~-~i~~~~llkia~A-~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          80 VINN-----TLNEHVNKALDILVIQGKRDKLEEIGREILKNN-EVSASILVAIANA-LRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             HHTT-----CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC--C-CSCHHHHHHHHHH-HHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHhc-----chHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC-CCCHHHHHHHHHH-HHHhcchhhHHHHHHHHHHHhHH
Confidence            2211     245566777888899999999999999977755 3444544445444 88899999999999999998875

>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=93.43  E-value=0.37  Score=28.26  Aligned_cols=67  Identities=15%  Similarity=0.047  Sum_probs=50.2

Q ss_pred             ccccc-hHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHCCCCCCcchhhhHH
Q 039342          139 FDDES-NWQMVEYVFDKLNCEGYGLGMRFYNALLEALWCLGLRERAARVLDEATKRGLFPELFRHNKLV  206 (248)
Q Consensus       139 ~~~~~-~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~li  206 (248)
                      +.+.. +.-.+.+-++.+......|++....+.+++|-+.+++..|..+|+-.+.+ +.++...|..++
T Consensus        15 F~~~~iD~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K-~~~~k~~y~yil   82 (105)
T d1v54e_          15 FNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVI   82 (105)
T ss_dssp             HTCTTCCHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHH
T ss_pred             hcCcCccHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-hcCcHHHHHHHH
Confidence            44443 44556666677777889999999999999999999999999999987754 233445566555

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=93.13  E-value=0.54  Score=29.19  Aligned_cols=110  Identities=5%  Similarity=-0.120  Sum_probs=49.5

Q ss_pred             chHHHHHHHHHHHHcCCCCCHHhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----cCChhHHH
Q 039342            3 LYKECQAILSRMSESGVARNSDSFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCF----AGLVDESK   78 (248)
Q Consensus         3 ~~~~a~~~~~~m~~~g~~~~~~~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~----~g~~~~a~   78 (248)
                      |+++|.+.|.+..+.|..   ..+..|.  .....+.++|++.+++..+.|.   ...+..|-..|..    ..+.++|.
T Consensus         8 d~~~A~~~~~kaa~~g~~---~a~~~l~--~~~~~~~~~a~~~~~~aa~~g~---~~a~~~Lg~~y~~g~~~~~d~~~A~   79 (133)
T d1klxa_           8 DLKKAIQYYVKACELNEM---FGCLSLV--SNSQINKQKLFQYLSKACELNS---GNGCRFLGDFYENGKYVKKDLRKAA   79 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCT---THHHHHH--TCTTSCHHHHHHHHHHHHHTTC---HHHHHHHHHHHHHCSSSCCCHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCh---hhhhhhc--cccccCHHHHHHHHhhhhcccc---hhhhhhHHHhhhhccccchhhHHHH
Confidence            456777777776665532   1222221  1223455666666666555442   2222223333322    23455566


Q ss_pred             HHHHHHHHCCCCcCHhhHHHHHHHHHh----cCCHHHHHHHHHHHHHCC
Q 039342           79 EQFQEIKSSGILPSVMCYCMLLAVYAK----SNRWDDAYGLLDEMHTNR  123 (248)
Q Consensus        79 ~~~~~m~~~~~~p~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~  123 (248)
                      ++|++..+.|.   +.....|-..|..    ..+.++|.++|++--+.|
T Consensus        80 ~~~~~aa~~g~---~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~G  125 (133)
T d1klxa_          80 QYYSKACGLND---QDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  125 (133)
T ss_dssp             HHHHHHHHTTC---HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHhhhhccCc---chHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHCC
Confidence            66655555442   2222223223322    234555555555544443

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=93.05  E-value=0.55  Score=29.13  Aligned_cols=16  Identities=25%  Similarity=0.455  Sum_probs=8.9

Q ss_pred             CHHHHHHHHHHHHHcC
Q 039342           38 RFEEAIKAYVEMEKVR   53 (248)
Q Consensus        38 ~~~~a~~~~~~m~~~~   53 (248)
                      |+++|.+.|++..+.|
T Consensus         8 d~~~A~~~~~kaa~~g   23 (133)
T d1klxa_           8 DLKKAIQYYVKACELN   23 (133)
T ss_dssp             HHHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHCC
Confidence            4555666666655544

>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=87.16  E-value=1.2  Score=27.39  Aligned_cols=71  Identities=8%  Similarity=-0.062  Sum_probs=50.0

Q ss_pred             CCCHHhHHHHHHHHHhc---CCHHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHhcCChhHHHHHHHHHHHCCCCcCH
Q 039342           20 ARNSDSFNAVIEAFRQG---GRFEEAIKAYVEMEKVRCDPNE-RTLEAVLSVYCFAGLVDESKEQFQEIKSSGILPSV   93 (248)
Q Consensus        20 ~~~~~~y~~li~~~~~~---~~~~~a~~~~~~m~~~~~~p~~-~t~~~ll~~~~~~g~~~~a~~~~~~m~~~~~~p~~   93 (248)
                      .|++.+-=..--++++.   .+.+++..+|++..+.+ +.+. ..+--|--+|.+.|++++|.+.++.+.+.  .|+.
T Consensus        32 ~~s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~~~~~-p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~i--eP~n  106 (124)
T d2pqrb1          32 TATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEA-ESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEH--ERNN  106 (124)
T ss_dssp             GSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHC-GGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTC
T ss_pred             CCCcchHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcC-chhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHcc--CCCc
Confidence            35666555555566655   45678999999987653 2333 34456667899999999999999999875  4543

>d1ug3a1 a.118.1.14 (A:1235-1427) Eukaryotic initiation factor eIF4G {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: MIF4G domain-like
domain: Eukaryotic initiation factor eIF4G
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.23  E-value=1  Score=30.14  Aligned_cols=65  Identities=12%  Similarity=0.092  Sum_probs=38.7

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC--ChhHHHHHHHHHHHCCCCc
Q 039342           25 SFNAVIEAFRQGGRFEEAIKAYVEMEKVRCDPNERTLEAVLSVYCFAG--LVDESKEQFQEIKSSGILP   91 (248)
Q Consensus        25 ~y~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~ll~~~~~~g--~~~~a~~~~~~m~~~~~~p   91 (248)
                      ...++|.-|...++.++|...++++......+  .....++......+  .-+.+..++..+.+.|+-+
T Consensus        12 k~~~il~Ey~~~~D~~Ea~~~l~el~~p~~~~--~~V~~~i~~~le~~~~~re~~~~Ll~~L~~~~~is   78 (193)
T d1ug3a1          12 KSKAIIEEYLHLNDMKEAVQCVQELASPSLLF--IFVRHGVESTLERSAIAREHMGQLLHQLLCAGHLS   78 (193)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHHTTCCGGGHH--HHHHHHHHHHTTTCHHHHHHHHHHHHHHHHTTSSC
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHcCCchhHH--HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHCCCCC
Confidence            45678888999999999999998875322221  11222333332222  2455566777777666543